| Year |
Citation |
Score |
| 2021 |
Kimmel JC, Yi N, Roy M, Hendrickson DG, Kelley DR. Differentiation reveals latent features of aging and an energy barrier in murine myogenesis. Cell Reports. 35: 109046. PMID 33910007 DOI: 10.1016/j.celrep.2021.109046 |
0.728 |
|
| 2021 |
Kimmel JC, Kelley DR. Semi-supervised adversarial neural networks for single-cell classification. Genome Research. PMID 33627475 DOI: 10.1101/gr.268581.120 |
0.721 |
|
| 2020 |
Bernstein NJ, Fong NL, Lam I, Roy MA, Hendrickson DG, Kelley DR. Solo: Doublet Identification in Single-Cell RNA-Seq via Semi-Supervised Deep Learning. Cell Systems. PMID 32592658 DOI: 10.1016/j.cels.2020.05.010 |
0.31 |
|
| 2020 |
Kimmel JC, Penland L, Rubinstein ND, Hendrickson DG, Kelley DR, Rosenthal AZ. Corrigendum: Murine single-cell RNA-seq reveals cell-identity- and tissue-specific trajectories of aging Genome Research. 30: 153_1-153_1. DOI: 10.1101/gr.259820.119 |
0.737 |
|
| 2019 |
Kimmel JC, Penland L, Rubinstein ND, Hendrickson DG, Kelley DR, Rosenthal AZ. Murine single-cell RNA-seq reveals cell-identity- and tissue-specific trajectories of aging. Genome Research. PMID 31754020 DOI: 10.1101/gr.253880.119 |
0.734 |
|
| 2017 |
Feigin ME, Garvin T, Bailey P, Waddell N, Chang DK, Kelley DR, Shuai S, Gallinger S, McPherson JD, Grimmond SM, Khurana E, Stein LD, Biankin AV, Schatz MC, Tuveson DA. Recurrent noncoding regulatory mutations in pancreatic ductal adenocarcinoma. Nature Genetics. PMID 28481342 DOI: 10.1038/Ng.3861 |
0.384 |
|
| 2014 |
Hacisuleyman E, Goff LA, Trapnell C, Williams A, Henao-Mejia J, Sun L, McClanahan P, Hendrickson DG, Sauvageau M, Kelley DR, Morse M, Engreitz J, Lander ES, Guttman M, Lodish HF, et al. Topological organization of multichromosomal regions by the long intergenic noncoding RNA Firre. Nature Structural & Molecular Biology. 21: 198-206. PMID 24463464 DOI: 10.1038/Nsmb.2764 |
0.502 |
|
| 2014 |
Trapnell C, Roberts A, Goff L, Pertea G, Kim D, Kelley DR, Pimentel H, Salzberg SL, Rinn JL, Pachter L. Erratum: Corrigendum: Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks Nature Protocols. 9: 2513-2513. DOI: 10.1038/Nprot1014-2513A |
0.602 |
|
| 2013 |
Gifford CA, Ziller MJ, Gu H, Trapnell C, Donaghey J, Tsankov A, Shalek AK, Kelley DR, Shishkin AA, Issner R, Zhang X, Coyne M, Fostel JL, Holmes L, Meldrim J, et al. Transcriptional and epigenetic dynamics during specification of human embryonic stem cells. Cell. 153: 1149-63. PMID 23664763 DOI: 10.1016/J.Cell.2013.04.037 |
0.534 |
|
| 2013 |
Sun L, Goff LA, Trapnell C, Alexander R, Lo KA, Hacisuleyman E, Sauvageau M, Tazon-Vega B, Kelley DR, Hendrickson DG, Yuan B, Kellis M, Lodish HF, Rinn JL. Long noncoding RNAs regulate adipogenesis. Proceedings of the National Academy of Sciences of the United States of America. 110: 3387-92. PMID 23401553 DOI: 10.1073/Pnas.1222643110 |
0.494 |
|
| 2012 |
Zimin AV, Kelley DR, Roberts M, Marçais G, Salzberg SL, Yorke JA. Mis-assembled "segmental duplications" in two versions of the Bos taurus genome. Plos One. 7: e42680. PMID 22880081 DOI: 10.1371/Journal.Pone.0042680 |
0.534 |
|
| 2012 |
Trapnell C, Roberts A, Goff L, Pertea G, Kim D, Kelley DR, Pimentel H, Salzberg SL, Rinn JL, Pachter L. Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks. Nature Protocols. 7: 562-78. PMID 22383036 DOI: 10.1038/Nprot.2012.016 |
0.702 |
|
| 2012 |
Kelley DR, Liu B, Delcher AL, Pop M, Salzberg SL. Gene prediction with Glimmer for metagenomic sequences augmented by classification and clustering. Nucleic Acids Research. 40: e9. PMID 22102569 DOI: 10.1093/Nar/Gkr1067 |
0.492 |
|
| 2011 |
Earl D, Bradnam K, St John J, Darling A, Lin D, Fass J, Yu HO, Buffalo V, Zerbino DR, Diekhans M, Nguyen N, Ariyaratne PN, Sung WK, Ning Z, Haimel M, ... ... Kelley DR, et al. Assemblathon 1: a competitive assessment of de novo short read assembly methods. Genome Research. 21: 2224-41. PMID 21926179 DOI: 10.1101/Gr.126599.111 |
0.71 |
|
| 2011 |
Kelley DR, Kingsford C. Extracting between-pathway models from E-MAP interactions using expected graph compression. Journal of Computational Biology : a Journal of Computational Molecular Cell Biology. 18: 379-90. PMID 21385041 DOI: 10.1089/cmb.2010.0268 |
0.557 |
|
| 2010 |
Kelley DR, Schatz MC, Salzberg SL. Quake: quality-aware detection and correction of sequencing errors. Genome Biology. 11: R116. PMID 21114842 DOI: 10.1186/gb-2010-11-11-r116 |
0.577 |
|
| 2010 |
Kelley DR, Salzberg SL. Clustering metagenomic sequences with interpolated Markov models. Bmc Bioinformatics. 11: 544. PMID 21044341 DOI: 10.1186/1471-2105-11-544 |
0.523 |
|
| 2010 |
Kelley DR, Salzberg SL. Detection and correction of false segmental duplications caused by genome mis-assembly. Genome Biology. 11: R28. PMID 20219098 DOI: 10.1186/gb-2010-11-3-r28 |
0.513 |
|
| 2010 |
Kelley D, Schatz M, Salzberg S. Quality-aware error correction of sequencing reads F1000research. 1. DOI: 10.7490/F1000Research.274.1 |
0.602 |
|
| 2009 |
Zimin AV, Delcher AL, Florea L, Kelley DR, Schatz MC, Puiu D, Hanrahan F, Pertea G, Van Tassell CP, Sonstegard TS, Marçais G, Roberts M, Subramanian P, Yorke JA, Salzberg SL. A whole-genome assembly of the domestic cow, Bos taurus. Genome Biology. 10: R42. PMID 19393038 DOI: 10.1186/Gb-2009-10-4-R42 |
0.619 |
|
| 2008 |
Salzberg SL, Sommer DD, Schatz MC, Phillippy AM, Rabinowicz PD, Tsuge S, Furutani A, Ochiai H, Delcher AL, Kelley D, Madupu R, Puiu D, Radune D, Shumway M, Trapnell C, et al. Genome sequence and rapid evolution of the rice pathogen Xanthomonas oryzae pv. oryzae PXO99A. Bmc Genomics. 9: 204. PMID 18452608 DOI: 10.1186/1471-2164-9-204 |
0.721 |
|
| 2008 |
Salzberg SL, Sommer DD, Schatz MC, Phillippy AM, Rabinowicz PD, Tsuge S, Furutani A, Ochiai H, Delcher AL, Kelley D, Madupu R, Puiu D, Radune D, Shumway M, Trapnell C, et al. Erratum to: Genome sequence and rapid evolution of the rice pathogen Xanthomonas oryzae pv. oryzae PXO99 A Bmc Genomics. 9: 534. DOI: 10.1186/1471-2164-9-534 |
0.586 |
|
| Show low-probability matches. |