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Three-dimensional genome rewiring in loci with human accelerated regions.
Keough KC, Whalen S, Inoue F, Przytycki PF, Fair T, Deng C, Steyert M, Ryu H, Lindblad-Toh K, Karlsson E; Zoonomia Consortium§; Nowakowski T, Ahituv N, Pollen A, Pollard KS. Keough KC, et al. Science. 2023 Apr 28;380(6643):eabm1696. doi: 10.1126/science.abm1696. Epub 2023 Apr 28. Science. 2023. PMID: 37104607 Free PMC article.
Broad Host Range of SARS-CoV-2 Predicted by Comparative and Structural Analysis of ACE2 in Vertebrates.
Damas J, Hughes GM, Keough KC, Painter CA, Persky NS, Corbo M, Hiller M, Koepfli KP, Pfenning AR, Zhao H, Genereux DP, Swofford R, Pollard KS, Ryder OA, Nweeia MT, Lindblad-Toh K, Teeling EC, Karlsson EK, Lewin HA. Damas J, et al. Among authors: keough kc. bioRxiv [Preprint]. 2020 Apr 18:2020.04.16.045302. doi: 10.1101/2020.04.16.045302. bioRxiv. 2020. PMID: 32511356 Free PMC article. Updated. Preprint.
Broad host range of SARS-CoV-2 predicted by comparative and structural analysis of ACE2 in vertebrates.
Damas J, Hughes GM, Keough KC, Painter CA, Persky NS, Corbo M, Hiller M, Koepfli KP, Pfenning AR, Zhao H, Genereux DP, Swofford R, Pollard KS, Ryder OA, Nweeia MT, Lindblad-Toh K, Teeling EC, Karlsson EK, Lewin HA. Damas J, et al. Among authors: keough kc. Proc Natl Acad Sci U S A. 2020 Sep 8;117(36):22311-22322. doi: 10.1073/pnas.2010146117. Epub 2020 Aug 21. Proc Natl Acad Sci U S A. 2020. PMID: 32826334 Free PMC article.
Comparative host-coronavirus protein interaction networks reveal pan-viral disease mechanisms.
Gordon DE, Hiatt J, Bouhaddou M, Rezelj VV, Ulferts S, Braberg H, Jureka AS, Obernier K, Guo JZ, Batra J, Kaake RM, Weckstein AR, Owens TW, Gupta M, Pourmal S, Titus EW, Cakir M, Soucheray M, McGregor M, Cakir Z, Jang G, O'Meara MJ, Tummino TA, Zhang Z, Foussard H, Rojc A, Zhou Y, Kuchenov D, Hüttenhain R, Xu J, Eckhardt M, Swaney DL, Fabius JM, Ummadi M, Tutuncuoglu B, Rathore U, Modak M, Haas P, Haas KM, Naing ZZC, Pulido EH, Shi Y, Barrio-Hernandez I, Memon D, Petsalaki E, Dunham A, Marrero MC, Burke D, Koh C, Vallet T, Silvas JA, Azumaya CM, Billesbølle C, Brilot AF, Campbell MG, Diallo A, Dickinson MS, Diwanji D, Herrera N, Hoppe N, Kratochvil HT, Liu Y, Merz GE, Moritz M, Nguyen HC, Nowotny C, Puchades C, Rizo AN, Schulze-Gahmen U, Smith AM, Sun M, Young ID, Zhao J, Asarnow D, Biel J, Bowen A, Braxton JR, Chen J, Chio CM, Chio US, Deshpande I, Doan L, Faust B, Flores S, Jin M, Kim K, Lam VL, Li F, Li J, Li YL, Li Y, Liu X, Lo M, Lopez KE, Melo AA, Moss FR 3rd, Nguyen P, Paulino J, Pawar KI, Peters JK, Pospiech TH Jr, Safari M, Sangwan S, Schaefer K, Thomas PV, Thwin AC, Trenker R, Tse E, Tsui TKM, Wang F, Whitis N, Yu Z, Zhang K, Zhang Y, Zhou F, Saltzberg D; QCRG Structural… See abstract for full author list ➔ Gordon DE, et al. Among authors: keough kc. Science. 2020 Dec 4;370(6521):eabe9403. doi: 10.1126/science.abe9403. Epub 2020 Oct 15. Science. 2020. PMID: 33060197 Free PMC article.
Single-cell epigenomics reveals mechanisms of human cortical development.
Ziffra RS, Kim CN, Ross JM, Wilfert A, Turner TN, Haeussler M, Casella AM, Przytycki PF, Keough KC, Shin D, Bogdanoff D, Kreimer A, Pollard KS, Ament SA, Eichler EE, Ahituv N, Nowakowski TJ. Ziffra RS, et al. Among authors: keough kc. Nature. 2021 Oct;598(7879):205-213. doi: 10.1038/s41586-021-03209-8. Epub 2021 Oct 6. Nature. 2021. PMID: 34616060 Free PMC article.
Machine learning dissection of human accelerated regions in primate neurodevelopment.
Whalen S, Inoue F, Ryu H, Fair T, Markenscoff-Papadimitriou E, Keough K, Kircher M, Martin B, Alvarado B, Elor O, Laboy Cintron D, Williams A, Hassan Samee MA, Thomas S, Krencik R, Ullian EM, Kriegstein A, Rubenstein JL, Shendure J, Pollen AA, Ahituv N, Pollard KS. Whalen S, et al. Neuron. 2023 Mar 15;111(6):857-873.e8. doi: 10.1016/j.neuron.2022.12.026. Epub 2023 Jan 13. Neuron. 2023. PMID: 36640767 Free PMC article.
An atlas of lamina-associated chromatin across twelve human cell types reveals an intermediate chromatin subtype.
Shah PP, Keough KC, Gjoni K, Santini GT, Abdill RJ, Wickramasinghe NM, Dundes CE, Karnay A, Chen A, Salomon REA, Walsh PJ, Nguyen SC, Whalen S, Joyce EF, Loh KM, Dubois N, Pollard KS, Jain R. Shah PP, et al. Among authors: keough kc. Genome Biol. 2023 Jan 23;24(1):16. doi: 10.1186/s13059-023-02849-5. Genome Biol. 2023. PMID: 36691074 Free PMC article.
Leveraging Base Pair Mammalian Constraint to Understand Genetic Variation and Human Disease.
Sullivan PF, Meadows JRS, Gazal S, Phan BN, Li X, Genereux DP, Dong MX, Bianchi M, Andrews G, Sakthikumar S, Nordin J, Roy A, Christmas MJ, Marinescu VD, Wallerman O, Xue JR, Li Y, Yao S, Sun Q, Szatkiewicz J, Wen J, Huckins LM, Lawler AJ, Keough KC, Zheng Z, Zeng J, Wray NR, Johnson J, Chen J; Zoonomia Consortium; Paten B, Reilly SK, Hughes GM, Weng Z, Pollard KS, Pfenning AR, Forsberg-Nilsson K, Karlsson EK, Lindblad-Toh K. Sullivan PF, et al. Among authors: keough kc. bioRxiv [Preprint]. 2023 Mar 10:2023.03.10.531987. doi: 10.1101/2023.03.10.531987. bioRxiv. 2023. PMID: 36945512 Free PMC article. Updated. Preprint.
Chiropterans Are a Hotspot for Horizontal Transfer of DNA Transposons in Mammalia.
Paulat NS, Storer JM, Moreno-Santillán DD, Osmanski AB, Sullivan KAM, Grimshaw JR, Korstian J, Halsey M, Garcia CJ, Crookshanks C, Roberts J, Smit AFA, Hubley R, Rosen J, Teeling EC, Vernes SC, Myers E, Pippel M, Brown T, Hiller M; Zoonomia Consortium; Rojas D, Dávalos LM, Lindblad-Toh K, Karlsson EK, Ray DA. Paulat NS, et al. Mol Biol Evol. 2023 May 2;40(5):msad092. doi: 10.1093/molbev/msad092. Mol Biol Evol. 2023. PMID: 37071810 Free PMC article.
24 results