Publication List

Oczko-Wojciechowska MSwierniak MKrajewska JKowalska MKowal MStokowy TWojtas BRusinek DPawlaczek ACzarniecka A, Szpak-Ulczok S, Gawlik T, Chmielik E, Tyszkiewicz T, Nikiel B, Lange D, Jarzab M, Wiench M, Jarzab B (2017)
Differences in the transcriptome of medullary thyroid cancer regarding the status and type of RET gene mutations
Sci Rep, 7, 42074
PubMed 28181547

Aksnes HGoris MStrømland ØDrazic AWaheed QReuter NArnesen T (2017)
Molecular Determinants of the N-Terminal Acetyltransferase Naa60 Anchoring to the Golgi Membrane
J Biol Chem (in press)
PubMed 28196861

Leiss L, Mutlu E, Øyan A, Yan T, Tsinkalovsky O, Sleire L, Petersen K, Rahman MA, Johannessen M, Mitra SS, Jacobsen HK, Talasila KM, Miletic H, Jonassen I, Li X, Brons NH, Kalland KH, Wang J, Enger PØ (2017)
Tumour-associated glial host cells display a stem-like phenotype with a distinct gene expression profile and promote growth of GBM xenografts
BMC Cancer, 17 (1), 108
PubMed 28173797

Sørhus E, Incardona JP, Furmanek T, Goetz GW, Scholz NL, Meier S, Edvardsen RB, Jentoft S (2017)
Novel adverse outcome pathways revealed by chemical genetics in a developing marine fish
Elife, 6
PubMed 28117666

Malde K, Seliussen BB, Quintela M, Dahle G, Besnier F, Skaug HJ, Øien N, Solvang HK, Haug T, Skern-Mauritzen R, Kanda N, Pastene LA, Jonassen I, Glover KA (2017)
Whole genome resequencing reveals diagnostic markers for investigating global migration and hybridization between minke whale species
BMC Genomics, 18 (1), 76
PubMed 28086785

Haugarvoll K, Johansson S, Rodriguez CE, Boman H, Haukanes BI, Bruland O, Roque F, Jonassen I, Blomqvist M, Telstad W, Månsson JE, Knappskog PM, Bindoff LA (2017)
GBA2 Mutations Cause a Marinesco-Sjögren-Like Syndrome: Genetic and Biochemical Studies
PLoS One, 12 (1), e0169309
PubMed 28052128

Steine IM, Zayats T, Stansberg C, Pallesen S, Mrdalj J, Håvik B, Soulé J, Haavik J, Milde AM, Skrede S, Murison R, Krystal J, Grønli J. (2016)
Implication of NOTCH1 gene in susceptibility to anxiety and depression among sexual abuse victims.
Transl Psychiatry. 13;6(12):e977
PubMed 27959334

Oczko-Wojciechowska M, Swierniak M, Krajewska J, Kowalska M, Kowal M, Stokowy T, Wojtas B, Rusinek D, Pawlaczek A, Czarniecka Mauland KK, Wik E, Hoivik EA, Kusonmano K, Halle MK, Berg A, Haugland HK, Øyan AM, Kalland KH, Stefansson IM, Akslen LA, Krakstad C, Trovik J, Werner HM, Salvesen HB (2016)
Aneuploidy related transcriptional changes in endometrial cancer link low expression of chromosome 15q genes to poor survival
Oncotarget (in press)
PubMed 28039471

Gjuvsland AB, Zörgö E, Samy JK, Stenberg S, Demirsoy IH, Roque F, Maciaszczyk-Dziubinska E, Migocka M, Alonso-Perez E, Zackrisson M, Wysocki R, Tamás MJ, Jonassen I, Omholt SW, Warringer J(2016)
Disentangling genetic and epigenetic determinants of ultrafast adaptation
Mol Syst Biol, 12 (12), 892
PubMed 27979908

Lereim RR, Oveland E, Berven FS, Vaudel M, Barsnes H (2016)
Visualization, Inspection and Interpretation of Shotgun Proteomics Identification Results
Adv Exp Med Biol, 919, 227-235
PubMed 27975220

Muth T, Rapp E, Berven FS, Barsnes H, Vaudel M (2016)
Tandem Mass Spectrum Sequencing: An Alternative to Database Search Engines in Shotgun Proteomics
Adv Exp Med Biol, 919, 217-226
PubMed 27975219

Verheggen K, Martens L, Berven FS, Barsnes H, Vaudel M (2016)
Database Search Engines: Paradigms, Challenges and Solutions
Adv Exp Med Biol, 919, 147-156
PubMed 27975215

Neveling K, Mensenkamp AR, Derks R, Kwint M, Ouchene H, Steehouwer M, van Lier B, Bosgoed E, Rikken A, Tychon M, Zafeiropoulou D, Castelein S, Hehir-Kwa J, Tjwan Thung D, Hofste T, Lelieveld SH, Bertens SM, Adan IB, Eijkelenboom A, Tops BB, Yntema H, Stokowy T, Knappskog PM, Høberg-Vetti H, Steen VM et al. (2016)
BRCA Testing by Single-Molecule Molecular Inversion Probes
Clin Chem, 63 (2), 503-512
PubMed 27974384

Waløen K, Kleppe R, Martinez A, Haavik J (2016)
Tyrosine and tryptophan hydroxylases as therapeutic targets in human disease
Expert Opin Ther Targets, 21 (2), 167-180
PubMed 27973928

Johansson BB, Irgens HU, Molnes J, Sztromwasser P, Aukrust I, Juliusson PB, Søvik O, Levy S, Skrivarhaug T, Joner G, Molven A, Johansson S, Njølstad PR (2016)
Targeted next-generation sequencing reveals MODY in up to 6.5% of antibody-negative diabetes cases listed in the Norwegian Childhood Diabetes Registry
Diabetologia (in press)
PubMed 27913849

Kleppe L, Edvardsen RB, Furmanek T, Andersson E, Juanchich A, Wargelius A (2016)
bmp15l, figla, smc1bl, and larp6l are preferentially expressed in germ cells in Atlantic salmon (Salmo salar L.)
Mol Reprod Dev, 84 (1), 76-87
PubMed 27893173

Guldbrandsen AFarag Y, Kroksveen AC, Oveland E, Lereim RR, Opsahl JA, Myhr KM, Berven FS, Barsnes H (2016)
CSF-PR 2.0: An Interactive Literature Guide to Quantitative Cerebrospinal Fluid Mass Spectrometry Data from Neurodegenerative Disorders
Mol Cell Proteomics, 16 (2), 300-309
PubMed 27890865

Bukowska-Ośko I, Perlejewski K, Nakamura S, Motooka D, Stokowy T, Kosińska J, Popiel M, Płoski R, Horban A, Lipowski D, Caraballo Cortés K, Pawełczyk A, Demkow U, Stępień A, Radkowski M, Laskus T (2017)
Sensitivity of Next-Generation Sequencing Metagenomic Analysis for Detection of RNA and DNA Viruses in Cerebrospinal Fluid: The Confounding Effect of Background Contamination
Adv Exp Med Biol, 944, 53-62
PubMed 27826891

Lereim RR, Oveland E, Xiao Y, Torkildsen Ø, Wergeland S, Myhr KM, Sun SC, Berven FS (2016)
The Brain Proteome of the Ubiquitin Ligase Peli1 Knock-Out Mouse during Experimental Autoimmune Encephalomyelitis
J Proteomics Bioinform, 9 (9), 209-219
PubMed 27746629

Kroksveen AC, Guldbrandsen A, Vaudel M, Lereim RRBarsnes H, Myhr KM, Torkildsen Ø, Berven FS (2016)
In-Depth Cerebrospinal Fluid Quantitative Proteome and Deglycoproteome Analysis: Presenting a Comprehensive Picture of Pathways and Processes Affected by Multiple Sclerosis
J Proteome Res, 16 (1), 179-194
PubMed 27728768

Vaudel M, Barsnes H, Ræder H, Berven FS (2016)
Using Proteomics Bioinformatics Tools and Resources in Proteogenomic Studies
Adv Exp Med Biol, 926, 65-75
PubMed 27686806

Khan HM, Grauffel C, Broer R, MacKerell AD, Havenith RW, Reuter N (2016)
Improving the Force Field Description of Tyrosine-Choline Cation-π Interactions: QM Investigation of Phenol-N(Me)4(+) Interactions
J Chem Theory Comput, 12 (11), 5585-5595
PubMed 27682345

Stokowy T, Gawel D, Wojtas B (2016)
Differences in miRNA and mRNA Profile of Papillary Thyroid Cancer Variants
Int J Endocrinol, 2016, 1427042
PubMed 27656207

Bukowska-Ośko I, Perlejewski K, Nakamura S, Motooka D, Stokowy T, Kosińska J, Popiel M, Płoski R, Horban A, Lipowski D, Caraballo Cortés K, Pawełczyk A, Demkow U, Stępień A, Radkowski M, Laskus T (2016)
Sensitivity of Next-Generation Sequencing Metagenomic Analysis for Detection of RNA and DNA Viruses in Cerebrospinal Fluid: The Confounding Effect of Background Contamination
Adv Exp Med Biol (in press)
PubMed 27645539

Saito TRehmsmeier M (2016)
Precrec: fast and accurate precision-recall and ROC curve calculations in R
Bioinformatics, 33 (1), 145-147
PubMed 27591081

Seale AC, Koech AC, Sheppard AE, Barsosio HC, Langat J, Anyango E, Mwakio S, Mwarumba S, Morpeth SC, Anampiu K, Vaughan A, Giess A, Mogeni P, Walusuna L, Mwangudzah H, Mwanzui D, Salim M, Kemp B, Jones C, Mturi N, Tsofa B, Mumbo E, Mulewa D, Bandika V, Soita M et al. (2016)
Maternal colonization with Streptococcus agalactiae and associated stillbirth and neonatal disease in coastal Kenya
Nat Microbiol, 1 (7), 16067
PubMed 27572968

Stokowy T, Wojtas B, Jarzab B, Krohn K, Fredman D, Dralle H, Musholt T, Hauptmann S, Lange D, Hegedüs L, Paschke R, Eszlinger M (2016)
Two-miRNA classifiers differentiate mutation-negative follicular thyroid carcinomas and follicular thyroid adenomas in fine needle aspirations with high specificity
Endocrine, 54 (2), 440-447
PubMed 27473101

Lanzén A, Lekang K, Jonassen I, Thompson EM, Troedsson C (2016)
High-throughput metabarcoding of eukaryotic diversity for environmental monitoring of offshore oil-drilling activities
Mol Ecol, 25 (17), 4392-406
PubMed 27454455

Moore CE, Giess A, Soeng S, Sar P, Kumar V, Nhoung P, Bousfield R, Turner P, Stoesser N, Day NP, Parry CM (2016)
Characterisation of Invasive Streptococcus pneumoniae Isolated from Cambodian Children between 2007 – 2012
PLoS One, 11 (7), e0159358
PubMed 27448096

Bukowska-Ośko I, Perlejewski K, Nakamura S, Motooka D, Stokowy T, Kosińska J, Popiel M, Płoski R, Horban A, Lipowski D, Caraballo Cortés K, Pawełczyk A, Demkow U, Stępień A, Radkowski M, Laskus T (2016)
Sensitivity of Next-Generation Sequencing Metagenomic Analysis for Detection of RNA and DNA Viruses in Cerebrospinal Fluid: The Confounding Effect of Background Contamination
Adv Exp Med Biol (in press)
PubMed 27405447

Martin-Almedina S, Martinez-Corral I, Holdhus R, Vicente A, Fotiou E, Lin S, Petersen K, Simpson MA, Hoischen A, Gilissen C, Jeffery H, Atton G, Karapouliou C, Brice G, Gordon K, Wiseman JW, Wedin M, Rockson SG, Jeffery S, Mortimer PS, Snyder MP, Berland S, Mansour S, Makinen T, Ostergaard P (2016)
EPHB4 kinase-inactivating mutations cause autosomal dominant lymphatic-related hydrops fetalis
J Clin Invest, 126 (8), 3080-8
PubMed 27400125

Gibson WJ, Hoivik EA, Halle MK, Taylor-Weiner A, Cherniack AD, Berg A, Holst F, Zack TI, Werner HM, Staby KM, Rosenberg M, Stefansson IM, Kusonmano K, Chevalier A, Mauland KK, Trovik J, Krakstad C, Giannakis M, Hodis E, Woie K, Bjorge L, Vintermyr OK, Wala JA, Lawrence MS, Getz G et al. (2016)
The genomic landscape and evolution of endometrial carcinoma progression and abdominopelvic metastasis
Nat Genet, 48 (8), 848-55
PubMed 27348297

Perlejewski K, Bukowska-Ośko I, Nakamura S, Motooka D, Stokowy T, Płoski R, Rydzanicz M, Zakrzewska-Pniewska B, Podlecka-Piętowska A, Nojszewska M, Gogol A, Caraballo Cortés K, Demkow U, Stępień A, Laskus T, Radkowski M (2016)
Metagenomic Analysis of Cerebrospinal Fluid from Patients with Multiple Sclerosis
Adv Exp Med Biol, 935, 89-98
PubMed 27311319

Stokowy T, Garbulowski M, Fiskerstrand T, Holdhus R, Labun KSztromwasser P, Gilissen C, Hoischen A, Houge G, Petersen KJonassen I, Steen VM (2016)
RareVariantVis: new tool for visualization of causative variants in rare monogenic disorders using whole genome sequencing data
Bioinformatics, 32 (19), 3018-20
PubMed 27288501

Swierniak M, Pfeifer A, Stokowy T, Rusinek D, Chekan M, Lange D, Krajewska J, Oczko-Wojciechowska M, Czarniecka A, Jarzab M, Jarzab B, Wojtas B (2016)
Somatic mutation profiling of follicular thyroid cancer by next generation sequencing
Mol Cell Endocrinol, 433, 130-7
PubMed 27283500

Thyme SB, Akhmetova L, Montague TG, Valen E, Schier AF (2016)
Internal guide RNA interactions interfere with Cas9-mediated cleavage
Nat Commun, 7, 11750
PubMed 27282953

Labun K, Montague TG, Gagnon JA, Thyme SB, Valen E (2016)
CHOPCHOP v2: a web tool for the next generation of CRISPR genome engineering
Nucleic Acids Res, 44 (W1), W272-6
PubMed 27185894

Tzoulis C, Sztromwasser P, Johansson S, Gjerde IO, Knappskog P, Bindoff LA (2017)
PNKP Mutations Identified by Whole-Exome Sequencing in a Norwegian Patient with Sporadic Ataxia and Edema
Cerebellum, 16 (1), 272-275
PubMed 27165045

Aasebø E, Mjaavatten O, Vaudel M, Farag Y, Selheim F, Berven F, Bruserud Ø, Hernandez-Valladares M (2016)
Freezing effects on the acute myeloid leukemia cell proteome and phosphoproteome revealed using optimal quantitative workflows
J Proteomics, 145, 214-25
PubMed 27107777

Yılmaz Ş, Victor B, Hulstaert N, Vandermarliere E, Barsnes H, Degroeve S, Gupta S, Sticker A, Gabriël S, Dorny P, Palmblad M, Martens L (2016)
A Pipeline for Differential Proteomics in Unsequenced Species
J Proteome Res, 15 (6), 1963-70
PubMed 27089233

Lien S, Koop BF, Sandve SR, Miller JR, Kent MP, Nome T, Hvidsten TR, Leong JS, Minkley DR, Zimin A, Grammes F, Grove H, Gjuvsland A, Walenz B, Hermansen RA, von Schalburg K, Rondeau EB, Di Genova A, Samy JK, Olav Vik J, Vigeland MD, Caler L, Grimholt U, Jentoft S, Våge DI et al. (2016)
The Atlantic salmon genome provides insights into rediploidization
Nature, 533 (7602), 200-5
PubMed 27088604

Sheppard AE, Stoesser N, Wilson DJ, Sebra R, Kasarskis A, Anson LW, Giess A, Pankhurst LJ, Vaughan A, Grim CJ, Cox HL, Yeh AJ, Modernising Medical Microbiology (MMM) Informatics Group, Sifri CD, Walker AS, Peto TE, Crook DW, Mathers AJ (2016)
Nested Russian Doll-Like Genetic Mobility Drives Rapid Dissemination of the Carbapenem Resistance Gene blaKPC
Antimicrob Agents Chemother, 60 (6), 3767-78
PubMed 27067320

Khan HM, He T, Fuglebakk EGrauffel C, Yang B, Roberts MF, Gershenson A, Reuter N (2016)
A Role for Weak Electrostatic Interactions in Peripheral Membrane Protein Binding
Biophys J, 110 (6), 1367-78
PubMed 27028646

Tiwari SPReuter N (2016)
Similarity in Shape Dictates Signature Intrinsic Dynamics Despite No Functional Conservation in TIM Barrel Enzymes
PLoS Comput Biol, 12 (3), e1004834
PubMed 27015412

Ou Y, Xia R, Kong F, Zhang X, Yu S, Jiang L, Zheng L, Lin L (2016)
Overexpression of DEK is an indicator of poor prognosis in patients with gastric adenocarcinoma
Oncol Lett, 11 (3), 1823-1828
PubMed 26998084

Bizuayehu TTFurmanek T, Karlsen Ø, van der Meeren T, Edvardsen RB, Rønnestad I, Hamre K, Johansen SD, Babiak I (2016)
First feed affects the expressions of microRNA and their targets in Atlantic cod – CORRIGENDUM
Br J Nutr, 115 (10), 1885
PubMed 26996320

Martin KR, Kantari-Mimoun C, Yin M, Pederzoli-Ribeil M, Angelot-Delettre F, Ceroi A, Grauffel C, Benhamou M, Reuter N, Saas P, Frachet P, Boulanger CM, Witko-Sarsat V (2016)
Proteinase 3 Is a Phosphatidylserine-binding Protein That Affects the Production and Function of Microvesicles
J Biol Chem, 291 (20), 10476-89
PubMed 26961880

Blomberg N, Oliveira A, Mons B, Persson B, Jonassen I (2015)
The ELIXIR channel in F1000Research
F1000Res, 4
PubMed 26913192

Mollet IG, Patel D, Govani FS, Giess A, Paschalaki K, Periyasamy M, Lidington EC, Mason JC, Jones MD, Game L, Ali S, Shovlin CL (2016)
Low Dose Iron Treatments Induce a DNA Damage Response in Human Endothelial Cells within Minutes
PLoS One, 11 (2), e0147990
PubMed 26866805

Flønes I, Sztromwasser P, Haugarvoll K, Dölle C, Lykouri M, Schwarzlmüller T, Jonassen I, Miletic H, Johansson S, Knappskog PM, Bindoff LA, Tzoulis C (2016)
Novel SLC19A3 Promoter Deletion and Allelic Silencing in Biotin-Thiamine-Responsive Basal Ganglia Encephalopathy
PLoS One, 11 (2), e0149055
PubMed 26863430

Opsahl JA, Vaudel M, Guldbrandsen A, Aasebø E, Van Pesch V, Franciotta D, Myhr KM, Barsnes H, Berle M, Torkildsen Ø, Kroksveen AC, Berven FS (2016)
Label-free analysis of human cerebrospinal fluid addressing various normalization strategies and revealing protein groups affected by multiple sclerosis
Proteomics, 16 (7), 1154-65
PubMed 26841090

Ghorbani S, Fossbakk A, Jorge-Finnigan A, Flydal MI, Haavik J, Kleppe R (2016)
Regulation of tyrosine hydroxylase is preserved across different homo- and heterodimeric 14-3-3 proteins
Amino Acids, 48 (5), 1221-9
PubMed 26825549

Hernández Sánchez LF, Aasebø E, Selheim F, Berven FS, Ræder H, Barsnes H, Vaudel M (2016)
Systemic Analysis of Regulated Functional Networks
Methods Mol Biol, 1394, 287-310
PubMed 26700057

Guldbrandsen ABarsnes H, Kroksveen AC, Berven FS, Vaudel M (2016)
A Simple Workflow for Large Scale Shotgun Glycoproteomics
Methods Mol Biol, 1394, 275-86
PubMed 26700056

Aasebø E, Berven FS, Selheim F, Barsnes H, Vaudel M (2016)
Interpretation of Quantitative Shotgun Proteomic Data
Methods Mol Biol, 1394, 261-73
PubMed 26700055

Brunetti D, Torsvik J, Dallabona C, Teixeira P, Sztromwasser P, Fernandez-Vizarra E, Cerutti R, Reyes A, Preziuso C, D’Amati G, Baruffini E, Goffrini P, Viscomi C, Ferrero I, Boman H, Telstad W, Johansson S, Glaser E, Knappskog PM, Zeviani M, Bindoff LA (2015)
Defective PITRM1 mitochondrial peptidase is associated with Aβ amyloidotic neurodegeneration
EMBO Mol Med, 8 (3), 176-90
PubMed 26697887

Nepal C, Coolen M, Hadzhiev Y, Cussigh D, Mydel P, Steen VM, Carninci P, Andersen JB, Bally-Cuif L, Müller F, Lenhard B (2015)
Transcriptional, post-transcriptional and chromatin-associated regulation of pri-miRNAs, pre-miRNAs and moRNAs
Nucleic Acids Res, 44 (7), 3070-81
PubMed 26673698

Waheed Q, Edholm O (2011)
Quantum Corrections to Classical Molecular Dynamics Simulations of Water and Ice
J Chem Theory Comput, 7 (9), 2903-9
PubMed 26605479

Fuglebakk EReuter N, Hinsen K (2013)
Evaluation of Protein Elastic Network Models Based on an Analysis of Collective Motions
J Chem Theory Comput, 9 (12), 5618-28
PubMed 26592296

Romanowska J, Nowiński KS, Trylska J (2012)
Determining Geometrically Stable Domains in Molecular Conformation Sets
J Chem Theory Comput, 8 (8), 2588-99
PubMed 26592104

Vrahatis AG, Dimitrakopoulou K, Balomenos P, Tsakalidis AK, Bezerianos A (2015)
CHRONOS: a time-varying method for microRNA-mediated subpathway enrichment analysis
Bioinformatics, 32 (6), 884-92
PubMed 26568631

Ison J, Rapacki K, Ménager H, Kalaš M, Rydza E, Chmura P, Anthon C, Beard N, Berka K, Bolser D, Booth T, Bretaudeau A, Brezovsky J, Casadio R, Cesareni G, Coppens F, Cornell M, Cuccuru G, Davidsen K, Vedova GD, Dogan T, Doppelt-Azeroual O, Emery L, Gasteiger E, Gatter T et al. (2015)
Tools and data services registry: a community effort to document bioinformatics resources
Nucleic Acids Res, 44 (D1), D38-47
PubMed 26538599

Mathelier A, Fornes O, Arenillas DJ, Chen CY, Denay G, Lee J, Shi W, Shyr C, Tan G, Worsley-Hunt R, Zhang AW, Parcy F, Lenhard B, Sandelin A, Wasserman WW (2015)
JASPAR 2016: a major expansion and update of the open-access database of transcription factor binding profiles
Nucleic Acids Res, 44 (D1), D110-5
PubMed 26531826

Verheggen K, Maddelein D, Hulstaert N, Martens L, Barsnes H, Vaudel M (2015)
Pladipus Enables Universal Distributed Computing in Proteomics Bioinformatics
J Proteome Res, 15 (3), 707-12
PubMed 26510693

Kleppe R, Herfindal L, Døskeland SO (2015)
Cell Death Inducing Microbial Protein Phosphatase Inhibitors–Mechanisms of Action
Mar Drugs, 13 (10), 6505-20
PubMed 26506362

Bredholt G, Mannelqvist M, Stefansson IM, Birkeland E, Bø TH, Øyan AM, Trovik J, Kalland KH, Jonassen I, Salvesen HB, Wik E, Akslen LA (2015)
Tumor necrosis is an important hallmark of aggressive endometrial cancer and associates with hypoxia, angiogenesis and inflammation responses
Oncotarget, 6 (37), 39676-91
PubMed 26485755

Vaudel M, Verheggen K, Csordas A, Raeder H, Berven FS, Martens L, Vizcaíno JA, Barsnes H (2015)
Exploring the potential of public proteomics data
Proteomics, 16 (2), 214-25
PubMed 26449181

Perlejewski K, Popiel M, Laskus T, Nakamura S, Motooka D, Stokowy T, Lipowski D, Pollak A, Lechowicz U, Caraballo Cortés K, Stępień A, Radkowski M, Bukowska-Ośko I (2015)
Next-generation sequencing (NGS) in the identification of encephalitis-causing viruses: Unexpected detection of human herpesvirus 1 while searching for RNA pathogens
J Virol Methods, 226, 1-6
PubMed 26424618

Chon NL, Osterberg JR, Henderson J, Khan HMReuter N, Knight JD, Lin H (2015)
Membrane Docking of the Synaptotagmin 7 C2A Domain: Computation Reveals Interplay between Electrostatic and Hydrophobic Contributions
Biochemistry, 54 (37), 5696-711
PubMed 26333120

Winge I, Teigen K, Fossbakk A, Mahootchi E, Kleppe R, Sköldberg F, Kämpe O, Haavik J (2015)
Mammalian CSAD and GADL1 have distinct biochemical properties and patterns of brain expression
Neurochem Int, 90, 173-84
PubMed 26327310

Krakstad C, Tangen IL, Hoivik EA, Halle MK, Berg A, Werner HM, Ræder MB, Kusonmano K, Zou JX, Øyan AM, Stefansson I, Trovik J, Kalland KH, Chen HW, Salvesen HB (2015)
ATAD2 overexpression links to enrichment of B-MYB-translational signatures and development of aggressive endometrial carcinoma
Oncotarget, 6 (29), 28440-52
PubMed 26308378

Vaudel M, Barsnes H, Bjerkvig R, Bikfalvi A, Selheim F, Berven FS, Daubon T (2016)
Practical Considerations for Omics Experiments in Biomedical Sciences
Curr Pharm Biotechnol, 17 (1), 105-14
PubMed 26278526

Jacobsen KK, Kleppe R, Johansson S, Zayats T, Haavik J (2015)
Epistatic and gene wide effects in YWHA and aromatic amino hydroxylase genes across ADHD and other common neuropsychiatric disorders: Association with YWHAE
Am J Med Genet B Neuropsychiatr Genet, 168 (6), 423-432
PubMed 26172220

Kroksveen AC, Jaffe JD, Aasebø E, Barsnes H, Bjørlykke Y, Franciotta D, Keshishian H, Myhr KM, Opsahl JA, van Pesch V, Teunissen CE, Torkildsen Ø, Ulvik RJ, Vethe H, Carr SA, Berven FS (2015)
Quantitative proteomics suggests decrease in the secretogranin-1 cerebrospinal fluid levels during the disease course of multiple sclerosis
Proteomics, 15 (19), 3361-9
PubMed 26152395

Martinez M, Bruce NJ, Romanowska J, Kokh DB, Ozboyaci M, Yu X, Öztürk MA, Richter S, Wade RC (2015)
SDA 7: A modular and parallel implementation of the simulation of diffusional association software
J Comput Chem, 36 (21), 1631-45
PubMed 26123630

Tröße C, Kongshaug H, Dondrup M, Nilsen F (2015)
Characterisation of iron regulatory protein 1A and 1B in the blood-feeding copepod Lepeophtheirus salmonis
Exp Parasitol, 157, 1-11
PubMed 26115940

Farag Y, Berven FS, Jonassen IPetersen KBarsnes H (2015)
Distributed and interactive visual analysis of omics data
J Proteomics, 129, 78-82
PubMed 26047716

Janus P, Stokowy T, Jaksik R, Szoltysek K, Handschuh L, Podkowinski J, Widlak W, Kimmel M, Widlak P (2015)
Cross talk between cytokine and hyperthermia-induced pathways: identification of different subsets of NF-κB-dependent genes regulated by TNFα and heat shock
Mol Genet Genomics, 290 (5), 1979-90
PubMed 25944781

Merkle FT, Neuhausser WM, Santos D, Valen E, Gagnon JA, Maas K, Sandoe J, Schier AF, Eggan K (2015)
Efficient CRISPR-Cas9-mediated generation of knockin human pluripotent stem cells lacking undesired mutations at the targeted locus
Cell Rep, 11 (6), 875-83
PubMed 25937281

Dimitrakopoulou K, Vrahatis AG, Bezerianos A (2015)
Integromics network meta-analysis on cardiac aging offers robust multi-layer modular signatures and reveals micronome synergism
BMC Genomics, 16, 147
PubMed 25887273

Stefansson IM, Raeder M, Wik E, Mannelqvist M, Kusonmano K, Knutsvik G, Haldorsen I, Trovik J, Øyan AM, Kalland KH, Staff AC, Salvesen HB, Akslen LA (2015)
Increased angiogenesis is associated with a 32-gene expression signature and 6p21 amplification in aggressive endometrial cancer
Oncotarget, 6 (12), 10634-45
PubMed 25860936

Vizcaíno JA, Barsnes H, Hermjakob H (2015)
Proteomics data visualisation
Proteomics, 15 (8), 1339-40
PubMed 25854789

Fjeld K, Weiss FU, Lasher D, Rosendahl J, Chen JM, Johansson BB, Kirsten H, Ruffert C, Masson E, Steine SJ, Bugert P, Cnop M, Grützmann R, Mayerle J, Mössner J, Ringdal M, Schulz HU, Sendler M, Simon P, Sztromwasser P, Torsvik J, Scholz M, Tjora E, Férec C, Witt H et al. (2015)
A recombined allele of the lipase gene CEL and its pseudogene CELP confers susceptibility to chronic pancreatitis
Nat Genet, 47 (5), 518-22
PubMed 25774637

Genikhovich G, Fried P, Prünster MM, Schinko JB, Gilles AF, Fredman D, Meier K, Iber D, Technau U (2015)
Axis Patterning by BMPs: Cnidarian Network Reveals Evolutionary Constraints
Cell Rep, 10 (10), 1646-1654
PubMed 25772352

Saito TRehmsmeier M (2015)
The precision-recall plot is more informative than the ROC plot when evaluating binary classifiers on imbalanced datasets
PLoS One, 10 (3), e0118432
PubMed 25738806

Tønne E, Holdhus R, Stansberg C, Stray-Pedersen A, Petersen K, Brunner HG, Gilissen C, Hoischen A, Prescott T, Steen VM, Fiskerstrand T (2015)
Syndromic X-linked intellectual disability segregating with a missense variant in RLIM
Eur J Hum Genet, 23 (12), 1652-6
PubMed 25735484

Bredrup C, Johansson S, Bindoff LA, Sztromwasser P, Kråkenes J, Mellgren AE, Brurås KR, Lind O, Boman H, Knappskog PM, Rødahl E (2015)
High myopia-excavated optic disc anomaly associated with a frameshift mutation in the MYC-binding protein 2 gene (MYCBP2)
Am J Ophthalmol, 159 (5), 973-9.e2
PubMed 25634536

Ghavidel FZ, Claesen J, Burzykowski T (2015)
A nonhomogeneous hidden markov model for gene mapping based on next-generation sequencing data
J Comput Biol, 22 (2), 178-88
PubMed 25611462

Vaudel M, Burkhart JM, Zahedi RP, Oveland E, Berven FS, Sickmann A, Martens L, Barsnes H (2015)
PeptideShaker enables reanalysis of MS-derived proteomics data sets
Nat Biotechnol, 33 (1), 22-4
PubMed 25574629

Dimitrakopoulos GN, Dimitrakopoulou K, Maraziotis IA, Sgarbas K, Bezerianos A (2014)
Supervised method for construction of microRNA-mRNA networks: application in cardiac tissue aging dataset
Conf Proc IEEE Eng Med Biol Soc, 2014, 318-21
PubMed 25569961

Mathers AJ, Stoesser N, Sheppard AE, Pankhurst L, Giess A, Yeh AJ, Didelot X, Turner SD, Sebra R, Kasarskis A, Peto T, Crook D, Sifri CD (2015)
Klebsiella pneumoniae carbapenemase (KPC)-producing K. pneumoniae at a single institution: insights into endemicity from whole-genome sequencing
Antimicrob Agents Chemother, 59 (3), 1656-63
PubMed 25561339

Tiwari SPFuglebakk EHollup SMSkjærven LCragnolini TGrindhaug SHTekle KMReuter N (2014)
WEBnm@ v2.0: Web server and services for comparing protein flexibility
BMC Bioinformatics, 15, 427
PubMed 25547242

Kroksveen AC, Opsahl JA, Guldbrandsen A, Myhr KM, Oveland E, Torkildsen Ø, Berven FS (2014)
Cerebrospinal fluid proteomics in multiple sclerosis
Biochim Biophys Acta, 1854 (7), 746-56
PubMed 25526888

Perica T, Kondo Y, Tiwari SP, McLaughlin SH, Kemplen KR, Zhang X, Steward A, Reuter N, Clarke J, Teichmann SA (2014)
Evolution of oligomeric state through allosteric pathways that mimic ligand binding
Science, 346 (6216), 1254346
PubMed 25525255

Danks GB, Raasholm M, Campsteijn C, Long AM, Manak JR, Lenhard B, Thompson EM (2014)
Trans-splicing and operons in metazoans: translational control in maternally regulated development and recovery from growth arrest
Mol Biol Evol, 32 (3), 585-99
PubMed 25525214

Yang B, Pu M, Khan HM, Friedman L, Reuter N, Roberts MF, Gershenson A (2014)
Quantifying transient interactions between Bacillus phosphatidylinositol-specific phospholipase-C and phosphatidylcholine-rich vesicles
J Am Chem Soc, 137 (1), 14-7
PubMed 25517221

Oveland E, Muth T, Rapp E, Martens L, Berven FS, Barsnes H (2015)
Viewing the proteome: how to visualize proteomics data?
Proteomics, 15 (8), 1341-55
PubMed 25504833

Myklebust LM, Van Damme P, Støve SI, Dörfel MJ, Abboud A, Kalvik TV, Grauffel C, Jonckheere V, Wu Y, Swensen J, Kaasa H, Liszczak G, Marmorstein R, Reuter N, Lyon GJ, Gevaert K, Arnesen T(2014)
Biochemical and cellular analysis of Ogden syndrome reveals downstream Nt-acetylation defects
Hum Mol Genet, 24 (7), 1956-76
PubMed 25489052

Möller S, Afgan E, Banck M, Bonnal RJ, Booth T, Chilton J, Cock PJ, Gumbel M, Harris N, Holland R, Kalaš M, Kaján L, Kibukawa E, Powel DR, Prins P, Quinn J, Sallou O, Strozzi F, Seemann T, Sloggett C, Soiland-Reyes S, Spooner W, Steinbiss S, Tille A, Travis AJ et al. (2014)
Community-driven development for computational biology at Sprints, Hackathons and Codefests
BMC Bioinformatics, 15 Suppl 14, S7
PubMed 25472764

Korfanty J, Stokowy T, Widlak P, Gogler-Piglowska A, Handschuh L, Podkowiński J, Vydra N, Naumowicz A, Toma-Jonik A, Widlak W (2014)
Crosstalk between HSF1 and HSF2 during the heat shock response in mouse testes
Int J Biochem Cell Biol, 57, 76-83
PubMed 25450459

Barsnes H, Vaudel M, Martens L (2015)
JSparklines: making tabular proteomics data come alive
Proteomics, 15 (8), 1428-31
PubMed 25422159

Berg A, Hoivik EA, Mjøs S, Holst F, Werner HM, Tangen IL, Taylor-Weiner A, Gibson WJ, Kusonmano K, Wik E, Trovik J, Halle MK, Øyan AM, Kalland KH, Cherniack AD, Beroukhim R, Stefansson I, Mills GB, Krakstad C, Salvesen HB (2015)
Molecular profiling of endometrial carcinoma precursor, primary and metastatic lesions suggests different targets for treatment in obese compared to non-obese patients
Oncotarget, 6 (2), 1327-39
PubMed 25415225

Andersson R, Refsing Andersen P, Valen E, Core LJ, Bornholdt J, Boyd M, Heick Jensen T, Sandelin A (2014)
Nuclear stability and transcriptional directionality separate functionally distinct RNA species
Nat Commun, 5, 5336
PubMed 25387874

Bjorlykke Y, Vethe H, Vaudel M, Barsnes H, Berven FS, Tjora E, Raeder H (2014)
Carboxyl-ester lipase maturity-onset diabetes of the young disease protein biomarkers in secretin-stimulated duodenal juice
J Proteome Res, 14 (1), 521-30
PubMed 25369532

Budnjo A, Narawane S, Grauffel CSchillinger AS, Fossen T, Reuter N, Haug BE (2014)
Reversible ketomethylene-based inhibitors of human neutrophil proteinase 3
J Med Chem, 57 (22), 9396-408
PubMed 25365140

Pauli A, Valen E, Schier AF (2014)
Identifying (non-)coding RNAs and small peptides: challenges and opportunities
Bioessays, 37 (1), 103-12
PubMed 25345765

Tangen IL, Werner HM, Berg A, Halle MK, Kusonmano K, Trovik J, Hoivik EA, Mills GB, Krakstad C, Salvesen HB (2014)
Loss of progesterone receptor links to high proliferation and increases from primary to metastatic endometrial cancer lesions
Eur J Cancer, 50 (17), 3003-10
PubMed 25281525

Fuglebakk ETiwari SPReuter N (2014)
Comparing the intrinsic dynamics of multiple protein structures using elastic network models
Biochim Biophys Acta, 1850 (5), 911-22
PubMed 25267310

Stokowy T, Wojtaś B, Krajewska J, Stobiecka E, Dralle H, Musholt T, Hauptmann S, Lange D, Hegedüs L, Jarząb B, Krohn K, Paschke R, Eszlinger M (2014)
A two miRNA classifier differentiates follicular thyroid carcinomas from follicular thyroid adenomas
Mol Cell Endocrinol, 399, 43-9
PubMed 25258301

Schillinger ASGrauffel CKhan HM, Halskau O, Reuter N (2014)
Two homologous neutrophil serine proteases bind to POPC vesicles with different affinities: When aromatic amino acids matter
Biochim Biophys Acta, 1838 (12), 3191-202
PubMed 25218402

Guldbrandsen A, Vethe H, Farag Y, Oveland E, Garberg H, Berle M, Myhr KM, Opsahl JA, Barsnes H, Berven FS (2014)
In-depth characterization of the cerebrospinal fluid (CSF) proteome displayed through the CSF proteome resource (CSF-PR)
Mol Cell Proteomics, 13 (11), 3152-63
PubMed 25038066

Wik E, Trovik J, Kusonmano K, Birkeland E, Raeder MB, Pashtan I, Hoivik EA, Krakstad C, Werner HM, Holst F, Mjøs S, Halle MK, Mannelqvist M, Mauland KK, Oyan AM, Stefansson IM, Petersen K, Simon R, Cherniack AD, Meyerson M, Kalland KH, Akslen LA, Salvesen HB (2014)
Endometrial Carcinoma Recurrence Score (ECARS) validates to identify aggressive disease and associates with markers of epithelial-mesenchymal transition and PI3K alterations
Gynecol Oncol, 134 (3), 599-606
PubMed 24995579

Pagarete A, Kusonmano KPetersen K, Kimmance SA, Martínez Martínez J, Wilson WH, Hehemann JH, Allen MJ, Sandaa RA (2014)
Dip in the gene pool: metagenomic survey of natural coccolithovirus communities
Virology, 466-467, 129-37
PubMed 24947907

Kleppe R, Rosati S, Jorge-Finnigan A, Alvira S, Ghorbani S, Haavik J, Valpuesta JM, Heck AJ, Martinez A (2014)
Phosphorylation dependence and stoichiometry of the complex formed by tyrosine hydroxylase and 14-3-3γ
Mol Cell Proteomics, 13 (8), 2017-30
PubMed 24947669

Gagnon JA, Valen E, Thyme SB, Huang P, Akhmetova L, Pauli A, Montague TG, Zimmerman S, Richter C, Schier AF (2014)
Efficient mutagenesis by Cas9 protein-mediated oligonucleotide insertion and large-scale assessment of single-guide RNAs
PLoS One, 9 (5), e98186
PubMed 24873830

Montague TG, Cruz JM, Gagnon JA, Church GM, Valen E (2014)
CHOPCHOP: a CRISPR/Cas9 and TALEN web tool for genome editing
Nucleic Acids Res, 42 (Web Server issue), W401-7
PubMed 24861617

Engerud H, Tangen IL, Berg A, Kusonmano K, Halle MK, Oyan AM, Kalland KH, Stefansson I, Trovik J, Salvesen HB, Krakstad C (2014)
High level of HSF1 associates with aggressive endometrial carcinoma and suggests potential for HSP90 inhibitors
Br J Cancer, 111 (1), 78-84
PubMed 24853175

Tangen IL, Krakstad C, Halle MK, Werner HM, Oyan AM, Kusonmano KPetersen K, Kalland KH, Akslen LA, Trovik J, Hurtado A, Salvesen HB (2014)
Switch in FOXA1 status associates with endometrial cancer progression
PLoS One, 9 (5), e98069
PubMed 24849812

Nygaard G, Herfindal L, Kopperud R, Aragay AM, Holmsen H, Døskeland SO, Kleppe R, Selheim F (2014)
Time-dependent inhibitory effects of cGMP-analogues on thrombin-induced platelet-derived microparticles formation, platelet aggregation, and P-selectin expression
Biochem Biophys Res Commun, 449 (3), 357-63
PubMed 24845383

Vaudel M, Barsnes H, Martens L, Berven FS (2014)
Bioinformatics for proteomics: opportunities at the interface between the scientists, their experiments, and the community
Methods Mol Biol, 1156, 239-48
PubMed 24791993

Taxt AM, Diaz Y, Bacle A, Grauffel C, Reuter N, Aasland R, Sommerfelt H, Puntervoll P (2014)
Characterization of immunological cross-reactivity between enterotoxigenic Escherichia coli heat-stable toxin and human guanylin and uroguanylin
Infect Immun, 82 (7), 2913-22
PubMed 24778111

Dudek M, Romanowska J, Wituła T, Trylska J (2014)
Interactions of amikacin with the RNA model of the ribosomal A-site: computational, spectroscopic and calorimetric studies
Biochimie, 102, 188-202
PubMed 24769038

Fossbakk A, Kleppe R, Knappskog PM, Martinez A, Haavik J (2014)
Functional studies of tyrosine hydroxylase missense variants reveal distinct patterns of molecular defects in Dopa-responsive dystonia
Hum Mutat, 35 (7), 880-90
PubMed 24753243

Herfindal L, Krakstad C, Myhren L, Hagland H, Kopperud R, Teigen K, Schwede F, Kleppe R, Døskeland SO (2014)
Introduction of aromatic ring-containing substituents in cyclic nucleotides is associated with inhibition of toxin uptake by the hepatocyte transporters OATP 1B1 and 1B3
PLoS One, 9 (4), e94926
PubMed 24740327

Vaudel M, Venne AS, Berven FS, Zahedi RP, Martens L, Barsnes H (2014)
Shedding light on black boxes in protein identification
Proteomics, 14 (9), 1001-5
PubMed 24678044

FANTOM Consortium and the RIKEN PMI and CLST (DGT), Forrest AR, Kawaji H, Rehli M, Baillie JK, de Hoon MJ, Haberle V, Lassmann T, Kulakovskiy IV, Lizio M, Itoh M, Andersson R, Mungall CJ, Meehan TF, Schmeier S, Bertin N, Jørgensen M, Dimont E, Arner E, Schmidl C, Schaefer U, Medvedeva YA, Plessy C, Vitezic M, Severin J et al. (2014)
A promoter-level mammalian expression atlas
Nature, 507 (7493), 462-70
PubMed 24670764

Andersson R, Gebhard C, Miguel-Escalada I, Hoof I, Bornholdt J, Boyd M, Chen Y, Zhao X, Schmidl C, Suzuki T, Ntini E, Arner E, Valen E, Li K, Schwarzfischer L, Glatz D, Raithel J, Lilje B, Rapin N, Bagger FO, Jørgensen M, Andersen PR, Bertin N, Rackham O, Burroughs AM et al. (2014)
An atlas of active enhancers across human cell types and tissues
Nature, 507 (7493), 455-61
PubMed 24670763

Kaján L, Hopf TA, Kalaš M, Marks DS, Rost B (2014)
FreeContact: fast and free software for protein contact prediction from residue co-evolution
BMC Bioinformatics, 15, 85
PubMed 24669753

Hoivik EA, Kusonmano K, Halle MK, Berg A, Wik E, Werner HM, Petersen K, Oyan AM, Kalland KH, Krakstad C, Trovik J, Widschwendter M, Salvesen HB (2014)
Hypomethylation of the CTCFL/BORIS promoter and aberrant expression during endometrial cancer progression suggests a role as an Epi-driver gene
Oncotarget, 5 (4), 1052-61
PubMed 24658009

Wojtas B, Ferraz C, Stokowy T, Hauptmann S, Lange D, Dralle H, Musholt T, Jarzab B, Paschke R, Eszlinger M (2014)
Differential miRNA expression defines migration and reduced apoptosis in follicular thyroid carcinomas
Mol Cell Endocrinol, 388 (1-2), 1-9
PubMed 24631480

Stokowy T, Eszlinger M, Świerniak M, Fujarewicz K, Jarząb B, Paschke R, Krohn K (2014)
Analysis options for high-throughput sequencing in miRNA expression profiling
BMC Res Notes, 7, 144
PubMed 24625073

Pascarella G, Lazarevic D, Plessy C, Bertin N, Akalin A, Vlachouli C, Simone R, Faulkner GJ, Zucchelli S, Kawai J, Daub CO, Hayashizaki Y, Lenhard B, Carninci P, Gustincich S (2014)
NanoCAGE analysis of the mouse olfactory epithelium identifies the expression of vomeronasal receptors and of proximal LINE elements
Front Cell Neurosci, 8, 41
PubMed 24600346

Furmanek T, Demski K, Banaś W, Haslam R, Napier J, Stymne S, Banaś A (2014)
The utilization of the acyl-CoA and the involvement PDAT and DGAT in the biosynthesis of erucic acid-rich triacylglycerols in Crambe seed oil
Lipids, 49 (4), 327-33
PubMed 24578031

Parulek J, Turkay C, Reuter N, Viola I (2013)
Visual cavity analysis in molecular simulations
BMC Bioinformatics, 14 Suppl 19, S4
PubMed 24564409

Sharma Y, Chilamakuri CS, Bakke M, Lenhard B (2014)
Computational characterization of modes of transcriptional regulation of nuclear receptor genes
PLoS One, 9 (2), e88880
PubMed 24551185

Zuin J, Franke V, van Ijcken WF, van der Sloot A, Krantz ID, van der Reijden MI, Nakato R, Lenhard B, Wendt KS (2014)
A cohesin-independent role for NIPBL at promoters provides insights in CdLS
PLoS Genet, 10 (2), e1004153
PubMed 24550742

Haberle V, Li N, Hadzhiev Y, Plessy C, Previti CNepal C, Gehrig J, Dong X, Akalin A, Suzuki AM, van IJcken WF, Armant O, Ferg M, Strähle U, Carninci P, Müller F, Lenhard B (2014)
Two independent transcription initiation codes overlap on vertebrate core promoters
Nature, 507 (7492), 381-5
PubMed 24531765

Hadziavdic K, Lekang K, Lanzen AJonassen I, Thompson EM, Troedsson C (2014)
Characterization of the 18S rRNA gene for designing universal eukaryote specific primers
PLoS One, 9 (2), e87624
PubMed 24516555

Dimitrakopoulou K, Dimitrakopoulos GN, Wilk E, Tsimpouris C, Sgarbas KN, Schughart K, Bezerianos A (2014)
Influenza A immunomics and public health omics: the dynamic pathway interplay in host response to H1N1 infection
OMICS, 18 (3), 167-83
PubMed 24512282

Katayama T, Wilkinson MD, Aoki-Kinoshita KF, Kawashima S, Yamamoto Y, Yamaguchi A, Okamoto S, Kawano S, Kim JD, Wang Y, Wu H, Kano Y, Ono H, Bono H, Kocbek S, Aerts J, Akune Y, Antezana E, Arakawa K, Aranda B, Baran J, Bolleman J, Bonnal RJ, Buttigieg PL, Campbell MP et al. (2014)
BioHackathon series in 2011 and 2012: penetration of ontology and linked data in life science domains
J Biomed Semantics, 5 (1), 5
PubMed 24495517

Tysnes BB, Satran HA, Mork SJ, Margaryan NV, Eide GE, Petersen K, Strizzi L, Hendrix MJ (2013)
Age-Dependent Association between Protein Expression of the Embryonic Stem Cell Marker Cripto-1 and Survival of Glioblastoma Patients
Transl Oncol, 6 (6), 732-41
PubMed 24466376

Pauli A, Norris ML, Valen E, Chew GL, Gagnon JA, Zimmerman S, Mitchell A, Ma J, Dubrulle J, Reyon D, Tsai SQ, Joung JK, Saghatelian A, Schier AF (2014)
Toddler: an embryonic signal that promotes cell movement via Apelin receptors
Science, 343 (6172), 1248636
PubMed 24407481

Narawane S, Budnjo A, Grauffel C, Haug BE, Reuter N (2014)
In silico design, synthesis, and assays of specific substrates for proteinase 3: influence of fluorogenic and charged groups
J Med Chem, 57 (3), 1111-5
PubMed 24397704

Ghavidel FZ, Mertens I, Baggerman G, Laukens K, Burzykowski T, Valkenborg D (2013)
The use of the isotopic distribution as a complementary quality metric to assess tandem mass spectra results
J Proteomics, 98, 150-8
PubMed 24384257

Goncearenco A, Ma BG, Berezovsky IN (2013)
Molecular mechanisms of adaptation emerging from the physics and evolution of nucleic acids and proteins
Nucleic Acids Res, 42 (5), 2879-92
PubMed 24371267

Kelchtermans P, Bittremieux W, De Grave K, Degroeve S, Ramon J, Laukens K, Valkenborg D, Barsnes H, Martens L (2014)
Machine learning applications in proteomics research: how the past can boost the future
Proteomics, 14 (4-5), 353-66
PubMed 24323524

Pedersen JS, Valen E, Velazquez AM, Parker BJ, Rasmussen M, Lindgreen S, Lilje B, Tobin DJ, Kelly TK, Vang S, Andersson R, Jones PA, Hoover CA, Tikhonov A, Prokhortchouk E, Rubin EM, Sandelin A, Gilbert MT, Krogh A, Willerslev E, Orlando L (2013)
Genome-wide nucleosome map and cytosine methylation levels of an ancient human genome
Genome Res, 24 (3), 454-66
PubMed 24299735

Dimitrakopoulou K, Dimitrakopoulos GN, Sgarbas KN, Bezerianos A (2013)
Tamoxifen integromics and personalized medicine: dynamic modular transformations underpinning response to tamoxifen in breast cancer treatment
OMICS, 18 (1), 15-33
PubMed 24299457

Muth T, Weilnböck L, Rapp E, Huber CG, Martens L, Vaudel M, Barsnes H (2014)
DeNovoGUI: an open source graphical user interface for de novo sequencing of tandem mass spectra
J Proteome Res, 13 (2), 1143-6
PubMed 24295440

Verheggen K, Barsnes H, Martens L (2013)
Distributed computing and data storage in proteomics: many hands make light work, and a stronger memory
Proteomics, 14 (4-5), 367-77
PubMed 24285552

Kleppe R, Ghorbani S, Martinez A, Haavik J (2013)
Modelling cellular signal communication mediated by phosphorylation dependent interaction with 14-3-3 proteins
FEBS Lett, 588 (1), 92-8
PubMed 24269229

Harmston N, Baresic A, Lenhard B (2013)
The mystery of extreme non-coding conservation
Philos Trans R Soc Lond B Biol Sci, 368 (1632), 20130021
PubMed 24218634

Mathelier A, Zhao X, Zhang AW, Parcy F, Worsley-Hunt R, Arenillas DJ, Buchman S, Chen CY, Chou A, Ienasescu H, Lim J, Shyr C, Tan G, Zhou M, Lenhard B, Sandelin A, Wasserman WW (2013)
JASPAR 2014: an extensively expanded and updated open-access database of transcription factor binding profiles
Nucleic Acids Res, 42 (Database issue), D142-7
PubMed 24194598

Wojtaś B, Pfeifer A, Jarząb M, Czarniecka A, Krajewska J, Swierniak M, Stokowy T, Rusinek D, Kowal M, Zebracka-Gala J, Tyszkiewicz T, Oczko-Wojciechowska M, Stobiecka E, Lange D, Paschke R, Jarząb B (2013)
Unsupervised analysis of follicular thyroid tumours transcriptome by oligonucleotide microarray gene expression profiling
Endokrynol Pol, 64 (5), 328-34
PubMed 24186587

Urich T, Lanzén A, Stokke R, Pedersen RB, Bayer C, Thorseth IH, Schleper C, Steen IH, Ovreas L (2013)
Microbial community structure and functioning in marine sediments associated with diffuse hydrothermal venting assessed by integrated meta-omics
Environ Microbiol, 16 (9), 2699-710
PubMed 24112684

Pfeifer A, Wojtas B, Oczko-Wojciechowska M, Kukulska A, Czarniecka A, Eszlinger M, Musholt T, Stokowy T, Swierniak M, Stobiecka E, Rusinek D, Tyszkiewicz T, Kowal M, Jarzab M, Hauptmann S, Lange D, Paschke R, Jarzab B (2013)
Molecular differential diagnosis of follicular thyroid carcinoma and adenoma based on gene expression profiling by using formalin-fixed paraffin-embedded tissues
BMC Med Genomics, 6, 38
PubMed 24099521

Gorbatenko A, Olesen CW, Mørup N, Thiel G, Kallunki T, Valen E, Pedersen SF (2013)
ErbB2 upregulates the Na+,HCO3(-)-cotransporter NBCn1/SLC4A7 in human breast cancer cells via Akt, ERK, Src, and Kruppel-like factor 4
FASEB J, 28 (1), 350-63
PubMed 24088818

Chavali S, Bruhn S, Tiemann K, Saetrom P, Barrenäs F, Saito T, Kanduri K, Wang H, Benson M (2013)
MicroRNAs act complementarily to regulate disease-related mRNA modules in human diseases
RNA, 19 (11), 1552-62
PubMed 24062574

Frangini A, Sjöberg M, Roman-Trufero M, Dharmalingam G, Haberle V, Bartke T, Lenhard B, Malumbres M, Vidal M, Dillon N (2013)
The aurora B kinase and the polycomb protein ring1B combine to regulate active promoters in quiescent lymphocytes
Mol Cell, 51 (5), 647-61
PubMed 24034696

Lanzén A, Simachew A, Gessesse A, Chmolowska D, Jonassen I, Øvreås L (2013)
Surprising prokaryotic and eukaryotic diversity, community structure and biogeography of Ethiopian soda lakes
PLoS One, 8 (8), e72577
PubMed 24023625

Malcher A, Rozwadowska N, Stokowy T, Kolanowski T, Jedrzejczak P, Zietkowiak W, Kurpisz M (2013)
Potential biomarkers of nonobstructive azoospermia identified in microarray gene expression analysis
Fertil Steril, 100 (6), 1686-94.e1-7
PubMed 24012201

Nepal C, Hadzhiev Y, Previti C, Haberle V, Li N, Takahashi H, Suzuki AM, Sheng Y, Abdelhamid RF, Anand S, Gehrig J, Akalin A, Kockx CE, van der Sloot AA, van Ijcken WF, Armant O, Rastegar S, Watson C, Strähle U, Stupka E, Carninci P, Lenhard B, Müller F (2013)
Dynamic regulation of the transcription initiation landscape at single nucleotide resolution during vertebrate embryogenesis
Genome Res, 23 (11), 1938-50
PubMed 24002785

Seitan VC, Faure AJ, Zhan Y, McCord RP, Lajoie BR, Ing-Simmons E, Lenhard B, Giorgetti L, Heard E, Fisher AG, Flicek P, Dekker J, Merkenschlager M (2013)
Cohesin-based chromatin interactions enable regulated gene expression within preexisting architectural compartments
Genome Res, 23 (12), 2066-77
PubMed 24002784

Karlsen BO, Klingan K, Emblem Å, Jørgensen TE, Jueterbock A, Furmanek T, Hoarau G, Johansen SD, Nordeide JT, Moum T (2013)
Genomic divergence between the migratory and stationary ecotypes of Atlantic cod
Mol Ecol, 22 (20), 5098-111
PubMed 23998762

Petersen K, Rajcevic U, Abdul Rahim SA, Jonassen I, Kalland KH, Jimenez CR, Bjerkvig R, Niclou SP (2013)
Gene set based integrated data analysis reveals phenotypic differences in a brain cancer model
PLoS One, 8 (7), e68288
PubMed 23874576

Malcher A, Rozwadowska N, Stokowy T, Jedrzejczak P, Zietkowiak W, Kurpisz M (2013)
The gene expression analysis of paracrine/autocrine factors in patients with spermatogenetic failure compared with normal spermatogenesis
Am J Reprod Immunol, 70 (6), 522-8
PubMed 23869807

Ntini E, Järvelin AI, Bornholdt J, Chen Y, Boyd M, Jørgensen M, Andersson R, Hoof I, Schein A, Andersen PR, Andersen PK, Preker P, Valen E, Zhao X, Pelechano V, Steinmetz LM, Sandelin A, Jensen TH(2013)
Polyadenylation site-induced decay of upstream transcripts enforces promoter directionality
Nat Struct Mol Biol, 20 (8), 923-8
PubMed 23851456

Ersland KM, Håvik B, Rinholm JE, Gundersen V, Stansberg C, Steen VM (2013)
LOC689986, a unique gene showing specific expression in restricted areas of the rodent neocortex
BMC Neurosci, 14, 68
PubMed 23844656

Dimitrakopoulou K, Vrahatis AG, Wilk E, Tsakalidis AK, Bezerianos A (2013)
OLYMPUS: an automated hybrid clustering method in time series gene expression. Case study: host response after Influenza A (H1N1) infection
Comput Methods Programs Biomed, 111 (3), 650-61
PubMed 23796450

Harmston N, Lenhard B (2013)
Chromatin and epigenetic features of long-range gene regulation
Nucleic Acids Res, 41 (15), 7185-99
PubMed 23766291

Goncearenco A, Mitternacht S, Yong T, Eisenhaber B, Eisenhaber F, Berezovsky IN (2013)
SPACER: Server for predicting allosteric communication and effects of regulation
Nucleic Acids Res, 41 (Web Server issue), W266-72
PubMed 23737445

Wang S, Kryvi H, Grotmol S, Wargelius A, Krossøy C, Epple M, Neues F, Furmanek T, Totland GK (2013)
Mineralization of the vertebral bodies in Atlantic salmon (Salmo salar L.) is initiated segmentally in the form of hydroxyapatite crystal accretions in the notochord sheath
J Anat, 223 (2), 159-70
PubMed 23711083

Chew GL, Pauli A, Rinn JL, Regev A, Schier AF, Valen E (2013)
Ribosome profiling reveals resemblance between long non-coding RNAs and 5′ leaders of coding RNAs
Development, 140 (13), 2828-34
PubMed 23698349

Armant O, März M, Schmidt R, Ferg M, Diotel N, Ertzer R, Bryne JC, Yang L, Baader I, Reischl M, Legradi J, Mikut R, Stemple D, van IJcken W, van der Sloot A, Lenhard B, Strähle U, Rastegar S (2013)
Genome-wide, whole mount in situ analysis of transcriptional regulators in zebrafish embryos
Dev Biol, 380 (2), 351-62
PubMed 23684812

Thongjuea S, Stadhouders R, Grosveld FG, Soler E, Lenhard B (2013)
r3Cseq: an R/Bioconductor package for the discovery of long-range genomic interactions from chromosome conformation capture and next-generation sequencing data
Nucleic Acids Res, 41 (13), e132
PubMed 23671339

Sandve GK, Gundersen S, Johansen M, Glad IK, Gunathasan K, Holden L, Holden M, Liestøl K, Nygård S, Nygaard V, Paulsen J, Rydbeck H, Trengereid K, Clancy T, Drabløs F, Ferkingstad E, Kalas M, Lien T, Rye MB, Frigessi A, Hovig E (2013)
The Genomic HyperBrowser: an analysis web server for genome-scale data
Nucleic Acids Res, 41 (Web Server issue), W133-41
PubMed 23632163

Bagi A, Pampanin DM, Lanzén A, Bilstad T, Kommedal R (2013)
Naphthalene biodegradation in temperate and arctic marine microcosms
Biodegradation, 25 (1), 111-25
PubMed 23624724

Xiao Y, Jin J, Chang M, Chang JH, Hu H, Zhou X, Brittain GC, Stansberg C, Torkildsen Ø, Wang X, Brink R, Cheng X, Sun SC (2013)
Peli1 promotes microglia-mediated CNS inflammation by regulating Traf3 degradation
Nat Med, 19 (5), 595-602
PubMed 23603814

Hulstaert N, Reisinger F, Rameseder J, Barsnes H, Vizcaíno JA, Martens L (2013)
Pride-asap: automatic fragment ion annotation of identified PRIDE spectra
J Proteomics, 95, 89-92
PubMed 23603108

Ghamari A, van de Corput MP, Thongjuea S, van Cappellen WA, van Ijcken W, van Haren J, Soler E, Eick D, Lenhard B, Grosveld FG (2013)
In vivo live imaging of RNA polymerase II transcription factories in primary cells
Genes Dev, 27 (7), 767-77
PubMed 23592796

Wik E, Birkeland E, Trovik J, Werner HM, Hoivik EA, Mjos S, Krakstad C, Kusonmano K, Mauland K, Stefansson IM, Holst F, Petersen K, Oyan AM, Simon R, Kalland KH, Ricketts W, Akslen LA, Salvesen HB (2013)
High phospho-Stathmin(Serine38) expression identifies aggressive endometrial cancer and suggests an association with PI3K inhibition
Clin Cancer Res, 19 (9), 2331-41
PubMed 23538402

Carvalho RH, Hou J, Haberle V, Aerts J, Grosveld F, Lenhard B, Philipsen S (2013)
Genomewide DNA methylation analysis identifies novel methylated genes in non-small-cell lung carcinomas
J Thorac Oncol, 8 (5), 562-73
PubMed 23524404

Grauffel C, Yang B, He T, Roberts MF, Gershenson A, Reuter N (2013)
Cation-π interactions as lipid-specific anchors for phosphatidylinositol-specific phospholipase C
J Am Chem Soc, 135 (15), 5740-50
PubMed 23506313

Sheffield NC, Thurman RE, Song L, Safi A, Stamatoyannopoulos JA, Lenhard B, Crawford GE, Furey TS (2013)
Patterns of regulatory activity across diverse human cell types predict tissue identity, transcription factor binding, and long-range interactions
Genome Res, 23 (5), 777-88
PubMed 23482648

Ison J, Kalas MJonassen I, Bolser D, Uludag M, McWilliam H, Malone J, Lopez R, Pettifer S, Rice P (2013)
EDAM: an ontology of bioinformatics operations, types of data and identifiers, topics and formats
Bioinformatics, 29 (10), 1325-32
PubMed 23479348

Eme L, Reigstad LJ, Spang A, Lanzén A, Weinmaier T, Rattei T, Schleper C, Brochier-Armanet C (2013)
Metagenomics of Kamchatkan hot spring filaments reveal two new major (hyper)thermophilic lineages related to Thaumarchaeota
Res Microbiol, 164 (5), 425-38
PubMed 23470515

Malde K, Furmanek T (2013)
Increasing sequence search sensitivity with transitive alignments
PLoS One, 8 (2), e54422
PubMed 23457449

Mylona A, Andrieu-Soler C, Thongjuea S, Martella A, Soler E, Jorna R, Hou J, Kockx C, van Ijcken W, Lenhard B, Grosveld F (2013)
Genome-wide analysis shows that Ldb1 controls essential hematopoietic genes/pathways in mouse early development and reveals novel players in hematopoiesis
Blood, 121 (15), 2902-13
PubMed 23390196

Barsnes H, Martens L (2013)
Crowdsourcing in proteomics: public resources lead to better experiments
Amino Acids, 44 (4), 1129-37
PubMed 23377569

Balzer S, Malde K, Grohme MA, Jonassen I (2013)
Filtering duplicate reads from 454 pyrosequencing data
Bioinformatics, 29 (7), 830-6
PubMed 23376350

Dimitrakopoulou K, Dimitrakopoulos G, Zacharaki EI, Maraziotis IA, Sgarbas K, Bezerianos A (2012)
Revealing the dynamic modularity of composite biological networks in breast cancer treatment
Conf Proc IEEE Eng Med Biol Soc, 2012, 5432-6
PubMed 23367158

Dimitrakopoulos G, Sgarbas K, Dimitrakopoulou K, Dragomir A, Bezerianos A, Maraziotis IA (2012)
Multi-scale modeling of gene regulatory networks via integration of temporal and topological biological data
Conf Proc IEEE Eng Med Biol Soc, 2012, 1242-5
PubMed 23366123

Cheng J, Karri S, Grauffel C, Wang F, Reuter N, Roberts MF, Wintrode PL, Gershenson A (2013)
Does changing the predicted dynamics of a phospholipase C alter activity and membrane binding?
Biophys J, 104 (1), 185-95
PubMed 23332071

Krakstad C, Birkeland E, Seidel D, Kusonmano K, Petersen K, Mjøs S, Hoivik EA, Wik E, Halle MK, Øyan AM, Kalland KH, Werner HM, Trovik J, Salvesen H (2012)
High-throughput mutation profiling of primary and metastatic endometrial cancers identifies KRAS, FGFR2 and PIK3CA to be frequently mutated
PLoS One, 7 (12), e52795
PubMed 23300780

Grauffel C, Abboud A, Liszczak G, Marmorstein R, Arnesen T, Reuter N (2012)
Specificity and versatility of substrate binding sites in four catalytic domains of human N-terminal acetyltransferases
PLoS One, 7 (12), e52642
PubMed 23285125

Waheed Q, Tjörnhammar R, Edholm O (2012)
Phase transitions in coarse-grained lipid bilayers containing cholesterol by molecular dynamics simulations
Biophys J, 103 (10), 2125-33
PubMed 23200046

Danks G, Campsteijn C, Parida M, Butcher S, Doddapaneni H, Fu B, Petrin R, Metpally R, Lenhard B, Wincker P, Chourrout D, Thompson EM, Manak JR (2012)
OikoBase: a genomics and developmental transcriptomics resource for the urochordate Oikopleura dioica
Nucleic Acids Res, 41 (Database issue), D845-53
PubMed 23185044

Lanzén A, Jørgensen SL, Huson DH, Gorfer M, Grindhaug SH, Jonassen I, Øvreås L, Urich T (2012)
CREST–classification resources for environmental sequence tags
PLoS One, 7 (11), e49334
PubMed 23145153

Sridhar S, Sharma A, Kongshaug H, Nilsen F, Jonassen I (2012)
Whole genome sequencing of the fish pathogen Francisella noatunensis subsp. orientalis Toba04 gives novel insights into Francisella evolution and pathogenecity
BMC Genomics, 13, 598
PubMed 23131096

Yadetie F, Karlsen OA, Lanzén A, Berg K, Olsvik P, Hogstrand C, Goksøyr A (2012)
Global transcriptome analysis of Atlantic cod (Gadus morhua) liver after in vivo methylmercury exposure suggests effects on energy metabolism pathways
Aquat Toxicol, 126, 314-25
PubMed 23103053

Werner HM, Berg A, Wik E, Birkeland E, Krakstad C, Kusonmano K, Petersen K, Kalland KH, Oyan AM, Akslen LA, Trovik J, Salvesen HB (2012)
ARID1A loss is prevalent in endometrial hyperplasia with atypia and low-grade endometrioid carcinomas
Mod Pathol, 26 (3), 428-34
PubMed 23080032

Kroksveen AC, Aasebø E, Vethe H, Van Pesch V, Franciotta D, Teunissen CE, Ulvik RJ, Vedeler C, Myhr KM, Barsnes H, Berven FS (2012)
Discovery and initial verification of differentially abundant proteins between multiple sclerosis patients and controls using iTRAQ and SID-SRM
J Proteomics, 78, 312-25
PubMed 23059536

Jorgensen SL, Hannisdal B, Lanzén A, Baumberger T, Flesland K, Fonseca R, Ovreås L, Steen IH, Thorseth IH, Pedersen RB, Schleper C (2012)
Correlating microbial community profiles with geochemical data in highly stratified sediments from the Arctic Mid-Ocean Ridge
Proc Natl Acad Sci U S A, 109 (42), E2846-55
PubMed 23027979

Blinn KS, Li X, Liu M, Bottomley LA, Liu M (2012)
Probing and mapping electrode surfaces in solid oxide fuel cells
J Vis Exp (67), e50161
PubMed 23023264

Thurman RE, Rynes E, Humbert R, Vierstra J, Maurano MT, Haugen E, Sheffield NC, Stergachis AB, Wang H, Vernot B, Garg K, John S, Sandstrom R, Bates D, Boatman L, Canfield TK, Diegel M, Dunn D, Ebersol AK, Frum T, Giste E, Johnson AK, Johnson EM, Kutyavin T, Lajoie B et al. (2012)
The accessible chromatin landscape of the human genome
Nature, 489 (7414), 75-82
PubMed 22955617

Côté RG, Griss J, Dianes JA, Wang R, Wright JC, van den Toorn HW, van Breukelen B, Heck AJ, Hulstaert N, Martens L, Reisinger F, Csordas A, Ovelleiro D, Perez-Rivevol Y, Barsnes H, Hermjakob H, Vizcaíno JA (2012)
The PRoteomics IDEntification (PRIDE) Converter 2 framework: an improved suite of tools to facilitate data submission to the PRIDE database and the ProteomeXchange consortium
Mol Cell Proteomics, 11 (12), 1682-9
PubMed 22949509

Kleppe L, Edvardsen RB, Kuhl H, Malde K, Furmanek T, Drivenes O, Reinhardt R, Taranger GL, Wargelius A (2012)
Maternal 3’UTRs: from egg to onset of zygotic transcription in Atlantic cod
BMC Genomics, 13, 443
PubMed 22937762

Romanowska J, Reuter N, Trylska J (2012)
Comparing aminoglycoside binding sites in bacterial ribosomal RNA and aminoglycoside modifying enzymes
Proteins, 81 (1), 63-80
PubMed 22907688

Logares R, Haverkamp TH, Kumar S, Lanzén A, Nederbragt AJ, Quince C, Kauserud H (2012)
Environmental microbiology through the lens of high-throughput DNA sequencing: synopsis of current platforms and bioinformatics approaches
J Microbiol Methods, 91 (1), 106-13
PubMed 22849829

Bouayad D, Pederzoli-Ribeil M, Mocek J, Candalh C, Arlet JB, Hermine O, Reuter N, Davezac N, Witko-Sarsat V (2012)
Nuclear-to-cytoplasmic relocalization of the proliferating cell nuclear antigen (PCNA) during differentiation involves a chromosome region maintenance 1 (CRM1)-dependent export and is a prerequisite for PCNA antiapoptotic activity in mature neutrophils
J Biol Chem, 287 (40), 33812-25
PubMed 22846997

Skavland J, Jørgensen KM, Hadziavdic K, Hovland R, Jonassen I, Bruserud O, Gjertsen BT (2011)
Specific cellular signal-transduction responses to in vivo combination therapy with ATRA, valproic acid and theophylline in acute myeloid leukemia
Blood Cancer J, 1 (2), e4
PubMed 22829110

van Riel B, Pakozdi T, Brouwer R, Monteiro R, Tuladhar K, Franke VBryne JC, Jorna R, Rijkers EJ, van Ijcken W, Andrieu-Soler C, Demmers J, Patient R, Soler E, Lenhard B, Grosveld F (2012)
A novel complex, RUNX1-MYEF2, represses hematopoietic genes in erythroid cells
Mol Cell Biol, 32 (19), 3814-22
PubMed 22801375

Fuglebakk E, Echave J, Reuter N (2012)
Measuring and comparing structural fluctuation patterns in large protein datasets
Bioinformatics, 28 (19), 2431-40
PubMed 22796957

Hosp J, Sagane Y, Danks G, Thompson EM (2012)
The evolving proteome of a complex extracellular matrix, the Oikopleura house
PLoS One, 7 (7), e40172
PubMed 22792236

Mishra CK, Choi TJ, Kang SC (2012)
Isolation and characterization of a bacteriophage F20 virulent to Enterobacter aerogenes
J Gen Virol, 93 (Pt 10), 2310-4
PubMed 22764320

Bengtsson MM, Sjøtun K, Lanzén A, Ovreås L (2012)
Bacterial diversity in relation to secondary production and succession on surfaces of the kelp Laminaria hyperborea
ISME J, 6 (12), 2188-98
PubMed 22763650

Lasry I, Seo YA, Ityel H, Shalva N, Pode-Shakked B, Glaser F, Berman B, Berezovsky IGoncearenco A, Klar A, Levy J, Anikster Y, Kelleher SL, Assaraf YG (2012)
A dominant negative heterozygous G87R mutation in the zinc transporter, ZnT-2 (SLC30A2), results in transient neonatal zinc deficiency
J Biol Chem, 287 (35), 29348-61
PubMed 22733820

Carvalho RH, Haberle V, Hou J, van Gent T, Thongjuea S, van Ijcken W, Kockx C, Brouwer R, Rijkers E, Sieuwerts A, Foekens J, van Vroonhoven M, Aerts J, Grosveld F, Lenhard B, Philipsen S (2012)
Genome-wide DNA methylation profiling of non-small cell lung carcinomas
Epigenetics Chromatin, 5 (1), 9
PubMed 22726460

Bartossek R, Spang A, Weidler G, Lanzen A, Schleper C (2012)
Metagenomic analysis of ammonia-oxidizing archaea affiliated with the soil group
Front Microbiol, 3, 208
PubMed 22723795

Sleutels F, Soochit W, Bartkuhn M, Heath H, Dienstbach S, Bergmaier P, Franke V, Rosa-Garrido M, van de Nobelen S, Caesar L, van der Reijden M, Bryne JC, van Ijcken W, Grootegoed JA, Delgado MD, Lenhard B, Renkawitz R, Grosveld F, Galjart N (2012)
The male germ cell gene regulator CTCFL is functionally different from CTCF and binds CTCF-like consensus sites in a nucleosome composition-dependent manner
Epigenetics Chromatin, 5 (1), 8
PubMed 22709888

Stavrum R, Valvatne H, Stavrum AK, Riley LW, Ulvestad E, Jonassen I, Doherty TM, Grewal HM (2012)
Mycobacterium tuberculosis Mce1 protein complex initiates rapid induction of transcription of genes involved in substrate trafficking
Genes Immun, 13 (6), 496-502
PubMed 22695749

Klingström T, Soldatova L, Stevens R, Roos TE, Swertz MA, Müller KM, Kalaš M, Lambrix P, Taussig MJ, Litton JE, Landegren U, Bongcam-Rudloff E (2012)
Workshop on laboratory protocol standards for the Molecular Methods Database
N Biotechnol, 30 (2), 109-13
PubMed 22687389

Haberle V, Lenhard B (2012)
Dissecting genomic regulatory elements in vivo
Nat Biotechnol, 30 (6), 504-6
PubMed 22678387

Cheevadhanarak S, Paithoonrangsarid K, Prommeenate P, Kaewngam W, Musigkain A, Tragoonrung S, Tabata S, Kaneko T, Chaijaruwanich J, Sangsrakru D, Tangphatsornruang S, Chanprasert J, Tongsima S, Kusonmano K, Jeamton W, Dulsawat S, Klanchui A, Vorapreeda T, Chumchua V, Khannapho C, Thammarongtham C, Plengvidhya V, Subudhi S, Hongsthong A, Ruengjitchatchawalya M et al. (2012)
Draft genome sequence of Arthrospira platensis C1 (PCC9438)
Stand Genomic Sci, 6 (1), 43-53
PubMed 22675597

Johansson S, Irgens H, Chudasama KK, Molnes J, Aerts J, Roque FS, Jonassen I, Levy S, Lima K, Knappskog PM, Bell GI, Molven A, Njølstad PR (2012)
Exome sequencing and genetic testing for MODY
PLoS One, 7 (5), e38050
PubMed 22662265

Kusonmano K, Netzer M, Baumgartner C, Dehmer M, Liedl KR, Graber A (2012)
Effects of pooling samples on the performance of classification algorithms: a comparative study
ScientificWorldJournal, 2012, 278352
PubMed 22654582

Goncearenco ABerezovsky IN (2012)
Exploring the evolution of protein function in Archaea
BMC Evol Biol, 12, 75
PubMed 22646318

Skjaerven L, Muga A, Reuter N, Martinez A (2012)
A dynamic model of long-range conformational adaptations triggered by nucleotide binding in GroEL-GroES
Proteins, 80 (10), 2333-46
PubMed 22576372

Aye TT, Low TY, Bjørlykke Y, Barsnes H, Heck AJ, Berven FS (2012)
Use of stable isotope dimethyl labeling coupled to selected reaction monitoring to enhance throughput by multiplexing relative quantitation of targeted proteins
Anal Chem, 84 (11), 4999-5006
PubMed 22548487

Ribeiro de Almeida C, Stadhouders R, Thongjuea S, Soler E, Hendriks RW (2012)
DNA-binding factor CTCF and long-range gene interactions in V(D)J recombination and oncogene activation
Blood, 119 (26), 6209-18
PubMed 22538856

Ray J, Dondrup M, Modha S, Steen IH, Sandaa RA, Clokie M (2012)
Finding a needle in the virus metagenome haystack–micro-metagenome analysis captures a snapshot of the diversity of a bacteriophage armoire
PLoS One, 7 (4), e34238
PubMed 22509283

Schroder K, Irvine KM, Taylor MS, Bokil NJ, Le Cao KA, Masterman KA, Labzin LI, Semple CA, Kapetanovic R, Fairbairn L, Akalin A, Faulkner GJ, Baillie JK, Gongora M, Daub CO, Kawaji H, McLachlan GJ, Goldman N, Grimmond SM, Carninci P, Suzuki H, Hayashizaki Y, Lenhard B, Hume DA, Sweet MJ (2012)
Conservation and divergence in Toll-like receptor 4-regulated gene expression in primary human versus mouse macrophages
Proc Natl Acad Sci U S A, 109 (16), E944-53
PubMed 22451944

Christoforou A, Dondrup M, Mattingsdal M, Mattheisen M, Giddaluru S, Nöthen MM, Rietschel M, Cichon S, Djurovic S, Andreassen OA, Jonassen I, Steen VM, Puntervoll P, Le Hellard S (2012)
Linkage-disequilibrium-based binning affects the interpretation of GWASs
Am J Hum Genet, 90 (4), 727-33
PubMed 22444669

Saini M, Tiwari S, Prasad J, Singh S, Kumar MS, Bala M (2010)
Hippophae leaf extract concentration regulates antioxidant and prooxidant effects on DNA
J Diet Suppl, 7 (1), 60-70
PubMed 22435574

Stokke R, Roalkvam I, Lanzen A, Haflidason H, Steen IH (2012)
Integrated metagenomic and metaproteomic analyses of an ANME-1-dominated community in marine cold seep sediments
Environ Microbiol, 14 (5), 1333-46
PubMed 22404914

Lenhard B, Sandelin A, Carninci P (2012)
Metazoan promoters: emerging characteristics and insights into transcriptional regulation
Nat Rev Genet, 13 (4), 233-45
PubMed 22392219

Ersland KM, Christoforou A, Stansberg C, Espeseth T, Mattheisen M, Mattingsdal M, Hardarson GA, Hansen T, Fernandes CP, Giddaluru S, Breuer R, Strohmaier J, Djurovic S, Nöthen MM, Rietschel M, Lundervold AJ, Werge T, Cichon S, Andreassen OA, Reinvang I, Steen VM, Le Hellard S (2012)
Gene-based analysis of regionally enriched cortical genes in GWAS data sets of cognitive traits and psychiatric disorders
PLoS One, 7 (2), e31687
PubMed 22384057

Radax R, Rattei T, Lanzen A, Bayer C, Rapp HT, Urich T, Schleper C (2012)
Metatranscriptomics of the marine sponge Geodia barretti: tackling phylogeny and function of its microbial community
Environ Microbiol, 14 (5), 1308-24
PubMed 22364353

Saito T, Sætrom P (2012)
Target gene expression levels and competition between transfected and endogenous microRNAs are strong confounding factors in microRNA high-throughput experiments
Silence, 3, 3
PubMed 22325809

Bizuayehu TT, Lanes CF, Furmanek T, Karlsen BO, Fernandes JM, Johansen SD, Babiak I (2012)
Differential expression patterns of conserved miRNAs and isomiRs during Atlantic halibut development
BMC Genomics, 13, 11
PubMed 22233483

Gundersen S, Kalaš M, Abul O, Frigessi A, Hovig E, Sandve GK (2011)
Identifying elemental genomic track types and representing them uniformly
BMC Bioinformatics, 12, 494
PubMed 22208806

Fredman D, Dong X, Lenhard B (2011)
Making enhancers from spare parts of the genome
Genome Biol, 12 (12), 138
PubMed 22206586

Plessy C, Pascarella G, Bertin N, Akalin A, Carrieri C, Vassalli A, Lazarevic D, Severin J, Vlachouli C, Simone R, Faulkner GJ, Kawai J, Daub CO, Zucchelli S, Hayashizaki Y, Mombaerts P, Lenhard B, Gustincich S, Carninci P (2011)
Promoter architecture of mouse olfactory receptor genes
Genome Res, 22 (3), 486-97
PubMed 22194471

Logue JB, Langenheder S, Andersson AF, Bertilsson S, Drakare S, Lanzén A, Lindström ES (2011)
Freshwater bacterioplankton richness in oligotrophic lakes depends on nutrient availability rather than on species-area relationships
ISME J, 6 (6), 1127-36
PubMed 22170419

Stadhouders R, Thongjuea S, Andrieu-Soler C, Palstra RJ, Bryne JC, van den Heuvel A, Stevens M, de Boer E, Kockx C, van der Sloot A, van den Hout M, van Ijcken W, Eick D, Lenhard B, Grosveld F, Soler E (2011)
Dynamic long-range chromatin interactions control Myb proto-oncogene transcription during erythroid development
EMBO J, 31 (4), 986-99
PubMed 22157820

Pauli A, Valen E, Lin MF, Garber M, Vastenhouw NL, Levin JZ, Fan L, Sandelin A, Rinn JL, Regev A, Schier AF (2011)
Systematic identification of long noncoding RNAs expressed during zebrafish embryogenesis
Genome Res, 22 (3), 577-91
PubMed 22110045

Skjaerven L, Reuter N, Martinez A (2011)
Dynamics, flexibility and ligand-induced conformational changes in biological macromolecules: a computational approach
Future Med Chem, 3 (16), 2079-100
PubMed 22098354

Chen Y, Jørgensen M, Kolde R, Zhao X, Parker B, Valen E, Wen J, Sandelin A (2011)
Prediction of RNA Polymerase II recruitment, elongation and stalling from histone modification data
BMC Genomics, 12, 544
PubMed 22047616

Stavrum R, Stavrum AK, Valvatne H, Riley LW, Ulvestad E, Jonassen I, Assmus J, Doherty TM, Grewal HM (2011)
Modulation of transcriptional and inflammatory responses in murine macrophages by the Mycobacterium tuberculosis mammalian cell entry (Mce) 1 complex
PLoS One, 6 (10), e26295
PubMed 22039457

Ribeiro de Almeida C, Stadhouders R, de Bruijn MJ, Bergen IM, Thongjuea SLenhard B, van Ijcken W, Grosveld F, Galjart N, Soler E, Hendriks RW (2011)
The DNA-binding protein CTCF limits proximal Vκ recombination and restricts κ enhancer interactions to the immunoglobulin κ light chain locus
Immunity, 35 (4), 501-13
PubMed 22035845

Clemente-Blanco A, Sen N, Mayan-Santos M, Sacristán MP, Graham B, Jarmuz A, Giess A, Webb E, Game L, Eick D, Bueno A, Merkenschlager M, Aragón L (2011)
Cdc14 phosphatase promotes segregation of telomeres through repression of RNA polymerase II transcription
Nat Cell Biol, 13 (12), 1450-6
PubMed 22020438

Taniya T, Tanaka S, Yamaguchi-Kabata Y, Hanaoka H, Yamasaki C, Maekawa H, Barrero RA, Lenhard B, Datta MW, Shimoyama M, Bumgarner R, Chakraborty R, Hopkinson I, Jia L, Hide W, Auffray C, Minoshima S, Imanishi T, Gojobori T (2011)
A prioritization analysis of disease association by data-mining of functional annotation of human genes
Genomics, 99 (1), 1-9
PubMed 22019378

Dimitrakopoulou K, Tsimpouris C, Papadopoulos G, Pommerenke C, Wilk E, Sgarbas KN, Schughart K, Bezerianos A (2011)
Dynamic gene network reconstruction from gene expression data in mice after influenza A (H1N1) infection
J Clin Bioinforma, 1, 27
PubMed 22017961

Royo JL, Hidalgo C, Roncero Y, Seda MA, Akalin ALenhard B, Casares F, Gómez-Skarmeta JL (2011)
Dissecting the transcriptional regulatory properties of human chromosome 16 highly conserved non-coding regions
PLoS One, 6 (9), e24824
PubMed 21935474

Valen E, Sandelin A (2011)
Genomic and chromatin signals underlying transcription start-site selection
Trends Genet, 27 (11), 475-85
PubMed 21924514

Kleppe R, Martinez A, Døskeland SO, Haavik J (2011)
The 14-3-3 proteins in regulation of cellular metabolism
Semin Cell Dev Biol, 22 (7), 713-9
PubMed 21888985

Zhao X, Valen E, Parker BJ, Sandelin A (2011)
Systematic clustering of transcription start site landscapes
PLoS One, 6 (8), e23409
PubMed 21887249

Star B, Nederbragt AJ, Jentoft S, Grimholt U, Malmstrøm M, Gregers TF, Rounge TB, Paulsen J, Solbakken MH, Sharma A, Wetten OF, Lanzén A, Winer R, Knight J, Vogel JH, Aken B, Andersen O, Lagesen K, Tooming-Klunderud A, Edvardsen RB, Tina KG, Espelund M, Nepal C, Previti C, Karlsen BO et al. (2011)
The genome sequence of Atlantic cod reveals a unique immune system
Nature, 477 (7363), 207-10
PubMed 21832995

Valen E, Preker P, Andersen PR, Zhao X, Chen Y, Ender C, Dueck A, Meister G, Sandelin A, Jensen TH (2011)
Biogenic mechanisms and utilization of small RNAs derived from human protein-coding genes
Nat Struct Mol Biol, 18 (9), 1075-82
PubMed 21822281

Kantari C, Millet A, Gabillet J, Hajjar E, Broemstrup T, Pluta P, Reuter N, Witko-Sarsat V (2011)
Molecular analysis of the membrane insertion domain of proteinase 3, the Wegener’s autoantigen, in RBL cells: implication for its pathogenic activity
J Leukoc Biol, 90 (5), 941-50
PubMed 21821719

Romanowska J, McCammon JA, Trylska J (2011)
Understanding the origins of bacterial resistance to aminoglycosides through molecular dynamics mutational study of the ribosomal A-site
PLoS Comput Biol, 7 (7), e1002099
PubMed 21814503

Sztromwasser PPuntervoll PPetersen K (2011)
Data partitioning enables the use of standard SOAP Web Services in genome-scale workflows
J Integr Bioinform, 8 (2), 163
PubMed 21788681

Berg K, Puntervoll P, Klungsøyr J, Goksøyr A (2011)
Brain proteome alterations of Atlantic cod (Gadus morhua) exposed to PCB 153
Aquat Toxicol, 105 (3-4), 206-17
PubMed 21762652

Goncearenco ABerezovsky IN (2011)
Computational reconstruction of primordial prototypes of elementary functional loops in modern proteins
Bioinformatics, 27 (17), 2368-75
PubMed 21724592

Colaert N, Barsnes H, Vaudel M, Helsens K, Timmerman E, Sickmann A, Gevaert K, Martens L (2011)
Thermo-msf-parser: an open source Java library to parse and visualize Thermo Proteome Discoverer msf files
J Proteome Res, 10 (8), 3840-3
PubMed 21714566

Hollup SM, Sadowski MI, Jonassen ITaylor WR (2011)
Exploring the limits of fold discrimination by structural alignment: a large scale benchmark using decoys of known fold
Comput Biol Chem, 35 (3), 174-88
PubMed 21704264

Wolff P, Weinhofer I, Seguin J, Roszak P, Beisel C, Donoghue MT, Spillane C, Nordborg M, Rehmsmeier M, Köhler C (2011)
High-resolution analysis of parent-of-origin allelic expression in the Arabidopsis Endosperm
PLoS Genet, 7 (6), e1002126
PubMed 21698132

Thomas LF, Saito T, Sætrom P (2011)
Inferring causative variants in microRNA target sites
Nucleic Acids Res, 39 (16), e109
PubMed 21693556

Balzer S, Malde K, Jonassen I (2011)
Systematic exploration of error sources in pyrosequencing flowgram data
Bioinformatics, 27 (13), i304-9
PubMed 21685085

Roalkvam I, Jørgensen SL, Chen Y, Stokke R, Dahle H, Hocking WP, Lanzén A, Haflidason H, Steen IH (2011)
New insight into stratification of anaerobic methanotrophs in cold seep sediments
FEMS Microbiol Ecol, 78 (2), 233-43
PubMed 21676010

Lanzén A, Jørgensen SL, Bengtsson MM, Jonassen I, Øvreås L, Urich T (2011)
Exploring the composition and diversity of microbial communities at the Jan Mayen hydrothermal vent field using RNA and DNA
FEMS Microbiol Ecol, 77 (3), 577-89
PubMed 21627670

Sheng YPreviti C (2011)
Genomic features and computational identification of human microRNAs under long-range developmental regulation
BMC Genomics, 12, 270
PubMed 21619633

Preker P, Almvig K, Christensen MS, Valen E, Mapendano CK, Sandelin A, Jensen TH (2011)
PROMoter uPstream Transcripts share characteristics with mRNAs and are produced upstream of all three major types of mammalian promoters
Nucleic Acids Res, 39 (16), 7179-93
PubMed 21596787

Berezovsky IN (2011)
The diversity of physical forces and mechanisms in intermolecular interactions
Phys Biol, 8 (3), 035002
PubMed 21572170

Engelen E, Akinci U, Bryne JC, Hou J, Gontan C, Moen M, Szumska D, Kockx C, van Ijcken W, Dekkers DH, Demmers J, Rijkers EJ, Bhattacharya S, Philipsen S, Pevny LH, Grosveld FG, Rottier RJ, Lenhard B, Poot RA (2011)
Sox2 cooperates with Chd7 to regulate genes that are mutated in human syndromes
Nat Genet, 43 (6), 607-11
PubMed 21532573

Kleppe R, Krakstad C, Selheim F, Kopperud R, Døskeland SO (2011)
The cAMP-dependent protein kinase pathway as therapeutic target: possibilities and pitfalls
Curr Top Med Chem, 11 (11), 1393-405
PubMed 21513494

Pecinka A, Fang W, Rehmsmeier M, Levy AA, Mittelsten Scheid O (2011)
Polyploidization increases meiotic recombination frequency in Arabidopsis
BMC Biol, 9, 24
PubMed 21510849

Kettunen P, Furmanek T, Chaulagain R, Kvinnsland IH, Luukko K (2011)
Developmentally regulated expression of intracellular Fgf11-13, hormone-like Fgf15 and canonical Fgf16, -17 and -20 mRNAs in the developing mouse molar tooth
Acta Odontol Scand, 69 (6), 360-6
PubMed 21449687

Allen MJ, Lanzén A, Bratbak G (2010)
Characterisation of the coccolithovirus intein
Mar Genomics, 4 (1), 1-7
PubMed 21429459

Skjaerven L, Grant B, Muga A, Teigen K, McCammon JA, Reuter N, Martinez A (2011)
Conformational sampling and nucleotide-dependent transitions of the GroEL subunit probed by unbiased molecular dynamics simulations
PLoS Comput Biol, 7 (3), e1002004
PubMed 21423709

Sissener NH, Hemre GI, Lall SP, Sagstad A, Petersen K, Williams J, Rohloff J, Sanden M (2011)
Are apparent negative effects of feeding GM MON810 maize to Atlantic salmon, Salmo salar, caused by confounding factors?
Br J Nutr, 106 (1), 42-56
PubMed 21418706

Apelseth TO, Hervig T, Wentzel-Larsen T, Petersen K, Reikvam H, Bruserud Ø (2011)
A prospective observational study of the effect of platelet transfusions on levels of platelet-derived cytokines, chemokines and interleukins in acute leukaemia patients with severe chemotherapy-induced cytopenia
Eur Cytokine Netw, 22 (1), 52-62
PubMed 21388914

Barsnes H, Vaudel M, Colaert N, Helsens K, Sickmann A, Berven FS, Martens L (2011)
compomics-utilities: an open-source Java library for computational proteomics
BMC Bioinformatics, 12, 70
PubMed 21385435

Vaudel M, Barsnes H, Berven FS, Sickmann A, Martens L (2011)
SearchGUI: An open-source graphical user interface for simultaneous OMSSA and X!Tandem searches
Proteomics, 11 (5), 996-9
PubMed 21337703

Barsnes H, Eidhammer I, Martens L (2011)
A global analysis of peptide fragmentation variability
Proteomics, 11 (6), 1181-8
PubMed 21328539

Mannelqvist M, Stefansson IM, Bredholt G, Hellem Bø T, Oyan AM, Jonassen I, Kalland KH, Salvesen HB, Akslen LA (2011)
Gene expression patterns related to vascular invasion and aggressive features in endometrial cancer
Am J Pathol, 178 (2), 861-71
PubMed 21281818

Quince C, Lanzen A, Davenport RJ, Turnbaugh PJ (2011)
Removing noise from pyrosequenced amplicons
BMC Bioinformatics, 12, 38
PubMed 21276213

Stansberg C, Ersland KM, van der Valk P, Steen VM (2011)
Gene expression in the rat brain: high similarity but unique differences between frontomedial-, temporal- and occipital cortex
BMC Neurosci, 12, 15
PubMed 21269499

Herfindal L, Myhren L, Kleppe R, Krakstad C, Selheim F, Jokela J, Sivonen K, Døskeland SO (2011)
Nostocyclopeptide-M1: a potent, nontoxic inhibitor of the hepatocyte drug transporters OATP1B3 and OATP1B1
Mol Pharm, 8 (2), 360-7
PubMed 21214185

Romanowska J, Larsson G, Eriksson M, Wikström BM, Westerlund H, Theorell T (2010)
Health effects on leaders and co-workers of an art-based leadership development program
Psychother Psychosom, 80 (2), 78-87
PubMed 21196805

Saito T, Sætrom P (2010)
A two-step site and mRNA-level model for predicting microRNA targets
BMC Bioinformatics, 11, 612
PubMed 21194446

Mitternacht SBerezovsky IN (2010)
A geometry-based generic predictor for catalytic and allosteric sites
Protein Eng Des Sel, 24 (4), 405-9
PubMed 21159618

Mitternacht SBerezovsky IN (2011)
On the importance of amino acid sequence and spatial proximity of interacting residues for protein folding
J Biomol Struct Dyn, 28 (4), 607-9; discussion 669-674
PubMed 21142232

Denoeud F, Henriet S, Mungpakdee S, Aury JM, Da Silva C, Brinkmann H, Mikhaleva J, Olsen LC, Jubin C, Cañestro C, Bouquet JM, Danks G, Poulain J, Campsteijn C, Adamski M, Cross I, Yadetie F, Muffato M, Louis A, Butcher S, Tsagkogeorga G, Konrad A, Singh S, Jensen MF, Huynh Cong E et al. (2010)
Plasticity of animal genome architecture unmasked by rapid evolution of a pelagic tunicate
Science, 330 (6009), 1381-5
PubMed 21097902

Barsnes H, Vizcaíno JA, Reisinger F, Eidhammer I, Martens L (2011)
Submitting proteomics data to PRIDE using PRIDE Converter
Methods Mol Biol, 694, 237-53
PubMed 21082439

Jørgensen KM, Hjelle SM, Øye OK, Puntervoll P, Reikvam H, Skavland J, Anderssen E, Bruserud Ø, Gjertsen BT (2010)
Untangling the intracellular signalling network in cancer–a strategy for data integration in acute myeloid leukaemia
J Proteomics, 74 (3), 269-81
PubMed 21075225

Arntzen MØ, Koehler CJ, Barsnes H, Berven FS, Treumann A, Thiede B (2010)
IsobariQ: software for isobaric quantitative proteomics using IPTL, iTRAQ, and TMT
J Proteome Res, 10 (2), 913-20
PubMed 21067241

Skjaerven L, Martinez A, Reuter N (2011)
Principal component and normal mode analysis of proteins; a quantitative comparison using the GroEL subunit
Proteins, 79 (1), 232-43
PubMed 21058295

Witko-Sarsat V, Mocek J, Bouayad D, Tamassia N, Ribeil JA, Candalh C, Davezac N, Reuter N, Mouthon L, Hermine O, Pederzoli-Ribeil M, Cassatella MA (2010)
Proliferating cell nuclear antigen acts as a cytoplasmic platform controlling human neutrophil survival
J Exp Med, 207 (12), 2631-45
PubMed 20975039

Jensen BO, Kleppe R, Kopperud R, Nygaard G, Døskeland SO, Holmsen H, Selheim F (2010)
Dipyridamole synergizes with nitric oxide to prolong inhibition of thrombin-induced platelet shape change
Platelets, 22 (1), 8-19
PubMed 20958117

Motti D, Le Duigou C, Eugène E, Chemaly N, Wittner L, Lazarevic D, Krmac H, Marstrand T, Valen E, Sanges R, Stupka E, Sandelin A, Cherubini E, Gustincich S, Miles R (2010)
Gene expression analysis of the emergence of epileptiform activity after focal injection of kainic acid into mouse hippocampus
Eur J Neurosci, 32 (8), 1364-79
PubMed 20950280

Ma BGBerezovsky IN (2010)
The MBLOSUM: a server for deriving mutation targets and position-specific substitution rates
J Biomol Struct Dyn, 28 (3), 415-9
PubMed 20919756

Davidson WS, Koop BF, Jones SJ, Iturra P, Vidal R, Maass A, Jonassen I, Lien S, Omholt SW (2010)
Sequencing the genome of the Atlantic salmon (Salmo salar)
Genome Biol, 11 (9), 403
PubMed 20887641

Hevrøy EM, Azpeleta C, Shimizu M, Lanzén A, Kaiya H, Espe M, Olsvik PA (2010)
Effects of short-term starvation on ghrelin, GH-IGF system, and IGF-binding proteins in Atlantic salmon
Fish Physiol Biochem, 37 (1), 217-32
PubMed 20878468

Kalas M, Puntervoll P, Joseph A, Bartaseviciūte E, Töpfer A, Venkataraman P, Pettifer S, Bryne JC, Ison J, Blanchet C, Rapacki K, Jonassen I (2010)
BioXSD: the common data-exchange format for everyday bioinformatics web services
Bioinformatics, 26 (18), i540-6
PubMed 20823319

Goncearenco ABerezovsky IN (2010)
Prototypes of elementary functional loops unravel evolutionary connections between protein functions
Bioinformatics, 26 (18), i497-503
PubMed 20823313

Balzer S, Malde K, Lanzén A, Sharma A, Jonassen I (2010)
Characteristics of 454 pyrosequencing data–enabling realistic simulation with flowsim
Bioinformatics, 26 (18), i420-5
PubMed 20823302

Soler E, Andrieu-Soler C, Boer Ed, Bryne JCThongjuea S, Rijkers E, Demmers J, van IJcken W, Grosveld F (2010)
A systems approach to analyze transcription factors in mammalian cells
Methods, 53 (2), 151-62
PubMed 20705139

Berg K, Puntervoll P, Valdersnes S, Goksøyr A (2010)
Responses in the brain proteome of Atlantic cod (Gadus morhua) exposed to methylmercury
Aquat Toxicol, 100 (1), 51-65
PubMed 20701987

Broemstrup TReuter N (2010)
Molecular dynamics simulations of mixed acidic/zwitterionic phospholipid bilayers
Biophys J, 99 (3), 825-33
PubMed 20682260

Grauffel C, Stote RH, Dejaegere A (2010)
Force field parameters for the simulation of modified histone tails
J Comput Chem, 31 (13), 2434-51
PubMed 20652987

Ma BG, Goncearenco A, Berezovsky IN (2010)
Thermophilic adaptation of protein complexes inferred from proteomic homology modeling
Structure, 18 (7), 819-28
PubMed 20637418

Berge EO, Knappskog S, Geisler S, Staalesen V, Pacal M, Børresen-Dale AL, Puntervoll P, Lillehaug JR, Lønning PE (2010)
Identification and characterization of retinoblastoma gene mutations disturbing apoptosis in human breast cancers
Mol Cancer, 9, 173
PubMed 20594292

Sørensen AR, Stidsen CE, Ribel U, Nishimura E, Sturis J, Jonassen I, Bouman SD, Kurtzhals P, Brand CL (2010)
Insulin detemir is a fully efficacious, low affinity agonist at the insulin receptor
Diabetes Obes Metab, 12 (8), 665-73
PubMed 20590743

Dankel SN, Fadnes DJ, Stavrum AK, Stansberg C, Holdhus R, Hoang T, Veum VL, Christensen BJ, Våge V, Sagen JV, Steen VM, Mellgren G (2010)
Switch from stress response to homeobox transcription factors in adipose tissue after profound fat loss
PLoS One, 5 (6), e11033
PubMed 20543949

Broemstrup T, Reuter N (2010)
How does proteinase 3 interact with lipid bilayers?
Phys Chem Chem Phys, 12 (27), 7487-96
PubMed 20532386

Hackenberg M, Barturen G, Carpena P, Luque-Escamilla PL, Previti C, Oliver JL (2010)
Prediction of CpG-island function: CpG clustering vs. sliding-window methods
BMC Genomics, 11, 327
PubMed 20500903

Mommens M, Fernandes JM, Bizuayehu TT, Bolla SL, Johnston IA, Babiak I (2010)
Maternal gene expression in Atlantic halibut (Hippoglossus hippoglossus L.) and its relation to egg quality
BMC Res Notes, 3, 138
Johansen SD, Karlsen BO, Furmanek T, Andreassen M, Jørgensen TE, Bizuayehu TT, Breines R, Emblem A, Kettunen P, Luukko K, Edvardsen RB, Nordeide JT, Coucheron DH, Moum T (2010)
RNA deep sequencing of the Atlantic cod transcriptome
Comp Biochem Physiol Part D Genomics Proteomics, 6 (1), 18-22
PubMed 20493789

Pettifer S, Ison J, Kalas M, Thorne D, McDermott P, Jonassen I, Liaquat A, Fernández JM, Rodriguez JM, INB-Partners, Pisano DG, Blanchet C, Uludag M, Rice P, Bartaseviciute E, Rapacki K, Hekkelman M, Sand O, Stockinger H, Clegg AB, Bongcam-Rudloff E, Salzemann J, Breton V, Attwood TK, Cameron G et al. (2010)
The EMBRACE web service collection
Nucleic Acids Res, 38 (Web Server issue), W683-8
PubMed 20462862

Côté R, Reisinger F, Martens L, Barsnes H, Vizcaino JA, Hermjakob H (2010)
The Ontology Lookup Service: bigger and better
Nucleic Acids Res, 38 (Web Server issue), W155-60
PubMed 20460452

Hajjar E, Broemstrup T, Kantari C, Witko-Sarsat V, Reuter N (2010)
Structures of human proteinase 3 and neutrophil elastase–so similar yet so different
FEBS J, 277 (10), 2238-54
PubMed 20423453

Pansoy A, Ahmed S, Valen E, Sandelin A, Matthews J (2010)
3-methylcholanthrene induces differential recruitment of aryl hydrocarbon receptor to human promoters
Toxicol Sci, 117 (1), 90-100
PubMed 20348232

Taxt A, Aasland R, Sommerfelt H, Nataro J, Puntervoll P (2010)
Heat-stable enterotoxin of enterotoxigenic Escherichia coli as a vaccine target
Infect Immun, 78 (5), 1824-31
PubMed 20231404

Saito T, Saetrom P (2010)
MicroRNAs–targeting and target prediction
N Biotechnol, 27 (3), 243-9
PubMed 20219708

Ravasi T, Suzuki H, Cannistraci CV, Katayama S, Bajic VB, Tan K, Akalin A, Schmeier S, Kanamori-Katayama M, Bertin N, Carninci P, Daub CO, Forrest AR, Gough J, Grimmond S, Han JH, Hashimoto T, Hide W, Hofmann O, Kamburov A, Kaur M, Kawaji H, Kubosaki A, Lassmann T, van Nimwegen E et al. (2010)
An atlas of combinatorial transcriptional regulation in mouse and man
Cell, 140 (5), 744-52
PubMed 20211142

Jain T, Koley KM, Vadlamudi VP, Ghosh RC, Roy S, Tiwari S, Sahu U (2009)
Diclofenac-induced biochemical and histopathological changes in white leghorn birds (Gallus domesticus)
Indian J Pharmacol, 41 (5), 237-41
PubMed 20177497

Punnamoottil B, Herrmann C, Pascual-Anaya J, D’Aniello S, Garcia-Fernàndez J, Akalin A, Becker TS, Rinkwitz S (2010)
Cis-regulatory characterization of sequence conservation surrounding the Hox4 genes
Dev Biol, 340 (2), 269-82
PubMed 20144609

Muth T, Vaudel M, Barsnes H, Martens L, Sickmann A (2010)
XTandem Parser: an open-source library to parse and analyse X!Tandem MS/MS search results
Proteomics, 10 (7), 1522-4
PubMed 20140905

Bartossek R, Nicol GW, Lanzen A, Klenk HP, Schleper C (2010)
Homologues of nitrite reductases in ammonia-oxidizing archaea: diversity and genomic context
Environ Microbiol, 12 (4), 1075-88
PubMed 20132279

Soler E, Andrieu-Soler C, de Boer E, Bryne JCThongjuea S, Stadhouders R, Palstra RJ, Stevens M, Kockx C, van Ijcken W, Hou J, Steinhoff C, Rijkers E, Lenhard B, Grosveld F (2010)
The genome-wide dynamics of the binding of Ldb1 complexes during erythroid differentiation
Genes Dev, 24 (3), 277-89
PubMed 20123907

Dong X, Akalin ASharma YLenhard B (2010)
Translog, a web browser for studying the expression divergence of homologous genes
BMC Bioinformatics, 11 Suppl 1, S59
PubMed 20122234

Ragvin A, Moro E, Fredman D, Navratilova P, Drivenes Ø, Engström PG, Alonso ME, de la Calle Mustienes E, Gómez Skarmeta JL, Tavares MJ, Casares F, Manzanares M, van Heyningen V, Molven A, Njølstad PR, Argenton F, Lenhard B, Becker TS (2009)
Long-range gene regulation links genomic type 2 diabetes and obesity risk regions to HHEX, SOX4, and IRX3
Proc Natl Acad Sci U S A, 107 (2), 775-80
PubMed 20080751

Barsnes H, Côté RG, Eidhammer I, Martens L (2010)
OLS dialog: an open-source front end to the ontology lookup service
BMC Bioinformatics, 11, 34
PubMed 20078892

Helsens K, Colaert N, Barsnes H, Muth T, Flikka K, Staes A, Timmerman E, Wortelkamp S, Sickmann A, Vandekerckhove J, Gevaert K, Martens L (2010)
ms_lims, a simple yet powerful open source laboratory information management system for MS-driven proteomics
Proteomics, 10 (6), 1261-4
PubMed 20058248

Barsnes H, Eidhammer I, Martens L (2010)
FragmentationAnalyzer: an open-source tool to analyze MS/MS fragmentation data
Proteomics, 10 (5), 1087-90
PubMed 20049869

Navratilova P, Fredman DLenhard B, Becker TS (2009)
Regulatory divergence of the duplicated chromosomal loci sox11a/b by subpartitioning and sequence evolution of enhancers in zebrafish
Mol Genet Genomics, 283 (2), 171-84
PubMed 20039180

Cheng L, Zhu J, Hui WH, Zhang X, Honig B, Fang Q, Zhou ZH (2009)
Backbone model of an aquareovirus virion by cryo-electron microscopy and bioinformatics
J Mol Biol, 397 (3), 852-63
PubMed 20036256

Dong X, Navratilova P, Fredman D, Drivenes Ø, Becker TS, Lenhard B (2009)
Exonic remnants of whole-genome duplication reveal cis-regulatory function of coding exons
Nucleic Acids Res, 38 (4), 1071-85
PubMed 19969543

Gould CM, Diella F, Via A, Puntervoll P, Gemünd C, Chabanis-Davidson S, Michael S, Sayadi A, Bryne JC, Chica C, Seiler M, Davey NE, Haslam N, Weatheritt RJ, Budd A, Hughes T, Pas J, Rychlewski L, Travé G, Aasland R, Helmer-Citterich M, Linding R, Gibson TJ (2009)
ELM: the status of the 2010 eukaryotic linear motif resource
Nucleic Acids Res, 38 (Database issue), D167-80
PubMed 19920119

Torkildsen Ø, Stansberg C, Angelskår SM, Kooi EJ, Geurts JJ, van der Valk P, Myhr KM, Steen VM, Bø L (2009)
Upregulation of immunoglobulin-related genes in cortical sections from multiple sclerosis patients
Brain Pathol, 20 (4), 720-9
PubMed 19919606

Waheed Q, Edholm O (2009)
Undulation contributions to the area compressibility in lipid bilayer simulations
Biophys J, 97 (10), 2754-60
PubMed 19917229

Valen E, Sandelin A, Winther O, Krogh A (2009)
Discovery of regulatory elements is improved by a discriminatory approach
PLoS Comput Biol, 5 (11), e1000562
PubMed 19911049

Vizcaíno JA, Côté R, Reisinger F, Barsnes H, Foster JM, Rameseder J, Hermjakob H, Martens L (2009)
The Proteomics Identifications database: 2010 update
Nucleic Acids Res, 38 (Database issue), D736-42
PubMed 19906717

Portales-Casamar E, Thongjuea S, Kwon AT, Arenillas D, Zhao X, Valen E, Yusuf D, Lenhard B, Wasserman WW, Sandelin A (2009)
JASPAR 2010: the greatly expanded open-access database of transcription factor binding profiles
Nucleic Acids Res, 38 (Database issue), D105-10
PubMed 19906716

Witko-Sarsat V, Reuter N, Mouthon L (2010)
Interaction of proteinase 3 with its associated partners: implications in the pathogenesis of Wegener’s granulomatosis
Curr Opin Rheumatol, 22 (1), 1-7
PubMed 19881350

Halskau Ø, Ying M, Baumann A, Kleppe R, Rodriguez-Larrea D, Almås B, Haavik J, Martinez A (2009)
Three-way interaction between 14-3-3 proteins, the N-terminal region of tyrosine hydroxylase, and negatively charged membranes
J Biol Chem, 284 (47), 32758-69
PubMed 19801645

Hajjar E, Dejaegere A, Reuter N (2009)
Challenges in pKa predictions for proteins: the case of Asp213 in human proteinase 3
J Phys Chem A, 113 (43), 11783-92
PubMed 19780520

Patel S, Malde K, Lanzén A, Olsen RH, Nerland AH (2009)
Identification of immune related genes in Atlantic halibut (Hippoglossus hippoglossus L.) following in vivo antigenic and in vitro mitogenic stimulation
Fish Shellfish Immunol, 27 (6), 729-38
PubMed 19751833

Taylor WR, Chelliah V, Hollup SM, MacDonald JT, Jonassen I (2009)
Probing the “dark matter” of protein fold space
Structure, 17 (9), 1244-52
PubMed 19748345

Roider HG, Lenhard B, Kanhere A, Haas SA, Vingron M (2009)
CpG-depleted promoters harbor tissue-specific transcription factor binding signals–implications for motif overrepresentation analyses
Nucleic Acids Res, 37 (19), 6305-15
PubMed 19736212

Piantek M, Schulze G, Koch M, Franke KJ, Leyssner F, Krüger A, Navío C, Miguel J, Bernien M, Wolf M, Kuch W, Tegeder P, Pascual JI (2009)
Reversing the thermal stability of a molecular switch on a gold surface: ring-opening reaction of nitrospiropyran
J Am Chem Soc, 131 (35), 12729-35
PubMed 19722719

Neuweger H, Persicke M, Albaum SP, Bekel T, Dondrup M, Hüser AT, Winnebald J, Schneider J, Kalinowski J, Goesmann A (2009)
Visualizing post genomics data-sets on customized pathway maps by ProMeTra-aeration-dependent gene expression and metabolism of Corynebacterium glutamicum as an example
BMC Syst Biol, 3, 82
PubMed 19698148

Dong X, Fredman DLenhard B (2009)
Synorth: exploring the evolution of synteny and long-range regulatory interactions in vertebrate genomes
Genome Biol, 10 (8), R86
PubMed 19698106

Rajcevic U, Petersen K, Knol JC, Loos M, Bougnaud S, Klychnikov O, Li KW, Pham TV, Wang J, Miletic H, Peng Z, Bjerkvig R, Jimenez CR, Niclou SP (2009)
iTRAQ-based proteomics profiling reveals increased metabolic activity and cellular cross-talk in angiogenic compared with invasive glioblastoma phenotype
Mol Cell Proteomics, 8 (11), 2595-612
PubMed 19674965

Quince C, Lanzén A, Curtis TP, Davenport RJ, Hall N, Head IM, Read LF, Sloan WT (2009)
Accurate determination of microbial diversity from 454 pyrosequencing data
Nat Methods, 6 (9), 639-41
PubMed 19668203

Bessa J, Tena JJ, de la Calle-Mustienes E, Fernández-Miñán A, Naranjo S, Fernández A, Montoliu L, Akalin ALenhard B, Casares F, Gómez-Skarmeta JL (2009)
Zebrafish enhancer detection (ZED) vector: a new tool to facilitate transgenesis and the functional analysis of cis-regulatory regions in zebrafish
Dev Dyn, 238 (9), 2409-17
PubMed 19653328

Barsnes H, Huber S, Sickmann A, Eidhammer I, Martens L (2009)
OMSSA Parser: an open-source library to parse and extract data from OMSSA MS/MS search results
Proteomics, 9 (14), 3772-4
PubMed 19639591

Eisenacher M, Martens L, Barsnes H, Hardt T, Kohl M, Häkkinen J, Apweiler R, Meyer HE, Stephan C (2009)
Proteomics Data Collection – 5th ProDaC Workshop: 4 March 2009, Kolympari, Crete, Greece
Proteomics, 9 (14), 3626-9
PubMed 19639582

Eisenacher M, Martens L, Hardt T, Kohl M, Barsnes H, Helsens K, Häkkinen J, Levander F, Aebersold R, Vandekerckhove J, Dunn MJ, Lisacek F, Siepen JA, Hubbard SJ, Binz PA, Blüggel M, Thiele H, Cottrell J, Meyer HE, Apweiler R, Stephan C (2009)
Getting a grip on proteomics data – Proteomics Data Collection (ProDaC)
Proteomics, 9 (15), 3928-33
PubMed 19637238

Fredman D, Engström PG, Lenhard B (2009)
Web-based tools and approaches to study long-range gene regulation in Metazoa
Brief Funct Genomic Proteomic, 8 (4), 231-42
PubMed 19605518

Trösse C, Waagbø R, Breck O, Stavrum AK, Petersen K, Olsvik PA (2009)
Genome-wide transcription analysis of histidine-related cataract in Atlantic salmon (Salmo salar L)
Mol Vis, 15, 1332-50
PubMed 19597568

Barsnes H, Vizcaíno JA, Eidhammer I, Martens L (2009)
PRIDE Converter: making proteomics data-sharing easy
Nat Biotechnol, 27 (7), 598-9
PubMed 19587657

Ahmed S, Valen E, Sandelin A, Matthews J (2009)
Dioxin increases the interaction between aryl hydrocarbon receptor and estrogen receptor alpha at human promoters
Toxicol Sci, 111 (2), 254-66
PubMed 19574409

Dittami SM, Scornet D, Petit JL, Ségurens B, Da Silva C, Corre E, Dondrup M, Glatting KH, König R, Sterck L, Rouzé P, Van de Peer Y, Cock JM, Boyen C, Tonon T (2009)
Global expression analysis of the brown alga Ectocarpus siliculosus (Phaeophyceae) reveals large-scale reprogramming of the transcriptome in response to abiotic stress
Genome Biol, 10 (6), R66
PubMed 19531237

Johansen SD, Coucheron DH, Andreassen M, Karlsen BO, Furmanek T, Jørgensen TE, Emblem A, Breines R, Nordeide JT, Moum T, Nederbragt AJ, Stenseth NC, Jakobsen KS (2009)
Large-scale sequence analyses of Atlantic cod
N Biotechnol, 25 (5), 263-71
PubMed 19491044

van Beijnum JR, Petersen K, Griffioen AW (2009)
Tumor endothelium is characterized by a matrix remodeling signature
Front Biosci (Schol Ed), 1, 216-25
PubMed 19482697

Siegel G, Obernosterer G, Fiore R, Oehmen M, Bicker S, Christensen M, Khudayberdiev S, Leuschner PF, Busch CJ, Kane C, Hübel K, Dekker F, Hedberg C, Rengarajan B, Drepper C, Waldmann H, Kauppinen S, Greenberg ME, Draguhn A, Rehmsmeier M, Martinez J, Schratt GM (2009)
A functional screen implicates microRNA-138-dependent regulation of the depalmitoylation enzyme APT1 in dendritic spine morphogenesis
Nat Cell Biol, 11 (6), 705-16
PubMed 19465924

Alves L, Niemeier S, Hauenschild A, Rehmsmeier M, Merkle T (2009)
Comprehensive prediction of novel microRNA targets in Arabidopsis thaliana
Nucleic Acids Res, 37 (12), 4010-21
PubMed 19417064

Leversen NA, de Souza GA, Målen H, Prasad SJonassen I, Wiker HG (2009)
Evaluation of signal peptide prediction algorithms for identification of mycobacterial signal peptides using sequence data from proteomic methods
Microbiology, 155 (Pt 7), 2375-83
PubMed 19389770

Previti C, Harari O, Zwir I, del Val C (2009)
Profile analysis and prediction of tissue-specific CpG island methylation classes
BMC Bioinformatics, 10, 116
PubMed 19383127

FANTOM Consortium, Suzuki H, Forrest AR, van Nimwegen E, Daub CO, Balwierz PJ, Irvine KM, Lassmann T, Ravasi T, Hasegawa Y, de Hoon MJ, Katayama S, Schroder K, Carninci P, Tomaru Y, Kanamori-Katayama M, Kubosaki A, Akalin A, Ando Y, Arner E, Asada M, Asahara H, Bailey T, Bajic VB, Bauer D et al. (2009)
The transcriptional network that controls growth arrest and differentiation in a human myeloid leukemia cell line
Nat Genet, 41 (5), 553-62
PubMed 19377474

Akalin AFredman D, Arner E, Dong X, Bryne JC, Suzuki H, Daub CO, Hayashizaki Y, Lenhard B (2009)
Transcriptional features of genomic regulatory blocks
Genome Biol, 10 (4), R38
PubMed 19374772

Lie KK, Lanzen A, Breilid H, Olsvik PA (2009)
Gene expression profiling in Atlantic cod (Gadus morhua L.) from two contaminated sites using a custom-made cDNA microarray
Environ Toxicol Chem, 28 (8), 1711-21
PubMed 19364188

Dondrup M, Hüser AT, Mertens D, Goesmann A (2009)
An evaluation framework for statistical tests on microarray data
J Biotechnol, 140 (1-2), 18-26
PubMed 19297690

Øyan AM, Anensen N, Bø THStordrange LJonassen I, Bruserud Ø, Kalland KH, Gjertsen BT (2009)
Genes of cell-cell interactions, chemotherapy detoxification and apoptosis are induced during chemotherapy of acute myeloid leukemia
BMC Cancer, 9, 77
PubMed 19265549

Ke XS, Qu Y, Rostad K, Li WC, Lin B, Halvorsen OJ, Haukaas SA, Jonassen IPetersen K, Goldfinger N, Rotter V, Akslen LA, Oyan AM, Kalland KH (2009)
Genome-wide profiling of histone h3 lysine 4 and lysine 27 trimethylation reveals an epigenetic signature in prostate carcinogenesis
PLoS One, 4 (3), e4687
PubMed 19262738

Salvesen HB, Carter SL, Mannelqvist M, Dutt A, Getz G, Stefansson IM, Raeder MB, Sos ML, Engelsen IB, Trovik J, Wik E, Greulich H, Bø THJonassen I, Thomas RK, Zander T, Garraway LA, Oyan AM, Sellers WR, Kalland KH, Meyerson M, Akslen LA, Beroukhim R (2009)
Integrated genomic profiling of endometrial carcinoma associates aggressive tumors with indicators of PI3 kinase activation
Proc Natl Acad Sci U S A, 106 (12), 4834-9
PubMed 19261849

Homann R, Fleer D, Giegerich R, Rehmsmeier M (2009)
mkESA: enhanced suffix array construction tool
Bioinformatics, 25 (8), 1084-5
PubMed 19246510

Henckel K, Runte KJ, Bekel T, Dondrup M, Jakobi T, Küster H, Goesmann A (2009)
TRUNCATULIX–a data warehouse for the legume community
BMC Plant Biol, 9, 19
PubMed 19210766

Dondrup M, Albaum SP, Griebel T, Henckel K, Jünemann S, Kahlke T, Kleindt CK, Küster H, Linke B, Mertens D, Mittard-Runte V, Neuweger H, Runte KJ, Tauch A, Tille F, Pühler A, Goesmann A (2009)
EMMA 2–a MAGE-compliant system for the collaborative analysis and integration of microarray data
BMC Bioinformatics, 10, 50
PubMed 19200358

Pendino F, Nguyen E, Jonassen I, Dysvik B, Azouz A, Lanotte M, Ségal-Bendirdjian E, Lillehaug JR (2009)
Functional involvement of RINF, retinoid-inducible nuclear factor (CXXC5), in normal and tumoral human myelopoiesis
Blood, 113 (14), 3172-81
PubMed 19182210

Lybaek H, Ørstavik KH, Prescott T, Hovland R, Breilid H, Stansberg C, Steen VM, Houge G (2009)
An 8.9 Mb 19p13 duplication associated with precocious puberty and a sporadic 3.9 Mb 2q23.3q24.1 deletion containing NR4A2 in mentally retarded members of a family with an intrachromosomal 19p-into-19q between-arm insertion
Eur J Hum Genet, 17 (7), 904-10
PubMed 19156171

Eisenacher M, Kohl M, Martens L, Barsnes H, Hardt T, Levander F, Häkkinen J, Apweiler R, Meyer HE, Stephan C (2009)
Proteomics data collection–4th ProDaC workshop 15 August 2008, Amsterdam, The Netherlands
Proteomics, 9 (2), 218-22
PubMed 19105180

Becker A, Barnett MJ, Capela D, Dondrup M, Kamp PB, Krol E, Linke B, Rüberg S, Runte K, Schroeder BK, Weidner S, Yurgel SN, Batut J, Long SR, Pühler A, Goesmann A (2008)
A portal for rhizobial genomes: RhizoGATE integrates a Sinorhizobium meliloti genome annotation update with postgenome data
J Biotechnol, 140 (1-2), 45-50
PubMed 19103235

Barsnes H, Mikalsen SO, Eidhammer I (2008)
Blind search for post-translational modifications and amino acid substitutions using peptide mass fingerprints from two proteases
BMC Res Notes, 1, 130
PubMed 19099572

Valen E, Pascarella G, Chalk A, Maeda N, Kojima M, Kawazu C, Murata M, Nishiyori H, Lazarevic D, Motti D, Marstrand TT, Tang MH, Zhao X, Krogh A, Winther O, Arakawa T, Kawai J, Wells C, Daub C, Harbers M, Hayashizaki Y, Gustincich S, Sandelin A, Carninci P (2008)
Genome-wide detection and analysis of hippocampus core promoters using DeepCAGE
Genome Res, 19 (2), 255-65
PubMed 19074369

Navratilova P, Fredman D, Hawkins TA, Turner K, Lenhard B, Becker TS (2008)
Systematic human/zebrafish comparative identification of cis-regulatory activity around vertebrate developmental transcription factor genes
Dev Biol, 327 (2), 526-40
PubMed 19073165

Tokuriki N, Oldfield CJ, Uversky VN, Berezovsky IN, Tawfik DS (2008)
Do viral proteins possess unique biophysical features?
Trends Biochem Sci, 34 (2), 53-9
PubMed 19062293

Barsnes H, Eidhammer I, Cruciani V, Mikalsen SO (2008)
Protease-dependent fractional mass and peptide properties
Eur J Mass Spectrom (Chichester), 14 (5), 311-7
PubMed 19023148

Hollup SM, Taylor WR, Jonassen I (2008)
Structural fragments in protein model refinement
Protein Pept Lett, 15 (9), 964-71
PubMed 18991773

Maraziotis IA, Dimitrakopoulou K, Bezerianos A (2008)
An in silico method for detecting overlapping functional modules from composite biological networks
BMC Syst Biol, 2, 93
PubMed 18976494

Romanowska J, Setny P, Trylska J (2008)
Molecular dynamics study of the ribosomal A-site
J Phys Chem B, 112 (47), 15227-43
PubMed 18973356

Hauenschild A, Ringrose L, Altmutter C, Paro R, Rehmsmeier M (2008)
Evolutionary plasticity of polycomb/trithorax response elements in Drosophila species
PLoS Biol, 6 (10), e261
PubMed 18959483

Saelensminde G, Halskau Ø, Jonassen I (2008)
Amino acid contacts in proteins adapted to different temperatures: hydrophobic interactions and surface charges play a key role
Extremophiles, 13 (1), 11-20
PubMed 18825305

Hughes T, Liberles DA (2008)
Whole-genome duplications in the ancestral vertebrate are detectable in the distribution of gene family sizes of tetrapod species
J Mol Evol, 67 (4), 343-57
PubMed 18815825

Olsvik PA, Lie KK, Mykkeltvedt E, Samuelsen OB, Petersen K, Stavrum AK, Lunestad BT (2008)
Pharmacokinetics and transcriptional effects of the anti-salmon lice drug emamectin benzoate in Atlantic salmon (Salmo salar L.)
BMC Pharmacol, 8, 16
PubMed 18786259

Neuweger H, Albaum SP, Dondrup M, Persicke M, Watt T, Niehaus K, Stoye J, Goesmann A (2008)
MeltDB: a software platform for the analysis and integration of metabolomics experiment data
Bioinformatics, 24 (23), 2726-32
PubMed 18765459

Kemmer D, Faxén M, Hodges E, Lim J, Herzog E, Ljungström E, Lundmark A, Olsen MK, Podowski R, Sonnhammer EL, Nilsson P, Reimers M, Lenhard B, Roberds SL, Wahlestedt C, Höög C, Agarwal P, Wasserman WW (2004)
Exploring the foundation of genomics: a northern blot reference set for the comparative analysis of transcript profiling technologies
Comp Funct Genomics, 5 (8), 584-95
PubMed 18629180

Schlüter A, Bekel T, Diaz NN, Dondrup M, Eichenlaub R, Gartemann KH, Krahn I, Krause L, Krömeke H, Kruse O, Mussgnug JH, Neuweger H, Niehaus K, Pühler A, Runte KJ, Szczepanowski R, Tauch A, Tilker A, Viehöver P, Goesmann A (2008)
The metagenome of a biogas-producing microbial community of a production-scale biogas plant fermenter analysed by the 454-pyrosequencing technology
J Biotechnol, 136 (1-2), 77-90
PubMed 18597880

de Souza GA, Målen H, Søfteland T, Saelensminde G, Prasad S, Jonassen I, Wiker HG (2008)
High accuracy mass spectrometry analysis as a tool to verify and improve gene annotation using Mycobacterium tuberculosis as an example
BMC Genomics, 9, 316
PubMed 18597682

Eidhammer I, Barsnes H, Mikalsen SO (2008)
MassSorter: peptide mass fingerprinting data analysis
Methods Mol Biol, 484, 345-59
PubMed 18592191

Urich T, Lanzén A, Qi J, Huson DH, Schleper C, Schuster SC (2008)
Simultaneous assessment of soil microbial community structure and function through analysis of the meta-transcriptome
PLoS One, 3 (6), e2527
PubMed 18575584

Koczyk GBerezovsky IN (2008)
Domain Hierarchy and closed Loops (DHcL): a server for exploring hierarchy of protein domain structure
Nucleic Acids Res, 36 (Web Server issue), W239-45
PubMed 18502776

Massey SE, Churbanov A, Rastogi S, Liberles DA (2008)
Characterizing positive and negative selection and their phylogenetic effects
Gene, 418 (1-2), 22-6
PubMed 18486364

Stavrum AK, Petersen KJonassen I, Dysvik B (2008)
Analysis of gene-expression data using J-Express
Curr Protoc Bioinformatics, Chapter 7, Unit 7.3
PubMed 18428687

Mungpakdee S, Seo HC, Angotzi AR, Dong X, Akalin A, Chourrout D (2008)
Differential evolution of the 13 Atlantic salmon Hox clusters
Mol Biol Evol, 25 (7), 1333-43
PubMed 18424774

Luukko K, Moe K, Sijaona A, Furmanek T, Hals Kvinnsland I, Midtbø M, Kettunen P (2008)
Secondary induction and the development of tooth nerve supply
Ann Anat, 190 (2), 178-87
PubMed 18413271

Stavrum R, Valvatne H, Bø TH, Jonassen I, Hinds J, Butcher PD, Grewal HM (2008)
Genomic diversity among Beijing and non-Beijing Mycobacterium tuberculosis isolates from Myanmar
PLoS One, 3 (4), e1973
PubMed 18398483

Hughes T, Liberles DA (2008)
The power-law distribution of gene family size is driven by the pseudogenisation rate’s heterogeneity between gene families
Gene, 414 (1-2), 85-94
PubMed 18378100

Lanzén A, Oinn T (2008)
The Taverna Interaction Service: enabling manual interaction in workflows
Bioinformatics, 24 (8), 1118-20
PubMed 18337261

Eichner C, Frost P, Dysvik B, Jonassen I, Kristiansen B, Nilsen F (2008)
Salmon louse (Lepeophtheirus salmonis) transcriptomes during post molting maturation and egg production, revealed using EST-sequencing and microarray analysis
BMC Genomics, 9, 126
PubMed 18331648

Oyan AM, Bø TH, Jonassen I, Ulvestad E, Tore Gjertsen B, Bruserud O, Kalland KH (2007)
Global gene expression in classification, pathogenetic understanding and identification of therapeutic targets in acute myeloid leukemia
Curr Pharm Biotechnol, 8 (6), 344-54
PubMed 18289043

Marstrand TT, Frellsen J, Moltke I, Thiim M, Valen E, Retelska D, Krogh A (2008)
Asap: a framework for over-representation statistics for transcription factor binding sites
PLoS One, 3 (2), e1623
PubMed 18286180

Engström PGFredman DLenhard B (2008)
Ancora: a web resource for exploring highly conserved noncoding elements and their association with developmental regulatory genes
Genome Biol, 9 (2), R34
PubMed 18279518

Liu Y, Gao H, Marstrand TT, Ström A, Valen E, Sandelin A, Gustafsson JA, Dahlman-Wright K (2008)
The genome landscape of ERalpha- and ERbeta-binding DNA regions
Proc Natl Acad Sci U S A, 105 (7), 2604-9
PubMed 18272478

Giegerich R, Brazma A, Jonassen I, Ukkonen E, Vingron M (2008)
The BREW workshop series: a stimulating experience in PhD education
Brief Bioinform, 9 (3), 250-3
PubMed 18216087

Kemmer D, Podowski RM, Yusuf D, Brumm J, Cheung W, Wahlestedt C, Lenhard B, Wasserman WW (2008)
Gene characterization index: assessing the depth of gene annotation
PLoS One, 3 (1), e1440
PubMed 18213364

Andersen MC, Engström PG, Lithwick S, Arenillas D, Eriksson P, Lenhard B, Wasserman WW, Odeberg J (2007)
In silico detection of sequence variations modifying transcriptional regulation
PLoS Comput Biol, 4 (1), e5
PubMed 18208319

Malde KJonassen I (2008)
Repeats and EST analysis for new organisms
BMC Genomics, 9, 23
PubMed 18205940

Taylor WR, Bartlett GJ, Chelliah V, Klose D, Lin K, Sheldon T, Jonassen I (2008)
Prediction of protein structure from ideal forms
Proteins, 70 (4), 1610-9
PubMed 18175329

Henningsen N, Franke KJ, Schulze G, Fernández-Torrente I, Priewisch B, Rück-Braun K, Pascual JI (2008)
Active intramolecular conformational dynamics controlling the assembly of azobenzene derivatives at surfaces
Chemphyschem, 9 (1), 71-3
PubMed 18098252

Genome Information Integration Project And H-Invitational 2, Yamasaki C, Murakami K, Fujii Y, Sato Y, Harada E, Takeda J, Taniya T, Sakate R, Kikugawa S, Shimada M, Tanino M, Koyanagi KO, Barrero RA, Gough C, Chun HW, Habara T, Hanaoka H, Hayakawa Y, Hilton PB, Kaneko Y, Kanno M, Kawahara Y, Kawamura T, Matsuya A et al. (2007)
The H-Invitational Database (H-InvDB), a comprehensive annotation resource for human genes and transcripts
Nucleic Acids Res, 36 (Database issue), D793-9
PubMed 18089548

Hajjar E, Mihajlovic M, Witko-Sarsat V, Lazaridis T, Reuter N (2008)
Computational prediction of the binding site of proteinase 3 to the plasma membrane
Proteins, 71 (4), 1655-69
PubMed 18076025

Kikuta H, Fredman D, Rinkwitz S, Lenhard B, Becker TS (2007)
Retroviral enhancer detection insertions in zebrafish combined with comparative genomics reveal genomic regulatory blocks – a fundamental feature of vertebrate genomes
Genome Biol, 8 Suppl 1, S4
PubMed 18047696

Neuweger H, Baumbach J, Albaum S, Bekel T, Dondrup M, Hüser AT, Kalinowski J, Oehm S, Pühler A, Rahmann S, Weile J, Goesmann A (2007)
CoryneCenter – an online resource for the integrated analysis of corynebacterial genome and transcriptome data
BMC Syst Biol, 1, 55
PubMed 18034885

Frith MC, Valen E, Krogh A, Hayashizaki Y, Carninci P, Sandelin A (2007)
A code for transcription initiation in mammalian genomes
Genome Res, 18 (1), 1-12
PubMed 18032727

Hajjar E, Korkmaz B, Reuter N (2007)
Differences in the substrate binding sites of murine and human proteinase 3 and neutrophil elastase
FEBS Lett, 581 (29), 5685-90
PubMed 18023421

Bryne JC, Valen E, Tang MH, Marstrand T, Winther O, da Piedade I, Krogh A, Lenhard B, Sandelin A (2007)
JASPAR, the open access database of transcription factor-binding profiles: new content and tools in the 2008 update
Nucleic Acids Res, 36 (Database issue), D102-6
PubMed 18006571

Engström PG, Ho Sui SJ, Drivenes O, Becker TS, Lenhard B (2007)
Genomic regulatory blocks underlie extensive microsynteny conservation in insects
Genome Res, 17 (12), 1898-908
PubMed 17989259

Winge I, McKinney JA, Ying M, D’Santos CS, Kleppe R, Knappskog PM, Haavik J (2008)
Activation and stabilization of human tryptophan hydroxylase 2 by phosphorylation and 14-3-3 binding
Biochem J, 410 (1), 195-204
PubMed 17973628

Daae Lampe O, Viola I, Reuter N, Hauser H (2007)
Two-level approach to efficient visualization of protein dynamics
IEEE Trans Vis Comput Graph, 13 (6), 1616-23
PubMed 17968117

Hughes T, Liberles DA (2007)
The pattern of evolution of smaller-scale gene duplicates in mammalian genomes is more consistent with neo- than subfunctionalisation
J Mol Evol, 65 (5), 574-88
PubMed 17957399

Maraziotis IA, Dimitrakopoulou K, Bezerianos A (2007)
Growing functional modules from a seed protein via integration of protein interaction and gene expression data
BMC Bioinformatics, 8, 408
PubMed 17956603

Kettunen P, Spencer-Dene B, Furmanek T, Kvinnsland IH, Dickson C, Thesleff I, Luukko K (2007)
Fgfr2b mediated epithelial-mesenchymal interactions coordinate tooth morphogenesis and dental trigeminal axon patterning
Mech Dev, 124 (11-12), 868-83
PubMed 17951031

Suhr ML, Dysvik B, Bruland O, Warnakulasuriya S, Amaratunga AN, Jonassen I, Vasstrand EN, Ibrahim SO (2007)
Gene expression profile of oral squamous cell carcinomas from Sri Lankan betel quid users
Oncol Rep, 18 (5), 1061-75
PubMed 17914555

Hjelmervik TO, Lindqvist AK, Petersen K, Johannesson M, Stavrum AK, Johansson A, Jonsson R, Holmdahl R, Bolstad AI (2007)
The influence of the NOD Nss1/Idd5 loci on sialadenitis and gene expression in salivary glands of congenic mice
Arthritis Res Ther, 9 (5), R99
PubMed 17900348

Sheng YEngström PGLenhard B (2007)
Mammalian microRNA prediction through a support vector machine model of sequence and structure
PLoS One, 2 (9), e946
PubMed 17895987

He X, Chang S, Zhang J, Zhao Q, Xiang H, Kusonmano K, Yang L, Sun ZS, Yang H, Wang J (2007)
MethyCancer: the database of human DNA methylation and cancer
Nucleic Acids Res, 36 (Database issue), D836-41
PubMed 17890243

Becker TS, Lenhard B (2007)
The random versus fragile breakage models of chromosome evolution: a matter of resolution
Mol Genet Genomics, 278 (5), 487-91
PubMed 17851692

Hystad ME, Myklebust JH, Bø TH, Sivertsen EA, Rian E, Forfang L, Munthe E, Rosenwald A, Chiorazzi M, Jonassen I, Staudt LM, Smeland EB (2007)
Characterization of early stages of human B cell development by gene expression profiling
J Immunol, 179 (6), 3662-71
PubMed 17785802

Flikka K, Meukens J, Helsens K, Vandekerckhove J, Eidhammer I, Gevaert K, Martens L (2007)
Implementation and application of a versatile clustering tool for tandem mass spectrometry data
Proteomics, 7 (18), 3245-58
PubMed 17708593

Skjaerven L, Jonassen IReuter N (2007)
TMM@: a web application for the analysis of transmembrane helix mobility
BMC Bioinformatics, 8, 232
PubMed 17601351

Stuhr LE, Raa A, Oyan AM, Kalland KH, Sakariassen PO, Petersen K, Bjerkvig R, Reed RK (2007)
Hyperoxia retards growth and induces apoptosis, changes in vascular density and gene expression in transplanted gliomas in nude rats
J Neurooncol, 85 (2), 191-202
PubMed 17557137

Hughes T, Ekman D, Ardawatia H, Elofsson A, Liberles DA (2007)
Evaluating dosage compensation as a cause of duplicate gene retention in Paramecium tetraurelia
Genome Biol, 8 (5), 213
PubMed 17521457

Sandelin A, Carninci P, Lenhard B, Ponjavic J, Hayashizaki Y, Hume DA (2007)
Mammalian RNA polymerase II core promoters: insights from genome-wide studies
Nat Rev Genet, 8 (6), 424-36
PubMed 17486122

Petersen K, Oyan AM, Rostad K, Olsen S, Bø TH, Salvesen HB, Gjertsen BT, Bruserud O, Halvorsen OJ, Akslen LA, Steen VM, Jonassen I, Kalland KH (2007)
Comparison of nucleic acid targets prepared from total RNA or poly(A) RNA for DNA oligonucleotide microarray hybridization
Anal Biochem, 366 (1), 46-58
PubMed 17449007

Saelensminde G, Halskau Ø, Helland R, Willassen NP, Jonassen I (2007)
Structure-dependent relationships between growth temperature of prokaryotes and the amino acid frequency in their proteins
Extremophiles, 11 (4), 585-96
PubMed 17429573

Stansberg C, Vik-Mo AO, Holdhus R, Breilid H, Srebro B, Petersen K, Jørgensen HA, Jonassen I, Steen VM (2007)
Gene expression profiles in rat brain disclose CNS signature genes and regional patterns of functional specialisation
BMC Genomics, 8, 94
PubMed 17408481

Kikuta H, Laplante M, Navratilova P, Komisarczuk AZ, Engström PG, Fredman D, Akalin A, Caccamo M, Sealy I, Howe K, Ghislain J, Pezeron G, Mourrain P, Ellingsen S, Oates AC, Thisse C, Thisse B, Foucher I, Adolf B, Geling A, Lenhard B, Becker TS (2007)
Genomic regulatory blocks encompass multiple neighboring genes and maintain conserved synteny in vertebrates
Genome Res, 17 (5), 545-55
PubMed 17387144

Halvorsen OJ, Rostad K, Øyan AM, Puntervoll H, Bø TH, Stordrange L, Olsen S, Haukaas SA, Hood L, Jonassen I, Kalland KH, Akslen LA (2007)
Increased expression of SIM2-s protein is a novel marker of aggressive prostate cancer
Clin Cancer Res, 13 (3), 892-7
PubMed 17289882

Raa A, Stansberg C, Steen VM, Bjerkvig R, Reed RK, Stuhr LE (2007)
Hyperoxia retards growth and induces apoptosis and loss of glands and blood vessels in DMBA-induced rat mammary tumors
BMC Cancer, 7, 23
PubMed 17263869

Pang KC, Stephen S, Dinger ME, Engström PG, Lenhard B, Mattick JS (2006)
RNAdb 2.0–an expanded database of mammalian non-coding RNAs
Nucleic Acids Res, 35 (Database issue), D178-82
PubMed 17145715

Rostad K, Mannelqvist M, Halvorsen OJ, Oyan AM, Bø TH, Stordrange L, Olsen S, Haukaas SA, Lin B, Hood L, Jonassen I, Akslen LA, Kalland KH (2007)
ERG upregulation and related ETS transcription factors in prostate cancer
Int J Oncol, 30 (1), 19-32
PubMed 17143509

Korkmaz B, Hajjar E, Kalupov T, Reuter N, Brillard-Bourdet M, Moreau T, Juliano L, Gauthier F (2006)
Influence of charge distribution at the active site surface on the substrate specificity of human neutrophil protease 3 and elastase. A kinetic and molecular modeling analysis
J Biol Chem, 282 (3), 1989-97
PubMed 17088257

Rayner TF, Rocca-Serra P, Spellman PT, Causton HC, Farne A, Holloway E, Irizarry RA, Liu J, Maier DS, Miller M, Petersen K, Quackenbush J, Sherlock G, Stoeckert CJ, White J, Whetzel PL, Wymore F, Parkinson H, Sarkans U, Ball CA, Brazma A (2006)
A simple spreadsheet-based, MIAME-supportive format for microarray data: MAGE-TAB
BMC Bioinformatics, 7, 489
PubMed 17087822

Küster H, Becker A, Firnhaber C, Hohnjec N, Manthey K, Perlick AM, Bekel T, Dondrup M, Henckel K, Goesmann A, Meyer F, Wipf D, Requena N, Hildebrandt U, Hampp R, Nehls U, Krajinski F, Franken P, Pühler A (2006)
Development of bioinformatic tools to support EST-sequencing, in silico- and microarray-based transcriptome profiling in mycorrhizal symbioses
Phytochemistry, 68 (1), 19-32
PubMed 17081576

Sakariassen PØ, Prestegarden L, Wang J, Skaftnesmo KO, Mahesparan R, Molthoff C, Sminia P, Sundlisaeter E, Misra A, Tysnes BB, Chekenya M, Peters H, Lende G, Kalland KH, Øyan AM, Petersen KJonassen I, van der Kogel A, Feuerstein BG, Terzis AJ, Bjerkvig R, Enger PØ (2006)
Angiogenesis-independent tumor growth mediated by stem-like cancer cells
Proc Natl Acad Sci U S A, 103 (44), 16466-71
PubMed 17056721

Ardawatia H, Liberles DA (2006)
A systematic analysis of lineage-specific evolution in metabolic pathways
Gene, 387 (1-2), 67-74
PubMed 17034962

Vidal OM, Merino R, Rico-Bautista E, Fernandez-Perez L, Chia DJ, Woelfle J, Ono M, Lenhard B, Norstedt G, Rotwein P, Flores-Morales A (2006)
In vivo transcript profiling and phylogenetic analysis identifies suppressor of cytokine signaling 2 as a direct signal transducer and activator of transcription 5b target in liver
Mol Endocrinol, 21 (1), 293-311
PubMed 17008382

Skovgaard M, Kodra JT, Gram DX, Knudsen SM, Madsen D, Liberles DA (2006)
Using evolutionary information and ancestral sequences to understand the sequence-function relationship in GLP-1 agonists
J Mol Biol, 363 (5), 977-88
PubMed 16989858

Jonassen I, Klose D, Taylor WR (2006)
Protein model refinement using structural fragment tessellation
Comput Biol Chem, 30 (5), 360-6
PubMed 16982212

Rehmsmeier M (2006)
Prediction of microRNA targets
Methods Mol Biol, 342, 87-99
PubMed 16957369

Bailey PJ, Klos JM, Andersson E, Karlén M, Källström M, Ponjavic J, Muhr J, Lenhard B, Sandelin A, Ericson J (2006)
A global genomic transcriptional code associated with CNS-expressed genes
Exp Cell Res, 312 (16), 3108-19
PubMed 16919269

Ponjavic J, Lenhard B, Kai C, Kawai J, Carninci P, Hayashizaki Y, Sandelin A (2006)
Transcriptional and structural impact of TATA-initiation site spacing in mammalian core promoters
Genome Biol, 7 (8), R78
PubMed 16916456

Brillard-Bourdet M, Hamdaoui A, Hajjar E, Boudier C, Reuter N, Ehret-Sabatier L, Bieth JG, Gauthier F (2006)
A novel locust (Schistocerca gregaria) serine protease inhibitor with a high affinity for neutrophil elastase
Biochem J, 400 (3), 467-76
PubMed 16839309

Roth C, Rastogi S, Arvestad L, Dittmar K, Light S, Ekman D, Liberles DA (2007)
Evolution after gene duplication: models, mechanisms, sequences, systems, and organisms
J Exp Zool B Mol Dev Evol, 308 (1), 58-73
PubMed 16838295

Malde K, Schneeberger K, Coward EJonassen I (2006)
RBR: library-less repeat detection for ESTs
Bioinformatics, 22 (18), 2232-6
PubMed 16837527

Rastogi S, Reuter NLiberles DA (2006)
Evaluation of models for the evolution of protein sequences and functions under structural constraint
Biophys Chem, 124 (2), 134-44
PubMed 16837122

Berglund-Sonnhammer AC, Steffansson P, Betts MJ, Liberles DA (2006)
Optimal gene trees from sequences and species trees using a soft interpretation of parsimony
J Mol Evol, 63 (2), 240-50
PubMed 16830091

Roth C, Liberles DA (2006)
A systematic search for positive selection in higher plants (Embryophytes)
BMC Plant Biol, 6, 12
PubMed 16784532

Taylor WR, Lin K, Klose D, Fraternali F, Jonassen I (2006)
Dynamic domain threading
Proteins, 64 (3), 601-14
PubMed 16752419

Frith MC, Ponjavic J, Fredman D, Kai C, Kawai J, Carninci P, Hayashizaki Y, Sandelin A (2006)
Evolutionary turnover of mammalian transcription start sites
Genome Res, 16 (6), 713-22
PubMed 16687732

Maeda N, Kasukawa T, Oyama R, Gough J, Frith M, Engström PG, Lenhard B, Aturaliya RN, Batalov S, Beisel KW, Bult CJ, Fletcher CF, Forrest AR, Furuno M, Hill D, Itoh M, Kanamori-Katayama M, Katayama S, Katoh M, Kawashima T, Quackenbush J, Ravasi T, Ring BZ, Shibata K, Sugiura K et al. (2006)
Transcript annotation in FANTOM3: mouse gene catalog based on physical cDNAs
PLoS Genet, 2 (4), e62
PubMed 16683036

Engström PG, Suzuki H, Ninomiya N, Akalin A, Sessa L, Lavorgna G, Brozzi A, Luzi L, Tan SL, Yang L, Kunarso G, Ng EL, Batalov S, Wahlestedt C, Kai C, Kawai J, Carninci P, Hayashizaki Y, Wells C, Bajic VB, Orlando V, Reid JF, Lenhard B, Lipovich L (2006)
Complex Loci in human and mouse genomes
PLoS Genet, 2 (4), e47
PubMed 16683030

Carninci P, Sandelin A, Lenhard B, Katayama S, Shimokawa K, Ponjavic J, Semple CA, Taylor MS, Engström PG, Frith MC, Forrest AR, Alkema WB, Tan SL, Plessy C, Kodzius R, Ravasi T, Kasukawa T, Fukuda S, Kanamori-Katayama M, Kitazume Y, Kawaji H, Kai C, Nakamura M, Konno H, Nakano K et al. (2006)
Genome-wide analysis of mammalian promoter architecture and evolution
Nat Genet, 38 (6), 626-35
PubMed 16645617

Arnesen T, Betts MJ, Pendino F, Liberles DA, Anderson D, Caro J, Kong X, Varhaug JE, Lillehaug JR (2006)
Characterization of hARD2, a processed hARD1 gene duplicate, encoding a human protein N-alpha-acetyltransferase
BMC Biochem, 7, 13
PubMed 16638120

Øyan AM, Bø TH, Jonassen I, Gjertsen BT, Bruserud Ø, Kalland KH (2006)
cDNA microarray analysis of non-selected cases of acute myeloid leukemia demonstrates distinct clustering independent of cytogenetic aberrations and consistent with morphological signs of differentiation
Int J Oncol, 28 (5), 1065-80
PubMed 16596222

Li T, Chamberlin SG, Caraco MD, Liberles DA, Gaucher EA, Benner SA (2006)
Analysis of transitions at two-fold redundant sites in mammalian genomes. Transition redundant approach-to-equilibrium (TREx) distance metrics
BMC Evol Biol, 6, 25
PubMed 16545144

Flikka K, Martens L, Vandekerckhove J, Gevaert K, Eidhammer I (2006)
Improving the reliability and throughput of mass spectrometry-based proteomics by spectrum quality filtering
Proteomics, 6 (7), 2086-94
PubMed 16518876

Andersen M, Lenhard B, Whatling C, Eriksson P, Odeberg J (2006)
Alternative promoter usage of the membrane glycoprotein CD36
BMC Mol Biol, 7, 8
PubMed 16515687

Dysvik B, Vasstrand EN, Løvlie R, Elgindi OA, Kross KW, Aarstad HJ, Johannessen AC, Jonassen I, Ibrahim SO (2006)
Gene expression profiles of head and neck carcinomas from Sudanese and Norwegian patients reveal common biological pathways regardless of race and lifestyle
Clin Cancer Res, 12 (4), 1109-20
PubMed 16489063

Hajjar E, Korkmaz B, Gauthier F, Brandsdal BO, Witko-Sarsat V, Reuter N (2006)
Inspection of the binding sites of proteinase3 for the design of a highly specific substrate
J Med Chem, 49 (4), 1248-60
PubMed 16480262

Barsnes H, Mikalsen SO, Eidhammer I (2006)
MassSorter: a tool for administrating and analyzing data from mass spectrometry experiments on proteins with known amino acid sequences
BMC Bioinformatics, 7, 42
PubMed 16438723

Gómez-Skarmeta JL, Lenhard B, Becker TS (2006)
New technologies, new findings, and new concepts in the study of vertebrate cis-regulatory sequences
Dev Dyn, 235 (4), 870-85
PubMed 16395688

Vlieghe D, Sandelin A, De Bleser PJ, Vleminckx K, Wasserman WW, van Roy F, Lenhard B (2006)
A new generation of JASPAR, the open-access repository for transcription factor binding site profiles
Nucleic Acids Res, 34 (Database issue), D95-7
PubMed 16381983

Karlsen OA, Kindingstad L, Angelskår SM, Bruseth LJ, Straume D, Puntervoll P, Fjellbirkeland A, Lillehaug JR, Jensen HB (2005)
Identification of a copper-repressible C-type heme protein of Methylococcus capsulatus (Bath). A member of a novel group of the bacterial di-heme cytochrome c peroxidase family of proteins
FEBS J, 272 (24), 6324-35
PubMed 16336269

Raeder MB, Fernø J, Glambek M, Stansberg C, Steen VM (2005)
Antidepressant drugs activate SREBP and up-regulate cholesterol and fatty acid biosynthesis in human glial cells
Neurosci Lett, 395 (3), 185-90
PubMed 16324787

Fernø J, Raeder MB, Vik-Mo AO, Skrede S, Glambek M, Tronstad KJ, Breilid H, Løvlie R, Berge RK, Stansberg C, Steen VM (2005)
Antipsychotic drugs activate SREBP-regulated expression of lipid biosynthetic genes in cultured human glioma cells: a novel mechanism of action?
Pharmacogenomics J, 5 (5), 298-304
PubMed  16027736

Pocanschi CL, Apell HJ, Puntervoll P, Høgh B, Jensen HB, Welte W, Kleinschmidt JH (2005)
The major outer membrane protein of Fusobacterium nucleatum (FomA) folds and inserts into lipid bilayers via parallel folding pathways
J Mol Biol, 355 (3), 548-61
PubMed 16310217

Liberles DA (2005)
Datasets for evolutionary comparative genomics
Genome Biol, 6 (8), 117
PubMed 16086856

Ellingsen S, Laplante MA, König M, Kikuta H, Furmanek T, Hoivik EA, Becker TS (2005)
Large-scale enhancer detection in the zebrafish genome
Development, 132 (17), 3799-811
PubMed 16049110

Dublet B, Ruello A, Pederzoli M, Hajjar E, Courbebaisse M, Canteloup S, Reuter N, Witko-Sarsat V (2005)
Cleavage of p21/WAF1/CIP1 by proteinase 3 modulates differentiation of a monocytic cell line. Molecular analysis of the cleavage site
J Biol Chem, 280 (34), 30242-53
PubMed 15975933

Ståhlberg N, Merino R, Hernández LH, Fernández-Pérez L, Sandelin A, Engström P, Tollet-Egnell P, Lenhard B, Flores-Morales A (2005)
Exploring hepatic hormone actions using a compilation of gene expression profiles
BMC Physiol, 5 (1), 8
PubMed 15953391

Rossnes R, Eidhammer I, Liberles DA (2005)
Phylogenetic reconstruction of ancestral character states for gene expression and mRNA splicing data
BMC Bioinformatics, 6, 127
PubMed 15921519

Berglund AC, Wallner B, Elofsson A, Liberles DA (2005)
Tertiary windowing to detect positive diversifying selection
J Mol Evol, 60 (4), 499-504
PubMed 15883884

Hjelmervik TO, Petersen KJonassen I, Jonsson R, Bolstad AI (2005)
Gene expression profiling of minor salivary glands clearly distinguishes primary Sjögren’s syndrome patients from healthy control subjects
Arthritis Rheum, 52 (5), 1534-44
PubMed 15880807

Schneeberger K, Malde K, Coward EJonassen I (2005)
Masking repeats while clustering ESTs
Nucleic Acids Res, 33 (7), 2176-80
PubMed 15831790

Rastogi S, Liberles DA (2005)
Subfunctionalization of duplicated genes as a transition state to neofunctionalization
BMC Evol Biol, 5, 28
PubMed 15831095

Bhushan S, Ståhl A, Nilsson S, Lefebvre B, Seki M, Roth C, McWilliam D, Wright SJ, Liberles DA, Shinozaki K, Bruce BD, Boutry M, Glaser E (2005)
Catalysis, subcellular localization, expression and evolution of the targeting peptides degrading protease, AtPreP2
Plant Cell Physiol, 46 (6), 985-96
PubMed 15827031

Hollup SM, Salensminde G, Reuter N (2005)
WEBnm@: a web application for normal mode analyses of proteins
BMC Bioinformatics, 6, 52
PubMed 15762993

Fjeld K, Kettunen P, Furmanek T, Kvinnsland IH, Luukko K (2005)
Dynamic expression of Wnt signaling-related Dickkopf1, -2, and -3 mRNAs in the developing mouse tooth
Dev Dyn, 233 (1), 161-6
PubMed 15759274

Stansberg C, Subramaniam S, Collet B, Secombes CJ, Cunningham C (2005)
Cloning of the Atlantic salmon (Salmo salar) IL-1 receptor associated protein
Fish Shellfish Immunol, 19 (1), 53-65
PubMed 15722231

Mottagui-Tabar S, Faghihi MA, Mizuno Y, Engström PG, Lenhard B, Wasserman WW, Wahlestedt C (2005)
Identification of functional SNPs in the 5-prime flanking sequences of human genes
BMC Genomics, 6, 18
PubMed 15717931

Bellinge RH, Liberles DA, Iaschi SP, O’brien PA, Tay GK (2005)
Myostatin and its implications on animal breeding: a review
Anim Genet, 36 (1), 1-6
PubMed 15670124

Oyan AM, Bø TH, Jonassen I, Ulvestad E, Gjertsen BT, Kalland KH, Bruserud O (2005)
CD34 expression in native human acute myelogenous leukemia blasts: differences in CD34 membrane molecule expression are associated with different gene expression profiles
Cytometry B Clin Cytom, 64 (1), 18-27
PubMed 15668952

Halvorsen OJ, Oyan AM, Bø TH, Olsen S, Rostad K, Haukaas SA, Bakke AM, Marzolf B, Dimitrov K, Stordrange L, Lin B, Jonassen I, Hood L, Akslen LA, Kalland KH (2005)
Gene expression profiles in prostate cancer: association with patient subgroups and tumour differentiation
Int J Oncol, 26 (2), 329-36
PubMed 15645116

Sandelin A, Bailey P, Bruce S, Engström PG, Klos JM, Wasserman WW, Ericson J, Lenhard B (2004)
Arrays of ultraconserved non-coding regions span the loci of key developmental genes in vertebrate genomes
BMC Genomics, 5 (1), 99
PubMed 15613238

Roth C, Betts MJ, Steffansson P, Saelensminde G, Liberles DA (2005)
The Adaptive Evolution Database (TAED): a phylogeny based tool for comparative genomics
Nucleic Acids Res, 33 (Database issue), D495-7
PubMed 15608245

Pang KC, Stephen S, Engström PG, Tajul-Arifin K, Chen W, Wahlestedt C, Lenhard B, Hayashizaki Y, Mattick JS (2005)
RNAdb–a comprehensive mammalian noncoding RNA database
Nucleic Acids Res, 33 (Database issue), D125-30
PubMed 15608161

Kettunen P, Løes S, Furmanek T, Fjeld K, Kvinnsland IH, Behar O, Yagi T, Fujisawa H, Vainio S, Taniguchi M, Luukko K (2004)
Coordination of trigeminal axon navigation and patterning with tooth organ formation: epithelial-mesenchymal interactions, and epithelial Wnt4 and Tgfbeta1 regulate semaphorin 3a expression in the dental mesenchyme
Development, 132 (2), 323-34
PubMed 15604101

Malde K, Coward EJonassen I (2004)
A graph based algorithm for generating EST consensus sequences
Bioinformatics, 21 (8), 1371-5
PubMed 15572463

Hinsen K, Reuter N, Navaza J, Stokes DL, Lacapère JJ (2004)
Normal mode-based fitting of atomic structure into electron density maps: application to sarcoplasmic reticulum Ca-ATPase
Biophys J, 88 (2), 818-27
PubMed 15542555

Tellgren A, Berglund AC, Savolainen P, Janis CM, Liberles DA (2004)
Myostatin rapid sequence evolution in ruminants predates domestication
Mol Phylogenet Evol, 33 (3), 782-90
PubMed 15522803

Korenjak M, Taylor-Harding B, Binné UK, Satterlee JS, Stevaux O, Aasland R, White-Cooper H, Dyson N, Brehm A (2004)
Native E2F/RBF complexes contain Myb-interacting proteins and repress transcription of developmentally controlled E2F target genes
Cell, 119 (2), 181-93
PubMed 15479636

Braun FN, Liberles DA (2004)
Repeat-modulated population genetic effects in fungal proteins
J Mol Evol, 59 (1), 97-102
PubMed 15383912

Katzov H, Bennet AM, Kehoe P, Wiman B, Gatz M, Blennow K, Lenhard B, Pedersen NL, de Faire U, Prince JA (2004)
A cladistic model of ACE sequence variation with implications for myocardial infarction, Alzheimer disease and obesity
Hum Mol Genet, 13 (21), 2647-57
PubMed 15367486

Flikka K, Yadetie F, Laegreid A, Jonassen I (2004)
XHM: a system for detection of potential cross hybridizations in DNA microarrays
BMC Bioinformatics, 5, 117
PubMed 15333145

Gaucher EA, Graddy LG, Li T, Simmen RC, Simmen FA, Schreiber DR, Liberles DA, Janis CM, Benner SA (2004)
The planetary biology of cytochrome P450 aromatases
BMC Biol, 2, 19
PubMed 15315709

Alkema WB, Lenhard B, Wasserman WW (2004)
Regulog analysis: detection of conserved regulatory networks across bacteria: application to Staphylococcus aureus
Genome Res, 14 (7), 1362-73
PubMed 15231752

Berven FS, Flikka K, Jensen HB, Eidhammer I (2004)
BOMP: a program to predict integral beta-barrel outer membrane proteins encoded within genomes of Gram-negative bacteria
Nucleic Acids Res, 32 (Web Server issue), W394-9
PubMed 15215418

Sandelin A, Wasserman WW, Lenhard B (2004)
ConSite: web-based prediction of regulatory elements using cross-species comparison
Nucleic Acids Res, 32 (Web Server issue), W249-52
PubMed 15215389

Taylor WR, Jonassen I (2004)
A structural pattern-based method for protein fold recognition
Proteins, 56 (2), 222-34
PubMed 15211507

Kleppe R, Haavik J (2004)
Different stabilities and denaturation pathways for structurally related aromatic amino acid hydroxylases
FEBS Lett, 565 (1-3), 155-9
PubMed 15135070

Küster H, Hohnjec N, Krajinski F, El YF, Manthey K, Gouzy J, Dondrup M, Meyer F, Kalinowski J, Brechenmacher L, van Tuinen D, Gianinazzi-Pearson V, Pühler A, Gamas P, Becker A (2004)
Construction and validation of cDNA-based Mt6k-RIT macro- and microarrays to explore root endosymbioses in the model legume Medicago truncatula
J Biotechnol, 108 (2), 95-113
PubMed 15129719

Hughes T, Hyun Y, Liberles DA (2004)
Visualising very large phylogenetic trees in three dimensional hyperbolic space
BMC Bioinformatics, 5, 48
PubMed 15117420

Imanishi T, Itoh T, Suzuki Y, O’Donovan C, Fukuchi S, Koyanagi KO, Barrero RA, Tamura T, Yamaguchi-Kabata Y, Tanino M, Yura K, Miyazaki S, Ikeo K, Homma K, Kasprzyk A, Nishikawa T, Hirakawa M, Thierry-Mieg J, Thierry-Mieg D, Ashurst J, Jia L, Nakao M, Thomas MA, Mulder N, Karavidopoulou Y et al. (2004)
Integrative annotation of 21,037 human genes validated by full-length cDNA clones
PLoS Biol, 2 (6), e162
PubMed 15103394

Subramaniam S, Stansberg C, Cunningham C (2004)
The interleukin 1 receptor family
Dev Comp Immunol, 28 (5), 415-28
PubMed 15062641

Stensvaag V, Furmanek T, Lønning K, Terzis AJ, Bjerkvig R, Visted T (2004)
Cryopreservation of alginate-encapsulated recombinant cells for antiangiogenic therapy
Cell Transplant, 13 (1), 35-44
PubMed 15040603

Johansson A, Katzov H, Zetterberg H, Feuk L, Johansson B, Bogdanovic N, Andreasen N, Lenhard B, Brookes AJ, Pedersen NL, Blennow K, Prince JA (2004)
Variants of CYP46A1 may interact with age and APOE to influence CSF Abeta42 levels in Alzheimer’s disease
Hum Genet, 114 (6), 581-7
PubMed 15034781

Bø TH, Dysvik B, Jonassen I (2004)
LSimpute: accurate estimation of missing values in microarray data with least squares methods
Nucleic Acids Res, 32 (3), e34
PubMed 14978222

Hüser AT, Becker A, Brune I, Dondrup M, Kalinowski J, Plassmeier J, Pühler A, Wiegräbe I, Tauch A (2003)
Development of a Corynebacterium glutamicum DNA microarray and validation by genome-wide expression profiling during growth with propionate as carbon source
J Biotechnol, 106 (2-3), 269-86
PubMed 14651867

Goesmann A, Linke B, Rupp O, Krause L, Bartels D, Dondrup M, McHardy AC, Wilke A, Pühler A, Meyer F (2003)
Building a BRIDGE for the integration of heterogeneous data from functional genomics into a platform for systems biology
J Biotechnol, 106 (2-3), 157-67
PubMed 14651858

Wilke A, Rückert C, Bartels D, Dondrup M, Goesmann A, Hüser AT, Kespohl S, Linke B, Mahne M, McHardy A, Pühler A, Meyer F (2003)
Bioinformatics support for high-throughput proteomics
J Biotechnol, 106 (2-3), 147-56
PubMed 14651857

Dondrup M, Goesmann A, Bartels D, Kalinowski J, Krause L, Linke B, Rupp O, Sczyrba A, Pühler A, Meyer F (2003)
EMMA: a platform for consistent storage and efficient analysis of microarray data
J Biotechnol, 106 (2-3), 135-46
PubMed 14651856

Wang J, Bø TH, Jonassen I, Myklebost O, Hovig E (2003)
Tumor classification and marker gene prediction by feature selection and fuzzy c-means clustering using microarray data
BMC Bioinformatics, 4, 60
PubMed 14651757

Braun FN, Liberles DA (2003)
Retention of enzyme gene duplicates by subfunctionalization
Int J Biol Macromol, 33 (1-3), 19-22
PubMed 14599579

Visted T, Furmanek T, Sakariassen P, Foegler WB, Sim K, Westphal H, Bjerkvig R, Lund-Johansen M (2003)
Prospects for delivery of recombinant angiostatin by cell-encapsulation therapy
Hum Gene Ther, 14 (15), 1429-40
PubMed 14577923

Mazet F, Yu JK, Liberles DA, Holland LZ, Shimeld SM (2003)
Phylogenetic relationships of the Fox (Forkhead) gene family in the Bilateria
Gene, 316, 79-89
PubMed 14563554

Reuter N, Hinsen K, Lacapère JJ (2003)
Transconformations of the SERCA1 Ca-ATPase: a normal mode study
Biophys J, 85 (4), 2186-97
PubMed 14507684

Roth C, Hughes T (2003)
From microarrays to genome duplications
Genome Biol, 4 (8), 332
PubMed 12914655

Stansberg C, Subramaniam S, Olsen L, Secombes CJ, Cunningham C (2003)
Cloning and characterisation of a putative ST2L homologue from Atlantic salmon (Salmo salar)
Fish Shellfish Immunol, 15 (3), 211-24
PubMed 12892743

Malde K, Coward EJonassen I (2003)
Fast sequence clustering using a suffix array algorithm
Bioinformatics, 19 (10), 1221-6
PubMed 12835265

Puntervoll P, Linding R, Gemünd C, Chabanis-Davidson S, Mattingsdal M, Cameron S, Martin DM, Ausiello G, Brannetti B, Costantini A, Ferrè F, Maselli V, Via A, Cesareni G, Diella F, Superti-Furga G, Wyrwicz L, Ramu C, McGuigan C, Gudavalli R, Letunic I, Bork P, Rychlewski L, Küster B, Helmer-Citterich M et al. (2003)
ELM server: A new resource for investigating short functional sites in modular eukaryotic proteins
Nucleic Acids Res, 31 (13), 3625-30
PubMed 12824381

Taylor WR, Munro RE, Petersen K, Bywater RP (2003)
Ab initio modelling of the N-terminal domain of the secretin receptors
Comput Biol Chem, 27 (2), 103-14
PubMed 12821307

Agasøster AV, Halskau Ø, Fuglebakk E, Frøystein NA, Muga A, Holmsen H, Martínez A (2003)
The interaction of peripheral proteins and membranes studied with alpha-lactalbumin and phospholipid bilayers of various compositions
J Biol Chem, 278 (24), 21790-7
PubMed 12660251

Luukko K, Løes S, Furmanek T, Fjeld K, Kvinnsland IH, Kettunen P (2003)
Identification of a novel putative signaling center, the tertiary enamel knot in the postnatal mouse molar tooth
Mech Dev, 120 (3), 270-6
PubMed 12591596

Petersen K, Taylor WR (2003)
Modelling zinc-binding proteins with GADGET: genetic algorithm and distance geometry for exploring topology
J Mol Biol, 325 (5), 1039-59
PubMed 12527307

Toska K, Kleppe R, Cohen P, Haavik J (2002)
Phosphorylation of tyrosine hydroxylase in isolated mice adrenal glands
Ann N Y Acad Sci, 971, 66-8
PubMed 12438091

Puntervoll P, Ruud M, Bruseth LJ, Kleivdal H, Høgh BT, Benz R, Jensen HB (2002)
Structural characterization of the fusobacterial non-specific porin FomA suggests a 14-stranded topology, unlike the classical porins
Microbiology, 148 (Pt 11), 3395-403
PubMed 12427931

Toska K, Kleppe R, Armstrong CG, Morrice NA, Cohen P, Haavik J (2002)
Regulation of tyrosine hydroxylase by stress-activated protein kinases
J Neurochem, 83 (4), 775-83
PubMed 12421349

Zhao Y, Kacskovics I, Pan Q, Liberles DA, Geli J, Davis SK, Rabbani H, Hammarstrom L (2002)
Artiodactyl IgD: the missing link
J Immunol, 169 (8), 4408-16
PubMed 12370374

Chekenya M, Enger PØ, Thorsen F, Tysnes BB, Al-Sarraj S, Read TA, Furmanek T, Mahesparan R, Levine JM, Butt AM, Pilkington GJ, Bjerkvig R (2002)
The glial precursor proteoglycan, NG2, is expressed on tumour neovasculature by vascular pericytes in human malignant brain tumours
Neuropathol Appl Neurobiol, 28 (5), 367-80
PubMed 12366818

Iversen H, Fuglebakk E, Holmsen H, Fukami MH (2002)
Identification of minor metabolites of phospholipid signal molecules in [(32)P]P(i)-labelled platelets
Platelets, 13 (5-6), 279-84
PubMed 12189013

Milchert LE, Liberles DA, Elofsson A (2002)
The salmon genome (and other issues in bioinformatics)
Genome Biol, 3 (7), REPORTS4022
PubMed 12184805

Lenhard B, Wasserman WW (2002)
TFBS: Computational framework for transcription factor binding site analysis
Bioinformatics, 18 (8), 1135-6
PubMed 12176838

Schöneboom JC, Lin H, Reuter N, Thiel W, Cohen S, Ogliaro F, Shaik S (2002)
The elusive oxidant species of cytochrome P450 enzymes: characterization by combined quantum mechanical/molecular mechanical (QM/MM) calculations
J Am Chem Soc, 124 (27), 8142-51
PubMed 12095360

Liberles DA, Wayne ML (2002)
Tracking adaptive evolutionary events in genomic sequences
Genome Biol, 3 (6), REVIEWS1018
PubMed 12093382

Bø T, Jonassen I (2002)
New feature subset selection procedures for classification of expression profiles
Genome Biol, 3 (4), RESEARCH0017
PubMed 11983058

Davids W, Gamieldien J, Liberles DA, Hide W (2002)
Positive selection scanning reveals decoupling of enzymatic activities of carbamoyl phosphate synthetase in Helicobacter pylori
J Mol Evol, 54 (4), 458-64
PubMed 11956684

Subramaniam S, Stansberg C, Olsen L, Zou J, Secombes CJ, Cunningham C (2002)
Cloning of a Salmo salar interleukin-1 receptor-like cDNA
Dev Comp Immunol, 26 (5), 415-31
PubMed 11906722

Jonassen I, Eidhammer I, Conklin D, Taylor WR (2002)
Structure motif discovery and mining the PDB
Bioinformatics, 18 (2), 362-7
PubMed 11847094

Conklin D, Jonassen I, Aasland R, Taylor WR (2002)
Association of nucleotide patterns with gene function classes: application to human 3′ untranslated sequences
Bioinformatics, 18 (1), 182-9
PubMed 11836227

Bø TH, Jonassen I, Eidhammer I, Helgesen C (2002)
A fast top-down method for constructing reliable radiation hybrid frameworks
Bioinformatics, 18 (1), 11-8
PubMed 11836206

Peltier JB, Emanuelsson O, Kalume DE, Ytterberg J, Friso G, Rudella A, Liberles DA, Söderberg L, Roepstorff P, von Heijne G, van Wijk KJ (2002)
Central functions of the lumenal and peripheral thylakoid proteome of Arabidopsis determined by experimentation and genome-wide prediction
Plant Cell, 14 (1), 211-36
PubMed 11826309

Krause A, Haas SA, Coward E, Vingron M (2002)
SYSTERS, GeneNest, SpliceNest: exploring sequence space from genome to protein
Nucleic Acids Res, 30 (1), 299-300
PubMed 11752319

Laprevotte I, Pupin M, Coward E, Didier G, Terzian C, Devauchelle C, Hénaut A (2001)
HIV-1 and HIV-2 LTR nucleotide sequences: assessment of the alignment by N-block presentation, “retroviral signatures” of overrepeated oligonucleotides, and a probable important role of scrambled stepwise duplications/deletions in molecular evolution
Mol Biol Evol, 18 (7), 1231-45
PubMed 11420363

Dysvik B, Jonassen I (2001)
J-Express: exploring gene expression data using Java
Bioinformatics, 17 (4), 369-70
PubMed 11301307

Apweiler R, Attwood TK, Bairoch A, Bateman A, Birney E, Biswas M, Bucher P, Cerutti L, Corpet F, Croning MD, Durbin R, Falquet L, Fleischmann W, Gouzy J, Hermjakob H, Hulo N, Jonassen I, Kahn D, Kanapin A, Karavidopoulou Y, Lopez R, Marx B, Mulder NJ, Oinn TM, Pagni M et al. (2000)
InterPro–an integrated documentation resource for protein families, domains and functional sites
Bioinformatics, 16 (12), 1145-50
PubMed 11159333

Eidhammer I, Jonassen I, Taylor WR (2000)
Structure comparison and structure patterns
J Comput Biol, 7 (5), 685-716
PubMed 11153094

Apweiler R, Attwood TK, Bairoch A, Bateman A, Birney E, Biswas M, Bucher P, Cerutti L, Corpet F, Croning MD, Durbin R, Falquet L, Fleischmann W, Gouzy J, Hermjakob H, Hulo N, Jonassen I, Kahn D, Kanapin A, Karavidopoulou Y, Lopez R, Marx B, Mulder NJ, Oinn TM, Pagni M et al. (2001)
The InterPro database, an integrated documentation resource for protein families, domains and functional sites
Nucleic Acids Res, 29 (1), 37-40
PubMed 11125043

Jonassen I, Eidhammer I, Grindhaug SH, Taylor WR (2000)
Searching the protein structure databank with weak sequence patterns and structural constraints
J Mol Biol, 304 (4), 599-619
PubMed 11099383

Jonassen I (2000)
Discovering patterns conserved in sets of unaligned protein sequences
Methods Mol Biol, 143, 33-52
PubMed 11084901

Vilo J, Brazma A, Jonassen I, Robinson A, Ukkonen E (2000)
Mining for putative regulatory elements in the yeast genome using gene expression data
Proc Int Conf Intell Syst Mol Biol, 8, 384-94
PubMed 10977099

Kurtzhals P, Schäffer L, Sørensen A, Kristensen C, Jonassen I, Schmid C, Trüb T (2000)
Correlations of receptor binding and metabolic and mitogenic potencies of insulin analogs designed for clinical use
Diabetes, 49 (6), 999-1005
PubMed 10866053

Coward E (1999)
Shufflet: shuffling sequences while conserving the k-let counts
Bioinformatics, 15 (12), 1058-9
PubMed 10745997

Klaerr-Blanchard M, Chiapello H, Coward E (2000)
Detecting localized repeats in genomic sequences: a new strategy and its application to Bacillus subtilis and Arabidopsis thaliana sequences
Comput Chem, 24 (1), 57-70
PubMed 10642880

Jonassen I, Eidhammer I, Taylor WR (1999)
Discovery of local packing motifs in protein structures
Proteins, 34 (2), 206-19
PubMed 10022356

Brazma A, Jonassen I, Vilo J, Ukkonen E (1998)
Predicting gene regulatory elements in silico on a genomic scale
Genome Res, 8 (11), 1202-15
PubMed 9847082

Coward E, Drabløs F (1998)
Detecting periodic patterns in biological sequences
Bioinformatics, 14 (6), 498-507
PubMed 9694988

Kjeldsen T, Pettersson AF, Drube L, Kurtzhals P, Jonassen I, Havelund S, Hansen PH, Markussen J (1998)
Secretory expression of human albumin domains in Saccharomyces cerevisiae and their binding of myristic acid and an acylated insulin analogue
Protein Expr Purif, 13 (2), 163-9
PubMed 9675058

Brazma A, Jonassen I, Eidhammer I, Gilbert D (1998)
Approaches to the automatic discovery of patterns in biosequences
J Comput Biol, 5 (2), 279-305
PubMed 9672833

Kurtzhals P, Havelund S, Jonassen I, Markussen J (1997)
Effect of fatty acids and selected drugs on the albumin binding of a long-acting, acylated insulin analogue
J Pharm Sci, 86 (12), 1365-8
PubMed 9423147

Jonassen I (1997)
Efficient discovery of conserved patterns using a pattern graph
Comput Appl Biosci, 13 (5), 509-22
PubMed 9367124

Whittingham JL, Havelund S, Jonassen I (1997)
Crystal structure of a prolonged-acting insulin with albumin-binding properties
Biochemistry, 36 (10), 2826-31
PubMed 9062110

Brazma A, Jonassen I, Ukkonen E, Vilo J (1996)
Discovering patterns and subfamilies in biosequences
Proc Int Conf Intell Syst Mol Biol, 4, 34-43
PubMed 8877502

Markussen J, Havelund S, Kurtzhals P, Andersen AS, Halstrøm J, Hasselager E, Larsen UD, Ribel U, Schäffer L, Vad K, Jonassen I (1996)
Soluble, fatty acid acylated insulins bind to albumin and show protracted action in pigs
Diabetologia, 39 (3), 281-8
PubMed 8721773

Kurtzhals P, Havelund S, Jonassen I, Kiehr B, Ribel U, Markussen J (1996)
Albumin binding and time action of acylated insulins in various species
J Pharm Sci, 85 (3), 304-8
PubMed 8699334

Kurtzhals P, Havelund S, Jonassen I, Kiehr B, Larsen UD, Ribel U, Markussen J (1995)
Albumin binding of insulins acylated with fatty acids: characterization of the ligand-protein interaction and correlation between binding affinity and timing of the insulin effect in vivo
Biochem J, 312 ( Pt 3), 725-31
PubMed 8554512

Jonassen I, Collins JF, Higgins DG (1995)
Finding flexible patterns in unaligned protein sequences
Protein Sci, 4 (8), 1587-95
PubMed 8520485

Tiwari SPReuter N (2016)
Similarity in Shape Dictates Signature Intrinsic Dynamics Despite No Functional Conservation in TIM Barrel Enzymes
PLoS One, 11 (3), e1004834

Skjaerven L, Hollup SM, Reuter N (2009)
Normal mode analysis for proteins
Theochem-J. Mol. Struct., 898 (1-3), 42-48

Kim J, Jonassen I (2005)
Guest editorial: WABI special section part II
IEEE-ACM Trans. Comput. Biol. Bioinform., 2 (1), 1-2

Soler E, Andrieu-Soler C, de Boer E, Bryne JC, Thongjuea S, Stadhouders R, Palstra RJ, Stevens M, Kockx C, van IJcken W, Hou J, Steinhoff C, Rijkers E, Lenhard B, Grosveld F (2010)
The genome-wide dynamics of the binding of Ldb1 complexes during erythroid differentiation (vol 24, pg 277, 2010)
Genes Dev., 24 (6), 623

Kim J, Jonassen I (2004)
Guest editorial: WABI special section part 1
IEEE-ACM Trans. Comput. Biol. Bioinform., 1 (4), 137-138

Lampe OD, Viola I, Reuter N, Hauser H (2007)
Two-level approach to efficient visualization of protein dynamics
IEEE Trans. Vis. Comput. Graph., 13 (6), 1616-1623

Menager H, Kalas M, Rapacki K, Ison J (2016)
Using registries to integrate bioinformatics tools and services into workbench environments
Int. J. Softw. Tools Technol. Transf., 18 (6), 581-586

Ragvin A, Moro E, Fredman D, Navratilova P, Drivenes O, Engstrom PG, Alonso ME, Mustienes ED, Skarmeta JLG, Tavares MJ, Casares F, Manzanares M, van Heyningen V, Molven A, Njolstad PR, Argenton F, Lenhard B, Becker TS (2011)
Long-range gene regulation links genomic type 2 diabetes and obesity risk regions to HHEX, SOX4, and IRX3 (vol 107, pg 775, 2009)
Proc. Natl. Acad. Sci. U. S. A., 108 (10), 4264