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CAGI6 ID-Challenge: Assessment of phenotype and variant predictions in 415 children with Neurodevelopmental Disorders (NDDs).
Aspromonte MC, Conte AD, Zhu S, Tan W, Shen Y, Zhang Y, Li Q, Wang MH, Babbi G, Bovo S, Martelli PL, Casadio R, Althagafi A, Toonsi S, Kulmanov M, Hoehndorf R, Katsonis P, Williams A, Lichtarge O, Xian S, Surento W, Pejaver V, Mooney SD, Sunderam U, Srinivasan R, Murgia A, Piovesan D, Tosatto SCE, Leonardi E. Aspromonte MC, et al. Among authors: shen y. Res Sq [Preprint]. 2023 Aug 2:rs.3.rs-3209168. doi: 10.21203/rs.3.rs-3209168/v1. Res Sq. 2023. Update in: Hum Genet. 2025 Jan 9. doi: 10.1007/s00439-024-02722-w PMID: 37577579 Free PMC article. Updated. Preprint.
Critical assessment of variant prioritization methods for rare disease diagnosis within the Rare Genomes Project.
Stenton SL, O'Leary M, Lemire G, VanNoy GE, DiTroia S, Ganesh VS, Groopman E, O'Heir E, Mangilog B, Osei-Owusu I, Pais LS, Serrano J, Singer-Berk M, Weisburd B, Wilson M, Austin-Tse C, Abdelhakim M, Althagafi A, Babbi G, Bellazzi R, Bovo S, Carta MG, Casadio R, Coenen PJ, De Paoli F, Floris M, Gajapathy M, Hoehndorf R, Jacobsen JOB, Joseph T, Kamandula A, Katsonis P, Kint C, Lichtarge O, Limongelli I, Lu Y, Magni P, Mamidi TKK, Martelli PL, Mulargia M, Nicora G, Nykamp K, Pejaver V, Peng Y, Pham THC, Podda MS, Rao A, Rizzo E, Saipradeep VG, Savojardo C, Schols P, Shen Y, Sivadasan N, Smedley D, Soru D, Srinivasan R, Sun Y, Sunderam U, Tan W, Tiwari N, Wang X, Wang Y, Williams A, Worthey EA, Yin R, You Y, Zeiberg D, Zucca S, Bakolitsa C, Brenner SE, Fullerton SM, Radivojac P, Rehm HL, O'Donnell-Luria A. Stenton SL, et al. Among authors: shen y. medRxiv [Preprint]. 2023 Aug 4:2023.08.02.23293212. doi: 10.1101/2023.08.02.23293212. medRxiv. 2023. Update in: Hum Genomics. 2024 Apr 29;18(1):44. doi: 10.1186/s40246-024-00604-w PMID: 37577678 Free PMC article. Updated. Preprint.
Critical assessment of variant prioritization methods for rare disease diagnosis within the rare genomes project.
Stenton SL, O'Leary MC, Lemire G, VanNoy GE, DiTroia S, Ganesh VS, Groopman E, O'Heir E, Mangilog B, Osei-Owusu I, Pais LS, Serrano J, Singer-Berk M, Weisburd B, Wilson MW, Austin-Tse C, Abdelhakim M, Althagafi A, Babbi G, Bellazzi R, Bovo S, Carta MG, Casadio R, Coenen PJ, De Paoli F, Floris M, Gajapathy M, Hoehndorf R, Jacobsen JOB, Joseph T, Kamandula A, Katsonis P, Kint C, Lichtarge O, Limongelli I, Lu Y, Magni P, Mamidi TKK, Martelli PL, Mulargia M, Nicora G, Nykamp K, Pejaver V, Peng Y, Pham THC, Podda MS, Rao A, Rizzo E, Saipradeep VG, Savojardo C, Schols P, Shen Y, Sivadasan N, Smedley D, Soru D, Srinivasan R, Sun Y, Sunderam U, Tan W, Tiwari N, Wang X, Wang Y, Williams A, Worthey EA, Yin R, You Y, Zeiberg D, Zucca S, Bakolitsa C, Brenner SE, Fullerton SM, Radivojac P, Rehm HL, O'Donnell-Luria A. Stenton SL, et al. Among authors: shen y. Hum Genomics. 2024 Apr 29;18(1):44. doi: 10.1186/s40246-024-00604-w. Hum Genomics. 2024. PMID: 38685113 Free PMC article.
Assessing predictions on fitness effects of missense variants in HMBS in CAGI6.
Zhang J, Kinch L, Katsonis P, Lichtarge O, Jagota M, Song YS, Sun Y, Shen Y, Kuru N, Dereli O, Adebali O, Alladin MA, Pal D, Capriotti E, Turina MP, Savojardo C, Martelli PL, Babbi G, Casadio R, Pucci F, Rooman M, Cia G, Tsishyn M, Strokach A, Hu Z, van Loggerenberg W, Roth FP, Radivojac P, Brenner SE, Cong Q, Grishin NV. Zhang J, et al. Among authors: shen y. Hum Genet. 2024 Aug 7. doi: 10.1007/s00439-024-02680-3. Online ahead of print. Hum Genet. 2024. PMID: 39110250
Assessing the predicted impact of single amino acid substitutions in calmodulin for CAGI6 challenges.
Turina P, Dal Cortivo G, Enriquez Sandoval CA, Alexov E, Ascher DB, Babbi G, Bakolitsa C, Casadio R, Fariselli P, Folkman L, Kamandula A, Katsonis P, Li D, Lichtarge O, Martelli PL, Panday SK, Pires DEV, Portelli S, Pucci F, Rodrigues CHM, Rooman M, Savojardo C, Schwersensky M, Shen Y, Strokach AV, Sun Y, Woo J, Radivojac P, Brenner SE, Dell'Orco D, Capriotti E. Turina P, et al. Among authors: shen y. Hum Genet. 2024 Dec 23. doi: 10.1007/s00439-024-02720-y. Online ahead of print. Hum Genet. 2024. PMID: 39714488
CAGI6 ID panel challenge: assessment of phenotype and variant predictions in 415 children with neurodevelopmental disorders (NDDs).
Aspromonte MC, Del Conte A, Zhu S, Tan W, Shen Y, Zhang Y, Li Q, Wang MH, Babbi G, Bovo S, Martelli PL, Casadio R, Althagafi A, Toonsi S, Kulmanov M, Hoehndorf R, Katsonis P, Williams A, Lichtarge O, Xian S, Surento W, Pejaver V, Mooney SD, Sunderam U, Srinivasan R, Murgia A, Piovesan D, Tosatto SCE, Leonardi E. Aspromonte MC, et al. Among authors: shen y. Hum Genet. 2025 Jan 9. doi: 10.1007/s00439-024-02722-w. Online ahead of print. Hum Genet. 2025. PMID: 39786577
Somatic estrogen receptor α mutations that induce dimerization promote receptor activity and breast cancer proliferation.
Irani S, Tan W, Li Q, Toy W, Jones C, Gadiya M, Marra A, Katzenellenbogen JA, Carlson KE, Katzenellenbogen BS, Karimi M, Segu Rajappachetty R, Del Priore IS, Reis-Filho JS, Shen Y, Chandarlapaty S. Irani S, et al. Among authors: shen y. J Clin Invest. 2024 Jan 2;134(1):e163242. doi: 10.1172/JCI163242. J Clin Invest. 2024. PMID: 37883178 Free PMC article.
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