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Page 1
The Complete Sequence and Comparative Analysis of Ape Sex Chromosomes.
Makova KD, Pickett BD, Harris RS, Hartley GA, Cechova M, Pal K, Nurk S, Yoo D, Li Q, Hebbar P, McGrath BC, Antonacci F, Aubel M, Biddanda A, Borchers M, Bomberg E, Bouffard GG, Brooks SY, Carbone L, Carrel L, Carroll A, Chang PC, Chin CS, Cook DE, Craig SJC, de Gennaro L, Diekhans M, Dutra A, Garcia GH, Grady PGS, Green RE, Haddad D, Hallast P, Harvey WT, Hickey G, Hillis DA, Hoyt SJ, Jeong H, Kamali K, Kosakovsky Pond SL, LaPolice TM, Lee C, Lewis AP, Loh YE, Masterson P, McCoy RC, Medvedev P, Miga KH, Munson KM, Pak E, Paten B, Pinto BJ, Potapova T, Rhie A, Rocha JL, Ryabov F, Ryder OA, Sacco S, Shafin K, Shepelev VA, Slon V, Solar SJ, Storer JM, Sudmant PH, Sweetalana, Sweeten A, Tassia MG, Thibaud-Nissen F, Ventura M, Wilson MA, Young AC, Zeng H, Zhang X, Szpiech ZA, Huber CD, Gerton JL, Yi SV, Schatz MC, Alexandrov IA, Koren S, O'Neill RJ, Eichler E, Phillippy AM. Makova KD, et al. Among authors: cook de. bioRxiv [Preprint]. 2023 Dec 1:2023.11.30.569198. doi: 10.1101/2023.11.30.569198. bioRxiv. 2023. Update in: Nature. 2024 Jun;630(8016):401-411. doi: 10.1038/s41586-024-07473-2 PMID: 38077089 Free PMC article. Updated. Preprint.
A deep-learning-based RNA-seq germline variant caller.
Cook DE, Venkat A, Yelizarov D, Pouliot Y, Chang PC, Carroll A, De La Vega FM. Cook DE, et al. Among authors: de la vega fm. Bioinform Adv. 2023 Jun 13;3(1):vbad062. doi: 10.1093/bioadv/vbad062. eCollection 2023. Bioinform Adv. 2023. PMID: 37416509 Free PMC article.
DeepSomatic: Accurate somatic small variant discovery for multiple sequencing technologies.
Park J, Cook DE, Chang PC, Kolesnikov A, Brambrink L, Mier JC, Gardner J, McNulty B, Sacco S, Keskus A, Bryant A, Ahmad T, Shetty J, Zhao Y, Tran B, Narzisi G, Helland A, Yoo B, Pushel I, Lansdon LA, Bi C, Walter A, Gibson M, Pastinen T, Farooqi MS, Robine N, Miga KH, Carroll A, Kolmogorov M, Paten B, Shafin K. Park J, et al. Among authors: cook de. bioRxiv [Preprint]. 2024 Aug 19:2024.08.16.608331. doi: 10.1101/2024.08.16.608331. bioRxiv. 2024. PMID: 39229187 Free PMC article. Preprint.
Highly accurate assembly polishing with DeepPolisher.
Mastoras M, Asri M, Brambrink L, Hebbar P, Kolesnikov A, Cook DE, Nattestad M, Lucas J, Won TS, Chang PC, Carroll A, Paten B, Shafin K. Mastoras M, et al. Among authors: cook de. bioRxiv [Preprint]. 2024 Sep 19:2024.09.17.613505. doi: 10.1101/2024.09.17.613505. bioRxiv. 2024. PMID: 39345401 Free PMC article. Preprint.
A robust benchmark for detecting low-frequency variants in the HG002 Genome In A Bottle NIST reference material.
Daniels CA, Abdulkadir A, Cleveland MH, McDaniel JH, Jáspez D, Rubio-Rodríguez LA, Muñoz-Barrera A, Lorenzo-Salazar JM, Flores C, Yoo B, Sahraeian SME, Wang Y, Rossi M, Visvanath A, Murray L, Chen WT, Catreux S, Han J, Mehio R, Parnaby G, Carroll A, Chang PC, Shafin K, Cook D, Kolesnikov A, Brambrink L, Mootor MFE, Patel Y, Yamaguchi TN, Boutros PC, Sienkiewicz K, Foox J, Mason CE, Lajoie BR, Ruiz-Perez CA, Kruglyak S, Zook JM, Olson ND. Daniels CA, et al. bioRxiv [Preprint]. 2024 Dec 5:2024.12.02.625685. doi: 10.1101/2024.12.02.625685. bioRxiv. 2024. PMID: 39677813 Free PMC article. Preprint.
Balancing selection maintains hyper-divergent haplotypes in Caenorhabditis elegans.
Lee D, Zdraljevic S, Stevens L, Wang Y, Tanny RE, Crombie TA, Cook DE, Webster AK, Chirakar R, Baugh LR, Sterken MG, Braendle C, Félix MA, Rockman MV, Andersen EC. Lee D, et al. Among authors: cook de. Nat Ecol Evol. 2021 Jun;5(6):794-807. doi: 10.1038/s41559-021-01435-x. Epub 2021 Apr 5. Nat Ecol Evol. 2021. PMID: 33820969 Free PMC article.
Local adaptation and spatiotemporal patterns of genetic diversity revealed by repeated sampling of Caenorhabditis elegans across the Hawaiian Islands.
Crombie TA, Battlay P, Tanny RE, Evans KS, Buchanan CM, Cook DE, Dilks CM, Stinson LA, Zdraljevic S, Zhang G, Roberto NM, Lee D, Ailion M, Hodgins KA, Andersen EC. Crombie TA, et al. Among authors: cook de. Mol Ecol. 2022 Apr;31(8):2327-2347. doi: 10.1111/mec.16400. Epub 2022 Feb 25. Mol Ecol. 2022. PMID: 35167162 Free PMC article.
Shared Genomic Regions Underlie Natural Variation in Diverse Toxin Responses.
Evans KS, Brady SC, Bloom JS, Tanny RE, Cook DE, Giuliani SE, Hippleheuser SW, Zamanian M, Andersen EC. Evans KS, et al. Among authors: cook de. Genetics. 2018 Dec;210(4):1509-1525. doi: 10.1534/genetics.118.301311. Epub 2018 Oct 19. Genetics. 2018. PMID: 30341085 Free PMC article.
130 results