| RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome B Li, CN Dewey BMC bioinformatics 12, 1-16, 2011 | 20039 | 2011 |
| De novo transcript sequence reconstruction from RNA-seq using the Trinity platform for reference generation and analysis BJ Haas, A Papanicolaou, M Yassour, M Grabherr, PD Blood, J Bowden, ... Nature protocols 8 (8), 1494-1512, 2013 | 8322 | 2013 |
| RNA-Seq gene expression estimation with read mapping uncertainty B Li, V Ruotti, RM Stewart, JA Thomson, CN Dewey Bioinformatics 26 (4), 493-500, 2010 | 1334 | 2010 |
| COVID-19 tissue atlases reveal SARS-CoV-2 pathology and cellular targets TM Delorey, CGK Ziegler, G Heimberg, R Normand, Y Yang, ... Nature 595 (7865), 107-113, 2021 | 713 | 2021 |
| A single-cell and single-nucleus RNA-Seq toolbox for fresh and frozen human tumors M Slyper, CBM Porter, O Ashenberg, J Waldman, E Drokhlyansky, ... Nature medicine 26 (5), 792-802, 2020 | 567 | 2020 |
| Accuracy assessment of fusion transcript detection via read-mapping and de novo fusion transcript assembly-based methods BJ Haas, A Dobin, B Li, N Stransky, N Pochet, A Regev Genome biology 20, 1-16, 2019 | 536 | 2019 |
| Decoding human fetal liver haematopoiesis DM Popescu, RA Botting, E Stephenson, K Green, S Webb, L Jardine, ... Nature 574 (7778), 365-371, 2019 | 526 | 2019 |
| Evaluation of de novo transcriptome assemblies from RNA-Seq data B Li, N Fillmore, Y Bai, M Collins, JA Thomson, R Stewart, CN Dewey Genome biology 15, 1-21, 2014 | 302 | 2014 |
| STAR-Fusion: fast and accurate fusion transcript detection from RNA-Seq BJ Haas, A Dobin, N Stransky, B Li, X Yang, T Tickle, A Bankapur, ... BioRxiv, 120295, 2017 | 254 | 2017 |
| Unannotated proteins expand the MHC-I-restricted immunopeptidome in cancer T Ouspenskaia, T Law, KR Clauser, S Klaeger, S Sarkizova, F Aguet, B Li, ... Nature biotechnology 40 (2), 209-217, 2022 | 237 | 2022 |
| Cumulus provides cloud-based data analysis for large-scale single-cell and single-nucleus RNA-seq B Li, J Gould, Y Yang, S Sarkizova, M Tabaka, O Ashenberg, Y Rosen, ... Nature methods 17 (8), 793-798, 2020 | 182 | 2020 |
| Nuclei multiplexing with barcoded antibodies for single-nucleus genomics JT Gaublomme, B Li, C McCabe, A Knecht, Y Yang, E Drokhlyansky, ... Nature communications 10 (1), 2907, 2019 | 161 | 2019 |
| Inherited myeloproliferative neoplasm risk affects haematopoietic stem cells EL Bao, SK Nandakumar, X Liao, AG Bick, J Karjalainen, M Tabaka, ... Nature 586 (7831), 769-775, 2020 | 126 | 2020 |
| Integrated scRNA-Seq identifies human postnatal thymus seeding progenitors and regulatory dynamics of differentiating immature thymocytes M Lavaert, KL Liang, N Vandamme, JE Park, J Roels, MS Kowalczyk, B Li, ... Immunity 52 (6), 1088-1104. e6, 2020 | 116 | 2020 |
| Blood and immune development in human fetal bone marrow and Down syndrome L Jardine, S Webb, I Goh, M Quiroga Londoño, G Reynolds, M Mather, ... Nature 598 (7880), 327-331, 2021 | 108 | 2021 |
| Discovering transcription factor binding sites in highly repetitive regions of genomes with multi-read analysis of ChIP-Seq data D Chung, PF Kuan, B Li, R Sanalkumar, K Liang, EH Bresnick, C Dewey, ... PLoS computational biology 7 (7), e1002111, 2011 | 107 | 2011 |
| macmanes MD BJ Haas, A Papanicolaou, M Yassour, M Grabherr, PD Blood, J Bowden, ... Ott M, Orvis J, Pochet N, Strozzi F, Weeks N, Westerman R, William T, Dewey …, 2013 | 64 | 2013 |
| Linking indirect effects of cytomegalovirus in transplantation to modulation of monocyte innate immune function P Sen, AR Wilkie, F Ji, Y Yang, IJ Taylor, M Velazquez-Palafox, ... Science Advances 6 (17), eaax9856, 2020 | 26 | 2020 |
| PROBer provides a general toolkit for analyzing sequencing-based toeprinting assays B Li, A Tambe, S Aviran, L Pachter Cell systems 4 (5), 568-574. e7, 2017 | 22 | 2017 |
| Metrics for rapid quality control in RNA structure probing experiments K Choudhary, NP Shih, F Deng, M Ledda, B Li, S Aviran Bioinformatics 32 (23), 3575-3583, 2016 | 19 | 2016 |
Colin DeweyProfessor of Biostatistics and Medical Informatics, University of Wisconsin-MadisonEmail verificata su biostat.wisc.edu