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HyPhy: hypothesis testing using phylogenies.
Pond SL, Frost SD, Muse SV. Pond SL, et al. Bioinformatics. 2005 Mar 1;21(5):676-9. doi: 10.1093/bioinformatics/bti079. Epub 2004 Oct 27. Bioinformatics. 2005. PMID: 15509596
Vocal learning-associated convergent evolution in mammalian proteins and regulatory elements.
Wirthlin ME, Schmid TA, Elie JE, Zhang X, Kowalczyk A, Redlich R, Shvareva VA, Rakuljic A, Ji MB, Bhat NS, Kaplow IM, Schäffer DE, Lawler AJ, Wang AZ, Phan BN, Annaldasula S, Brown AR, Lu T, Lim BK, Azim E; Zoonomia Consortium; Clark NL, Meyer WK, Pond SLK, Chikina M, Yartsev MM, Pfenning AR, Andrews G, Armstrong JC, Bianchi M, Birren BW, Bredemeyer KR, Breit AM, Christmas MJ, Clawson H, Damas J, Di Palma F, Diekhans M, Dong MX, Eizirik E, Fan K, Fanter C, Foley NM, Forsberg-Nilsson K, Garcia CJ, Gatesy J, Gazal S, Genereux DP, Goodman L, Grimshaw J, Halsey MK, Harris AJ, Hickey G, Hiller M, Hindle AG, Hubley RM, Hughes GM, Johnson J, Juan D, Kaplow IM, Karlsson EK, Keough KC, Kirilenko B, Koepfli KP, Korstian JM, Kowalczyk A, Kozyrev SV, Lawler AJ, Lawless C, Lehmann T, Levesque DL, Lewin HA, Li X, Lind A, Lindblad-Toh K, Mackay-Smith A, Marinescu VD, Marques-Bonet T, Mason VC, Meadows JRS, Meyer WK, Moore JE, Moreira LR, Moreno-Santillan DD, Morrill KM, Muntané G, Murphy WJ, Navarro A, Nweeia M, Ortmann S, Osmanski A, Paten B, Paulat NS, Pfenning AR, Phan BN, Pollard KS, Pratt HE, Ray DA, Reilly SK, Rosen JR, Ruf I, Ryan L, Ryder OA, Sabeti PC, Schäffer DE, Serres A, Shap… See abstract for full author list ➔ Wirthlin ME, et al. Among authors: pond slk. Science. 2024 Mar 29;383(6690):eabn3263. doi: 10.1126/science.abn3263. Epub 2024 Mar 29. Science. 2024. PMID: 38422184 Free PMC article.
HIV-1 and SARS-CoV-2: Patterns in the evolution of two pandemic pathogens.
Fischer W, Giorgi EE, Chakraborty S, Nguyen K, Bhattacharya T, Theiler J, Goloboff PA, Yoon H, Abfalterer W, Foley BT, Tegally H, San JE, de Oliveira T; Network for Genomic Surveillance in South Africa (NGS-SA); Gnanakaran S, Korber B. Fischer W, et al. Cell Host Microbe. 2021 Jul 14;29(7):1093-1110. doi: 10.1016/j.chom.2021.05.012. Epub 2021 Jun 3. Cell Host Microbe. 2021. PMID: 34242582 Free PMC article. Review.
Escape of SARS-CoV-2 501Y.V2 from neutralization by convalescent plasma.
Cele S, Gazy I, Jackson L, Hwa SH, Tegally H, Lustig G, Giandhari J, Pillay S, Wilkinson E, Naidoo Y, Karim F, Ganga Y, Khan K, Bernstein M, Balazs AB, Gosnell BI, Hanekom W, Moosa MS; Network for Genomic Surveillance in South Africa; COMMIT-KZN Team; Lessells RJ, de Oliveira T, Sigal A. Cele S, et al. Nature. 2021 May;593(7857):142-146. doi: 10.1038/s41586-021-03471-w. Epub 2021 Mar 29. Nature. 2021. PMID: 33780970 Free PMC article.
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, Bornberg-Bauer 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, Pond SLK, LaPolice TM, Lee C, Lewis AP, Loh YE, Masterson P, McGarvey KM, 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 EE, Phillippy AM. Makova KD, et al. Among authors: pond slk. Nature. 2024 Jun;630(8016):401-411. doi: 10.1038/s41586-024-07473-2. Epub 2024 May 29. Nature. 2024. PMID: 38811727 Free PMC article.
57 results