Publications and preprints

Michael I. Love, Charlotte Soneson, and Rob Patro. Swimming downstream: statistical analysis of differential transcript usage following Salmon quantification F1000Research, June 2018. doi: 10.12688/f1000research.15398.1 rnaseqDTU workflow

Anqi Zhu, Joseph G. Ibrahim, Michael I. Love. Heavy-tailed prior distributions for sequence count data: removing the noise and preserving large differences. bioRxiv, April 2018. doi: 10.1101/303255, apeglm software

Yuchen Yang, Ruth Huh, Houston W. Culpepper, Yuan Lin, Michael I. Love, Yun Li SAFE-clustering: Single-cell Aggregated (From Ensemble) Clustering for Single-cell RNA-seq Data. bioRxiv, March 2018. doi: 10.1101/215723

Edward W. Pietryk, Kiristin Clement, Marwa Elnagheeb, Ryan Kuster, Kayla Kilpatrick, Michael I. Love, Folami Y. Ideraabdullah. Intergenerational response to the endocrine disruptor vinclozolin is influenced by maternal genotype and crossing scheme. Reproducitive Toxicology, March 2018. doi: 10.1016/j.reprotox.2018.03.005

Koen Van den Berge (1), Fanny Perraudeau (1), Charlotte Soneson, Michael I. Love, Davide Risso, Jean-Philippe Vert, Mark D. Robinson, Sandrine Dudoit (N), Lieven Clement (N). Observation weights unlock bulk RNA-seq tools for zero inflation and single-cell applications. Genome Biology, February 2018. doi: 10.1186/s13059-018-1406-4, ZINB-WaVE software vignette for DE analysis

Lindsay A. Williams, Hazel B. Nichols, Katherine A. Hoadley, Chiu Kit Tse, Joseph Geradts, Mary Elizabeth Bell, Charles M. Perou, Michael I. Love, Andrew F. Olshan, Melissa A. Troester. Reproductive risk factor associations with lobular and ductal carcinoma in the Carolina Breast Cancer Study. Cancer Causes & Control, November 2017. doi: 10.1007/s10552-017-0977-9

Doug H. Phanstiel, Kevin Van Bortle, Damek Spacek, Gaelen T. Hess, Muhammad S. Shamim, Ido Machol, Michael I. Love, Erez L. Aiden, Michael C. Bassik, Michael P. Snyder. Static and Dynamic DNA Loops form AP-1-Bound Activation Hubs during Macrophage Development. Molecular Cell, September 2017. PMC, doi: 10.1016/j.molcel.2017.08.006

Rob Patro, Geet Duggal, Michael I. Love, Rafael A. Irizarry, Carl Kingsford. Salmon provides fast and bias-aware quantification of transcript expression. Nature Methods, March 2017. PMC, doi: 10.1038/nmeth.4197, CMU PR, Salmon software

Michael I. Love, Matthew Huska, Marcel Jurk, Robert Schöpflin, Stephan Starick, Kevin Schwahn, Samantha Cooper, Keith Yamamoto, Morgane Thomas-Chollier, Martin Vingron, Sebastiaan Meijsing. Role of the chromatin landscape and sequence in determining cell type-specific genomic glucocorticoid receptor binding and gene regulation. Nucleic Acids Research, November 2016. doi: 10.1093/nar/gkw1163

Leonardo Collado Torres, Abhinav Nellore, Alyssa C. Frazee, Christopher Wilks, Michael I. Love, Ben Langmead, Rafael A. Irizarry, Jeffrey Leek, Andrew E. Jaffe. Flexible expressed region analysis for RNA-seq with derfinder. Nucleic Acids Research, October 2016. PMC, doi: 10.1093/nar/gkw852, derfinder package

Michael I. Love, John B. Hogenesch, Rafael A. Irizarry. Modeling of RNA-seq fragment sequence bias reduces systematic errors in transcript abundance estimation. Nature Biotechnology, 34(12):1287-1291, September 2016. PMC, doi: 10.1038/nbt.3682, blog post, YouTube, alpine package

Mingxiang Teng, Michael I. Love, Carrie A. Davis, Sarah Djebali, Alexander Dobin, Brenton R. Graveley, Sheng Li, Christopher E. Mason, Sara Olson, Dmitri Pervouchine, Cricket A. Sloan, Xintao Wei, Lijun Zhan, Rafael A. Irizarry. A benchmark for RNA-seq quantification pipelines. Genome Biology, 17(74), April 2016. PMC, doi: 10.1186/s13059-016-0940-1

Charlotte Soneson, Michael I. Love, Mark D. Robinson. Differential analyses for RNA-seq: transcript-level estimates improve gene-level inferences. F1000Research, 4(1521), December 2015. PMC, doi: 10.12688/f1000research.7563.1, tximport package

Michael I. Love, Simon Anders, Vladislav Kim, Wolfgang Huber. RNA-seq workflow: gene-level exploratory analysis and differential expression. F1000Research, 4(1070), October 2015. PMC, doi: 10.12688/f1000research.7035.1, live workflow

Raman Kumar, et al. Increased STAG2 dosage defines a novel cohesinopathy with intellectual disability and behavioural problems. Human Molecular Genetics, October 2015. doi: 10.1093/hmg/ddv414

Stephan R. Starick, Jonas Ibn-Salem, Marcel Jurk, Céline Hernandez, Michael I. Love, Ho-Ryun Chung, Martin Vingron, Morgane Thomas-Chollier, Sebastiaan H. Meijsing. ChIP-exo signal associated with DNA-binding motifs provides insight into the genomic binding of the glucocorticoid receptor and cooperating transcription factors. Genome Research, 25(6):825–835, June 2015. doi: 10.1101/gr.185157.114

Wolfgang Huber, Vincent J. Carey, Robert Gentleman, Simon Anders, Marc Carlson, Benilton S. Carvalho, Hector Corrada C. Bravo, Sean Davis, Laurent Gatto, Thomas Girke, Raphael Gottardo, Florian Hahne, Kasper D. Hansen, Rafael A. Irizarry, Michael Lawrence, Michael I. Love, James MacDonald, Valerie Obenchain, Andrzej K. Oleś, Hervé Pagès, Alejandro Reyes, Paul Shannon, Gordon K. Smyth, Dan Tenenbaum, Levi Waldron, Martin Morgan. Orchestrating high-throughput genomic analysis with Bioconductor. Nature Methods, 12(2):115–121, February 2015. PMC, doi: 10.1038/nmeth.3252

Hao Hu, et al. X-exome sequencing of 405 unresolved families identifies seven novel intellectual disability genes. Molecular Psychiatry, February 2015. doi: 10.1038/mp.2014.193

Michael I. Love, Wolfgang Huber, Simon Anders. Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome Biology, 15(12):550+, December 2014. PMC, doi: 10.1186/s13059-014-0550-8, DESeq2 package

Wei Li, Han Xu, Tengfei Xiao, Le Cong, Michael I. Love, Feng Zhang, Rafael A. Irizarry, Jun S. Liu, Myles Brown, X. S. Liu. MAGeCK enables robust identification of essential genes from genome-scale CRISPR/cas9 knockout screens. Genome Biology, 15(12):554+, December 2014. PMC, doi: 10.1186/s13059-014-0554-4

Jonas Ibn-Salem (1), Sebastian Köhler (1), Michael I. Love, Ho-Ryun Chung, Ni Huang, Matthew E. Hurles, Melissa Haendel, Nicole L. Washington, Damian Smedley, Christopher J. Mungall, Suzanna E. Lewis, Claus-Eric Ott, Sebastian Bauer, Paul N. Schofield, Stefan Mundlos, Malte Spielmann (N), Peter N. Robinson (N). Deletions of chromosomal regulatory boundaries are associated with congenital disease. Genome Biology, 15(9):423+, September 2014. PMC, doi: 10.1186/s13059-014-0423-1

Owen D. Solberg (1), Edwin J. Ostrin (1), Michael I. Love, Jeffrey C. Peng, Nirav R. Bhakta, Lydia Hou, Christine Nguyen, Margaret Solon, Cindy Nguyen, Andrea J. Barczak, Lorna T. Zlock, Denitza P. Blagev, Walter E. Finkbeiner, K. Mark Ansel, Joseph R. Arron, David J. Erle (N), Prescott G. Woodruff (N). Airway epithelial miRNA expression is altered in asthma. American Journal of Respiratory and Critical Care Medicine, 186(10):965–974, November 2012. PMC, doi: 10.1164/rccm.201201-0027OC

Ruping Sun, Michael I. Love, Tomasz Zemojtel, Anne-Katrin Emde, Ho-Ryun Chung, Martin Vingron, Stefan A. Haas. Breakpointer: using local mapping artifacts to support sequence breakpoint discovery from single-end reads. Bioinformatics, 28(7):1024–1025, April 2012. doi: 10.1093/bioinformatics/bts064

Michael I. Love, Alena Myšičková, Ruping Sun, Vera Kalscheuer, Martin Vingron, Stefan A. Haas. Modeling read counts for CNV detection in exome sequencing data. Statistical Applications in Genetics and Molecular Biology, 10(1), January 2011. PMC, doi: 10.2202/1544-6115.1732, exomeCopy package