Joshi Group – Medical Genomics

Research summary:

We study epigenetic and transcription mechanisms of mammalian gene control during development and disease, with potential long-term applications in developing alternative, gene-based therapies. We facilitate the use of genome-wide data through the development of new computational  methods and tools (theme 1) as well as perform integrative analysis of –omics data (theme 2). Alongside this, we collaborate with several experimental labs (theme 3). The three main themes of research along with a list of exemplar publications for each theme is below:

Development of new computational methods and tools to study mammalian epigenetic and transcription control 

  1. Devailly G, Mantsoki A, Joshi A. Heat*seq: an interactive web tool for highthroughput sequencing experiment comparison with public data. Bioinformatics, 32(21):3354–3356 (2016). ISSN 1367-4811. doi:10.1093/bioinformatics/btw407
  2. Pooley C, Ruau D, Lombard P, Göttgens B, Joshi A. TRES predicts transcription control in embryonic stem cells. Bioinformatics, 30(20):2983–2985 (2014). ISSN 1367-4811. doi: 10.1093/bioinformatics/btu399

Data exploration, integration and analysis of genome-wide data to learn new biology

  1. Mantsoki A, Devailly G, Joshi A. Dynamics of promoter bivalency and RNAP II pausing in mouse stem and differentiated cells. BMC Developmental Biology, 18(1):2 (2018). ISSN 1471-213X. doi: 10.1186/s12861-018-0163-7
  2. Mantsoki A, Devailly G, Joshi A. CpG island erosion, polycomb occupancy and sequence motif enrichment at bivalent promoters in mammalian embryonic stem cells. Scientific Reports, 5:16791 (2015). ISSN 2045-2322. doi:10.1038/srep16791.
  3. Joshi A. Mammalian transcriptional hotspots are enriched for tissue specific enhancers near cell type specific highly expressed genes and are predicted to act as transcriptional activator hubs. BMC Bioinformatics, 15:412 (2014). ISSN 14712105. doi:10.1186/s12859-014-0412-0.

Collaborative projects with experimental research groups with clinical implications

  1. Sugiyama D, Joshi A, Kulkeaw K, Tan KS, Yokoo-Inoue T, Mizuochi-Yanagi C, Yasuda K, Doi A, Iino T, Itoh M, Nagao-Sato S, Tani K, Akashi K, Hayashizaki Y, Suzuki H, Kawaji H, Carninci P, Forrest ARR. A Transcriptional Switch Point During Hematopoietic Stem and Progenitor Cell Ontogeny. Stem Cells and Development, 26(5):314–327 (2017). ISSN 1557-8534. doi:10.1089/scd.2016.0194
  2. Joshi A, Pooley C, Freeman TC, Lennartsson A, Babina M, Schmidl C, Geijtenbeek T, FANTOM Consortium, Michoel T, Severin J, Itoh M, Lassmann T, Kawaji H, Hayashizaki Y, Carninci P, Forrest ARR, Rehli M, Hume DA. Technical Advance: Transcription factor, promoter, and enhancer utilization in human myeloid cells. Journal of Leukocyte Biology, 97(5):985–995 (2015). ISSN 1938-3673. doi: 10.1189/jlb.6TA1014-477RR.