Publications

2024
Semancik CS, Zhao N, Koestler DC, Boerwinkle E, Bressler J, Buchsbaum RJ, Kelsey KT, Platz EA, Michaud DS. DNA Methylation-Derived Immune Cell Proportions and Cancer Risk, Including Lung Cancer, in Black Participants. medRxiv. 2024 ;.
Murugan M, Yuan B, Venner E, Ballantyne CM, Robinson KM, Coons JC, Wang L, Empey PE, Gibbs RA. Empowering personalized pharmacogenomics with generative AI solutions. J Am Med Inform Assoc. 2024 ;31(6):1356-1366.
Zhang Y, Chen F, Balic M, Creighton CJ. An essential gene signature of breast cancer metastasis reveals targetable pathways. Breast Cancer Res. 2024 ;26(1):98.
Copeland I, Wonkam-Tingang E, Gupta-Malhotra M, S Hashmi S, Han Y, Jajoo A, Hall NJ, Hernández PP, Lie N, Liu D, Xu J, Rosenfeld J, Haldipur A, Desire Z, Coban-Akdemir ZH, Scott DA, Li Q, Chao H-T, Zaske AM, Lupski JR, Milewicz DM, Shete S, Posey JE, Hanchard NA. Exome sequencing implicates ancestry-related Mendelian variation at SYNE1 in childhood-onset essential hypertension. JCI Insight. 2024 ;9(9).
Almannai M, Marafi D, Zaki MS, Maroofian R, Efthymiou S, Saadi NWaill, Filimban B, Dafsari HSalimi, Rahman F, Maqbool S, Faqeih E, Mutairi FAl, Alsharhan H, Abdelaty O, Bin-Hasan S, Duan R, Noureldeen MM, Alqattan A, Houlden H, Hunter JV, Posey JE, Lupski JR, El-Hattab AW. Expanding the phenotype of PPP1R21-related neurodevelopmental disorder. Clin Genet. 2024 ;105(6):620-629.
Wright A, Wilkinson MD, Mungall C, Cain S, Richards S, Sternberg P, Provin E, Jacobs JL, Geib S, Raciti D, Yook K, Stein L, Molik DC. FAIR Header Reference genome: a TRUSTworthy standard. Brief Bioinform. 2024 ;25(3).
Venner E, Patterson K, Kalra D, Wheeler MM, Chen Y-J, Kalla SE, Yuan B, Karnes JH, Walker K, Smith JD, McGee S, Radhakrishnan A, Haddad A, Empey PE, Wang Q, Lichtenstein L, Toledo D, Jarvik G, Musick A, Gibbs RA. The frequency of pathogenic variation in the All of Us cohort reveals ancestry-driven disparities. Commun Biol. 2024 ;7(1):174.
Bu C, Zheng X, Zhao X, Xu T, Bai X, Jia Y, Chen M, Hao L, Xiao J, Zhang Z, Zhao W, Tang B, Bào Y. GenBase: A Nucleotide Sequence Database. Genomics Proteomics Bioinformatics. 2024 ;.
de Vries PS, Reventun P, Brown MR, Heath AS, Huffman JE, Le N-Q, Bebo A, Brody JA, Temprano-Sagrera G, Raffield LM, Ozel ABilge, Thibord F, Jain D, Lewis JP, Rodriguez BAT, Pankratz N, Taylor KD, Polasek O, Chen M-H, Yanek LR, Carrasquilla GD, Marioni RE, Kleber ME, Trégouët D-A, Yao J, Li-Gao R, Joshi PK, Trompet S, Martinez-Perez A, Ghanbari M, Howard TE, Reiner AP, Arvanitis M, Ryan KA, Bartz TM, Rudan I, Faraday N, Linneberg A, Ekunwe L, Davies G, Delgado GE, Suchon P, Guo X, Rosendaal FR, Klaric L, Noordam R, van Rooij F, Curran JE, Wheeler MM, Osburn WO, O'Connell JR, Boerwinkle E, Beswick A, Psaty BM, Kolcic I, Souto JCarlos, Becker LC, Hansen T, Doyle MF, Harris SE, Moissl AP, Deleuze J-F, Rich SS, Vlieg Avan Hylcka, Campbell H, Stott DJ, Soria JManuel, de Maat MPM, Almasy L, Brody LC, Auer PL, Mitchell BD, Ben-Shlomo Y, Fornage M, Hayward C, Mathias RA, Kilpeläinen TO, Lange LA, Cox SR, Marz W, Morange P-E, Rotter JI, Mook-Kanamori DO, Wilson JF, van der Harst P, J Jukema W, M Ikram A, Blangero J, Kooperberg C, Desch KC, Johnson AD, Sabater-Lleal M, Lowenstein CJ, Smith NL, Morrison AC. A genetic association study of circulating coagulation factor VIII and von Willebrand factor levels. Blood. 2024 ;143(18):1845-1855.
Wang J, Wang M, Moshiri A, Harris RA, Raveendran M, Nguyen T, Kim S, Young L, Wang K, Wiseman R, O'Connor DH, Johnson Z, Martinez M, Montague MJ, Sayers K, Lyke M, Vallender E, Stout T, Li Y, Thomasy SM, Rogers J, Chen R. Genetic diversity of 1,845 rhesus macaques improves genetic variation interpretation and identifies disease models. Nat Commun. 2024 ;15(1):5658.
Hu J, Korchina V, Zouk H, Harden MV, Murdock DR, Macbeth A, Harrison SM, Lennon N, Kovar C, Balasubramanian A, Zhang L, Chandanavelli G, Pasham D, Rowley R, Wiley K, Smith ME, Gordon A, Jarvik GP, Sleiman P, Kelly MA, Bland HT, Murugan M, Venner E, Boerwinkle E, Prows C, Mahanta L, Rehm HL, Gibbs RA, Muzny DM. Genetic sex validation for sample tracking in next-generation sequencing clinical testing. BMC Res Notes. 2024 ;17(1):62.
Patel H, Harris RA, Qian JH, Oezguen N, Watson A, Szigeti RG, Cho S, Ruan W, Britto S, Opekun A, Preidis G, Kellermayer R. Genetic Variation Between Small Bowel and Colon-Predominant Crohn's Disease. Cell Mol Gastroenterol Hepatol. 2024 ;17(6):1069-1071.
Keaton JM, Kamali Z, Xie T, Vaez A, Williams A, Goleva SB, Ani A, Evangelou E, Hellwege JN, Yengo L, Young WJ, Traylor M, Giri A, Zheng Z, Zeng J, Chasman DI, Morris AP, Caulfield MJ, Hwang S-J, Kooner JS, Conen D, Attia JR, Morrison AC, Loos RJF, Kristiansson K, Schmidt R, Hicks AA, Pramstaller PP, Nelson CP, Samani NJ, Risch L, Gyllensten U, Melander O, Riese H, Wilson JF, Campbell H, Rich SS, Psaty BM, Lu Y, Rotter JI, Guo X, Rice KM, Vollenweider P, Sundström J, Langenberg C, Tobin MD, Giedraitis V, Luan J'an, Tuomilehto J, Kutalik Z, Ripatti S, Salomaa V, Girotto G, Trompet S, J Jukema W, van der Harst P, Ridker PM, Giulianini F, Vitart V, Goel A, Watkins H, Harris SE, Deary IJ, van der Most PJ, Oldehinkel AJ, Keavney BD, Hayward C, Campbell A, Boehnke M, Scott LJ, Boutin T, Mamasoula C, Jarvelin M-R, Peters A, Gieger C, Lakatta EG, Cucca F, Hui J, Knekt P, Enroth S, de Borst MH, Polasek O, Concas MPina, Catamo E, Cocca M, Li-Gao R, Hofer E, Schmidt H, Spedicati B, Waldenberger M, Strachan DP, Laan M, Teumer A, Dörr M, Gudnason V, Cook JP, Ruggiero D, Kolcic I, Boerwinkle E, Traglia M, Lehtimäki T, Raitakari OT, Johnson AD, Newton-Cheh C, Brown MJ, Dominiczak AF, Sever PJ, Poulter N, Chambers JC, Elosua R, Siscovick D, Esko T, Metspalu A, Strawbridge RJ, Laakso M, Hamsten A, Hottenga J-J, de Geus E, Morris AD, Palmer CNA, Nolte IM, Milaneschi Y, Marten J, Wright A, Zeggini E, Howson JMM, O'Donnell CJ, Spector T, Nalls MA, Simonsick EM, Liu Y, van Duijn CM, Butterworth AS, Danesh JN, Menni C, Wareham NJ, Khaw K-T, Sun YV, Wilson PWF, Cho K, Visscher PM, Denny JC, Levy D, Edwards TL, Munroe PB, Snieder H, Warren HR. Genome-wide analysis in over 1 million individuals of European ancestry yields improved polygenic risk scores for blood pressure traits. Nat Genet. 2024 ;56(5):778-791.
Genomic data in the All of Us Research Program. Nature. 2024 ;.
Martin-Giacalone BA, Li H, Scheurer ME, Casey DL, Dugan-Perez S, Marquez-Do DA, Muzny DM, Gibbs RA, Barkauskas DA, Hall D, Stewart DR, Schiffman JD, McEvoy MT, Khan J, Malkin D, Linardic CM, Crompton BD, Shern JF, Skapek SX, Venkatramani R, Hawkins DS, Sabo A, Plon SE, Lupo PJ. Germline Genetic Testing and Survival Outcomes Among Children With Rhabdomyosarcoma: A Report From the Children's Oncology Group. JAMA Netw Open. 2024 ;7(3):e244170.
Chen F, Zhang Y, Sedlazeck FJ, Creighton CJ. Germline structural variation globally impacts the cancer transcriptome including disease-relevant genes. Cell Rep Med. 2024 ;5(3):101446.
Wang Z, Peters BA, Yu B, Grove ML, Wang T, Xue X, Thyagarajan B, Daviglus ML, Boerwinkle E, Hu G, Mossavar-Rahmani Y, Isasi CR, Knight R, Burk RD, Kaplan RC, Qi Q. Gut Microbiota and Blood Metabolites Related to Fiber Intake and Type 2 Diabetes. Circ Res. 2024 ;134(7):842-854.
Du H, Dardas Z, Jolly A, Grochowski CM, Jhangiani SN, Li H, Muzny DM, Fatih JM, Yesil G, Elcioglu NH, Gezdirici A, Marafi D, Pehlivan D, Calame DG, Carvalho CMB, Posey JE, Gambin T, Coban-Akdemir Z, Lupski JR. HMZDupFinder: a robust computational approach for detecting intragenic homozygous duplications from exome sequencing data. Nucleic Acids Res. 2024 ;52(4):e18.
Ma M, Ganapathi M, Zheng Y, Tan K-L, Kanca O, Bove KE, Quintanilla N, Sag SO, Temel SG, LeDuc CA, McPartland AJ, Pereira EM, Shen Y, Hagen J, Thomas CP, Galván NThao Nguye, Pan X, Lu S, Rosenfeld JA, Calame DG, Wangler MF, Lupski JR, Pehlivan D, Hertel PM, Chung WK, Bellen HJ. Homozygous missense variants in YKT6 result in loss of function and are associated with developmental delay, with or without severe infantile liver disease and risk for hepatocellular carcinoma. Genet Med. 2024 ;26(7):101125.
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 FEnnes, 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 CChuen, Lee J, Tan P, Lim WKhong, Kitchener AC, Zinner D, Gut I, Melin AD, Guschanski K, Schierup MHeide, Beck RMD, Karakikes I, Wang KC, Umapathy G, Roos C, Boubli JP, Siepel A, Kundaje A, Paten B, Lindblad-Toh K, Rogers J, Bonet TMarques, Farh KKai-How. Identification of constrained sequence elements across 239 primate genomes. Nature. 2024 ;625(7996):735-742.
Madasu C, Liao Z, Parks SE, Sharma KL, Bohren KM, Ye Q, Li F, Palaniappan M, Tan Z, Yuan F, Creighton CJ, Tang S, Masand RP, Guan X, Young DW, Monsivais D, Matzuk MM. Identification of potent pan-ephrin receptor kinase inhibitors using DNA-encoded chemistry technology. Proc Natl Acad Sci U S A. 2024 ;121(19):e2322934121.
Chen N-C, Paulin LF, Sedlazeck FJ, Koren S, Phillippy AM, Langmead B. Improved sequence mapping using a complete reference genome and lift-over. Nat Methods. 2024 ;21(1):41-49.
Horesh ME, Martin-Fernandez M, Gruber C, Buta S, Le Voyer T, Puzenat E, Lesmana H, Wu Y, Richardson A, Stein D, Hodeib S, Youssef M, Kurowski JA, Feuille E, Pedroza LA, Fuleihan RL, Haseley A, Hovnanian A, Quartier P, Rosain J, Davis G, Mullan D, Stewart O'J, Patel R, Lee AE, Rubinstein R, Ewald L, Maheshwari N, Rahming V, Chinn IK, Lupski JR, Orange JS, Sancho-Shimizu V, Casanova J-L, Abul-Husn NS, Itan Y, Milner JD, Bustamante J, Bogunovic D. Individuals with JAK1 variants are affected by syndromic features encompassing autoimmunity, atopy, colitis, and dermatitis. J Exp Med. 2024 ;221(6).
Dylus D, Altenhoff A, Majidian S, Sedlazeck FJ, Dessimoz C. Inference of phylogenetic trees directly from raw sequencing reads using Read2Tree. Nat Biotechnol. 2024 ;42(1):139-147.
Dunn TN, Cope DI, Tang S, Sirupangi T, Parks SE, Liao Z, Yuan F, Creighton CJ, Masand RP, Radilla LAlpuing, Guan X, Detti L, Monsivais D, Matzuk MM. Inhibition of CSF1R and KIT With Pexidartinib Reduces Inflammatory Signaling and Cell Viability in Endometriosis. Endocrinology. 2024 ;165(4).