Citations & Publications

  • Regulation of RNA editing by intracellular acidification. Turnee N Malik, Erin E Doherty, Vandana M Gaded, Theodore M Hill, Peter A Beal, Ronald B Emeson. Nucleic Acids Research, 2021 Read it
    (CDS contribution: Data processing and analysis of RNA editing sites)
  • A developmental lineage-based gene co-expression network for mouse pancreatic β-cells reveals a role for Zfp800 in pancreas development. Osipovich AB, Dudek KD, Greenfest-Allen E, Cartailler JP, Manduchi E, Potter Case L, Choi E, Chapman AG, Clayton HW, Gu G, Stoeckert CJ Jr, Magnuson MA. Development. 2021 Mar 2:dev.196964. doi: 10.1242/dev.196964. Epub ahead of print. PMID: 33653874. Read it
    (CDS contribution: Network analysis, web app development)
  • Combinatorial transcription factor profiles predict mature and functional human islet α and β cells. Shristi Shrestha, Diane C. Saunders, John T. Walker, Joan Camunas-Soler, Xiao-Qing Dai, Rachana Haliyur, Radhika Aramandla, Greg Poffenberger, Nripesh Prasad, Rita Bottino, Roland Stein, Jean-Philippe Cartailler, Stephen C. J. Parker, Patrick E. MacDonald, Shawn E. Levy, Alvin C. Powers, Marcela Brissova. bioRxiv 2021.02.23.432522; doi: Read it
    (CDS contribution: )
  • Pancreatlas™: applying an adaptable framework to map the human pancreas in health and disease. Diane C. Saunders, James Messmer, Irina Kusmartseva, Maria L. Beery, Mingder Yang, Mark A. Atkinson, Alvin C. Powers, Jean-Philippe Cartailler, Marcela Brissova. BioRxiv. 2020. doi: Read it
    (CDS contribution: Informatics, imaging, infrastructure, programming)
  • Quantitative Analysis of Adenosine-to-Inosine RNA Editing. Malik TN, Cartailler JP, Emeson RB. Methods Mol Biol. 2021;2181:97-111. doi:10.1007/978-1-0716-0787-9_7 Read it
    (CDS contribution: Bioinformatics)
  • Loss of the transcription factor MAFB limits β-cell derivation from human PSCs Ronan Russell, Phichitpol P. Carnese, Thomas G. Hennings, Emily M. Walker, Holger A. Russ, Jennifer S. Liu, Simone Giacometti, Roland Stein & Matthias Hebrok. Nature Communications. 2020 Read it
    (CDS contribution: ChIP-Seq data processing and analysis, data deposition to ArrayExpress, protocols write-ups)
  • Excitotoxicity and overnutrition additively impair metabolic function and identity of pancreatic β-cells Osipovich et al. (pending acceptance)
    (CDS contribution: Bioinformatics, RNA-Seq data processing and analysis, functional gene enrichment analysis)
  • Human iPSC-derived cerebral organoids model features of Leigh Syndrome and reveal abnormal corticogenesis Alejandra I. Romero-Morales, Anuj Rastogi, Hoor Temuri, Megan L. Rasmussen, Gregory Scott McElroy, Lawrence Hsu, Paula M. Almonacid, Bryan A. Millis, Navdeep S Chandel, Jean-Phillippe Cartailler, Vivian Gama. BioRxiv. 2020. doi: Read it
    (CDS contribution: Bioinformatics, variant calling analysis, visualization, enrichment analysis)
  • Transgene-associated human growth hormone expression in pancreatic β-cells impairs identification of sex-based gene expression differences. Stancill JS, Osipovich AB, Cartailler JP, Magnuson MA. Am J Physiol Endocrinol Metab. 2019 Feb 1;316(2):E196-E209. doi: 10.1152/ajpendo.00229.2018 Read it
    (CDS contribution: Bulk RNA-Seq data processing and analysis)
  • iterativeWGCNA: iterative refinement to improve module detection from WGCNA co-expression networks. Emily Greenfest-Allen, Jean-Philippe Cartailler, Mark A. Magnuson, Christian J. Stoeckert Jr. BioRxiv. 2017. doi: Read it
    (CDS contribution: Method validation and application to new datasets)
  • Chronic β-Cell Depolarization Impairs β-Cell Identity by Disrupting a Network of Ca2+-Regulated Genes. Stancill JS, Cartailler JP, Clayton HW, O'Connor JT, Dickerson MT, Dadi PK, Osipovich AB, Jacobson DA, Magnuson MA. Diabetes. 2017 Aug;66(8):2175-2187. doi: 10.2337/db16-1355 Read it
    (CDS contribution: Bulk RNA-Seq data processing and analysis)
  • New ideas connecting the cell cycle and pancreatic endocrine-lineage specification. Bechard ME, Wright CV. Cell Cycle. 2017 Feb 16;16(4):301-303. doi: 10.1080/15384101.2016.1256149 Read it
    (CDS contribution: Figure 1 illustration)
  • Setd5 is essential for mammalian development and the co-transcriptional regulation of histone acetylation. Osipovich AB, Gangula R, Vianna PG, Magnuson MA. Development. 2016 Dec 15;143(24):4595-4607 Read it
    (CDS contribution: Bulk RNA-Seq data processing and analysis)
  • Research resource: dkCOIN, the National Institute of Diabetes, Digestive and Kidney Diseases (NIDDK) consortium interconnectivity network: a pilot program to aggregate research resources generated by multiple research consortia. McKenna NJ, Howard CL, Aufiero M, Easton-Marks J, Steffen DL, Becnel LB, Magnuson MA, McIndoe RA, Cartailler JP. Mol Endocrinol. 2012 Oct;26(10):1675-81 Read it
    (CDS contribution: Informatics, strategy, leadership)


Data Repositories

Code Repositories