Of 30 papers, those that were co-authored are marked as such:

Differential Signaling Effects of Escherichia Coli and Staphylococcus Aureus in Human Whole Blood Indicate Distinct Regulation of the NRF2 Pathway.. Pourquoi A, Miller MR, Koch SR, Boyle K, Surratt V, Nguyen H, Panja S, Cartailler JP, Shrestha S, Stark RJ. Shock 61(4):p 557-563, April 2024. | DOI: 10.1097/SHK.0000000000002305 Read it
(CDS contribution: Bioinformatics, RNA-Seq, differential gene expression)

From goal to outcome: Analyzing the progression of biomedical sciences PhD careers in a longitudinal study using an expanded taxonomy. Brown AM, Meyers LC, Varadarajan J, Ward NJ, Cartailler JP, Chalkley RG, Gould KL, Petrie KA. FASEB BioAdvances. 2023; 00: 1-26. doi:10.1096/fba.2023-00072 Read it
(CDS contribution: Database architecture and development, ETL, publication/software engineering, documentation, infrastructure)

Deletion of Ascl1 in pancreatic β-cells improves insulin secretion, promotes parasympathetic innervation, and attenuates dedifferentiation during metabolic stress. Osipovich AB, Zhou FY, Chong JJ, Trinh LT, Cottam MA, Shrestha S, Cartailler JP, Magnuson MA. Mol Metab. 2023 Sep 26:101811. doi: 10.1016/j.molmet.2023.101811. Epub ahead of print. PMID: 37769990. Read it
(CDS contribution: Bioinformatics, RNA-Seq)

ZFP92, a KRAB domain zinc finger protein enriched in pancreatic islets, binds to B1/Alu SINE transposable elements and regulates retroelements and genes. Osipovich AB, Dudek KD, Trinh LT, Kim LH, Shrestha S, Cartailler JP, Magnuson MA. PLoS Genet. 2023 May 8;19(5):e1010729. doi: 10.1371/journal.pgen.1010729. PMID: 37155670. Read it
(CDS contribution: Bulk RNA-Seq analysis, transcriptomics, transposable elements, data visualization, enrichment analysis)

Single-cell RNA sequencing of Sox17-expressing lineages reveals distinct gene regulatory networks and dynamic developmental trajectories. Stem Cells. Trinh LT, Osipovich AB, Liu B, Shrestha S, Cartailler JP, Wright CVE, Magnuson MA. 2023 Apr 21:sxad030. doi: 10.1093/stmcls/sxad030. Epub ahead of print. PMID: 37085274. Read it
(CDS contribution: Bioinformatics, pySCENIC, single cell transcriptomics, computational analysis)

Protein kinase D1 (Prkd1) deletion in brown adipose tissue leads to altered myogenic gene expression after cold exposure, while thermogenesis remains intact. Crowder, MK, Shrestha, S, Cartailler, JP, & Collins, S (2023). Physiological Reports, 11, e15576. https://doi.org/10.14814/phy2.15576 Read it
(CDS contribution: Bioinformatics, bulk RNA-Seq analysis, transcriptomics, data visualization, enrichment analysis)

Human pancreatic capillaries and nerve fibers persist in type 1 diabetes despite beta cell loss. Richardson TM, Saunders DC, Haliyur R, Shrestha S, Cartailler JP, Reinert RB, Petronglo J, Bottino R, Aramandla R, Bradley AM, Jenkins R, Phillips S, Kang H; Human Pancreas Analysis Program; Caidedo A, Powers AC, Brissova M. Am J Physiol Endocrinol Metab. 2023 Jan 25. doi: 10.1152/ajpendo.00246.2022. Epub ahead of print. PMID: 36696598. Read it
(CDS contribution: Single cell transcriptomics, computational analysis)

Lhx2 is a progenitor-intrinsic modulator of Sonic Hedgehog signaling during early retinal neurogenesis. Li X, Gordon PJ, Gaynes JA, Fuller AW, Ringuette R, Santiago CP, Wallace V, Blackshaw S, Li P, Levine EM. Elife. 2022 Dec 2;11:e78342. doi: 10.7554/eLife.78342. PMID: 36459481; PMCID: PMC9718532. Read it
(CDS contribution: Bioinformatics, RNA-Seq, differential gene expression)

Aging compromises human islet beta cell function and identity by decreasing transcription factor activity and inducing ER stress. Shrestha S, Erikson G, Lyon J, Spigelman AF, Bautista A, Manning Fox JE, Dos Santos C, Shokhirev M, Cartailler JP, Hetzer MW, MacDonald PE, Arrojo E Drigo R. Sci Adv. 2022 Oct 7;8(40):eabo3932. doi: 10.1126/sciadv.abo3932. Epub 2022 Oct 5. PMID: 36197983; PMCID: PMC9534504. Read it
(CDS contribution: Single cell transcriptomics, pySCENIC, computational analysis)

Distinct Patterns of Clonal Evolution Drive Myelodysplastic Syndrome Progression to Secondary Acute Myeloid Leukemia. Guess T, Potts CR, Bhat P, Cartailler JA, Brooks A, Holt C, Yenamandra A, Wheeler FC, Savona MR, Cartailler JP, Ferrell PB. Blood Cancer Discov. 2022 Jul 6;3(4):316-329. doi: 10.1158/2643-3230.BCD-21-0128. Read it
(CDS contribution: Bioinformatics, single cell transcriptomics, data visualization)

Human iPSC-derived cerebral organoids model features of Leigh syndrome and reveal abnormal corticogenesis. Romero-Morales AI, Robertson GL, Rastogi A, Rasmussen ML, Temuri H, McElroy GS, Chakrabarty RP, Hsu L, Almonacid PM, Millis BA, Chandel NS, Cartailler JP, Gama V. Development. 2022 Oct 15;149(20):dev199914. doi: 10.1242/dev.199914. Epub 2022 Jul 6. Read it
(CDS contribution: Bioinformatics, data visualization)

Isocitrate dehydrogenase mutations are associated with altered IL-1β responses in acute myeloid leukemia. Sunthankar KI, Jenkins MT, Cote CH, Patel SB, Welner RS, Ferrell PB. Leukemia. 2022 Apr;36(4):923-934. doi: 10.1038/s41375-021-01487-9. Epub 2021 Dec 2. PMID: 34857894; PMCID: PMC9066619. Read it
(CDS contribution: Single cell transcriptomics)

Influence of basal media composition on barrier fidelity within human pluripotent stem cell-derived blood-brain barrier models. Neal EH, Katdare KA, Shi Y, Marinelli NA, Hagerla KA, Lippmann ES. J Neurochem. 2021 Dec;159(6):980-991. doi: 10.1111/jnc.15532. Epub 2021 Nov 18. PMID: 34716922; PMCID: PMC8688328. Read it
(CDS contribution: Discussion about RNA-Seq experimental design)

Regulation and Functional Consequences of mGlu4 RNA Editing Hofmann CS, Carrington S, Keller AN, Gregory KJ, Niswender CM. RNA. 2021 Oct;27(10):1220-1240. doi: 10.1261/rna.078729.121 Read it
(CDS contribution: Bioinformatics of RNA editing events from NGS FastQ files)

Mouse models of patent ductus arteriosus (PDA) and their relevance for human PDA. Yarboro MT, Gopal SH, Su RL, Morgan TM, Reese J. Dev Dyn. 2021 Aug 4. doi: 10.1002/dvdy.408. Read it
(CDS contribution: Protein-protein interaction analysis, data interpretation, and figure construction)

Insm1, Neurod1, and Pax6 promote murine pancreatic endocrine cell development through overlapping yet distinct RNA transcription and splicing programs. Dudek KD, Osipovich AB, Cartailler JP, Gu G, Magnuson MA. G3 Genes|Genomes|Genetics, 2021 Read it
(CDS contribution: Bulk RNA-Seq analysis, RNA alternate splicing analysis)

Combinatorial transcription factor profiles predict mature and functional human islet α and β cells. Shrestha S, Saunders DC, Walker JT, Camunas-Soler J, Dai XQ, Haliyur R, Aramandla R, Poffenberger G, Prasad N, Bottino R, Stein R, Cartailler JP, Parker SC, MacDonald PE, Levy SE, Powers AC, Brissova M. JCI Insight. 2021 Aug 24:151621. doi: 10.1172/jci.insight.151621. Read it
(CDS contribution: Single cell RNA-Seq analysis)

Regulation of RNA editing by intracellular acidification. Malik TN, Doherty EE, Gaded VM, Hill TM, Beal PA, Emeson RB. 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. Read it
(CDS contribution: Network analysis, web app development)

Pancreatlas™: applying an adaptable framework to map the human pancreas in health and disease. Saunders DC, Messmer J, Kusmartseva I, Beery ML, Yang M, Atkinson MA, Powers AC, Cartailler JP, Brissova M. Patterns (N Y). 2020 Oct 5;1(8):100120. doi: 10.1016/j.patter.2020.100120. 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 Russell R, Carnese PP, Hennings TG, Walker EM, Russ HA, Liu JS, Giacometti S, Stein R & Hebrok M. Nature Communications. 2020 Read it
(CDS contribution: ChIP-Seq Analysis)

Excitotoxicity and overnutrition additively impair metabolic function and identity of pancreatic β-cells Osipovich AB, Stancill JS, Cartailler JP, Dudek KD, Magnuson MA. Diabetes. 2020 Jul;69(7):1476-1491. doi: 10.2337/db19-1145 Read it
(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: https://doi.org/10.1101/2020.04.21.054361 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. Greenfest-Allen E, Cartailler JP, Magnuson MA, Stoeckert CJ. BioRxiv. 2017. doi: https://doi.org/10.1101/234062 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

• E-MTAB-4726 (ArrayExpress)
• E-MTAB-5189 (ArrayExpress)
• E-MTAB-6329 (ArrayExpress)
• E-MTAB-6615 (ArrayExpress)
• E-MTAB-8643 (ArrayExpress)
• E-MTAB-8612 (ArrayExpress)
• E-MTAB-8802 (ArrayExpress)
• PRJNA626388 (NCBI)
• 7311202 (Zenodo)

Code & Data Repositories

Published code, apps and data:

• Code - A developmental lineage-based gene co-expression network for mouse pancreatic beta-cells
• Code - iterativeWGCNA: a WGCNA extension
• Code - Modeling the effect of Leigh syndrome-associated mutations using human cerebral organoids
• Code - Freezer configuration generator for Core Informatics LIMS (Python)
• Code - Generate Leaflet-based heatmap from collaborator-location data
• Code - Single cell Islets - R Shiny App
• Code - FFIND is a generalized framework for connecting to managed data and metadata from diverse sources and making it accessible via an integrated web application that promotes the exploration and discovery of the data.
• App - Single cell gene expression atlas of human pancreatic islets
• Code - Aging compromises human islet beta cell function and identity by decreasing transcription factor activity and inducing ER stress
• Data - Aging compromises human islet beta cell function and identity by decreasing transcription factor activity and inducing ER stress