Publications and preprints

Nil Aygün, Angela L. Elwell, Dan Liang, Michael J. Lafferty, Kerry E. Cheek, Kenan P. Courtney, Jessica Mory, Ellie Hadden-Ford, Oleh Krupa, Luis de la Torre-Ubieta, Daniel H. Geschwind, Michael I. Love, Jason L. Stein. Brain-trait-associated variants impact cell-type-specific gene regulation during neurogenesis. American Journal of Human Genetics, September 2021. doi: 10.1016/j.ajhg.2021.07.011

Gieira S. Jones, Katherine A. Hoadley, Linnea T. Olsson, Alina M. Hamilton, Arjun Bhattacharya, Erin L. Kirk, Heather J. Tipaldos, Jodie M. Fleming, Michael I. Love, Hazel B. Nichols, Andrew F. Olshan, Melissa A. Troester Hepatocyte growth factor pathway expression in breast cancer by race and subtype. Breast Cancer Research, August 2021. doi: 10.1186/s13058-021-01460-5

(Open Letter) Kim-Anh Lê Cao, Al J. Abadi, Emily F. Davis-Marcisak, Lauren Hsu, Arshi Arora, Alexis Coullomb, Atul Deshpande, Yuzhou Feng, Pratheepa Jeganathan, Melanie Loth, Chen Meng, Wancen Mu, Vera Pancaldi, Kris Sankaran, Amrit Singh, Joshua S. Sodicoff, Genevieve L. Stein-O’Brien, Ayshwarya Subramanian, Joshua D. Welch, Yue You, Ricard Argelaguet, Vincent J. Carey, Ruben Dries, Casey S. Greene, Susan Holmes, Michael I. Love, Matthew E. Ritchie, Guo-Cheng Yuan, Aedin C. Culhane, Elana Fertig. Community-wide hackathons to identify central themes in single-cell multi-omics. Genome Biology, August 2021. doi: 10.1186/s13059-021-02433-9

Sean D. McCabe, Andrew B. Nobel, Michael I. Love. ACTOR: a latent Dirichlet model to compare expressed isoform proportions to a reference panel. Biostatistics, May 2021. doi: 10.1093/biostatistics/kxab013, actor R package

Dan Liang, Angela L. Elwell, Nil Aygün, Oleh Krupa, Justin M. Wolter, Felix A. Kyere, Michael J. Lafferty, Kerry E. Cheek, Kenan P. Courtney, Marianna Yusupova, Melanie E. Garrett, Allison Ashley-Koch, Gregory E. Crawford, Michael I. Love, Luis de la Torre-Ubieta, Daniel H. Geschwind, Jason L. Stein. Cell-type specific effects of genetic variation on chromatin accessibility during human neuronal differentiation. Nature Neuroscience, May 2021. doi: 10.1038/s41593-021-00858-w

Ying Chen, Nadia M. Davidson, Yuk Kei Wan, Harshil Patel, Fei Yao, Hwee Meng Low, Christopher Hendra, Laura Watten, Andre Sim, Chelsea Sawyer, Viktoriia Iakovleva, Puay Leng Lee, Lixia Xin, Hui En Vanessa Ng, Jia Min Loo, Xuewen Ong, Hui Qi Amanda Ng, Jiaxu Wang, Wei Qian Casslynn Koh, Suk Yeah Polly Poon, Dominik Stanojevic, Hoang-Dai Tran, Kok Hao Edwin Lim, Shen Yon Toh, Philip Andrew Ewels, Huck-Hui Ng, N.Gopalakrishna Iyer, Alexandre Thiery, Wee Joo Chng, Leilei Chen, Ramanuj DasGupta, Mile Sikic, Yun-Shen Chan, Boon Ooi Patrick Tan, Yue Wan, Wai Leong Tam, Qiang Yu, Chiea Chuan Khor, Torsten Wüstefeld, Ploy N. Pratanwanich, Michael I. Love, Wee Siong Sho Goh, Sarah B. Ng, Alicia Oshlack, Jonathan Göke, SG-NEx consortium. A systematic benchmark of Nanopore long read RNA sequencing for transcript level analysis in human cell lines. bioRxiv, April 2021. doi: 10.1101/2021.04.21.440736

Anqi Zhu (1), Nana Matoba (1), Emmaleigh Wilson, Amanda L. Tapia, Yun Li, Joseph G. Ibrahim, Jason L. Stein, Michael I. Love. MRLocus: identifying causal genes mediating a trait through Bayesian estimation of allelic heterogeneity. PLOS Genetics, April 2021. doi: 10.1371/journal.pgen.1009455, MRLocus R package

Anushka Rajesh, Yutong Chang, Malak S. Abedalthagafi, Annie Wong-Beringer, Michael I Love, Serghei Mangul. Improving the completeness of public metadata accompanying omics studies. Genome Biology, April 2021. doi: 10.1186/s13059-021-02332-z (Commentary)

Achal Patel, Montserrat García-Closas, Andrew F. Olshan, Charles M. Perou, Melissa A. Troester, Michael I. Love, Arjun Bhattacharya. Transcriptome-wide association study of risk of recurrence in Black and White breast cancer patients. medRxiv, March 2021. doi: 10.1101/2021.03.19.21253983

Arjun Bhattacharya, Yun Li, Michael I. Love. Multi-omic strategies for transcriptome-wide prediction and association studies. PLOS Genetics, March 2021. doi: 10.1371/journal.pgen.1009398, MOSTWAS R package

Hyo Young Choi, Heejoon Jo, Xiaobei Zhao, Katherine A. Hoadley, Scott Newman, Jeremiah Holt, Michele C. Hayward, Michael I. Love, J. S. Marron, D. Neil Hayes. SCISSOR: a framework for identifying structural changes in RNA transcripts. Nature Communications, January 2021. doi: 10.1038/s41467-020-20593-3

Arjun Bhattacharya, Alina M. Hamilton, Melissa A. Troester, Michael I. Love. DeCompress: tissue compartment deconvolution of targeted mRNA expression panels using compressed sensing. Nucleic Acids Research, January 2021. doi: 10.1093/nar/gkab031, DeCompress R package

Scott Van Buren, Hirak Sarkar, Avi Srivastava, Naim U. Rashid, Rob Patro, Michael I. Love. Compression of quantification uncertainty for scRNA-seq counts. Bioinformatics, January 2021. doi: 10.1093/bioinformatics/btab001, makeInfReps in fishpond R/Bioconductor package

Joshua P. Zitovsky, Michael I. Love. Fast effect size shrinkage software for beta-binomial models of allelic imbalance. F1000Research, December 2020. doi: 10.12688/f1000research.20916.2, method="betabinCR" in apeglm R/Bioconductor package

Nana Matoba, Michael I. Love, Jason L. Stein. Evaluating brain structure traits as endophenotypes using polygenicity and discoverability. Human Brain Mapping, October, 2020. doi: 10.1002/hbm.25257

Halei C. Benefield, Katherine E. Reeder-Hayes, Hazel B. Nichols, Benjamin C. Calhoun, Michael I. Love, Erin L. Kirk, Joseph Geradts, Katherine A. Hoadley, Stephen R. Cole, H. Shelton Earp, Andrew F. Olshan, Lisa A. Carey, Charles M. Perou, Melissa A. Troester. Outcomes of Hormone-Receptor Positive, HER2-Negative Breast Cancers by Race and Tumor Biological Features. JNCI Cancer Spectrum, September 2020. doi: 10.1093/jncics/pkaa072

Miheer Dewaskar, John Palowitch, Mark He, Michael I. Love, Andrew Nobel. Finding Stable Groups of Cross-Correlated Features in Multi-View data. arXiv, September 2020. arXiv: 2009.05079

Avi Srivastava, Laraib Malik, Hirak Sarkar, Mohsen Zakeri, Fatemeh Almodaresi, Charlotte Soneson, Michael I. Love, Carl Kingsford, Rob Patro. Alignment and mapping methodology influence transcript abundance estimation. Genome Biology, September 2020. doi: 10.1186/s13059-020-02151-8

Arjun Bhattacharya (1), Alina M. Hamilton (1), Helena Furberg, Eugene Pietzak, Mark P. Purdue, Melissa A. Troester, Katherine A. Hoadley (N), Michael I. Love (N). An approach for normalization and quality control for NanoString RNA expression data. Briefings in Bioinformatics, August 2020. doi: 10.1093/bib/bbaa163, PMC8138885

Hirak Sarkar, Avi Srivastava, Hector Corrada Bravo, Michael I. Love, Rob Patro. Terminus enables the discovery of data-driven, robust transcript groups from RNA-seq data. Bioinformatics, July 2020. doi: 10.1093/bioinformatics/btaa448, Terminus software

Sarah A. Reifeis, Michael G. Hudgens, Mete Civelek, Karen L. Mohlke, Michael I. Love. Assessing exposure effects on gene expression. Genetic Epidemiology, June, 2020. doi: 10.1002/gepi.22324, PMC7429346

Charlotte Soneson, Federico Marini, Florian Geier, Michael I. Love, Michael B. Stadler. ExploreModelMatrix: Interactive exploration for improved understanding of design matrices and linear models in R. F1000Research, June 2020. doi: 10.12688/f1000research.24187.1, ExploreModelMatrix R/Bioconductor package

Michael I. Love, Charlotte Soneson, Peter F. Hickey, Lisa K. Johnson, N. Tessa Pierce, Lori Shepherd, Martin Morgan, Rob Patro. Tximeta: Reference sequence checksums for provenance identification in RNA-seq. PLOS Computational Biology, February 2020. doi: 10.1371/journal.pcbi.1007664, tximeta R/Bioconductor package

Arjun Bhattacharya, Montserrat Garcia-Closas, Andrew F. Olshan, Charles M. Perou, Melissa A. Troester, Michael I. Love. A framework for transcriptome-wide association studies in breast cancer in diverse study populations. Genome Biology, February 2020. doi: 10.1186/s13059-020-1942-6

Stuart Lee, Michael Lawrence, Michael I. Love. Fluent genomics with plyranges and tximeta. F1000Research, February 2020. doi: 10.12688/f1000research.22259.1, fluentGenomics workflow

Lourdes Cruz-Garcia, Grainne O’Brien, Botond Sipos, Simon Mayes, Michael I. Love, Daniel J. Turner, Christophe Badie. Generation of a Transcriptional Radiation Exposure Signature in Human Blood Using Long-Read Nanopore Sequencing. Radiation Research, December 2019. doi: 10.1667/RR15476.1

Chelsea K. Raulerson, Arthur Ko, John C. Kidd, Kevin W. Currin, Sarah M. Brotman, Maren E. Cannon, Ying Wu, Cassandra N. Spracklen, Anne U. Jackson, Heather M. Stringham, Ryan P. Welch, Christian Fuchsberger, Adam E. Locke, Narisu Narisu, Aldons J. Lusis, Mete Civelek, Terrence S. Furey, Johanna Kuusisto, Francis S. Collins, Michael Boehnke, Laura J. Scott, Dan-Yu Lin, Michael I. Love, Markku Laakso, Päivi Pajukanta, Karen L. Mohlke. Adipose Tissue Gene Expression Associations Reveal Hundreds of Candidate Genes for Cardiometabolic Traits. Americal Journal of Human Genetics, October 2019. doi: 10.1016/j.ajhg.2019.09.001

Anqi Zhu, Avi Srivastava, Joseph G. Ibrahim, Rob Patro, Michael I. Love. Nonparametric expression analysis using inferential replicate counts. Nucleic Acids Research, August 2019. doi: 10.1093/nar/gkz622, swish supplement PDF, swish function in the fishpond R/Bioconductor package

Sean D. McCabe, Dan-Yu Lin, Michael I. Love. Consistency and overfitting of multi-omics methods on experimental data. Briefings in Bioinformatics, July 2019. doi: 10.1093/bib/bbz070, PMC7373174, movie R package

Charlotte Soneson, Michael I. Love, Rob Patro, Shobbir Hussain, Dheeraj Malhotra, Mark D. Robinson. A junction coverage compatibility score to quantify the reliability of transcript abundance estimates and annotation catalogs. Life Science Alliance, January 2019. doi: 10.26508/lsa.201800175

Lindsay A. Williams, Katherine A. Hoadley, Hazel B. Nichols, Joseph Geradts, Charles M. Perou, Michael I. Love, Andrew F. Olshan, Melissa A. Troester. Differences in race, molecular and tumor characteristics among women diagnosed with invasive ductal and lobular breast carcinomas. Cancer Causes & Control, January 2019. doi: 10.1007/s10552-018-1121-1

Yoh Isogai, Zheng Wu, Michael I.Love, Michael Ho-Young Ahn, Dhananjay Bambah-Mukku, Vivian Hua, Karolina Farrell, Catherine Dulac. Multisensory Logic of Infant-Directed Aggression by Males. Cell, December 2018. doi: 10.1016/j.cell.2018.11.032

(Review) Koen Van Den Berge, Katharina Hembach, Charlotte Soneson, Simone Tiberi, Lieven Clement, Michael I. Love, Rob Patro, Mark Robinson. RNA sequencing data: hitchhiker’s guide to expression analysis. Annual Review of Biomedical Data Science, April 2019. doi: 10.1146/annurev-biodatasci-072018-021255, https://peerj.com/manuscripts/33040/ (Review)

Anqi Zhu, Joseph G. Ibrahim, Michael I. Love. Heavy-tailed prior distributions for sequence count data: removing the noise and preserving large differences. Bioinformatics, November 2018. doi: 10.1093/bioinformatics/bty895, apeglm R/Bioconductor package

Michael I. Love, Charlotte Soneson, and Rob Patro. Swimming downstream: statistical analysis of differential transcript usage following Salmon quantification. F1000Research, October 2018. doi: 10.12688/f1000research.15398.3 rnaseqDTU workflow

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. Bioinformatics, September 2018. doi: 10.1093/bioinformatics/bty793

Alena van Bömmel, Michael I. Love, Ho-Ryun Chung, Martin Vingron. coTRaCTE predicts co-occurring transcription factors within cell-type specific enhancers. PLOS Computational Biology, August 2018. doi: 10.1371/journal.pcbi.1006372

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 vignette

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 R 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, September 2016. PMC, doi: 10.1038/nbt.3682, blog post, YouTube, alpine R/Bioconductor 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, 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, December 2015. PMC, doi: 10.12688/f1000research.7563.1, tximport R/Bioconductor package

Michael I. Love, Simon Anders, Vladislav Kim, Wolfgang Huber. RNA-seq workflow: gene-level exploratory analysis and differential expression. F1000Research, October 2015. PMC, doi: 10.12688/f1000research.7035.1, rnaseqGene 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, 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, 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, December 2014. PMC, doi: 10.1186/s13059-014-0550-8, DESeq2 R/Bioconductor 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, 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, 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, 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, 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, January 2011. PMC, doi: 10.2202/1544-6115.1732