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2023
Zhang Y, Chen F, Creighton CJ. Pan-cancer molecular subtypes of metastasis reveal distinct and evolving transcriptional programs. Cell Rep Med. 2023 ;4(2):100932.
Hale RC, Owen N, Yuan B, Chinn IK. Phenotypic Variability of SOCS1 Haploinsufficiency. J Clin Immunol. 2023 ;43(5):902-906.
Shao Y, Zhou L, Li F, Zhao L, Zhang B-L, Shao F, Chen J-W, Chen C-Y, Bi X, Zhuang X-L, Zhu H-L, Hu J, Sun Z, Li X, Wang D, Rivas-González I, Wang S, Wang Y-M, Chen W, Li G, Lu H-M, Liu Y, Kuderna LFK, Farh KKai-How, Fan P-F, Yu L, Li M, Liu Z-J, Tiley GP, Yoder AD, Roos C, Hayakawa T, Marques-Bonet T, Rogers J, Stenson PD, Cooper DN, Schierup MHeide, Yao Y-G, Zhang Y-P, Wang W, Qi X-G, Zhang G, Wu D-D. Phylogenomic analyses provide insights into primate evolution. Science. 2023 ;380(6648):913-924.
Li X, Quick C, Zhou H, Gaynor SM, Liu Y, Chen H, Selvaraj MSunitha, Sun R, Dey R, Arnett DK, Bielak LF, Bis JC, Blangero J, Boerwinkle E, Bowden DW, Brody JA, Cade BE, Correa A, L Cupples A, Curran JE, de Vries PS, Duggirala R, Freedman BI, Göring HHH, Guo X, Haessler J, Kalyani RR, Kooperberg C, Kral BG, Lange LA, Manichaikul A, Martin LW, McGarvey ST, Mitchell BD, Montasser ME, Morrison AC, Naseri T, O'Connell JR, Palmer ND, Peyser PA, Psaty BM, Raffield LM, Redline S, Reiner AP, Reupena M'aSefuiva, Rice KM, Rich SS, Sitlani CM, Smith JA, Taylor KD, Vasan RS, Willer CJ, Wilson JG, Yanek LR, Zhao W, Rotter JI, Natarajan P, Peloso GM, Li Z, Lin X. Powerful, scalable and resource-efficient meta-analysis of rare variant associations in large whole genome sequencing studies. Nat Genet. 2023 ;55(1):154-164.
Ufomadu P, Fu S, Huynh D. Prevalence of Rhabdomyosarcoma in the U.S. from 2017-2018: A SEER study. J Natl Med Assoc. 2023 ;115(4):403-404.
Tin A, Sullivan KJ, Walker KA, Bressler J, Talluri R, Yu B, Simino J, Gudmundsdottir V, Emilsson V, Jennings LL, Launer L, Mei H, Boerwinkle E, B Windham G, Gottesman R, Gudnason V, Coresh J, Fornage M, Mosley TH. Proteomic Analysis Identifies Circulating Proteins Associated With Plasma Amyloid-β and Incident Dementia. Biol Psychiatry Glob Open Sci. 2023 ;3(3):490-499.
Walker KA, Chen J, Shi L, Yang Y, Fornage M, Zhou L, Schlosser P, Surapaneni A, Grams ME, Duggan MR, Peng Z, Gomez GT, Tin A, Hoogeveen RC, Sullivan KJ, Ganz P, Lindbohm JV, Kivimaki M, Nevado-Holgado AJ, Buckley N, Gottesman RF, Mosley TH, Boerwinkle E, Ballantyne CM, Coresh J. Proteomics analysis of plasma from middle-aged adults identifies protein markers of dementia risk in later life. Sci Transl Med. 2023 ;15(705):eadf5681.
2022
Smith HStevens, Sanchez CE, Maag R, Buentello A, Murdock DR, Metcalf GA, Hadley TD, Riconda DL, Boerwinkle E, Wehrens XHT, Ballantyne CM, Gibbs RA, McGuire AL, Pereira S. Patient and Clinician Perceptions of Precision Cardiology Care: Findings From the HeartCare Study. Circ Genom Precis Med. 2022 ;15(6):e003605.
Lima AR, Ferreira BM, Zhang C, Jolly A, Du H, White JJ, Dawood M, Lins TC, Chiabai MA, van Beusekom E, Cordoba MS, Rosa ECCCaldas, Kayserili H, Kimonis V, Wu E, Mellado C, Aggarwal V, Richieri-Costa A, Brunoni D, Canó TM, Jorge AAL, Kim CA, Honjo R, Bertola DR, Dandalo-Girardi RM, Bayram Y, Gezdirici A, Yilmaz-Gulec E, Gumus E, Yilmaz GC, Okamoto N, Ohashi H, Coban-Akdemir Z, Mitani T, Jhangiani SN, Muzny DM, Regattieri NAP, Pogue R, Pereira RW, Otto PA, Gibbs RA, Ali BR, van Bokhoven H, Brunner HG, V Sutton R, Lupski JR, Vianna-Morgante AM, Carvalho CMB, Mazzeu JF. Phenotypic and mutational spectrum of ROR2-related Robinow syndrome. Hum Mutat. 2022 ;43(7):900-918.
Zhang J, Dutta D, Köttgen A, Tin A, Schlosser P, Grams ME, Harvey B, Yu B, Boerwinkle E, Coresh J, Chatterjee N. Plasma proteome analyses in individuals of European and African ancestry identify cis-pQTLs and models for proteome-wide association studies. Nat Genet. 2022 ;54(5):593-602.
Hu X, Qiao D, Kim W, Moll M, Balte PP, Lange LA, Bartz TM, Kumar R, Li X, Yu B, Cade BE, Laurie CA, Sofer T, Ruczinski I, Nickerson DA, Muzny DM, Metcalf GA, Doddapaneni H, Gabriel S, Gupta N, Dugan-Perez S, L Cupples A, Loehr LR, Jain D, Rotter JI, Wilson JG, Psaty BM, Fornage M, Morrison AC, Vasan RS, Washko G, Rich SS, O'Connor GT, Bleecker E, Kaplan RC, Kalhan R, Redline S, Gharib SA, Meyers D, Ortega V, Dupuis J, London SJ, Lappalainen T, Oelsner EC, Silverman EK, R Barr G, Thornton TA, Wheeler HE, Cho MH, Im HKyung, Manichaikul A. Polygenic transcriptome risk scores for COPD and lung function improve cross-ethnic portability of prediction in the NHLBI TOPMed program. Am J Hum Genet. 2022 ;109(5):857-870.
Olson ND, Wagner J, McDaniel J, Stephens SH, Westreich ST, Prasanna AG, Johanson E, Boja E, Maier EJ, Serang O, Jáspez D, Lorenzo-Salazar JM, Muñoz-Barrera A, Rubio-Rodríguez LA, Flores C, Kyriakidis K, Malousi A, Shafin K, Pesout T, Jain M, Paten B, Chang P-C, Kolesnikov A, Nattestad M, Baid G, Goel S, Yang H, Carroll A, Eveleigh R, Bourgey M, Bourque G, Li G, Ma CX, Tang LQ, Du YP, Zhang SW, Morata J, Tonda R, Parra G, Trotta J-R, Brueffer C, Demirkaya-Budak S, Kabakci-Zorlu D, Turgut D, Kalay Ö, Budak G, Narcı K, Arslan E, Brown R, Johnson IJ, Dolgoborodov A, Semenyuk V, Jain A, H Tetikol S, Jain V, Ruehle M, Lajoie B, Roddey C, Catreux S, Mehio R, Ahsan MUmair, Liu Q, Wang K, Sahraeian SMohammad E, Fang LTai, Mohiyuddin M, Hung C, Jain C, Feng H, Li Z, Chen L, Sedlazeck FJ, Zook JM. PrecisionFDA Truth Challenge V2: Calling variants from short and long reads in difficult-to-map regions. Cell Genom. 2022 ;2(5).
Zhang Y, Chen F, Chandrashekar DS, Varambally S, Creighton CJ. Proteogenomic characterization of 2002 human cancers reveals pan-cancer molecular subtypes and associated pathways. Nat Commun. 2022 ;13(1):2669.
Anurag M, Jaehnig EJ, Krug K, Lei JT, Bergstrom EJ, Kim B-J, Vashist TD, Huynh AMinh Tran, Dou Y, Gou X, Huang C, Shi Z, Wen B, Korchina V, Gibbs RA, Muzny DM, Doddapaneni H, Dobrolecki LE, Rodriguez H, Robles AI, Hiltke T, Lewis MT, Nangia JR, Shafaee MNemati, Li S, Hagemann IS, Hoog J, Lim B, C Osborne K, Mani DR, Gillette MA, Zhang B, Echeverria GV, Miles G, Rimawi MF, Carr SA, Ademuyiwa FO, Satpathy S, Ellis MJ. Proteogenomic Markers of Chemotherapy Resistance and Response in Triple-Negative Breast Cancer. Cancer Discov. 2022 ;12(11):2586-2605.
2021
Zhang Y, Chen F, Donehower LA, Scheurer ME, Creighton CJ. A pediatric brain tumor atlas of genes deregulated by somatic genomic rearrangement. Nat Commun. 2021 ;12(1):937.
Petty LE, Phillippi-Falkenstein K, H Kubisch M, Raveendran M, Harris RA, Vallender EJ, Huff CD, Bohm RP, Rogers J, Below JE. Pedigree reconstruction and distant pairwise relatedness estimation from genome sequence data: A demonstration in a population of rhesus macaques (Macaca mulatta). Mol Ecol Resour. 2021 ;21(4):1333-1346.
Foox J, Tighe SW, Nicolet CM, Zook JM, Byrska-Bishop M, Clarke WE, Khayat MM, Mahmoud M, Laaguiby PK, Herbert ZT, Warner D, Grills GS, Jen J, Levy S, Xiang J, Alonso A, Zhao X, Zhang W, Teng F, Zhao Y, Lu H, Schroth GP, Narzisi G, Farmerie W, Sedlazeck FJ, Baldwin DA, Mason CE. Performance assessment of DNA sequencing platforms in the ABRF Next-Generation Sequencing Study. Nat Biotechnol. 2021 ;39(9):1129-1140.
Wohler E, Martin R, Griffith S, Rodrigues Eda S, Antonescu C, Posey JE, Coban-Akdemir Z, Jhangiani SN, Doheny KF, Lupski JR, Valle D, Hamosh A, Sobreira N. PhenoDB, GeneMatcher and VariantMatcher, tools for analysis and sharing of sequence data. Orphanet J Rare Dis. 2021 ;16(1):365.
Khayat MM, Li H, Chander V, Hu J, Hansen AW, Li S, Traynelis J, Shen H, Weissenberger G, Stossi F, Johnson HL, Lupski JR, Posey JE, Sabo A, Meng Q, Murdock DR, Wangler M, Gibbs RA. Phenotypic and protein localization heterogeneity associated with AHDC1 pathogenic protein-truncating alleles in Xia-Gibbs syndrome. Hum Mutat. 2021 ;42(5):577-591.
Xu J, Liu G, Hegde SM, Palta P, Boerwinkle E, Gabriel KP, Yu B. Physical Activity-Related Metabolites Are Associated with Mortality: Findings from the Atherosclerosis Risk in Communities (ARIC) Study. Metabolites. 2021 ;11(1).
Damotte V, van der Lee SJ, Chouraki V, Grenier-Boley B, Simino J, Adams H, Tosto G, White C, Terzikhan N, Cruchaga C, Knol MJ, Li S, Schraen S, Grove ML, Satizabal C, Amin N, Berr C, Younkin S, Gottesman RF, Buée L, Beiser A, Knopman DS, Uitterlinden A, DeCarli C, Bressler J, DeStefano A, Dartigues J-F, Yang Q, Boerwinkle E, Tzourio C, Fornage M, M Ikram A, Amouyel P, de Jager P, Reitz C, Mosley TH, Lambert J-C, Seshadri S, van Duijn CM. Plasma amyloid β levels are driven by genetic variants near APOE, BACE1, APP, PSEN2: A genome-wide association study in over 12,000 non-demented participants. Alzheimers Dement. 2021 ;17(10):1663-1674.
Seplyarskiy VB, Soldatov RA, Koch E, McGinty RJ, Goldmann JM, Hernandez RD, Barnes K, Correa A, Burchard EG, Ellinor PT, McGarvey ST, Mitchell BD, Vasan RS, Redline S, Silverman E, Weiss ST, Arnett DK, Blangero J, Boerwinkle E, He J, Montgomery C, Rao DC, Rotter JI, Taylor KD, Brody JA, Chen Y-DIda, Fuentes Lde Las, Hwu C-M, Rich SS, Manichaikul AW, Mychaleckyj JC, Palmer ND, Smith JA, Kardia SLR, Peyser PA, Bielak LF, O'Connor TD, Emery LS, Gilissen C, Wong WSW, Kharchenko PV, Sunyaev S. Population sequencing data reveal a compendium of mutational processes in the human germ line. Science. 2021 ;373(6558):1030-1035.
Creighton CJ. Portals for Exploring Noncoding Variants in Pediatric Cancer. Trends Genet. 2021 ;37(4):297-298.
Pursell T, Clinton JLSpencer, Tan J, Peng R, Qin X, Doddapaneni H, Menon V, Momin Z, Kottapalli K, Howard L, Latimer E, Heaggans S, Hayward GS, Ling PD. Primary Infection May Be an Underlying Factor Contributing to Lethal Hemorrhagic Disease Caused by Elephant Endotheliotropic Herpesvirus 3 in African Elephants (). Microbiol Spectr. 2021 ;9(2):e0098321.
Mahmoud M, Doddapaneni H, Timp W, Sedlazeck FJ. PRINCESS: comprehensive detection of haplotype resolved SNVs, SVs, and methylation. Genome Biol. 2021 ;22(1):268.