Publications

Candice Byers, Catrina Spruce, Haley J Fortin, Anne Czechanski, Steven C Munger, Laura G Reinholdt, Daniel A Skelly, Christopher L Baker (2021). Genetic control of pluripotency epigenome determines differentiation bias in mouse embryonic stem cells. bioRxiv.

Yuka Takemon, Joel M Chick, Isabela Gerdes Gyuricza, Daniel M Skelly, Oliver Devuyst, Steven Gygi, Gary A Churchill, Ron Korstanje (2020). Proteomic and transcriptomic profiling reveal different aspects of aging in the kidney. bioRxiv.

Hongtian Stanley Yang, Kristen D Onos, Kwangbom Choi, Kelly J Keezer, Daniel A Skelly, Gregory W Carter, Gareth R Howell (2020). Natural genetic variation determines microglia heterogeneity in wild-derived mouse models of Alzheimer's disease. Available at SSRN 3650597.

Daniel Ortmann, Stephanie Brown, Anne Czechanski, Selcan Aydin, Daniele Muraro, Yuanhua Huang, Rute A Tomaz, Anna Osnato, Giovanni Canu, Brandon T Wesley, others (2020). Naive pluripotent stem cells exhibit phenotypic variability that is driven by genetic variation. Cell stem cell.

Daniel A Skelly, Anne Czechanski, Candice Byers, Selcan Aydin, Catrina Spruce, Chris Olivier, Kwangbom Choi, Daniel M Gatti, Narayanan Raghupathy, Gregory R Keele, others (2020). Mapping the effects of genetic variation on chromatin state and gene expression reveals loci that control ground state pluripotency. Cell Stem Cell.

Vishnu Hosur, Daniel A Skelly, Christopher Francis, Benjamin E Low, Vivek Kohar, Lisa M Burzenski, Mansoor A Amiji, Leonard D Shultz, Michael V Wiles (2020). Improved mouse models and advanced genetic and genomic technologies for the study of neutrophils. Drug discovery today.

Elvira Forte, Daniel A Skelly, Mandy Chen, Sandra Daigle, Kaesi A Morelli, Olivia Hon, Vivek M Philip, Mauro W Costa, Nadia A Rosenthal, Milena B Furtado (2020). Dynamic interstitial cell response during myocardial infarction predicts resilience to rupture in genetically diverse mice. Cell reports.

Elvira Forte, Bryant Perkins, Amalia Sintou, Harkaran S Kalkat, Angelos Papanikolaou, Catherine Jenkins, Mashael Alsubaie, Rasheda A Chowdhury, Theodore M Duffy, Daniel A Skelly, others (2020). Cross-Priming Dendritic Cells Exacerbate Immunopathology after Ischemic Tissue Damage in the Heart. Circulation.

Kwangbom Choi, Yang Chen, Daniel A Skelly, Gary A Churchill (2020). Bayesian model selection reveals biological origins of zero inflation in single-cell transcriptomics. Genome biology.

Marion Bouvet, Olivier Claude, Maguelonne Roux, Dan Skelly, Nihar Masurkar, Nathalie Mougenot, Sophie Nadaud, Catherine Blanc, Clément Delacroix, Solenne Chardonnet, others (2020). Anti-integrin α v therapy improves cardiac fibrosis after myocardial infarction by blunting cardiac PW1+ stromal cells. Scientific Reports.

Daniel A Skelly, Narayanan Raghupathy, Raymond F Robledo, Joel H Graber, Elissa J Chesler (2019). Reference trait analysis reveals correlations between gene expression and quantitative traits in disjoint samples. Genetics.

Sriram Vijayraghavan, Stanislav G Kozmin, Pooja K Strope, Daniel A Skelly, Zhenguo Lin, John Kennell, Paul M Magwene, Fred S Dietrich, John H McCusker (2019). Mitochondrial genome variation affects multiple respiration and nonrespiration phenotypes in Saccharomyces cerevisiae. Genetics.

Micheal A McLellan, Daniel A Skelly, Malathi SI Dona, Galen T Squiers, Gabriella E Farrugia, Taylah L Gaynor, Charles D Cohen, Raghav Pandey, Henry Diep, Antony Vin, others (2019). High-resolution transcriptomic profiling of the heart during chronic stress reveals cellular drivers of cardiac fibrosis and hypertrophy. bioRxiv.

Daniel A Skelly, Anne Czechanski, Candice Byers, Selcan Aydin, Catrina Spruce, Chris Olivier, Kwangbom Choi, Daniel M Gatti, Narayanan Raghupathy, Alexander Stanton, others (2019). Genetic variation influences pluripotent ground state stability in mouse embryonic stem cells through a hierarchy of molecular phenotypes. bioRxiv.

Daniel A Skelly, Galen T Squiers, Micheal A McLellan, Mohan T Bolisetty, Paul Robson, Nadia A Rosenthal, Alexander R Pinto (2018). Single-cell transcriptional profiling reveals cellular diversity and intercommunication in the mouse heart. Cell reports.

Molly A Bogue, Stephen C Grubb, David O Walton, Vivek M Philip, Georgi Kolishovski, Tim Stearns, Matthew H Dunn, Daniel A Skelly, Beena Kadakkuzha, Gregg TeHennepe, others (2018). Mouse Phenome Database: an integrative database and analysis suite for curated empirical phenotype data from laboratory mice. Nucleic acids research.

Daniel A Skelly, John H McCusker, Eric A Stone, Paul M Magwene (2017). Private haplotype barcoding facilitates inexpensive high-resolution genotyping of multiparent crosses. bioRxiv.

Daniel A Skelly, Paul M Magwene, Brianna Meeks, Helen A Murphy (2017). Known mutator alleles do not markedly increase mutation rate in clinical Saccharomyces cerevisiae strains. Proceedings of the Royal Society B: Biological Sciences.

Daniel A Skelly, Paul M Magwene, Eric A Stone (2016). Sporadic, global linkage disequilibrium between unlinked segregating sites. Genetics.

Daniel A Skelly, Paul M Magwene (2016). Population perspectives on functional genomic variation in yeast. Briefings in functional genomics.

Pooja K Strope, Daniel A Skelly, Stanislav G Kozmin, Gayathri Mahadevan, Eric A Stone, Paul M Magwene, Fred S Dietrich, John H McCusker (2015). The 100-genomes strains, an S. cerevisiae resource that illuminates its natural phenotypic and genotypic variation and emergence as an opportunistic pathogen. Genome research.

Pooja K Strope, Stanislav G Kozmin, Daniel A Skelly, Paul M Magwene, Fred S Dietrich, John H McCusker (2015). 2μ plasmid in Saccharomyces species and in Saccharomyces cerevisiae. FEMS yeast research.

Caitlin F Connelly, Daniel A Skelly, Maitreya J Dunham, Joshua M Akey (2013). Population genomics and transcriptional consequences of regulatory motif variation in globally diverse Saccharomyces cerevisiae strains. Molecular biology and evolution.

Daniel A Skelly, Gennifer E Merrihew, Michael Riffle, Caitlin F Connelly, Emily O Kerr, Marnie Johansson, Daniel Jaschob, Beth Graczyk, Nicholas J Shulman, Jon Wakefield, others (2013). Integrative phenomics reveals insight into the structure of phenotypic diversity in budding yeast. Genome research.

Daniel A Skelly, Marnie Johansson, Jennifer Madeoy, Jon Wakefield, Joshua M Akey (2011). A powerful and flexible statistical framework for testing hypotheses of allele-specific gene expression from RNA-seq data. Genome research.

Stanley I Dodson, Daniel A Skelly, Carol Eunmi Lee (2010). Out of Alaska: morphological diversity within the genus Eurytemora from its ancestral Alaskan range (Crustacea, Copepoda). Fifty years after the ‘‘Homage to Santa Rosalia’’: Old and new paradigms on biodiversity in aquatic ecosystems.

Daniel A Skelly, James Ronald, Caitlin F Connelly, Joshua M Akey (2009). Population genomics of intron splicing in 38 Saccharomyces cerevisiae genome sequences. Genome biology and evolution.

Daniel A Skelly, James Ronald, Joshua M Akey (2009). Inherited variation in gene expression. Annual review of genomics and human genetics.