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Orchestrating high-throughput genomic analysis with Bioconductor W Huber, VJ Carey, R Gentleman, S Anders, M Carlson, BS Carvalho, ... Nature methods 12 (2), 115-121, 2015 | 3558 | 2015 |
Differential abundance analysis for microbial marker-gene surveys JN Paulson, OC Stine, HC Bravo, M Pop Nature methods 10 (12), 1200-1202, 2013 | 2239 | 2013 |
Tackling the widespread and critical impact of batch effects in high-throughput data JT Leek, RB Scharpf, HC Bravo, D Simcha, B Langmead, WE Johnson, ... Nature Reviews Genetics 11 (10), 733-739, 2010 | 2168 | 2010 |
Increased methylation variation in epigenetic domains across cancer types KD Hansen, W Timp, HC Bravo, S Sabunciyan, B Langmead, ... Nature genetics 43 (8), 768-775, 2011 | 1212 | 2011 |
Multivariable association discovery in population-scale meta-omics studies H Mallick, A Rahnavard, LJ McIver, S Ma, Y Zhang, LH Nguyen, TL Tickle, ... PLoS computational biology 17 (11), e1009442, 2021 | 1192 | 2021 |
Comparative cellular analysis of motor cortex in human, marmoset and mouse TE Bakken, NL Jorstad, Q Hu, BB Lake, W Tian, BE Kalmbach, M Crow, ... Nature 598 (7879), 111-119, 2021 | 454 | 2021 |
Automated classification of bird and amphibian calls using machine learning: A comparison of methods MA Acevedo, CJ Corrada-Bravo, H Corrada-Bravo, LJ Villanueva-Rivera, ... Ecological Informatics 4 (4), 206-214, 2009 | 383 | 2009 |
A multimodal cell census and atlas of the mammalian primary motor cortex Principal manuscript editors, Analysis coordination, ... Nature 598 (7879), 86-102, 2021 | 311 | 2021 |
Diarrhea in young children from low-income countries leads to large-scale alterations in intestinal microbiota composition M Pop, AW Walker, J Paulson, B Lindsay, M Antonio, MA Hossain, ... Genome biology 15, 1-12, 2014 | 276 | 2014 |
A system for operational aerosol optical depth data assimilation over global oceans C Kuang, PH McMurry, AV McCormick, FL Eisele, SH Lee, LH Young, ... J. Geophys. Res 113 (D10), D10208, 2007 | 262 | 2007 |
Reporting guidelines for human microbiome research: the STORMS checklist C Mirzayi, A Renson, Genomic Standards Consortium, ... Nature medicine 27 (11), 1885-1892, 2021 | 243 | 2021 |
A transcriptomic and epigenomic cell atlas of the mouse primary motor cortex Z Yao, H Liu, F Xie, S Fischer, RS Adkins, AI Aldridge, SA Ament, ... Nature 598 (7879), 103-110, 2021 | 238 | 2021 |
metagenomeSeq: Statistical analysis for sparse high-throughput sequencing JN Paulson, M Pop, HC Bravo Bioconductor package 1 (0), 191, 2013 | 237 | 2013 |
Large hypomethylated blocks as a universal defining epigenetic alteration in human solid tumors W Timp, HC Bravo, OG McDonald, M Goggins, C Umbricht, M Zeiger, ... Genome medicine 6, 1-11, 2014 | 205 | 2014 |
Benchmarking deep learning interpretability in time series predictions AA Ismail, M Gunady, H Corrada Bravo, S Feizi Advances in neural information processing systems 33, 6441-6452, 2020 | 190 | 2020 |
Transcriptome Remodeling in Trypanosoma cruzi and Human Cells during Intracellular Infection Y Li, S Shah-Simpson, K Okrah, AT Belew, J Choi, KL Caradonna, ... PLoS pathogens 12 (4), e1005511, 2016 | 170 | 2016 |
Influence of host gene transcription level and orientation on HIV-1 latency in a primary-cell model L Shan, HC Yang, SA Rabi, HC Bravo, NS Shroff, RA Irizarry, H Zhang, ... Journal of virology 85 (11), 5384-5393, 2011 | 148 | 2011 |
matrixStats: Functions that Apply to Rows and Columns of Matrices (and to Vectors) H Bengtsson R package version 0.52 2, 2017, 2017 | 145 | 2017 |
Overcoming bias and systematic errors in next generation sequencing data MA Taub, H Corrada Bravo, RA Irizarry Genome medicine 2, 1-5, 2010 | 142 | 2010 |