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Page 1
Integrative single-cell analysis of cardiogenesis identifies developmental trajectories and non-coding mutations in congenital heart disease.
Ameen M, Sundaram L, Shen M, Banerjee A, Kundu S, Nair S, Shcherbina A, Gu M, Wilson KD, Varadarajan A, Vadgama N, Balsubramani A, Wu JC, Engreitz JM, Farh K, Karakikes I, Wang KC, Quertermous T, Greenleaf WJ, Kundaje A. Ameen M, et al. Among authors: farh k. Cell. 2022 Dec 22;185(26):4937-4953.e23. doi: 10.1016/j.cell.2022.11.028. Cell. 2022. PMID: 36563664 Free PMC article.
High-throughput SARS-CoV-2 and host genome sequencing from single nasopharyngeal swabs.
Gorzynski JE, De Jong HN, Amar D, Hughes CR, Ioannidis A, Bierman R, Liu D, Tanigawa Y, Kistler A, Kamm J, Kim J, Cappello L, Neff NF, Rubinacci S, Delaneau O, Shoura MJ, Seo K, Kirillova A, Raja A, Sutton S, Huang C, Sahoo MK, Mallempati KC, Montero-Martin G, Osoegawa K, Jimenez-Morales D, Watson N, Hammond N, Joshi R, Fernandez-Vina M, Christle JW, Wheeler MT, Febbo P, Farh K, Schroth G, Desouza F, Palacios J, Salzman J, Pinsky BA, Rivas MA, Bustamante CD, Ashley EA, Parikh VN. Gorzynski JE, et al. Among authors: farh k. medRxiv [Preprint]. 2020 Sep 1:2020.07.27.20163147. doi: 10.1101/2020.07.27.20163147. medRxiv. 2020. PMID: 32766602 Free PMC article. Preprint.
Discovery of stimulation-responsive immune enhancers with CRISPR activation.
Simeonov DR, Gowen BG, Boontanrart M, Roth TL, Gagnon JD, Mumbach MR, Satpathy AT, Lee Y, Bray NL, Chan AY, Lituiev DS, Nguyen ML, Gate RE, Subramaniam M, Li Z, Woo JM, Mitros T, Ray GJ, Curie GL, Naddaf N, Chu JS, Ma H, Boyer E, Van Gool F, Huang H, Liu R, Tobin VR, Schumann K, Daly MJ, Farh KK, Ansel KM, Ye CJ, Greenleaf WJ, Anderson MS, Bluestone JA, Chang HY, Corn JE, Marson A. Simeonov DR, et al. Among authors: farh kk. Nature. 2017 Sep 7;549(7670):111-115. doi: 10.1038/nature23875. Epub 2017 Aug 30. Nature. 2017. PMID: 28854172 Free PMC article.
Predicting the clinical impact of human mutation with deep neural networks.
Sundaram L, Gao H, Padigepati SR, McRae JF, Li Y, Kosmicki JA, Fritzilas N, Hakenberg J, Dutta A, Shon J, Xu J, Batzoglou S, Li X, Farh KK. Sundaram L, et al. Nat Genet. 2018 Aug;50(8):1161-1170. doi: 10.1038/s41588-018-0167-z. Epub 2018 Jul 23. Nat Genet. 2018. PMID: 30038395 Free PMC article.
Identification of constrained sequence elements across 239 primate genomes.
Kuderna LFK, Ulirsch JC, Rashid S, Ameen M, Sundaram L, Hickey G, Cox AJ, Gao H, Kumar A, Aguet F, Christmas MJ, Clawson H, Haeussler M, Janiak MC, Kuhlwilm M, Orkin JD, Bataillon T, Manu S, Valenzuela A, Bergman J, Rouselle M, Silva FE, Agueda L, Blanc J, Gut M, de Vries D, Goodhead I, Harris RA, Raveendran M, Jensen A, Chuma IS, Horvath JE, Hvilsom C, Juan D, Frandsen P, Schraiber JG, de Melo FR, Bertuol F, Byrne H, Sampaio I, Farias I, Valsecchi J, Messias M, da Silva MNF, Trivedi M, Rossi R, Hrbek T, Andriaholinirina N, Rabarivola CJ, Zaramody A, Jolly CJ, Phillips-Conroy J, Wilkerson G, Abee C, Simmons JH, Fernandez-Duque E, Kanthaswamy S, Shiferaw F, Wu D, Zhou L, Shao Y, Zhang G, Keyyu JD, Knauf S, Le MD, Lizano E, Merker S, Navarro A, Nadler T, Khor CC, Lee J, Tan P, Lim WK, Kitchener AC, Zinner D, Gut I, Melin AD, Guschanski K, Schierup MH, Beck RMD, Karakikes I, Wang KC, Umapathy G, Roos C, Boubli JP, Siepel A, Kundaje A, Paten B, Lindblad-Toh K, Rogers J, Marques Bonet T, Farh KK. Kuderna LFK, et al. Among authors: farh kk. Nature. 2024 Jan;625(7996):735-742. doi: 10.1038/s41586-023-06798-8. Epub 2023 Nov 29. Nature. 2024. PMID: 38030727 Free PMC article.
Author Correction: Discovery of stimulation-responsive immune enhancers with CRISPR activation.
Simeonov DR, Gowen BG, Boontanrart M, Roth TL, Gagnon JD, Mumbach MR, Satpathy AT, Lee Y, Bray NL, Chan AY, Lituiev DS, Nguyen ML, Gate RE, Subramaniam M, Li Z, Woo JM, Mitros T, Ray GJ, Curie GL, Naddaf N, Chu JS, Ma H, Boyer E, Van Gool F, Huang H, Liu R, Tobin VR, Schumann K, Daly MJ, Farh KK, Ansel KM, Ye CJ, Greenleaf WJ, Anderson MS, Bluestone JA, Chang HY, Corn JE, Marson A. Simeonov DR, et al. Among authors: farh kk. Nature. 2018 Jul;559(7715):E13. doi: 10.1038/s41586-018-0227-7. Nature. 2018. PMID: 29899441
The landscape of tolerated genetic variation in humans and primates.
Gao H, Hamp T, Ede J, Schraiber JG, McRae J, Singer-Berk M, Yang Y, Dietrich ASD, Fiziev PP, Kuderna LFK, Sundaram L, Wu Y, Adhikari A, Field Y, Chen C, Batzoglou S, Aguet F, Lemire G, Reimers R, Balick D, Janiak MC, Kuhlwilm M, Orkin JD, Manu S, Valenzuela A, Bergman J, Rousselle M, Silva FE, Agueda L, Blanc J, Gut M, de Vries D, Goodhead I, Harris RA, Raveendran M, Jensen A, Chuma IS, Horvath JE, Hvilsom C, Juan D, Frandsen P, de Melo FR, Bertuol F, Byrne H, Sampaio I, Farias I, do Amaral JV, Messias M, da Silva MNF, Trivedi M, Rossi R, Hrbek T, Andriaholinirina N, Rabarivola CJ, Zaramody A, Jolly CJ, Phillips-Conroy J, Wilkerson G, Abee C, Simmons JH, Fernandez-Duque E, Kanthaswamy S, Shiferaw F, Wu D, Zhou L, Shao Y, Zhang G, Keyyu JD, Knauf S, Le MD, Lizano E, Merker S, Navarro A, Bataillon T, Nadler T, Khor CC, Lee J, Tan P, Lim WK, Kitchener AC, Zinner D, Gut I, Melin A, Guschanski K, Schierup MH, Beck RMD, Umapathy G, Roos C, Boubli JP, Lek M, Sunyaev S, O'Donnell-Luria A, Rehm HL, Xu J, Rogers J, Marques-Bonet T, Farh KK. Gao H, et al. Among authors: farh kk. Science. 2023 Jun 2;380(6648):eabn8153. doi: 10.1126/science.abn8197. Epub 2023 Jun 2. Science. 2023. PMID: 37262156 Free PMC article.
68 results