• Home
  • Students
  • Student Publications

Student Publications

Below is a list of publications by year of current students and recent graduates. Students' names are highlighted in bold. 
2024

  • Tan Y, Wang L, Zhang H, Pan M, Liu DJ, Zhan X, Li B. Interpretable GWAS by linking clinical phenotypes to quantifiable immune repertoire components. Commun Biol. 2024 Oct 20;7(1):1357. doi: 10.1038/s42003-024-07010-x. PMID: 39428403. [PubMed]

  • Hou B, Wen Z, Bao J, Zhang R, Tong B, Yang S, Wen J, Cui Y, Moore JH, Saykin AJ, Huang H, Thompson PM, Ritchie MD, Davatzikos C, Shen L; Alzheimer’s Disease Neuroimaging Initiative. Interpretable deep clustering survival machines for Alzheimer's disease subtype discovery. Med Image Anal. 2024 Oct;97:103231. doi: 10.1016/j.media.2024.103231. Epub 2024 Jun 14. PMID: 38941858; PMCID: PMC11365808. [Pubmed]
  • Wenz BM, He Y, Chen NC, Pickrell JK, Li JH, Dudek MF, Li T, Keener R, Voight BF, Brown CD, Battle A. Genotype inference from aggregated chromatin accessibility data reveals genetic regulatory mechanisms. bioRxiv [Preprint]. 2024 Sep 5:2024.09.04.610850. doi: 10.1101/2024.09.04.610850. PMID: 39282458; PMCID: PMC11398312. [Pubmed]
  • Wang D, Gazzara MR, Jewell S, Wales-McGrath B, Brown CD, Choi PS, Barash Y. A Deep Dive into Statistical Modeling of RNA Splicing QTLs Reveals New Variants that Explain Neurodegenerative Disease. bioRxiv [Preprint]. 2024 Sep 3:2024.09.01.610696. doi: 10.1101/2024.09.01.610696. PMID: 39282456; PMCID: PMC11398334. [Pubmed]
  • Lam JC, Aboreden NG, Midla SC, Wang S, Huang A, Keller CA, Giardine B, Henderson KA, Hardison RC, Zhang H, Blobel GA. YY1-controlled regulatory connectivity and transcription are influenced by the cell cycle. Nat Genet. 2024 Sep;56(9):1938-1952. doi: 10.1038/s41588-024-01871-y. Epub 2024 Aug 29. PMID: 39210046. [Pubmed]
  • Zhang D, Schroeder A, Yan H, Yang H, Hu J, Lee MYY, Cho KS, Susztak K, Xu GX, Feldman MD, Lee EB, Furth EE, Wang L, Li M. Inferring super-resolution tissue architecture by integrating spatial transcriptomics with histology. Nat Biotechnol. 2024 Sep;42(9):1372-1377. doi: 10.1038/s41587-023-02019-9. Epub 2024 Jan 2. PMID: 38168986; PMCID: PMC11260191. [Pubmed]
  • Barnhart KT, Bollig KJ, Senapati S, Takacs P, Robins JC, Haisenleder DJ, Beer LA, Savaris RF, Koelper NC, Speicher DW, Chittams J, Bao J, Wen Z, Feng Y, Kim M, Mumford S, Shen L, Gimotty P. Multiplexed serum biomarkers to discriminate nonviable and ectopic pregnancy. Fertil Steril. 2024 Sep;122(3):482-493. doi: 10.1016/j.fertnstert.2024.04.028. Epub 2024 Apr 26. PMID: 38677710. [Pubmed]
  • Conlon DM, Kanakala S, Cherlin T, Ko YA, Vitali C, Gurunathan S, Venkatesh R, Woerner J, Guare LA, Biobank PM, Verma A, Verma SS, Guerraty MA. Genotype-First Approach Identifies an Association between rs28374544/FOG2S657G and Liver Disease through Alterations in mTORC1 Signaling. Genes (Basel). 2024 Aug 21;15(8):1098. doi: 10.3390/genes15081098. PMID: 39202457; PMCID: PMC11353451. [Pubmed]
  • Lu Z, Verginadis I, Kumazoe M, Castillo GM, Yao Y, Guerra RE, Bicher S, You M, McClung G, Qiu R, Xiao Z, Miao Z, George SS, Beiting DP, Nojiri T, Tanaka Y, Fujimura Y, Onda H, Hatakeyama Y, Nishimoto-Ashfield A, Bykova K, Guo W, Fan Y, Buynov NM, Diehl JA, Stanger BZ, Tachibana H, Gade TP, Puré E, Koumenis C, Bolotin EM, Fuchs SY. Modified C-type natriuretic peptide normalizes tumor vasculature, reinvigorates antitumor immunity, and improves solid tumor therapies. Sci Transl Med. 2024 Aug 21;16(761):eadn0904. doi: 10.1126/scitranslmed.adn0904. Epub 2024 Aug 21. PMID: 39167664. [Pubmed]
  • Zhang DY, Levin MG, Duda JT, Landry LG, Witschey WR, Damrauer SM, Ritchie MD, Rader DJ. Protein-truncating variant in APOL3 increases chronic kidney disease risk in epistasis with APOL1 risk alleles. JCI Insight. 2024 Aug 20:e181238. doi: 10.1172/jci.insight.181238. Epub ahead of print. PMID: 39163132. [Pubmed]
  • DePaolo J, Zhang DY, Damrauer SM. Leveraging genetic data to improve the care of patients with thoracic aortic dilation. Eur Heart J. 2024 Aug 16:ehae499. doi: 10.1093/eurheartj/ehae499. Epub ahead of print. PMID: 39150456. [Pubmed]
  • Rendel MD, Vitali C, Creasy KT, Zhang D, Scorletti E, Huang H, Seeling KS, Park J, Hehl L, Vell MS, Conlon D, Hayat S; Regeneron Center; Phillips MC, Schneider KM, Rader DJ, Schneider CV. The common p.Ile291Val variant of ERLIN1 enhances TM6SF2 function and is associated with protection against MASLD. Med. 2024 Aug 9;5(8):963-980.e5. doi: 10.1016/j.medj.2024.04.010. Epub 2024 May 21. PMID: 38776916. [Pubmed]
  • Moore A, Venkatesh R, Levin MG, Damrauer SM, Reza N, Cappola TP, Ritchie MD. Connecting intermediate phenotypes to disease using multi-omics in heart failure. medRxiv [Preprint]. 2024 Aug 7:2024.08.06.24311572. doi: 10.1101/2024.08.06.24311572. PMID: 39148828; PMCID: PMC11326335. [Pubmed]
  • Nam Y, Kim J, Jung SH, Woerner J, Suh EH, Lee DG, Shivakumar M, Lee ME, Kim D. Harnessing Artificial Intelligence in Multimodal Omics Data Integration: Paving the Path for the Next Frontier in Precision Medicine. Annu Rev Biomed Data Sci. 2024 Aug;7(1):225-250. doi: 10.1146/annurev-biodatasci-102523-103801. Epub 2024 Jul 24. PMID: 38768397. [Pubmed]
  • Bao J, Lee BN, Wen J, Kim M, Mu S, Yang S, Davatzikos C, Long Q, Ritchie MD, Shen L. Employing Informatics Strategies in Alzheimer's Disease Research: A Review from Genetics, Multiomics, and Biomarkers to Clinical Outcomes. Annu Rev Biomed Data Sci. 2024 Aug;7(1):391-418. doi: 10.1146/annurev-biodatasci-102423-121021. Epub 2024 Jul 24. PMID: 38848574. [Pubmed]
  • Jasper EA, Hellwege JN, Breeyear JH, Xiao B, Jarvik GP, Stanaway IB, Leppig KA, Chittoor G, Hayes MG, Dikilitas O, Kullo IJ, Holm IA, Verma SS, Edwards TL, Velez Edwards DR. Genetic predictors of blood pressure traits are associated with preeclampsia. Sci Rep. 2024 Jul 30;14(1):17613. doi: 10.1038/s41598-024-68469-6. PMID: 39080328; PMCID: PMC11289248. [Pubmed]
  • Abramowitz SA, Boulier K, Keat K, Cardone KM, Shivakumar M, DePaolo J, Judy R, Kim D, Rader DJ, Ritchie, Voight BF, Pasaniuc B, Levin MG, Damrauer SM. Population Performance and Individual Agreement of Coronary Artery Disease Polygenic Risk Scores. medRxiv [Preprint]. 2024 Jul 29:2024.07.25.24310931. doi: 10.1101/2024.07.25.24310931. PMID: 39108513; PMCID: PMC11302700. [Pubmed]
  • Katsuda T, Sussman JH, Zaret KS, Stanger BZ. The yin and yang of pioneer transcription factors: Dual roles in repression and activation. Bioessays. 2024 Jul 26:e2400138. doi: 10.1002/bies.202400138. Epub ahead of print. PMID: 39058903. [Pubmed]
  • Verma A, Huffman JE, Rodriguez A, Conery M, Liu M, Ho YL, Kim Y, Heise DA, Guare L, Panickan VA, Garcon H, Linares F, Costa L, Goethert I, Tipton R, Honerlaw J, Davies L, Whitbourne S, Cohen J, Posner DC, Sangar R, Murray M, Wang X, Dochtermann DR, Devineni P, Shi Y, Nandi TN, Assimes TL, Brunette CA, Carroll RJ, Clifford R, Duvall S, Gelernter J, Hung A, Iyengar SK, Joseph J, Kember R, Kranzler H, Kripke CM, Levey D, Luoh SW, Merritt VC, Overstreet C, Deak JD, Grant SFA, Polimanti R, Roussos P, Shakt G, Sun YV, Tsao N, Venkatesh S, Voloudakis G, Justice A, Begoli E, Ramoni R, Tourassi G, Pyarajan S, Tsao P, O'Donnell CJ, Muralidhar S, Moser J, Casas JP, Bick AG, Zhou W, Cai T, Voight BF, Cho K, Gaziano JM, Madduri RK, Damrauer S, Liao KP. Diversity and scale: Genetic architecture of 2068 traits in the VA Million Veteran Program. Science. 2024 Jul 19;385(6706):eadj1182. doi: 10.1126/science.adj1182. Epub 2024 Jul 19. PMID: 39024449. [Pubmed]
  • Sussman JH, Kim N, Kemp SB, Traum D, Katsuda T, Kahn BM, Xu J, Kim IK, Eskandarian C, Delman D, Beatty GL, Kaestner KH, Simpson AL, Stanger BZ. Multiplexed Imaging Mass Cytometry Analysis Characterizes the Vascular Niche in Pancreatic Cancer. Cancer Res. 2024 Jul 15;84(14):2364-2376. doi: 10.1158/0008-5472.CAN-23-2352. PMID: 38695869; PMCID: PMC11250934. [Pubmed]
  • Hui D, Sanford E, Lorenz K, Damrauer SM, Assimes TL, Thom CS, Voight BF. Mendelian randomization analyses clarify the effects of height on cardiovascular diseases. PLoS One. 2024 Jul 3;19(7):e0298786. doi: 10.1371/journal.pone.0298786. PMID: 38959188; PMCID: PMC11221663. [Pubmed]
  • Schnell J, Miao Z, Achieng M, Fausto CC, Wang V, Kuyper F, Thornton ME, Grubbs B, Kim J, Lindström NO. Stepwise developmental mimicry generates proximal-biased kidney organoids. bioRxiv [Preprint]. 2024 Jul 2:2024.06.28.601028. doi: 10.1101/2024.06.28.601028. PMID: 39005387; PMCID: PMC11244853. [Pubmed]
  • Wan F, Torres MDT, Peng J, de la Fuente-Nunez C. Deep-learning-enabled antibiotic discovery through molecular de-extinction. Nat Biomed Eng. 2024 Jul;8(7):854-871. doi: 10.1038/s41551-024-01201-x. Epub 2024 Jun 11. PMID: 38862735; PMCID: PMC11310081. [Pubmed]
  • White EK, Uberoi A, Pan JT, Ort JT, Campbell AE, Murga-Garrido SM, Harris JC, Bhanap P, Wei M, Robles NY, Gardner SE, Grice EA. Alcaligenes faecalis corrects aberrant matrix metalloproteinase expression to promote reepithelialization of diabetic wounds. Sci Adv. 2024 Jun 28;10(26):eadj2020. doi: 10.1126/sciadv.adj2020. Epub 2024 Jun 26. PMID: 38924411; PMCID: PMC11204295. [Pubmed]
  • Bandyopadhyay S, Duffy MP, Ahn KJ, Sussman JH, Pang M, Smith D, Duncan G, Zhang I, Huang J, Lin Y, Xiong B, Imtiaz T, Chen CH, Thadi A, Chen C, Xu J, Reichart M, Martinez Z, Diorio C, Chen C, Pillai V, Snaith O, Oldridge D, Bhattacharyya S, Maillard I, Carroll M, Nelson C, Qin L, Tan K. Mapping the cellular biogeography of human bone marrow niches using single-cell transcriptomics and proteomic imaging. Cell. 2024 Jun 6;187(12):3120-3140.e29. doi: 10.1016/j.cell.2024.04.013. Epub 2024 May 6. PMID: 38714197; PMCID: PMC11162340. [Pubmed]
  • Zhao H, Lin Y, Lin E, Liu F, Shu L, Jing D, Wang B, Wang M, Shan F, Zhang L, Lam JC, Midla SC, Giardine BM, Keller CA, Hardison RC, Blobel GA, Zhang H. Genome folding principles uncovered in condensin-depleted mitotic chromosomes. Nat Genet. 2024 Jun;56(6):1213-1224. doi: 10.1038/s41588-024-01759-x. Epub 2024 May 27. PMID: 38802567. [Pubmed]
  • Rodriguez A, Kim Y, Nandi TN, Keat K, Kumar R, Bhukar R, Conery M, Liu M, Hessington J, Maheshwari K, Schmidt D; VA Million Veteran Program; Begoli E, Tourassi G, Muralidhar S, Natarajan P, Voight BF, Cho K, Gaziano JM, Damrauer SM, Liao KP, Zhou W, Huffman JE, Verma A, Madduri RK. Accelerating Genome- and Phenome-Wide Association Studies using GPUs - A case study using data from the Million Veteran Program. bioRxiv [Preprint]. 2024 May 22:2024.05.17.594583. doi: 10.1101/2024.05.17.594583. PMID: 38826407; PMCID: PMC11142062. [Pubmed]
  • Kumar R, Venkatesh R, Ritchie MD. SABER: Statistical Identification of Loci of Interest in GWAS Summary Statistics using a Bayesian Gaussian Mixture Model. AMIA Jt Summits Transl Sci Proc. 2024 May 31;2024:575-583. PMID: 38827044; PMCID: PMC11141805. [Pubmed]
  • Littleton SH, Trang KB, Volpe CM, Cook K, DeBruyne N, Maguire JA, Weidekamp MA, Hodge KM, Boehm K, Lu S, Chesi A, Bradfield JP, Pippin JA, Anderson SA, Wells AD, Pahl MC, Grant SFA. Variant-to-function analysis of the childhood obesity chr12q13 locus implicates rs7132908 as a causal variant within the 3' UTR of FAIM2. Cell Genom. 2024 May 8;4(5):100556. doi: 10.1016/j.xgen.2024.100556. Epub 2024 May 1. PMID: 38697123; PMCID: PMC11099382. [Pubmed]
  • Leiby JS, Lee ME, Shivakumar M, Choe EK, Kim D. Deep learning imaging phenotype can classify metabolic syndrome and is predictive of cardiometabolic disorders. J Transl Med. 2024 May 8;22(1):434. doi: 10.1186/s12967-024-05163-1. PMID: 38720370; PMCID: PMC11077781. [Pubmed]
  • Li W, Ballard J, Zhao Y, Long Q. Knowledge-guided learning methods for integrative analysis of multi-omics data. Comput Struct Biotechnol J. 2024 Apr 30;23:1945-1950. doi: 10.1016/j.csbj.2024.04.053. PMID: 38736693; PMCID: PMC11087912. [Pubmed]
  • Harris JC, Trigg NA, Goshu B, Yokoyama Y, Dohnalová L, White EK, Harman A, Murga-Garrido SM, Ting-Chun Pan J, Bhanap P, Thaiss CA, Grice EA, Conine CC, Kambayashi T. The microbiota and T cells non-genetically modulate inherited phenotypes transgenerationally. Cell Rep. 2024 Apr 23;43(4):114029. doi: 10.1016/j.celrep.2024.114029. Epub 2024 Apr 4. PMID: 38573852; PMCID: PMC11102039. [Pubmed]
  • Romano JD, Truong V, Kumar R, Venkatesan M, Graham BE, Hao Y, Matsumoto N, Li X, Wang Z, Ritchie MD, Shen L, Moore JH. The Alzheimer's Knowledge Base: A Knowledge Graph for Alzheimer Disease Research. J Med Internet Res. 2024 Apr 18;26:e46777. doi: 10.2196/46777. PMID: 38635981; PMCID: PMC11066745. [Pubmed]
  • Agrawal P, Jain N, Gopalan V, Timon A, Singh A, Rajagopal PS, Hannenhalli S. Network-based approach elucidates critical genes in BRCA subtypes and chemotherapy response in triple negative breast cancer. iScience. 2024 Apr 16;27(5):109752. doi: 10.1016/j.isci.2024.109752. PMID: 38699227; PMCID: PMC11063905. [Pubmed]
  • Hui D, Dudek S, Kiryluk K, Walunas TL, Kullo IJ, Wei WQ, Tiwari HK, Peterson JF, Chung WK, Davis B, Khan A, Kottyan L, Limdi NA, Feng Q, Puckelwartz MJ, Weng C, Smith JL, Karlson EW; Regeneron Genetics Center; Jarvik GP, Ritchie MD. Risk factors affecting polygenic score performance across diverse cohorts. medRxiv [Preprint]. 2024 Apr 10:2023.05.10.23289777. doi: 10.1101/2023.05.10.23289777. PMID: 38645167; PMCID: PMC11030495. [Pubmed]
  • Wang Y, Xie Z, Kutschera E, Adams JI, Kadash-Edmondson KE, Xing Y. rMATS-turbo: an efficient and flexible computational tool for alternative splicing analysis of large-scale RNA-seq data. Nat Protoc. 2024 Apr;19(4):1083-1104. doi: 10.1038/s41596-023-00944-2. Epub 2024 Feb 23. PMID: 38396040. [Pubmed]
  • Hackley RK, Hwang S, Herb JT, Bhanap P, Lam K, Vreugdenhil A, Darnell CL, Pastor MM, Martin JH, Maupin-Furlow JA, Schmid AK. TbsP and TrmB jointly regulate gapII to influence cell development phenotypes in the archaeon Haloferax volcanii. Mol Microbiol. 2024 Apr;121(4):742-766. doi: 10.1111/mmi.15225. Epub 2024 Jan 11. PMID: 38204420; PMCID: PMC11023807. [Pubmed]
  • Pavani G, Klein JG, Nations CC, Sussman JH, Tan K, An HH, Abdulmalik O, Thom CS, Gearhart PA, Willett CM, Maguire JA, Chou ST, French DL, Gadue P. Modeling primitive and definitive erythropoiesis with induced pluripotent stem cells. Blood Adv. 2024 Mar 26;8(6):1449-1463. doi: 10.1182/bloodadvances.2023011708. PMID: 38290102; PMCID: PMC10955655. [Pubmed]
  • Wei M, Knight SAB, Fazelinia H, Spruce L, Roof J, Chu E, Kim DY, Bhanap P, Walsh J, Flowers L, Zhu J, Grice EA. An exploration of mechanisms underlying Desemzia incerta colonization resistance to methicillin-resistant Staphylococcus aureus on the skin. mSphere. 2024 Mar 26;9(3):e0063623. doi: 10.1128/msphere.00636-23. Epub 2024 Feb 28. PMID: 38415632; PMCID: PMC10964421. [Pubmed]
  • Jung SH, Lee YC, Shivakumar M, Kim J, Yun JS, Park WY, Won HH; Penn Medicine Biobank; Kim D. Association between genetic risk and adherence to healthy lifestyle for developing age-related hearing loss. BMC Med. 2024 Mar 26;22(1):141. doi: 10.1186/s12916-024-03364-5. PMID: 38532472; PMCID: PMC10964689. [Pubmed]
  • Miao Z, Wang J, Park K, Kuang D, Kim J. PACS allows comprehensive dissection of multiple factors governing chromatin accessibility from snATAC-seq data. bioRxiv [Preprint]. 2024 Mar 24:2023.07.30.551108. doi: 10.1101/2023.07.30.551108. PMID: 37577623; PMCID: PMC10418058. [Pubmed]
  • Wen J, Zhao B, Yang Z, Erus G, Skampardoni I, Mamourian E, Cui Y, Hwang G, Bao J, Boquet-Pujadas A, Zhou Z, Veturi Y, Ritchie MD, Shou H, Thompson PM, Shen L, Toga AW, Davatzikos C. The genetic architecture of multimodal human brain age. Nat Commun. 2024 Mar 23;15(1):2604. doi: 10.1038/s41467-024-46796-6. PMID: 38521789; PMCID: PMC10960798. [Pubmed]
  • Conery M, Pippin JA, Wagley Y, Trang K, Pahl MC, Villani DA, Favazzo LJ, Ackert-Bicknell CL, Zuscik MJ, Katsevich E, Wells AD, Zemel BS, Voight BF, Hankenson KD, Chesi A, Grant SFA. GWAS-informed data integration and non-coding CRISPRi screen illuminate genetic etiology of bone mineral density. bioRxiv [Preprint]. 2024 Mar 20:2024.03.19.585778. doi: 10.1101/2024.03.19.585778. PMID: 38562830; PMCID: PMC10983984. [Pubmed]
  • Lee YC, Jung SH, Shivakumar M, Cha S, Park WY, Won HH, Eun YG, Biobank PM, Kim D. Polygenic risk score-based phenome-wide association study of head and neck cancer across two large biobanks. BMC Med. 2024 Mar 14;22(1):120. doi: 10.1186/s12916-024-03305-2. PMID: 38486201; PMCID: PMC10941505. [Pubmed]
  • Sussman JH, Oldridge DA, Yu W, Chen CH, Zellmer AM, Rong J, Parvaresh-Rizi A, Thadi A, Xu J, Bandyopadhyay S, Sun Y, Wu D, Hunter CE, Brosius S, Ahn KJ, Baxter AE, Koptyra MP, Vanguri RS, McGrory S, Resnick AC, Storm PB, Amankulor NM, Santi M, Viaene AN, Zhang N, Raedt T, Cole K, Tan K. A longitudinal single-cell and spatial multiomic atlas of pediatric high-grade glioma. bioRxiv [Preprint]. 2024 Mar 8:2024.03.06.583588. doi: 10.1101/2024.03.06.583588. PMID: 38496580; PMCID: PMC10942465. [Pubmed]
  • Woerner J, Sriram V, Nam Y, Verma A, Kim D. Uncovering genetic associations in the human diseasome using an endophenotype-augmented disease network. Bioinformatics. 2024 Mar 4;40(3):btae126. doi: 10.1093/bioinformatics/btae126. PMID: 38527901; PMCID: PMC10963079. [Pubmed]
  • Marquis KA, Merenstein C, Bushman FD. 2-Hydroxyisovalerate Is Produced During Bacterial Vaginosis and Boosts HIV Infection in Resting T Cells. AIDS Res Hum Retroviruses. 2024 Mar;40(3):158-170. doi: 10.1089/AID.2022.0171. Epub 2023 Aug 29. PMID: 37548528; PMCID: PMC10924192. [Pubmed]
  • Nguyen AQ, Rodriguez C, Kumar R, Gupta S, Anderson DE, Saifi C. Biomechanical analysis of complications following T10-Pelvis spinal fusion: A population based computational study. J Biomech. 2024 Mar;165:111969. doi: 10.1016/j.jbiomech.2024.111969. Epub 2024 Feb 16. PMID: 38394952. [Pubmed]
  • Katsuda T, Sussman JH, Ito K, Katznelson A, Yuan S, Takenaka N, Li J, Merrell AJ, Cure H, Li Q, Rasool RU, Asangani IA, Zaret KS, Stanger BZ. Cellular reprogramming in vivo initiated by SOX4 pioneer factor activity. Nat Commun. 2024 Feb 26;15(1):1761. doi: 10.1038/s41467-024-45939-z. PMID: 38409161; PMCID: PMC10897393. [Pubmed]
  • Williams DKA, Christophers B, Keyes T, Kumar R, Granovetter MC, Adigun A, Olivera J, Pura-Bryant J, Smith C, Okafor C, Shibre M, Daye D, Akabas MH. Sociodemographic factors and research experience impact MD-PhD program acceptance. JCI Insight. 2024 Feb 8;9(3):e176146. doi: 10.1172/jci.insight.176146. PMID: 38329127; PMCID: PMC10967469. [Pubmed]
  • Lee MYY, Li M. Integration of multi-modal single-cell data. Nat Biotechnol. 2024 Feb;42(2):190-191. doi: 10.1038/s41587-023-01826-4. PMID: 37231264. [Pubmed]
  • Hu Y, Rong J, Xu Y, Xie R, Peng J, Gao L, Tan K. Unsupervised and supervised discovery of tissue cellular neighborhoods from cell phenotypes. Nat Methods. 2024 Feb;21(2):267-278. doi: 10.1038/s41592-023-02124-2. Epub 2024 Jan 8. PMID: 38191930; PMCID: PMC10864185. [Pubmed]
  • Leung YY, Naj AC, Chou YF, Valladares O, Schmidt M, Hamilton-Nelson K, Wheeler N, Lin H, Gangadharan P, Qu L, Clark K, Kuzma AB, Lee WP, Cantwell L, Nicaretta H; Alzheimer’s Disease Sequencing Project; Haines J, Farrer L, Seshadri S, Brkanac Z, Cruchaga C, Pericak-Vance M, Mayeux RP, Bush WS, Destefano A, Martin E, Schellenberg GD, Wang LS. Human whole-exome genotype data for Alzheimer's disease. Nat Commun. 2024 Jan 23;15(1):684. doi: 10.1038/s41467-024-44781-7. PMID: 38263370; PMCID: PMC10805795. [Pubmed]
  • Mason K, Sathe A, Hess PR, Rong J, Wu CY, Furth E, Susztak K, Levinsohn J, Ji HP, Zhang N. Niche-DE: niche-differential gene expression analysis in spatial transcriptomics data identifies context-dependent cell-cell interactions. Genome Biol. 2024 Jan 12;25(1):14. doi: 10.1186/s13059-023-03159-6. PMID: 38217002; PMCID: PMC10785550. [Pubmed]
  • Yang Z, Wen J, Abdulkadir A, Cui Y, Erus G, Mamourian E, Melhem R, Srinivasan D, Govindarajan ST, Chen J, Habes M, Masters CL, Maruff P, Fripp J, Ferrucci L, Albert MS, Johnson SC, Morris JC, LaMontagne P, Marcus DS, Benzinger TLS, Wolk DA, Shen L, Bao J, Resnick SM, Shou H, Nasrallah IM, Davatzikos C. Gene-SGAN: discovering disease subtypes with imaging and genetic signatures via multi-view weakly-supervised deep clustering. Nat Commun. 2024 Jan 8;15(1):354. doi: 10.1038/s41467-023-44271-2. PMID: 38191573; PMCID: PMC10774282. [Pubmed]
  • Chu J, Rong J, Feng X, Li H. ntsm: an alignment-free, ultra-low-coverage, sequencing technology agnostic, intraspecies sample comparison tool for sample swap detection. Gigascience. 2024 Jan 2;13:giae024. doi: 10.1093/gigascience/giae024. PMID: 38832466; PMCID: PMC11148594. [Pubmed]
  • Kember RL, Verma SS, Verma A, Xiao B, Lucas A, Kripke CM, Judy R, Chen J, Damrauer SM, Rader DJ, Ritchie MD. Polygenic risk scores for cardiometabolic traits demonstrate importance of ancestry for predictive precision medicine. Pac Symp Biocomput. 2024;29:611-626. PMID: 38160310; PMCID: PMC10947742. [Pubmed]
  • Miao Z, Kim J. Uniform quantification of single-nucleus ATAC-seq data with Paired-Insertion Counting (PIC) and a model-based insertion rate estimator. Nat Methods. 2024 Jan;21(1):32-36. doi: 10.1038/s41592-023-02103-7. Epub 2023 Dec 4. PMID: 38049698; PMCID: PMC10776405. [Pubmed]
  • Cardone KM, Dudek S, Keat K, Bradford Y, Cindi Z, Daar ES, Gulick R, Riddler SA, Lennox JL, Sinxadi P, Haas DW, Ritchie MD. Lymphocyte Count Derived Polygenic Score and Interindividual Variability in CD4 T-cell Recovery in Response to Antiretroviral Therapy. Pac Symp Biocomput. 2024;29:594-610. PMID: 38160309; PMCID: PMC10764076. [Pubmed]
2023
  • Davidson NR, Barnard ME, Hippen AA, Campbell A, Johnson CE, Way GP, Dalley BK, Berchuck A, Salas LA, Peres LC, Marks JR, Schildkraut JM, Greene CS, Doherty JA. Molecular subtypes of high-grade serous ovarian cancer across racial groups and gene expression platforms. bioRxiv [Preprint]. 2023 Dec 2:2023.11.01.565179. doi: 10.1101/2023.11.01.565179. Update in: Cancer Epidemiol Biomarkers Prev. 2024 Aug 1;33(8):1114-1125. doi: 10.1158/1055-9965.EPI-24-0113. PMID: 37961178; PMCID: PMC10635053. [Pubmed]
  • Bae JH, Jung YM, Lee J, Shivakumar M, Park CW, Park JS, Jun JK, Kim D, Kim SK, Lee SM. Future risk of metabolic syndrome after recurrent pregnancy loss: a cohort study using UK Biobank. Fertil Steril. 2023 Dec;120(6):1227-1233. doi: 10.1016/j.fertnstert.2023.09.012. PMID: 38008468. [Pubmed]
  • Wong AC, Devason AS, Umana IC, Cox TO, Dohnalová L, Litichevskiy L, Perla J, Lundgren P, Etwebi Z, Izzo LT, Kim J, Tetlak M, Descamps HC, Park SL, Wisser S, McKnight AD, Pardy RD, Kim J, Blank N, Patel S, Thum K, Mason S, Beltra JC, Michieletto MF, Ngiow SF, Miller BM, Liou MJ, Madhu B, Dmitrieva-Posocco O, Huber AS, Hewins P, Petucci C, Chu CP, Baraniecki-Zwil G, Giron LB, Baxter AE, Greenplate AR, Kearns C, Montone K, Litzky LA, Feldman M, Henao-Mejia J, Striepen B, Ramage H, Jurado KA, Wellen KE, O'Doherty U, Abdel-Mohsen M, Landay AL, Keshavarzian A, Henrich TJ, Deeks SG, Peluso MJ, Meyer NJ, Wherry EJ, Abramoff BA, Cherry S, Thaiss CA, Levy M. Serotonin reduction in post-acute sequelae of viral infection. Cell. 2023 Oct 26;186(22):4851-4867.e20. doi: 10.1016/j.cell.2023.09.013. Epub 2023 Oct 16. PMID: 37848036; PMCID: PMC11227373. [Pubmed]
  • Lundgren P, Sharma PV, Dohnalová L, Coleman K, Uhr GT, Kircher S, Litichevskiy L, Bahnsen K, Descamps HC, Demetriadou C, Chan J, Chellappa K, Cox TO, Heyman Y, Pather SR, Shoffler C, Petucci C, Shalem O, Raj A, Baur JA, Snyder NW, Wellen KE, Levy M, Seale P, Li M, Thaiss CA. A subpopulation of lipogenic brown adipocytes drives thermogenic memory. Nat Metab. 2023 Oct;5(10):1691-1705. doi: 10.1038/s42255-023-00893-w. Epub 2023 Oct 2. PMID: 37783943; PMCID: PMC11309804. [Pubmed]
  • Osman A, Mervosh NL, Strat AN, Euston TJ, Zipursky G, Pollak RM, Meckel KR, Tyler SR, Chan KL, Buxbaum Grice A, Drapeau E, Litichevskiy L, Gill J, Zeldin SM, Thaiss CA, Buxbaum JD, Breen MS, Kiraly DD. Acetate supplementation rescues social deficits and alters transcriptional regulation in prefrontal cortex of Shank3 deficient mice. Brain Behav Immun. 2023 Nov;114:311-324. doi: 10.1016/j.bbi.2023.08.020. Epub 2023 Aug 30. PMID: 37657643; PMCID: PMC10955506. [Pubmed]
  • Suh EH, Lee G, Jung SH, Wen Z, Bao J, Nho K, Huang H, Davatzikos C, Saykin AJ, Thompson PM, Shen L, Kim D; Alzheimer’s Disease Neuroimaging Initiative. An interpretable Alzheimer's disease oligogenic risk score informed by neuroimaging biomarkers improves risk prediction and stratification. Front Aging Neurosci. 2023 Oct 26;15:1281748. doi: 10.3389/fnagi.2023.1281748. PMID: 37953885; PMCID: PMC10637854. [Pubmed]
  • Lee MYY, Kaestner KH, Li M. Benchmarking algorithms for joint integration of unpaired and paired single-cell RNA-seq and ATAC-seq data. Genome Biol. 2023 Oct 24;24(1):244. doi: 10.1186/s13059-023-03073-x. PMID: 37875977; PMCID: PMC10594700. [Pubmed]
  • Campbell AE, McCready-Vangi AR, Uberoi A, Murga-Garrido SM, Lovins VM, White EK, Pan JT, Knight SAB, Morgenstern AR, Bianco C, Planet PJ, Gardner SE, Grice EA. Variable staphyloxanthin production by Staphylococcus aureus drives strain-dependent effects on diabetic wound-healing outcomes. Cell Rep. 2023 Oct 31;42(10):113281. doi: 10.1016/j.celrep.2023.113281. Epub 2023 Oct 19. PMID: 37858460; PMCID: PMC10680119. [Pubmed]
  • Tan K, Xu J, Chen C, Vincent T, Pölönen P, Hu J, Yoshimura S, Yu W, Sussman J, Chen CH, Li E, Diorio C, Shraim R, Newman H, Uppuluri L, Li A, Chen G, Bandyopadhyay S, Wu D, Ding YY, Xu J, Lim T, Hsu M, Thadi A, Ahn KJ, Wu CY, Peng J, Sun Y, Wang A, Mehta R, Frank D, Meyer L, Loh M, Raetz E, Chen Z, Wood B, Devidas M, Dunsmore K, Winter S, Chang TC, Wu G, Pounds S, Zhang N, Carroll W, Hunger S, Bernt K, Yang J, Mullighan C, Teachey D. Identification and targeting of treatment resistant progenitor populations in T-cell Acute Lymphoblastic Leukemia. Res Sq [Preprint]. 2023 Oct 30:rs.3.rs-3487715. doi: 10.21203/rs.3.rs-3487715/v1. PMID: 37961674; PMCID: PMC10635362. [Pubmed]
  • Bao J, Wen J, Wen Z, Yang S, Cui Y, Yang Z, Erus G, Saykin AJ, Long Q, Davatzikos C, Shen L. Brain-wide genome-wide colocalization study for integrating genetics, transcriptomics and brain morphometry in Alzheimer's disease. Neuroimage. 2023 Oct 15;280:120346. doi: 10.1016/j.neuroimage.2023.120346. Epub 2023 Aug 25. PMID: 37634885; PMCID: PMC10552907. [Pubmed]
  • Li B, Sangkuhl K, Whaley R, Woon M, Keat K, Whirl-Carrillo M, Ritchie MD, Klein TE. Frequencies of pharmacogenomic alleles across biogeographic groups in a large-scale biobank. Am J Hum Genet. 2023 Oct 5;110(10):1628-1647. doi: 10.1016/j.ajhg.2023.09.001. Epub 2023 Sep 26. PMID: 37757824; PMCID: PMC10577080. [Pubmed]
  • Lee DSM, Cardone KM, Zhang DY, Abramowitz S, DePaolo JS, Aragam KG, Biddinger K, Conery M, Dilitikas O, Hoffman-Andrews L, Judy RL, Khan A, Kulo I, Puckelwartz MJ, Reza N, Satterfield BA, Singhal P; Regeneron Genetics Center; Arany ZP, Cappola TP, Carruth E, Day SM, Do R, Haggarty CM, Joseph J, McNally E, Nadkarni G, Owens AT, Rader DJ, Ritchie MD, Sun Y, Voight BF, Levin MG, Damrauer SM. Common- and rare-variant genetic architecture of heart failure across the allele frequency spectrum. medRxiv [Preprint]. 2023 Oct 2:2023.07.16.23292724. doi: 10.1101/2023.07.16.23292724. PMID: 37503172; PMCID: PMC10371173. [Pubmed]
  • Sha J, Bao J, Liu K, Yang S, Wen Z, Wen J, Cui Y, Tong B, Moore JH, Saykin AJ, Davatzikos C, Long Q, Shen L; Alzheimer's Disease Neuroimaging Initiative. Preference matrix guided sparse canonical correlation analysis for mining brain imaging genetic associations in Alzheimer's disease. Methods. 2023 Oct;218:27-38. doi: 10.1016/j.ymeth.2023.07.007. Epub 2023 Jul 27. PMID: 37507059; PMCID: PMC10528049. [Pubmed]
  • Wang R, Helbig I, Edmondson AC, Lin L, Xing Y. Splicing defects in rare diseases: transcriptomics and machine learning strategies towards genetic diagnosis. Brief Bioinform. 2023 Sep 20;24(5):bbad284. doi: 10.1093/bib/bbad284. PMID: 37580177; PMCID: PMC10516351. [Pubmed]
  • Gregg JT, Moore JH. STAR_outliers: a python package that separates univariate outliers from non-normal distributions. BioData Min. 2023 Sep 4;16(1):25. doi: 10.1186/s13040-023-00342-0. PMID: 37667378; PMCID: PMC10476292. [Pubmed]
  • Anderson TL, Nande A, Merenstein C, Raynor B, Oommen A, Kelly BJ, Levy MZ, Hill AL. Quantifying individual-level heterogeneity in infectiousness and susceptibility through household studies. Epidemics. 2023 Sep;44:100710. doi: 10.1016/j.epidem.2023.100710. Epub 2023 Jul 22. PMID: 37556994; PMCID: PMC10594662. [Pubmed]
  • Lee SM, Shivakumar M, Xiao B, Jung SH, Nam Y, Yun JS, Choe EK, Jung YM, Oh S, Park JS, Jun JK, Kim D. Genome-wide polygenic risk scores for hypertensive disease during pregnancy can also predict the risk for long-term cardiovascular disease. Am J Obstet Gynecol. 2023 Sep;229(3):298.e1-298.e19. doi: 10.1016/j.ajog.2023.03.013. Epub 2023 Mar 16. PMID: 36933686; PMCID: PMC10504416. [Pubmed]
  • Kim J, Nath K, Schmidlin K, Schaufelberger H, Quattropani C, Vannini S, Mossi S, Thumshirn M, Manz M, Litichevskiy L, Fan J, Dmitrieva-Posocco O, Li M, Levy M, Schär P, Zwahlen M, Thaiss CA, Truninger K. Hierarchical contribution of individual lifestyle factors and their interactions on adenomatous and serrated polyp risk. J Gastroenterol. 2023 Sep;58(9):856-867. doi: 10.1007/s00535-023-02004-8. Epub 2023 Jun 10. PMID: 37300599; PMCID: PMC10423128. [Pubmed]
  • Wei M, Flowers L, Knight SAB, Zheng Q, Murga-Garrido S, Uberoi A, Pan JT, Walsh J, Schroeder E, Chu EW, Campbell A, Shin D, Bradley CW, Duran-Struuck R, Grice EA. Harnessing diversity and antagonism within the pig skin microbiota to identify novel mediators of colonization resistance to methicillin-resistant Staphylococcus aureus. mSphere. 2023 Aug 24;8(4):e0017723. doi: 10.1128/msphere.00177-23. Epub 2023 Jul 5. PMID: 37404023; PMCID: PMC10449522. [Pubmed]
  • Sussman JH, Xu J, Amankulor N, Tan K. Dissecting the tumor microenvironment of epigenetically driven gliomas: Opportunities for single-cell and spatial multiomics. Neurooncol Adv. 2023 Aug 21;5(1):vdad101. doi: 10.1093/noajnl/vdad101. PMID: 37706202; PMCID: PMC10496944. [Pubmed]
  • Merenstein C, Fitzgerald AS, Khatib LA, Graham-Wooten J, Bushman FD, Collman RG. Effects of Mask Reuse on the Oropharyngeal, Skin, and Mask Microbiome. J Infect Dis. 2023 Aug 16;228(4):479-486. doi: 10.1093/infdis/jiad167. PMID: 37217829; PMCID: PMC10428194. [Pubmed]
  • Schneider CV, Li T, Zhang D, Mezina AI, Rattan P, Huang H, Creasy KT, Scorletti E, Zandvakili I, Vujkovic M, Hehl L, Fiksel J, Park J, Wangensteen K, Risman M, Chang KM, Serper M, Carr RM, Schneider KM, Chen J, Rader DJ. Large-scale identification of undiagnosed hepatic steatosis using natural language processing. EClinicalMedicine. 2023 Aug 9;62:102149. doi: 10.1016/j.eclinm.2023.102149. PMID: 37599905; PMCID: PMC10432816. [Pubmed]
  • Wang F, Xu Y, Wang R, Zhang B, Smith N, Notaro A, Gaerlan S, Kutschera E, Kadash-Edmondson KE, Xing Y, Lin L. TEQUILA-seq: a versatile and low-cost method for targeted long-read RNA sequencing. Nat Commun. 2023 Aug 8;14(1):4760. doi: 10.1038/s41467-023-40083-6. PMID: 37553321; PMCID: PMC10409798. [Pubmed]
  • Gregg JT, Himes BE, Asselbergs FW, Moore JH. Improving Genetic Association Studies with a Novel Methodology that Unveils the Hidden Complexity of All-Cause Heart Failure. medRxiv [Preprint]. 2023 Aug 4:2023.08.02.23293567. doi: 10.1101/2023.08.02.23293567. PMID: 37577697; PMCID: PMC10418568. [Pubmed]
  • Katsuda T, Cure H, Sussman J, Simeonov KP, Krapp C, Arany Z, Grompe M, Stanger BZ. Rapid in vivo multiplexed editing (RIME) of the adult mouse liver. Hepatology. 2023 Aug 1;78(2):486-502. doi: 10.1002/hep.32759. Epub 2022 Oct 13. PMID: 36037289; PMCID: PMC11088813. [Pubmed]
  • Clark K, Fu W, Liu CL, Ho PC, Wang H, Lee WP, Chou SY, Wang LS, Tzeng JY. The prediction of Alzheimer's disease through multi-trait genetic modeling. Front Aging Neurosci. 2023 Jul 27;15:1168638. doi: 10.3389/fnagi.2023.1168638. PMID: 37577355; PMCID: PMC10416111. [Pubmed]
  • Katsuda T, Sussman J, Li J, Merrell AJ, Vostrejs W, Secreto A, Matsuzaki J, Ochiya T, Stanger BZ. Evidence for in vitro extensive proliferation of adult hepatocytes and biliary epithelial cells. Stem Cell Reports. 2023 Jul 11;18(7):1436-1450. doi: 10.1016/j.stemcr.2023.05.016. Epub 2023 Jun 22. PMID: 37352852; PMCID: PMC10362498. [Pubmed]
  • Adams CJ, Conery M, Auerbach BJ, Jensen ST, Mathieson I, Voight BF. Regularized sequence-context mutational trees capture variation in mutation rates across the human genome. PLoS Genet. 2023 Jul 7;19(7):e1010807. doi: 10.1371/journal.pgen.1010807. PMID: 37418489; PMCID: PMC10355397. [Pubmed]
  • White EK, Uberoi A, Pan JT, Ort JT, Campbell AE, Murga-Garrido SM, Harris JC, Bhanap P, Wei M, Robles NY, Gardner SE, Grice EA. Wound microbiota-mediated correction of matrix metalloproteinase expression promotes re-epithelialization of diabetic wounds. bioRxiv [Preprint]. 2023 Jun 30:2023.06.30.547263. doi: 10.1101/2023.06.30.547263. PMID: 37425836; PMCID: PMC10327199. [Pubmed]
  • Tong B, Risacher SL, Bao J, Feng Y, Wang X, Ritchie MD, Moore JH, Urbanowicz R, Saykin AJ, Shen L. Comparing Amyloid Imaging Normalization Strategies for Alzheimer's Disease Classification using an Automated Machine Learning Pipeline. AMIA Jt Summits Transl Sci Proc. 2023 Jun 16;2023:525-533. PMID: 37350880; PMCID: PMC10283108. [Pubmed]
  • Wang X, Feng Y, Tong B, Bao J, Ritchie MD, Saykin AJ, Moore JH, Urbanowicz R, Shen L. Exploring Automated Machine Learning for Cognitive Outcome Prediction from Multimodal Brain Imaging using STREAMLINE. AMIA Jt Summits Transl Sci Proc. 2023 Jun 16;2023:544-553. PMID: 37350896; PMCID: PMC10283099. [Pubmed]
  • Schneider KM, Blank N, Alvarez Y, Thum K, Lundgren P, Litichevskiy L, Sleeman M, Bahnsen K, Kim J, Kardo S, Patel S, Dohnalová L, Uhr GT, Descamps HC, Kircher S, McSween AM, Ardabili AR, Nemec KM, Jimenez MT, Glotfelty LG, Eisenberg JD, Furth EE, Henao-Mejia J, Bennett FC, Pierik MJ, Romberg-Camps M, Mujagic Z, Prinz M, Schneider CV, Wherry EJ, Bewtra M, Heuckeroth RO, Levy M, Thaiss CA. The enteric nervous system relays psychological stress to intestinal inflammation. Cell. 2023 Jun 22;186(13):2823-2838.e20. doi: 10.1016/j.cell.2023.05.001. Epub 2023 May 25. PMID: 37236193; PMCID: PMC10330875. [Pubmed]
  • Govek KW, Nicodemus P, Lin Y, Crawford J, Saturnino AB, Cui H, Zoga K, Hart MP, Camara PG. CAJAL enables analysis and integration of single-cell morphological data using metric geometry. Nat Commun. 2023 Jun 21;14(1):3672. doi: 10.1038/s41467-023-39424-2. PMID: 37339989; PMCID: PMC10282047. [Pubmed]
  • Honigberg MC, Truong B, Khan RR, Xiao B, Bhatta L, Vy HMT, Guerrero RF, Schuermans A, Selvaraj MS, Patel AP, Koyama S, Cho SMJ, Vellarikkal SK, Trinder M, Urbut SM, Gray KJ, Brumpton BM, Patil S, Zöllner S, Antopia MC, Saxena R, Nadkarni GN, Do R, Yan Q, Pe'er I, Verma SS, Gupta RM, Haas DM, Martin HC, van Heel DA, Laisk T, Natarajan P. Polygenic prediction of preeclampsia and gestational hypertension. Nat Med. 2023 Jun;29(6):1540-1549. doi: 10.1038/s41591-023-02374-9. Epub 2023 May 29. PMID: 37248299; PMCID: PMC10330886. [Pubmed]
  • Liu J, Cheng L, El-Mekkoussi H, Assenmacher CA, Lee MYY, Jaffe DR, Garvin-Darby K, Morgan A, Manduchi E, Schug J, Kaestner KH. Advanced precision modeling reveals divergent responses of hepatocellular carcinoma to combinatorial immunotherapy. Cancer Commun (Lond). 2023 Jun;43(6):706-710. doi: 10.1002/cac2.12421. Epub 2023 Apr 10. PMID: 37037491; PMCID: PMC10259666. [Pubmed]
  • Gawronski KAB, Bone WP, Park Y, Pashos EE, Wenz BM, Dudek MF, Wang X, Yang W, Rader DJ, Musunuru K, Voight BF, Brown CD. Evaluating the Contribution of Cell Type-Specific Alternative Splicing to Variation in Lipid Levels. Circ Genom Precis Med. 2023 Jun;16(3):248-257. doi: 10.1161/CIRCGEN.120.003249. Epub 2023 May 11. PMID: 37165871; PMCID: PMC10284136. [Pubmed]
  • Pan Y, Phillips JW, Zhang BD, Noguchi M, Kutschera E, McLaughlin J, Nesterenko PA, Mao Z, Bangayan NJ, Wang R, Tran W, Yang HT, Wang Y, Xu Y, Obusan MB, Cheng D, Lee AH, Kadash-Edmondson KE, Champhekar A, Puig-Saus C, Ribas A, Prins RM, Seet CS, Crooks GM, Witte ON, Xing Y. IRIS: Discovery of cancer immunotherapy targets arising from pre-mRNA alternative splicing. Proc Natl Acad Sci U S A. 2023 May 23;120(21):e2221116120. doi: 10.1073/pnas.2221116120. Epub 2023 May 16. PMID: 37192158; PMCID: PMC10214192. [Pubmed]
  • Li B, Sangkuhl K, Keat K, Whaley RM, Woon M, Verma S, Dudek S, Tuteja S, Verma A, Whirl-Carrillo M, Ritchie MD, Klein TE. How to Run the Pharmacogenomics Clinical Annotation Tool (PharmCAT). Clin Pharmacol Ther. 2023 May;113(5):1036-1047. doi: 10.1002/cpt.2790. Epub 2022 Dec 23. PMID: 36350094; PMCID: PMC10121724. [Pubmed]
  • Heil BJ, Crawford J, Greene CS. The effect of non-linear signal in classification problems using gene expression. PLoS Comput Biol. 2023 Mar 27;19(3):e1010984. doi: 10.1371/journal.pcbi.1010984. PMID: 36972227; PMCID: PMC10079219. [Pubmed]
  • Patterson A, Elbasir A, Tian B, Auslander N. Computational Methods Summarizing Mutational Patterns in Cancer: Promise and Limitations for Clinical Applications. Cancers (Basel). 2023 Mar 24;15(7):1958. doi: 10.3390/cancers15071958. PMID: 37046619; PMCID: PMC10093138. [Pubmed]
  • Fu Y, Kim H, Adams JI, Grimes SM, Huang S, Lau BT, Sathe A, Hess P, Ji HP, Zhang NR. Single cell and spatial alternative splicing analysis with long read sequencing. Res Sq [Preprint]. 2023 Mar 21:rs.3.rs-2674892. doi: 10.21203/rs.3.rs-2674892/v1. PMID: 36993612; PMCID: PMC10055662. [Pubmed]
  • Bao J, Chang C, Zhang Q, Saykin AJ, Shen L, Long Q; Alzheimer’s Disease Neuroimaging Initiative. Integrative analysis of multi-omics and imaging data with incorporation of biological information via structural Bayesian factor analysis. Brief Bioinform. 2023 Mar 19;24(2):bbad073. doi: 10.1093/bib/bbad073. PMID: 36882008; PMCID: PMC10387302. [Pubmed]
  • Xiao B, Velez Edwards DR, Lucas A, Drivas T, Gray K, Keating B, Weng C, Jarvik GP, Hakonarson H, Kottyan L, Elhadad N, Wei WQ, Luo Y, Kim D, Ritchie M, Verma SS; Regeneron Genetics Center *. Inference of Causal Relationships Between Genetic Risk Factors for Cardiometabolic Phenotypes and Female-Specific Health Conditions. J Am Heart Assoc. 2023 Mar 7;12(5):e026561. doi: 10.1161/JAHA.121.026561. Epub 2023 Feb 27. Erratum in: J Am Heart Assoc. 2024 Mar 5;13(5):e027760. doi: 10.1161/JAHA.121.027760. PMID: 36846987; PMCID: PMC10111435. [Pubmed]
  • Shi L, Shen W, Davis MI, Kong K, Vu P, Saha SK, Adil R, Kreuzer J, Egan R, Lee TD, Greninger P, Shrimp JH, Zhao W, Wei TY, Zhou M, Eccleston J, Sussman J, Manocha U, Weerasekara V, Kondo H, Vijay V, Wu MJ, Kearney SE, Ho J, McClanaghan J, Murchie E, Crowther GS, Patnaik S, Boxer MB, Shen M, Ting DT, Kim WY, Stanger BZ, Deshpande V, Ferrone CR, Benes CH, Haas W, Hall MD, Bardeesy N. SULT1A1-dependent sulfonation of alkylators is a lineage-dependent vulnerability of liver cancers. Nat Cancer. 2023 Mar;4(3):365-381. doi: 10.1038/s43018-023-00523-0. Epub 2023 Mar 13. PMID: 36914816; PMCID: PMC11090616. [Pubmed]
  • Hazuga MA, Grant SFA. Awakening new sleep biology with machine learning. Sleep. 2023 Feb 8;46(2):zsac284. doi: 10.1093/sleep/zsac284. PMID: 36422063; PMCID: PMC9905772. [Pubmed]
  • Conery M, Grant SFA. Human height: a model common complex trait. Ann Hum Biol. 2023 Feb;50(1):258-266. doi: 10.1080/03014460.2023.2215546. PMID: 37343163; PMCID: PMC10368389. [Pubmed]
  • Hui D, Mehrabi S, Quimby AE, Chen T, Chen S, Park J, Li B; Regeneron Genetics Center; Penn Medicine Biobank; Ruckenstein MJ, Rader DJ, Ritchie MD, Brant JA, Epstein DJ, Mathieson I. Gene burden analysis identifies genes associated with increased risk and severity of adult-onset hearing loss in a diverse hospital-based cohort. PLoS Genet. 2023 Jan 19;19(1):e1010584. doi: 10.1371/journal.pgen.1010584. PMID: 36656851; PMCID: PMC9888707. [Pubmed]
  • Keeler EL, Merenstein C, Reddy S, Taylor LJ, Cobián-Güemes AG, Zankharia U, Collman RG, Bushman FD. Widespread, human-associated redondoviruses infect the commensal protozoan Entamoeba gingivalis. Cell Host Microbe. 2023 Jan 11;31(1):58-68.e5. doi: 10.1016/j.chom.2022.11.002. Epub 2022 Dec 1. PMID: 36459997; PMCID: PMC9969835. [Pubmed]
  • Heil BJ, Greene CS. The Field-Dependent Nature of PageRank Values in Citation Networks. bioRxiv [Preprint]. 2023 Jan 6:2023.01.05.522943. doi: 10.1101/2023.01.05.522943. PMID: 36711900; PMCID: PMC9881996. [Pubmed]
  • Wang D, Quesnel-Vallieres M, Jewell S, Elzubeir M, Lynch K, Thomas-Tikhonenko A, Barash Y. A Bayesian model for unsupervised detection of RNA splicing based subtypes in cancers. Nat Commun. 2023 Jan 4;14(1):63. doi: 10.1038/s41467-022-35369-0. PMID: 36599821; PMCID: PMC9813260. [Pubmed]
  • Nam Y, Jung SH, Yun JS, Sriram V, Singhal P, Byrska-Bishop M, Verma A, Shin H, Park WY, Won HH, Kim D. Discovering comorbid diseases using an inter-disease interactivity network based on biobank-scale PheWAS data. Bioinformatics. 2023 Jan 1;39(1):btac822. doi: 10.1093/bioinformatics/btac822. PMID: 36571484; PMCID: PMC9825330. [Pubmed]
  • Keat K, Hui D, Xiao B, Bradford Y, Cindi Z, Daar ES, Gulick R, Riddler SA, Sinxadi P, Haas DW, Ritchie MD. Leveraging Multi-Ancestry Polygenic Risk Scores for Body Mass Index to Predict Antiretroviral Therapy-Induced Weight Gain. Pac Symp Biocomput. 2023;28:233-244. PMID: 36540980; PMCID: PMC10091400. [Pubmed]
  • Hui D, Xiao B, Dikilitas O, Freimuth RR, Irvin MR, Jarvik GP, Kottyan L, Kullo I, Limdi NA, Liu C, Luo Y, Namjou B, Puckelwartz MJ, Schaid D, Tiwari H, Wei WQ, Verma S, Kim D, Ritchie MD. Quantifying factors that affect polygenic risk score performance across diverse ancestries and age groups for body mass index. Pac Symp Biocomput. 2023;28:437-448. PMID: 36540998; PMCID: PMC10018532. [Pubmed]
2022
  • Himmelstein DS, Zietz M, Rubinetti V, Kloster K, Heil BJ, Alquaddoomi F, Hu D, Nicholson DN, Hao Y, Sullivan BD, Nagle MW, Greene CS. Hetnet connectivity search provides rapid insights into how biomedical entities are related. Gigascience. 2022 Dec 28;12:giad047. doi: 10.1093/gigascience/giad047. Epub 2023 Jul 28. PMID: 37503959; PMCID: PMC10375517.
  • Park J, MacLean MT, Lucas AM, Torigian DA, Schneider CV, Cherlin T, Xiao B, Miller JE, Bradford Y, Judy RL; Regeneron Genetics Center; Verma A, Damrauer SM, Ritchie MD, Witschey WR, Rader DJ. Exome-wide association analysis of CT imaging-derived hepatic fat in a medical biobank. Cell Rep Med. 2022 Dec 20;3(12):100855. doi: 10.1016/j.xcrm.2022.100855. Epub 2022 Dec 12. PMID: 36513072; PMCID: PMC9798024. [Pubmed]
  • Dohnalová L, Lundgren P, Carty JRE, Goldstein N, Wenski SL, Nanudorn P, Thiengmag S, Huang KP, Litichevskiy L, Descamps HC, Chellappa K, Glassman A, Kessler S, Kim J, Cox TO, Dmitrieva-Posocco O, Wong AC, Allman EL, Ghosh S, Sharma N, Sengupta K, Cornes B, Dean N, Churchill GA, Khurana TS, Sellmyer MA, FitzGerald GA, Patterson AD, Baur JA, Alhadeff AL, Helfrich EJN, Levy M, Betley JN, Thaiss CA. A microbiome-dependent gut-brain pathway regulates motivation for exercise. Nature. 2022 Dec;612(7941):739-747. doi: 10.1038/s41586-022-05525-z. Epub 2022 Dec 14. PMID: 36517598; PMCID: PMC11162758. [Pubmed]
  • Sha J, Bao J, Liu K, Yang S, Wen Z, Cui Y, Wen J, Davatzikos C, Moore JH, Saykin AJ, Long Q, Shen L; ADNI. Preference Matrix Guided Sparse Canonical Correlation Analysis for Genetic Study of Quantitative Traits in Alzheimer's Disease. Proceedings (IEEE Int Conf Bioinformatics Biomed). 2022 Dec;2022:541-548. doi: 10.1109/bibm55620.2022.9995342. PMID: 36845995; PMCID: PMC9944667. [Pubmed]
  • Verma SS, Keat K, Li B, Hoffecker G, Risman M; Regeneron Genetics Center; Sangkuhl K, Whirl-Carrillo M, Dudek S, Verma A, Klein TE, Ritchie MD, Tuteja S. Evaluating the frequency and the impact of pharmacogenetic alleles in an ancestrally diverse Biobank population. J Transl Med. 2022 Nov 28;20(1):550. doi: 10.1186/s12967-022-03745-5. PMID: 36443877; PMCID: PMC9703665. [Pubmed]
  • Way GP, Natoli T, Adeboye A, Litichevskiy L, Yang A, Lu X, Caicedo JC, Cimini BA, Karhohs K, Logan DJ, Rohban MH, Kost-Alimova M, Hartland K, Bornholdt M, Chandrasekaran SN, Haghighi M, Weisbart E, Singh S, Subramanian A, Carpenter AE. Morphology and gene expression profiling provide complementary information for mapping cell state. Cell Syst. 2022 Nov 16;13(11):911-923.e9. doi: 10.1016/j.cels.2022.10.001. Epub 2022 Oct 28. PMID: 36395727; PMCID: PMC10246468. [Pubmed]
  • Hippen AA, Crawford J, Gardner JR, Greene CS. wenda_gpu: fast domain adaptation for genomic data. Bioinformatics. 2022 Nov 15;38(22):5129-5130. doi: 10.1093/bioinformatics/btac663. PMID: 36193991; PMCID: PMC9665854. [Pubmed]
  • Levin MG, Tsao NL, Singhal P, Liu C, Vy HMT, Paranjpe I, Backman JD, Bellomo TR, Bone WP, Biddinger KJ, Hui Q, Dikilitas O, Satterfield BA, Yang Y, Morley MP, Bradford Y, Burke M, Reza N, Charest B; Regeneron Genetics Center; Judy RL, Puckelwartz MJ, Hakonarson H, Khan A, Kottyan LC, Kullo I, Luo Y, McNally EM, Rasmussen-Torvik LJ, Day SM, Do R, Phillips LS, Ellinor PT, Nadkarni GN, Ritchie MD, Arany Z, Cappola TP, Margulies KB, Aragam KG, Haggerty CM, Joseph J, Sun YV, Voight BF, Damrauer SM. Genome-wide association and multi-trait analyses characterize the common genetic architecture of heart failure. Nat Commun. 2022 Nov 14;13(1):6914. doi: 10.1038/s41467-022-34216-6. PMID: 36376295; PMCID: PMC9663424. [Pubmed]
  • Auerbach BJ, FitzGerald GA, Li M. Tempo: an unsupervised Bayesian algorithm for circadian phase inference in single-cell transcriptomics. Nat Commun. 2022 Nov 2;13(1):6580. doi: 10.1038/s41467-022-34185-w. PMID: 36323668; PMCID: PMC9630322. [Pubmed]
  • Truong VQ, Woerner JA, Cherlin TA, Bradford Y, Lucas AM, Okeh CC, Shivakumar MK, Hui DH, Kumar R, Pividori M, Jones SC, Bossa AC, Turner SD, Ritchie MD, Verma SS. Quality Control Procedures for Genome-Wide Association Studies. Curr Protoc. 2022 Nov;2(11):e603. doi: 10.1002/cpz1.603. PMID: 36441943.
  • Johnson KE, Adams CJ, Voight BF. Identifying rare variants inconsistent with identity-by-descent in population-scale whole-genome sequencing data. Methods Ecol Evol. 2022 Nov;13(11):2429-2442. doi: 10.1111/2041-210x.13991. Epub 2022 Oct 11. PMID: 38938451; PMCID: PMC11210625. [Pubmed]
  • Lakkis J, Schroeder A, Su K, Lee MYY, Bashore AC, Reilly MP, Li M. A multi-use deep learning method for CITE-seq and single-cell RNA-seq data integration with cell surface protein prediction and imputation. Nat Mach Intell. 2022 Nov;4(11):940-952. doi: 10.1038/s42256-022-00545-w. Epub 2022 Oct 27. PMID: 36873621; PMCID: PMC9979929. [Pubmed]
  • Lee SM, Shivakumar M, Park JW, Jung YM, Choe EK, Kwak SH, Oh S, Park JS, Jun JK, Kim D, Yun JS. Long-term cardiovascular outcomes of gestational diabetes mellitus: a prospective UK Biobank study. Cardiovasc Diabetol. 2022 Oct 29;21(1):221. doi: 10.1186/s12933-022-01663-w. PMID: 36309714; PMCID: PMC9618212. [Pubmed]
  • Adams JI, Ferebee T, Minto M, Pennerman KK, Chambwe N. Ten simple rules for creating a global network in computational biology. PLoS Comput Biol. 2022 Oct 27;18(10):e1010528. doi: 10.1371/journal.pcbi.1010528. PMID: 36301818; PMCID: PMC9612568. [Pubmed]
  • Shao A, Gearhart MD, Chan SC, Miao Z, Susztak K, Igarashi P. Multiomics analysis reveals that hepatocyte nuclear factor 1β regulates axon guidance genes in the developing mouse kidney. Sci Rep. 2022 Oct 20;12(1):17586. doi: 10.1038/s41598-022-22327-5. PMID: 36266461; PMCID: PMC9585060. [Pubmed]
  • Lee AJ, Mould DL, Crawford J, Hu D, Powers RK, Doing G, Costello JC, Hogan DA, Greene CS. SOPHIE: Generative Neural Networks Separate Common and Specific Transcriptional Responses. Genomics Proteomics Bioinformatics. 2022 Oct;20(5):912-927. doi: 10.1016/j.gpb.2022.09.011. Epub 2022 Oct 7. [Pubmed]
  • Merenstein C, Bushman FD, Collman RG. Alterations in the respiratory tract microbiome in COVID-19: current observations and potential significance. Microbiome. 2022 Oct 5;10(1):165. doi: 10.1186/s40168-022-01342-8. PMID: 36195943; PMCID: PMC9532226. [Pubmed]
  • Mai H, Bao J, Thompson PM, Kim D, Shen L. Identifying genes associated with brain volumetric differences through tissue specific transcriptomic inference from GWAS summary data. BMC Bioinformatics. 2022 Sep 28;23(Suppl 3):398. doi: 10.1186/s12859-022-04947-w. PMID: 36171548; PMCID: PMC9520794. [Pubmed]
  • Lee SM, Nam Y, Choi ES, Jung YM, Sriram V, Leiby JS, Koo JN, Oh IH, Kim BJ, Kim SM, Kim SY, Kim GM, Joo SK, Shin S, Norwitz ER, Park CW, Jun JK, Kim W, Kim D, Park JS. Development of early prediction model for pregnancy-associated hypertension with graph-based semi-supervised learning. Sci Rep. 2022 Sep 22;12(1):15793. doi: 10.1038/s41598-022-15391-4. PMID: 36138035; PMCID: PMC9499925. [Pubmed]
  • Patterson A, Auslander N. Mutated processes predict immune checkpoint inhibitor therapy benefit in metastatic melanoma. Nat Commun. 2022 Sep 19;13(1):5151. doi: 10.1038/s41467-022-32838-4. Erratum in: Nat Commun. 2023 Sep 21;14(1):5865. doi: 10.1038/s41467-023-41662-3. PMID: 36123351; PMCID: PMC9485158. [Pubmed]
  • Chen BY, Bone WP, Lorenz K, Levin M, Ritchie MD, Voight BF. ColocQuiaL: a QTL-GWAS colocalization pipeline. Bioinformatics. 2022 Sep 15;38(18):4409-4411. doi: 10.1093/bioinformatics/btac512. PMID: 35894642; PMCID: PMC9477517. [Pubmed]
  • Litichevskiy L, Thaiss CA. Microbiome complexity shapes metabolism. PLoS Biol. 2022 Sep 21;20(9):e3001793. doi: 10.1371/journal.pbio.3001793. PMID: 36129892; PMCID: PMC9491537. [Pubmed]
  • Choe EK, Shivakumar M, Lee SM, Verma A, Kim D. Dissecting the clinical relevance of polygenic risk score for obesity-a cross-sectional, longitudinal analysis. Int J Obes (Lond). 2022 Sep;46(9):1686-1693. doi: 10.1038/s41366-022-01168-2. Epub 2022 Jun 25. PMID: 35752651; PMCID: PMC10362905. [Pubmed]
  • Hao Y, Romano JD, Moore JH. Knowledge-guided deep learning models of drug toxicity improve interpretation. Patterns (N Y). 2022 Aug 24;3(9):100565. doi: 10.1016/j.patter.2022.100565. PMID: 36124309; PMCID: PMC9481960. [Pubmed]
  • Wu R, Bao J, Kim M, Saykin AJ, Moore JH, Shen L, On Behalf Of Adni. Mining High-Level Imaging Genetic Associations via Clustering AD Candidate Variants with Similar Brain Association Patterns. Genes (Basel). 2022 Aug 24;13(9):1520. doi: 10.3390/genes13091520. PMID: 36140686; PMCID: PMC9498881. [Pubmed]
  • Liu H, Doke T, Guo D, Sheng X, Ma Z, Park J, Vy HMT, Nadkarni GN, Abedini A, Miao Z, Palmer M, Voight BF, Li H, Brown CD, Ritchie MD, Shu Y, Susztak K. Epigenomic and transcriptomic analyses define core cell types, genes and targetable mechanisms for kidney disease. Nat Genet. 2022 Jul;54(7):950-962. doi: 10.1038/s41588-022-01097-w. Epub 2022 Jun 16. PMID: 35710981. [Pubmed]
  • Litichevskiy L, Thaiss CA. The Oscillating Gut Microbiome and Its Effects on Host Circadian Biology. Annu Rev Nutr. 2022 Aug 22;42:145-164. doi: 10.1146/annurev-nutr-062320-111321. Epub 2022 May 16. PMID: 35576592. [Pubmed]
  • Yun JS, Jung SH, Shivakumar M, Xiao B, Khera AV, Park WY, Won HH, Kim D. Associations between polygenic risk of coronary artery disease and type 2 diabetes, lifestyle, and cardiovascular mortality: A prospective UK Biobank study. Front Cardiovasc Med. 2022 Aug 17;9:919374. doi: 10.3389/fcvm.2022.919374. PMID: 36061534; PMCID: PMC9428483. [Pubmed]
  • Romano JD, Hao Y, Moore JH, Penning TM. Automating Predictive Toxicology Using ComptoxAI. Chem Res Toxicol. 2022 Aug 15;35(8):1370-1382. doi: 10.1021/acs.chemrestox.2c00074. Epub 2022 Jul 12. PMID: 35819939; PMCID: PMC9805296. [Pubmed]
  • Lee AJ, Reiter T, Doing G, Oh J, Hogan DA, Greene CS. Using genome-wide expression compendia to study microorganisms. Comput Struct Biotechnol J. 2022 Aug 10;20:4315-4324. doi: 10.1016/j.csbj.2022.08.012. [Pubmed]
  • Ju D, Hui D, Hammond DA, Wonkam A, Tishkoff SA. Importance of Including Non-European Populations in Large Human Genetic Studies to Enhance Precision Medicine. Annu Rev Biomed Data Sci. 2022 Aug 10;5:321-339. doi: 10.1146/annurev-biodatasci-122220-112550. Epub 2022 May 16. PMID: 35576557; PMCID: PMC9904154. [Pubmed]
  • Yun JS, Jung SH, Shivakumar M, Xiao B, Khera AV, Won HH, Kim D. Polygenic risk for type 2 diabetes, lifestyle, metabolic health, and cardiovascular disease: a prospective UK Biobank study. Cardiovasc Diabetol. 2022 Jul 14;21(1):131. doi: 10.1186/s12933-022-01560-2. PMID: 35836215; PMCID: PMC9284808. [Pubmed]
  • Leiby JS, Hao J, Kang GH, Park JW, Kim D. Attention-based multiple instance learning with self-supervision to predict microsatellite instability in colorectal cancer from histology whole-slide images. Annu Int Conf IEEE Eng Med Biol Soc. 2022 Jul;2022:3068-3071. doi: 10.1109/EMBC48229.2022.9871553. PMID: 36085965. [Pubmed]
  • Crawford J, Christensen BC, Chikina M, Greene CS. Widespread redundancy in -omics profiles of cancer mutation states. Genome Biol. 2022 Jun 27;23(1):137. doi: 10.1186/s13059-022-02705-y. PMID: 35761387; PMCID: PMC9238138. [Pubmed]
  • Neff SL, Hampton TH, Puerner C, Cengher L, Doing G, Lee AJ, Koeppen K, Cheung AL, Hogan DA, Cramer RA, Stanton BA. CF-Seq, an accessible web application for rapid re-analysis of cystic fibrosis pathogen RNA sequencing studies. Sci Data. 2022 Jun 16;9(1):343. doi: 10.1038/s41597-022-01431-1. [Pubmed]
  • Zhang X, Lucas AM, Veturi Y, Drivas TG, Bone WP, Verma A, Chung WK, Crosslin D, Denny JC, Hebbring S, Jarvik GP, Kullo I, Larson EB, Rasmussen-Torvik LJ, Schaid DJ, Smoller JW, Stanaway IB, Wei WQ, Weng C, Ritchie MD. Large-scale genomic analyses reveal insights into pleiotropy across circulatory system diseases and nervous system disorders. Nat Commun. 2022 Jun 14;13(1):3428. doi: 10.1038/s41467-022-30678-w. PMID: 35701404; PMCID: PMC9198016. [Pubmed]
  • Babb PL, Gregorič M, Lahens NF, Nicholson DN, Hayashi CY, Higgins L, Kuntner M, Agnarsson I, Voight BF. Characterization of the genome and silk-gland transcriptomes of Darwin's bark spider (Caerostris darwini). PLoS One. 2022 Jun 6;17(6):e0268660. doi: 10.1371/journal.pone.0268660. PMID: 35666730; PMCID: PMC9170102. [Pubmed]
  • Baik JY, Kim M, Bao J, Long Q, Shen L; Alzheimer’s Disease Neuroimaging Initiative. Identifying Alzheimer's genes via brain transcriptome mapping. BMC Med Genomics. 2022 May 19;15(Suppl 2):116. doi: 10.1186/s12920-022-01260-6. PMID: 35590321; PMCID: PMC9118564. [Pubmed]
  • Wen J, Fu CHY, Tosun D, Veturi Y, Yang Z, Abdulkadir A, Mamourian E, Srinivasan D, Skampardoni I, Singh A, Nawani H, Bao J, Erus G, Shou H, Habes M, Doshi J, Varol E, Mackin RS, Sotiras A, Fan Y, Saykin AJ, Sheline YI, Shen L, Ritchie MD, Wolk DA, Albert M, Resnick SM, Davatzikos C; iSTAGING consortium, ADNI, BIOCARD, and BLSA. Characterizing Heterogeneity in Neuroimaging, Cognition, Clinical Symptoms, and Genetics Among Patients With Late-Life Depression. JAMA Psychiatry. 2022 May 1;79(5):464-474. doi: 10.1001/jamapsychiatry.2022.0020. PMID: 35262657; PMCID: PMC8908227. [Pubmed]
  • Wing A, Xu J, Meng W, Rosenfeld AM, Li EY, Wertheim G, Paessler M, Bagg A, Frank D, Tan K, Teachey DT, Lim MS, Prak EL, Fajgenbaum DC, Pillai V. Transcriptome and unique cytokine microenvironment of Castleman disease. Mod Pathol. 2022 Apr;35(4):451-461. doi: 10.1038/s41379-021-00950-3. Epub 2021 Oct 22. PMID: 34686774; PMCID: PMC9272352. [Pubmed]
  • Temprano-Sagrera G, Sitlani CM, Bone WP, Martin-Bornez M, Voight BF, Morrison AC, Damrauer SM, de Vries PS, Smith NL, Sabater-Lleal M. Multi-phenotype analyses of hemostatic traits with cardiovascular events reveal novel genetic associations. J Thromb Haemost. 2022 Jun;20(6):1331-1349. doi: 10.1111/jth.15698. Epub 2022 Mar 29. PMID: 35285134; PMCID: PMC9314075. [Pubmed]
  • Jha A, Quesnel-Vallières M, Wang D, Thomas-Tikhonenko A, Lynch KW, Barash Y. Identifying common transcriptome signatures of cancer by interpreting deep learning models. Genome Biol. 2022 May 17;23(1):117. doi: 10.1186/s13059-022-02681-3. PMID: 35581644; PMCID: PMC9112525. [Pubmed]
  • Cucolo L, Chen Q, Qiu J, Yu Y, Klapholz M, Budinich KA, Zhang Z, Shao Y, Brodsky IE, Jordan MS, Gilliland DG, Zhang NR, Shi J, Minn AJ. The interferon-stimulated gene RIPK1 regulates cancer cell intrinsic and extrinsic resistance to immune checkpoint blockade. Immunity. 2022 Apr 12;55(4):671-685.e10. doi: 10.1016/j.immuni.2022.03.007. PMID: 35417675; PMCID: PMC11289737. [Pubmed]
  • Ahmadmehrabi S, Li B, Hui D, Park J, Ritchie M, Rader DJ, Ruckenstein MJ, Epstein DJ, Brant J. A Genome-First Approach to Rare Variants in Dominant Postlingual Hearing Loss Genes in a Large Adult Population. Otolaryngol Head Neck Surg. 2022 Apr;166(4):746-752. doi: 10.1177/01945998211029544. Epub 2021 Jul 20. PMID: 34281439. [Pubmed]
  • Hippen AA, Davidson NR, Greene CS. Computational audits combat disparities in recognition. Nat Hum Behav. 2022 Apr;6(4):473-474. doi: 10.1038/s41562-021-01279-2. PMID: 35039653. [Pubmed]
  • Sriram V, Shivakumar M, Jung SH, Nam Y, Bang L, Verma A, Lee S, Choe EK, Kim D. NETMAGE: A human disease phenotype map generator for the network-based visualization of phenome-wide association study results. Gigascience. 2022 Feb 15;11:giac002. doi: 10.1093/gigascience/giac002. PMID: 35166337; PMCID: PMC8848314. [Pubmed]
  • Bellomo TR, Bone WP, Chen BY, Gawronski KAB, Zhang D, Park J, Levin M, Tsao N, Klarin D, Lynch J, Assimes TL, Gaziano JM, Wilson PW, Cho K, Vujkovic M, O'Donnell CJ, Chang KM, Tsao PS, Rader DJ, Ritchie MD, Damrauer SM, Voight BF. Multi-Trait Genome-Wide Association Study of Atherosclerosis Detects Novel Pleiotropic Loci. Front Genet. 2022 Feb 2;12:787545. doi: 10.3389/fgene.2021.787545. PMID: 35186008; PMCID: PMC8847690. [Pubmed]
  • Blacher E, Tsai C, Litichevskiy L, Shipony Z, Iweka CA, Schneider KM, Chuluun B, Heller HC, Menon V, Thaiss CA, Andreasson KI. Aging disrupts circadian gene regulation and function in macrophages. Nat Immunol. 2022 Feb;23(2):229-236. doi: 10.1038/s41590-021-01083-0. Epub 2021 Dec 23. PMID: 34949832; PMCID: PMC9704320. [Pubmed]
  • Xing Y, Wang R, Davidson BL. Mis-splicing in Huntington's disease: harnessing the power of comparative transcriptomics. Trends Neurosci. 2022 Feb;45(2):91-93. doi: 10.1016/j.tins.2021.10.009. Epub 2021 Nov 6. PMID: 34753605; PMCID: PMC10550193. [Pubmed]
  • Nicholson DN, Rubinetti V, Hu D, Thielk M, Hunter LE, Greene CS. Examining linguistic shifts between preprints and publications. PLoS Biol. 2022 Feb 1;20(2):e3001470. doi: 10.1371/journal.pbio.3001470. PMID: 35104289; PMCID: PMC8806061. [Pubmed]
  • Romano JD, Le TT, La Cava W, Gregg JT, Goldberg DJ, Chakraborty P, Ray NL, Himmelstein D, Fu W, Moore JH. PMLB v1.0: an open-source dataset collection for benchmarking machine learning methods. Bioinformatics. 2022 Jan 12;38(3):878-880. doi: 10.1093/bioinformatics/btab727. PMID: 34677586; PMCID: PMC8756190. [Pubmed]
  • Romano JD, Hao Y, Moore JH. Improving QSAR Modeling for Predictive Toxicology using Publicly Aggregated Semantic Graph Data and Graph Neural Networks. Pac Symp Biocomput. 2022;27:187-198. PMID: 34890148; PMCID: PMC8714189. [Pubmed]
  • Nam Y, Jung SH, Verma A, Sriram V, Won HH, Yun JS; Regeneron Genetics Center; Kim D. netCRS: Network-based comorbidity risk score for prediction of myocardial infarction using biobank-scaled PheWAS data. Pac Symp Biocomput. 2022;27:325-336. PMID: 34890160; PMCID: PMC8682919. [Pubmed]
  • Clark K, Leung YY, Lee WP, Voight B, Wang LS. Polygenic Risk Scores in Alzheimer's Disease Genetics: Methodology, Applications, Inclusion, and Diversity. J Alzheimers Dis. 2022;89(1):1-12. doi: 10.3233/JAD-220025. PMID: 35848019; PMCID: PMC9484091. [Pubmed]
  • Kuksa PP, Liu CL, Fu W, Qu L, Zhao Y, Katanic Z, Clark K, Kuzma AB, Ho PC, Tzeng KT, Valladares O, Chou SY, Naj AC, Schellenberg GD, Wang LS, Leung YY. Alzheimer's Disease Variant Portal: A Catalog of Genetic Findings for Alzheimer's Disease. J Alzheimers Dis. 2022;86(1):461-477. doi: 10.3233/JAD-215055. PMID: 35068457; PMCID: PMC9028687. [Pubmed]
  • Bao J, Wen Z, Kim M, Saykin AJ, Thompson PM, Zhao Y, Shen L; Alzheimer’s Disease Neuroimaging Initiative. Identifying imaging genetic associations via regional morphometricity estimation. Pac Symp Biocomput. 2022;27:97-108. PMID: 34890140; PMCID: PMC8730533. [Pubmed]
  • Bao J, Wen Z, Kim M, Zhao X, Lee BN, Jung SH, Davatzikos C, Saykin AJ, Thompson PM, Kim D, Zhao Y, Shen L; Alzheimer’s Disease Neuroimaging Initiative. Identifying highly heritable brain amyloid phenotypes through mining Alzheimer's imaging and sequencing biobank data. Pac Symp Biocomput. 2022;27:109-120. PMID: 34890141; PMCID: PMC8730532. [Pubmed]
2021
  • Sriram V, Nam Y, Shivakumar M, Verma A, Jung SH, Lee SM, Kim D. A Network-Based Analysis of Disease Complication Associations for Obstetric Disorders in the UK Biobank. J Pers Med. 2021 Dec 17;11(12):1382. doi: 10.3390/jpm11121382. PMID: 34945853; PMCID: PMC8705804. [Pubmed]
  • Good CR, Aznar MA, Kuramitsu S, Samareh P, Agarwal S, Donahue G, Ishiyama K, Wellhausen N, Rennels AK, Ma Y, Tian L, Guedan S, Alexander KA, Zhang Z, Rommel PC, Singh N, Glastad KM, Richardson MW, Watanabe K, Tanyi JL, O'Hara MH, Ruella M, Lacey SF, Moon EK, Schuster SJ, Albelda SM, Lanier LL, Young RM, Berger SL, June CH. An NK-like CAR T cell transition in CAR T cell dysfunction. Cell. 2021 Dec 9;184(25):6081-6100.e26. doi: 10.1016/j.cell.2021.11.016. Epub 2021 Dec 2. PMID: 34861191; PMCID: PMC8827167. [Pubmed]
  • Lee WP, Tucci AA, Conery M, Leung YY, Kuzma AB, Valladares O, Chou YF, Lu W, Wang LS, Schellenberg GD, Tzeng JY. Copy Number Variation Identification on 3,800 Alzheimer's Disease Whole Genome Sequencing Data from the Alzheimer's Disease Sequencing Project. Front Genet. 2021 Nov 4;12:752390. doi: 10.3389/fgene.2021.752390. PMID: 34804120; PMCID: PMC8599981. [Pubmed]
  • Wu M, Lee MYY, Bahl V, Traum D, Schug J, Kusmartseva I, Atkinson MA, Fan G; HPAP Consortium; Kaestner KH. Single-cell analysis of the human pancreas in type 2 diabetes using multi-spectral imaging mass cytometry. Cell Rep. 2021 Nov 2;37(5):109919. doi: 10.1016/j.celrep.2021.109919. PMID: 34731614; PMCID: PMC8609965. [Pubmed]
  • Kondo A, Ma S, Lee MYY, Ortiz V, Traum D, Schug J, Wilkins B, Terry NA, Lee H, Kaestner KH. Highly Multiplexed Image Analysis of Intestinal Tissue Sections in Patients With Inflammatory Bowel Disease. Gastroenterology. 2021 Dec;161(6):1940-1952. doi: 10.1053/j.gastro.2021.08.055. Epub 2021 Sep 14. PMID: 34529988; PMCID: PMC8606000. [Pubmed]
  • Hao Y, Moore JH. TargetTox: A Feature Selection Pipeline for Identifying Predictive Targets Associated with Drug Toxicity. J Chem Inf Model. 2021 Nov 22;61(11):5386-5394. doi: 10.1021/acs.jcim.1c00733. Epub 2021 Nov 10. PMID: 34757743. [Pubmed]
  • Miao Z, Humphreys BD, McMahon AP, Kim J. Multi-omics integration in the age of million single-cell data. Nat Rev Nephrol. 2021 Nov;17(11):710-724. doi: 10.1038/s41581-021-00463-x. Epub 2021 Aug 20. PMID: 34417589; PMCID: PMC9191639. [Pubmed]
  • Rando HM, MacLean AL, Lee AJ, Lordan R, Ray S, Bansal V, Skelly AN, Sell E, Dziak JJ, Shinholster L, D'Agostino McGowan L, Ben Guebila M, Wellhausen N, Knyazev S, Boca SM, Capone S, Qi Y, Park Y, Mai D, Sun Y, Boerckel JD, Brueffer C, Byrd JB, Kamil JP, Wang J, Velazquez R, Szeto GL, Barton JP, Goel RR, Mangul S, Lubiana T; COVID-19 Review Consortium; Gitter A, Greene CS. Pathogenesis, Symptomatology, and Transmission of SARS-CoV-2 through Analysis of Viral Genomics and Structure. mSystems. 2021 Oct 26;6(5):e0009521. doi: 10.1128/mSystems.00095-21. Epub 2021 Oct 26. Erratum in: mSystems. 2022 Feb 22;7(1):e0144721. doi: 10.1128/msystems.01447-21. PMID: 34698547; PMCID: PMC8547481. [Pubmed]
  • Auerbach BJ, Hu J, Reilly MP, Li M. Applications of single-cell genomics and computational strategies to study common disease and population-level variation. Genome Res. 2021 Oct;31(10):1728-1741. doi: 10.1101/gr.275430.121. PMID: 34599006; PMCID: PMC8494214. [Pubmed]
  • Heil BJ, Hoffman MM, Markowetz F, Lee SI, Greene CS, Hicks SC. Reproducibility standards for machine learning in the life sciences. Nat Methods. 2021 Oct;18(10):1132-1135. doi: 10.1038/s41592-021-01256-7. PMID: 34462593; PMCID: PMC9131851. [Pubmed]
  • Weber LM, Hippen AA, Hickey PF, Berrett KC, Gertz J, Doherty JA, Greene CS, Hicks SC. Genetic demultiplexing of pooled single-cell RNA-sequencing samples in cancer facilitates effective experimental design. Gigascience. 2021 Sep 22;10(9):giab062. doi: 10.1093/gigascience/giab062. PMID: 34553212; PMCID: PMC8458035. [Pubmed]
  • Le TT, Himmelstein DS, Hippen AA, Gazzara MR, Greene CS. Analysis of scientific society honors reveals disparities. Cell Syst. 2021 Sep 22;12(9):900-906.e5. doi: 10.1016/j.cels.2021.07.007. Epub 2021 Aug 16. PMID: 34555325. [Pubmed]
  • Ding YY, Kim H, Madden K, Loftus JP, Chen GM, Allen DH, Zhang R, Xu J, Chen CH, Hu Y, Tasian SK, Tan K. Network Analysis Reveals Synergistic Genetic Dependencies for Rational Combination Therapy in Philadelphia Chromosome-Like Acute Lymphoblastic Leukemia. Clin Cancer Res. 2021 Sep 15;27(18):5109-5122. doi: 10.1158/1078-0432.CCR-21-0553. Epub 2021 Jul 1. PMID: 34210682; PMCID: PMC8448976. [Pubmed]
  • Maoz A, Merenstein C, Koga Y, Potter A, Gower AC, Liu G, Zhang S, Liu H, Stevenson C, Spira A, Reid ME, Campbell JD, Mazzilli SA, Lenburg ME, Beane J. Elevated T cell repertoire diversity is associated with progression of lung squamous cell premalignant lesions. J Immunother Cancer. 2021 Sep;9(9):e002647. doi: 10.1136/jitc-2021-002647. PMID: 34580161; PMCID: PMC8477334. [Pubmed]
  • Sheng X, Guan Y, Ma Z, Wu J, Liu H, Qiu C, Vitale S, Miao Z, Seasock MJ, Palmer M, Shin MK, Duffin KL, Pullen SS, Edwards TL, Hellwege JN, Hung AM, Li M, Voight BF, Coffman TM, Brown CD, Susztak K. Mapping the genetic architecture of human traits to cell types in the kidney identifies mechanisms of disease and potential treatments. Nat Genet. 2021 Sep;53(9):1322-1333. doi: 10.1038/s41588-021-00909-9. Epub 2021 Aug 12. PMID: 34385711; PMCID: PMC9338440. [Pubmed]
  • Merenstein C, Liang G, Whiteside SA, Cobián-Güemes AG, Merlino MS, Taylor LJ, Glascock A, Bittinger K, Tanes C, Graham-Wooten J, Khatib LA, Fitzgerald AS, Reddy S, Baxter AE, Giles JR, Oldridge DA, Meyer NJ, Wherry EJ, McGinniss JE, Bushman FD, Collman RG. Signatures of COVID-19 Severity and Immune Response in the Respiratory Tract Microbiome. mBio. 2021 Aug 31;12(4):e0177721. doi: 10.1128/mBio.01777-21. Epub 2021 Aug 17. Erratum in: mBio. 2022 Oct 26;13(5):e0229322. doi: 10.1128/mbio.02293-22. PMID: 34399607; PMCID: PMC8406335. [Pubmed]
  • Dele-Oni DO, Christianson KE, Egri SB, Vaca Jacome AS, DeRuff KC, Mullahoo J, Sharma V, Davison D, Ko T, Bula M, Blanchard J, Young JZ, Litichevskiy L, Lu X, Lam D, Asiedu JK, Toder C, Officer A, Peckner R, MacCoss MJ, Tsai LH, Carr SA, Papanastasiou M, Jaffe JD. Proteomic profiling dataset of chemical perturbations in multiple biological backgrounds. Sci Data. 2021 Aug 25;8(1):226. doi: 10.1038/s41597-021-01008-4. PMID: 34433823; PMCID: PMC8387426. [Pubmed]
  • Hippen AA, Falco MM, Weber LM, Erkan EP, Zhang K, Doherty JA, Vähärautio A, Greene CS, Hicks SC. miQC: An adaptive probabilistic framework for quality control of single-cell RNA-sequencing data. PLoS Comput Biol. 2021 Aug 24;17(8):e1009290. doi: 10.1371/journal.pcbi.1009290. PMID: 34428202; PMCID: PMC8415599. [Pubmed]
  • Wu CY, Lau BT, Kim HS, Sathe A, Grimes SM, Ji HP, Zhang NR. Integrative single-cell analysis of allele-specific copy number alterations and chromatin accessibility in cancer. Nat Biotechnol. 2021 Oct;39(10):1259-1269. doi: 10.1038/s41587-021-00911-w. Epub 2021 May 20. PMID: 34017141; PMCID: PMC9127226. [Pubmed]
  • Zhang H, Lam J, Zhang D, Lan Y, Vermunt MW, Keller CA, Giardine B, Hardison RC, Blobel GA. CTCF and transcription influence chromatin structure re-configuration after mitosis. Nat Commun. 2021 Aug 27;12(1):5157. doi: 10.1038/s41467-021-25418-5. PMID: 34453048; PMCID: PMC8397779. [Pubmed]
  • Uberoi A, Bartow-McKenney C, Zheng Q, Flowers L, Campbell A, Knight SAB, Chan N, Wei M, Lovins V, Bugayev J, Horwinski J, Bradley C, Meyer J, Crumrine D, Sutter CH, Elias P, Mauldin E, Sutter TR, Grice EA. Commensal microbiota regulates skin barrier function and repair via signaling through the aryl hydrocarbon receptor. Cell Host Microbe. 2021 Aug 11;29(8):1235-1248.e8. doi: 10.1016/j.chom.2021.05.011. Epub 2021 Jul 1. PMID: 34214492; PMCID: PMC8364505. [Pubmed]
  • Hu J, Schroeder A, Coleman K, Chen C, Auerbach BJ, Li M. Statistical and machine learning methods for spatially resolved transcriptomics with histology. Comput Struct Biotechnol J. 2021 Jul 1;19:3829-3841. doi: 10.1016/j.csbj.2021.06.052. PMID: 34285782; PMCID: PMC8273359. [Pubmed]
  • Rando HM, Wellhausen N, Ghosh S, Lee AJ, Dattoli AA, Hu F, Byrd JB, Rafizadeh DN, Lordan R, Qi Y, Sun Y, Brueffer C, Field JM, Guebila MB, Jadavji NM, Skelly AN, Ramsundar B, Wang J, Goel RR, Park Y; COVID-19 Review Consortium; Boca SM, Gitter A, Greene CS. Identification and Development of Therapeutics for COVID-19. ArXiv [Preprint]. 2021 Mar 3:arXiv:2103.02723v3. Update in: mSystems. 2021 Dec 21;6(6):e0023321. doi: 10.1128/mSystems.00233-21. [Pubmed]
  • Zhang D, Lam J, Blobel GA. Engineering three-dimensional genome folding. Nat Genet. 2021 May;53(5):602-611. doi: 10.1038/s41588-021-00860-9. Epub 2021 May 6. [Pubmed]
  • Miao Z, Balzer MS, Ma Z, Liu H, Wu J, Shrestha R, Aranyi T, Kwan A, Kondo A, Pontoglio M, Kim J, Li M, Kaestner KH, Susztak K. Single cell regulatory landscape of the mouse kidney highlights cellular differentiation programs and disease targets. Nat Commun. 2021 Apr 15;12(1):2277. doi: 10.1038/s41467-021-22266-1. [Pubmed]
  • Chen GM, Chen C, Das RK, Gao P, Chen CH, Bandyopadhyay S, Ding YY, Uzun Y, Yu W, Zhu Q, Myers RM, Grupp SA, Barrett DM, Tan K. Integrative bulk and single-cell profiling of pre-manufacture T-cell populations reveals factors mediating long-term persistence of CAR T-cell therapy. Cancer Discov. 2021 Apr 5:candisc.1677.2020. doi: 10.1158/2159-8290.CD-20-1677. [Pubmed]
  • Moore JH, Truong VQ, Robbins AB, Nicholson D, Williams-Devane CL. Ten important roles for academic leaders to promote equity, diversity, and inclusion in data science. BioData Min. 2021 Mar 30;14(1):22. doi: 10.1186/s13040-021-00256-9. [Pubmed]
  • Ahmadmehrabi S, Li B, Park J, Devkota B, Vujkovic M, Ko YA, Van Wagoner D, Tang WHW, Krantz I, Ritchie M; Regeneron Genetics Center, Brant J, Ruckenstein MJ, Epstein DJ, Rader DJ. Genome-first approach to rare EYA4 variants and cardio-auditory phenotypes in adults. Hum Genet. 2021 Mar 21. doi: 10.1007/s00439-021-02263-6. Epub ahead of print. PMID: 33745059. [Pubmed]
  • Gregg JT, Le TT, Moore JH. (2021). REGENS: an open source Python package for simulating realistic autosomal genotypes. Journal of Open Source Software, 6(59), 2743, https://doi.org/10.21105/joss.02743. [Link to paper]
  • Lee DSM, Park J, Kromer A, Baras A, Rader DJ, Ritchie MD, Ghanem LR, Barash Y. Disrupting upstream translation in mRNAs is associated with human disease. Nat Commun. 2021 Mar 9;12(1):1515. doi: 10.1038/s41467-021-21812-1. PMID: 33750777; PMCID: PMC7943595. [Pubmed]

  • Rando HM, Wellhausen N, Ghosh S, Lee AJ, Dattoli AA, Hu F, Byrd JB, Rafizadeh DN, Lordan R, Qi Y, Sun Y, Brueffer C, Field JM, Guebila MB, Jadavji NM, Skelly AN, Ramsundar B, Wang J, Goel RR, Park Y; COVID-19 Review Consortium; Boca SM, Gitter A, Greene CS. Identification and Development of Therapeutics for COVID-19. ArXiv [Preprint]. 2021 Mar 3:arXiv:2103.02723v3. Update in: mSystems. 2021 Dec 21;6(6):e0023321. doi: 10.1128/mSystems.00233-21. [Pubmed]

  • Bone WP, Siewert KM, Jha A, Klarin D, Damrauer SM; VA Million Veteran Program, Chang KM, Tsao PS, Assimes TL, Ritchie MD, Voight BF. Multi-trait association studies discover pleiotropic loci between Alzheimer's disease and cardiometabolic traits. Alzheimers Res Ther. 2021 Feb 4;13(1):34. doi: 10.1186/s13195-021-00773-z. PMCID: PMC7860582. [Pubmed]

  • Gu X, Yang H, Sheng X, Ko YA, Qiu C, Park J, Huang S, Kember R, Judy RL, Park J, Damrauer SM, Nadkarni G, Loos RJF, My VTH, Chaudhary K, Bottinger EP, Paranjpe I, Saha A, Brown C, Akilesh S, Hung AM, Palmer M, Baras A, Overton JD, Reid J, Ritchie M, Rader DJ, Susztak K. Kidney disease genetic risk variants alter lysosomal beta-mannosidase (MANBA) expression and disease severity. Sci Transl Med. 2021 Jan 13;13(576):eaaz1458. doi: 10.1126/scitranslmed.aaz1458. [Pubmed]

  • Park J, Lucas AM, Zhang X, Chaudhary K, Cho JH, Nadkarni G, Dobbyn A, Chittoor G, Josyula NS, Katz N, Breeyear JH, Ahmadmehrabi S, Drivas TG, Chavali VRM, Fasolino M, Sawada H, Daugherty A, Li Y, Zhang C, Bradford Y, Weaver J, Verma A, Judy RL, Kember RL, Overton JD, Reid JG, Ferreira MAR, Li AH, Baras A, LeMaire SA, Shen YH, Naji A, Kaestner KH, Vahedi G, Edwards TL, Chen J, Damrauer SM, Justice AE, Do R, Ritchie MD, Rader DJ. Exome-wide evaluation of rare coding variants using electronic health records identifies new gene-phenotype associations. Nat Med. 2021 Jan;27(1):66-72. doi: 10.1038/s41591-020-1133-8. Epub 2021 Jan 11. [Pubmed]

2020

  • Sanford EM, Emert BL, Coté A, Raj A. Gene regulation gravitates toward either addition or multiplication when combining the effects of two signals. Elife. 2020 Dec 7;9:e59388. doi: 10.7554/eLife.59388. PMCID: PMC7771960. [Pubmed]

  • Hippen AA, Greene CS. Expanding and Remixing the Metadata Landscape. Trends Cancer. 2021 Apr;7(4):276-278. doi: 10.1016/j.trecan.2020.10.011. Epub 2020 Nov 20. [Pubmed]

  • Lee AJ, Park Y, Doing G, Hogan DA, Greene CS. Correcting for experiment-specific variability in expression compendia can remove underlying signals. Gigascience. 2020 Nov 3;9(11):giaa117. doi: 10.1093/gigascience/giaa117. PMCID: PMC7607552. [Pubmed]

  • Pan H, Xue C, Auerbach BJ, Fan J, Bashore AC, Cui J, Yang DY, Trignano SB, Liu W, Shi J, Ihuegbu CO, Bush EC, Worley J, Vlahos L, Laise P, Solomon RA, Connolly ES, Califano A, Sims PA, Zhang H, Li M, Reilly MP. Single-Cell Genomics Reveals a Novel Cell State During Smooth Muscle Cell Phenotypic Switching and Potential Therapeutic Targets for Atherosclerosis in Mouse and Human. Circulation. 2020 Sep 23. doi: 10.1161/CIRCULATIONAHA.120.048378. Epub ahead of print. [Pubmed]

  • Wu X, Niculite CM, Preda MB, Rossi A, Tebaldi T, Butoi E, White MK, Tudoran OM, Petrusca DN, Jannasch AS, Bone WP, Zong X, Fang F, Burlacu A, Paulsen MT, Hancock BA, Sandusky GE, Mitra S, Fishel ML, Buechlein A, Ivan C, Oikonomopoulos S, Gorospe M, Mosley A, Radovich M, Davé UP, Ragoussis J, Nephew KP, Mari B, McIntyre A, Konig H, Ljungman M, Cousminer DL, Macchi P, Ivan M. Regulation of cellular sterol homeostasis by the oxygen responsive noncoding RNA lincNORS. Nat Commun. 2020 Sep 21;11(1):4755. doi: 10.1038/s41467-020-18411-x. [Pubmed]

  • He B, Gao P, Ding YY, Chen CH, Chen G, Chen C, Kim H, Tasian SK, Hunger SP, Tan K. Diverse noncoding mutations contribute to deregulation of cis-regulatory landscape in pediatric cancers. Sci Adv. 2020 Jul 24;6(30):eaba3064. doi: 10.1126/sciadv.aba3064. PMCID: PMC7439310.  [Pubmed]
  • Paul MR, Pan TC, Pant DK, Shih NN, Chen Y, Harvey KL, Solomon A, Lieberman D, Morrissette JJD, Soucier-Ernst D, Goodman NG, Stavropoulos SW, Maxwell KN, Clark C, Belka GK, Feldman M, DeMichele A and Chodosh LA. Genomic landscape of metastatic breast cancer identifies preferentially dysregulated pathways and targets [published online ahead of print, 2020 Jul 13]. J Clin Invest. 2020;129941. doi:10.1172/JCI129941. [Pubmed]

  • Jha A, K Aicher J, R Gazzara M, Singh D, Barash Y. Enhanced Integrated Gradients: improving interpretability of deep learning models using splicing codes as a case study. Genome Biol. 2020 Jun 19;21(1):149. doi: 10.1186/s13059-020-02055-7. PMCID: PMC7305616. [Pubmed]

  • Gao P, Chen C, Howell ED, Li Y, Tober J, Uzan Y, He B, Gao L, Zhu Q, Siekmann A, Speck N, Tan K. Transcriptional regulatory network controlling the ontogeny of hematopoietic stem cells [published online ahead of print, 2020 Jun 4]. Genes Dev. 2020;10.1101/gad.338202.120. doi:10.1101/gad.338202.120 [Pubmed]

  • Zhu, Q.*, Gao, P.*, Tober, J.*, Bennett, L., Chen, C., Uzun, Y., Li, Y., Mumau, M., Yu, W., He, B., Speck, N. & Tan K. (2020). Developmental trajectory of pre-hematopoietic stem cell formation from endothelium. Blood Journal. Blood-2020004801. [Pubmed]

  • Yu, W., Uzun, Y., Zhu, Q., Chen, C. and Tan, K., 2020. scATAC-pro: a comprehensive workbench for single-cell chromatin accessibility sequencing data. Genome biology. 21, pp.1-17. [Pubmed]

  • Aicher JK, Jewell P, Vaquero-Garcia J, Barash Y, Bhoj EJ. Mapping RNA splicing variations in clinically accessible and nonaccessible tissues to facilitate Mendelian disease diagnosis using RNA-seq. Genet Med. 2020 Mar 30. doi: 10.1038/s41436-020-0780-y. [Pubmed]

  • Bellissimo DC, Chen CH, Zhu Q, Bagga S, Lee CT, He B, Wertheim GB, Jordan M, Tan K, Worthen GS, Gilliland DG, Speck NA. Runx1 negatively regulates inflammatory cytokine production by neutrophils in response to Toll-like receptor signaling. Blood Adv. 2020 Mar 24;4(6):1145-1158. doi: 10.1182/bloodadvances.2019000785. [Pubmed]

  • Chen GM, Azzam A, Ding YY, Barrett DM, Grupp SA, Tan K. Dissecting the tumor-immune landscape in chimeric antigen receptor T-cell therapy: key challenges and opportunities for a systems immunology approach. Clin Cancer Res. 2020 Mar 3. pii: clincanres.3888.2019. doi: 10.1158/1078-0432.CCR-19-3888. [Pubmed]

  • Zhou Z, Ye C, Wang J, Zhang NR. Surface protein imputation from single cell transcriptomes by deep neural networks. Nat Commun. 2020 Jan 31;11(1):651. doi: 10.1038/s41467-020-14391-0. [Pubmed]
  • Clay M, Hammond J, Zhong F, Chen X, Kowalski C, Lee AJ, Porter M, Hampton T, Greene C, Pletneva E, Hogan D. (2020). Pseudomonas aeruginosa lasR mutant fitness in microoxia is supported by an Anr-regulated oxygen-binding hemerythrin. Proceedings of the National Academy of Sciences. 117. 201917576. 10.1073/pnas.1917576117. [Pubmed]

  • Zhou Z, Xu B, Minn A, Zhang NR. DENDRO: genetic heterogeneity profiling and subclone detection by single-cell RNA sequencing. Genome Biol. 2020 Jan 14;21(1):10. doi: 10.1186/s13059-019-1922-x. PMCID: PMC6961311. [Pubmed]

2019

  • Benson KK, Hu W, Weller AH, Bennett AH, Chen ER, Khetarpal SA, Yoshino S, Bone WP, Wang L, Rabinowitz JD, Voight BF, Soccio RE. Natural human genetic variation determines basal and inducible expression of PM20D1, an obesity-associated gene. Proc Natl Acad Sci U S A. 2019 Nov 12;116(46):23232-23242. doi: 10.1073/pnas.1913199116. Epub 2019 Oct 28. PMCID: PMC6859347. [Pubmed]

  • Zhou N, Jiang Y, Bergquist TR, Lee AJ, et al. The CAFA challenge reports improved protein function prediction and new functional annotations for hundreds of genes through experimental screens. Genome Biol. 2019 Nov 19;20(1):244. doi: 10.1186/s13059-019-1835-8. PMCID: PMC6864930. [Pubmed]

  • Ransick, A.*, Lindström, N. O.*, Liu, J.*, Zhu, Q., Guo, J. J., Alvarado, G. F., Kim, A. D., Black, H. G., Kim, J. & McMahon, A. P. (2019). Single-Cell Profiling Reveals Sex, Lineage, and Regional Diversity in the Mouse Kidney. Developmental cell. 51(3), pp.399-413. [Pubmed]

  • Park J, Damrauer SM, Baras A, Reid JG, Overton JD, Gonzalez-Alegre P. Epidemiology of DYT1 dystonia: Estimating prevalence via genetic ascertainment. Neurol Genet. 2019 Sep 13;5(5):e358. doi: 10.1212/NXG.0000000000000358. eCollection 2019 Oct. PMCID: PMC6745720. [Pubmed]
  • *Packer JS, *Zhu Q, Huynh C, Sivaramakrishnan P, Preston E, Dueck H, Stefanik D, Tan K, Trapnell C, Kim J, Waterston RH, Murray JI. A lineage-resolved molecular atlas of C. elegans embryogenesis at single-cell resolution. Science. 2019 Sep 5.pii: eaax1971. doi: 10.1126/science.aax1971. [Pubmed] *contributed equally

  • Wang J, Agarwal D, Huang M, Hu G, Zhou Z, Ye C, Zhang NR. Data denoising with transfer learning in single-cell transcriptomics. Nat Methods. 2019 Sep;16(9):875-878. doi: 10.1038/s41592-019-0537-1. Epub 2019 Aug 30. PubMed PMID:31471617. [Pubmed]

  • Benci JL, Johnson LR, Choa R, Xu Y, Qiu J, Zhou Z, Xu B, Ye D, Nathanson KL, June CH, Wherry EJ, Zhang NR, Ishwaran H, Hellmann MD, Wolchok JD, Kambayashi T,  Minn AJ. Opposing Functions of Interferon Coordinate Adaptive and Innate Immune Responses to Cancer Immune Checkpoint Blockade. Cell. 2019 Aug 8;178(4):933-948.e14. doi: 10.1016/j.cell.2019.07.019. PMCID: PMC6830508. [Pubmed]

  • Park J, Levin MG, Haggerty CM, Hartzel DN, Judy R, Kember RL, Reza N; Regeneron Genetics Center, Ritchie MD, Owens AT, Damrauer SM, Rader DJ. A genome-first approach to aggregating rare genetic variants in LMNA for association with electronic health record phenotypes. Genet Med. 2019 Aug 6. doi: 10.1038/s41436-019-0625-8. [Pubmed]

  • Peng T, Zhu Q, Yin P, Tan K. SCRABBLE: single-cell RNA-seq imputation constrained by bulk RNA-seq data. Genome Biol. 2019 May 6;20(1):88. doi: 10.1186/s13059-019-1681-8. PMCID: PMC6501316. [Pubmed]

  • Fan S, Kelly DE, Beltrame MH, Hansen MEB, Mallick S, Ranciaro A, Hirbo J, Thompson S, Beggs W, Nyambo T, Omar SA, Meskel DW, Belay G, Froment A, Patterson  N, Reich D, Tishkoff SA. African evolutionary history inferred from whole genome sequence data of 44 indigenous African populations. Genome Biol. 2019 Apr 26;20(1):82. doi: 10.1186/s13059-019-1679-2. PMCID: PMC6485071. [Pubmed]

  • Shields EJ, Petracovici AF, Bonasio R. lncRedibly versatile: biochemical and biological functions of long noncoding RNAs. Biochem J. 2019 Apr 10;476(7):1083-1104. doi: 10.1042/BCJ20180440. Review. PMCID: PMC6745715. [Pubmed]

  • Zhang X, Basile AO, Pendergrass SA, Ritchie MD. Real world scenarios in rare variant association analysis: the impact of imbalance and sample size on the power in silico. BMC Bioinformatics. 2019 Jan 22;20(1):46. Doi: 10.1186/s12859-018-2591-6. PMCID: PMC6343276.  [Pubmed]

  • Zhang X, Veturi Y, Verma S, Bone W, Verma A, Lucas A, Hebbring S, Denny JC, Stanaway IB, Jarvik GP, Crosslin D, Larson EB, Rasmussen-Torvik L, Pendergrass SA, Smoller JW, Hakonarson H, Sleiman P, Weng C, Fasel D, Wei WQ, Kullo I, Schaid D, Chung WK, Ritchie MD. Detecting potential pleiotropy across cardiovascular and neurological diseases using univariate, bivariate, and multivariate methods on 43,870 individuals from the eMERGE network. Pac Symp Biocomput. 2019;24:272-283. PMCID: PMC6457436. [Pubmed]

  • Shan M, Anderson ZD, Gregory BD. Computationally Characterizing Protein-Bound Long Noncoding RNAs and Their Secondary Structure Using Protein Interaction Profile Sequencing (PIP-Seq) in Plants. Methods Mol Biol. 2019;1933:363-380. doi:10.1007/978-1-4939-9045-0_22. [Pubmed]

2018
  • Siewert KM, Voight BF. Bivariate Genome-Wide Association Scan Identifies 6 Novel Loci Associated With Lipid Levels and Coronary Artery Disease. Circ Genom Precis Med. 2018 Dec;11(12):e002239. doi: 10.1161/CIRCGEN.118.002239. PMCID: PMC6291836. [Pubmed]
  • Rouhanifard SH, Mellis IA, Dunagin M, Bayatpour S, Jiang CL, Dardani I, Symmons O, Emert B, Torre E, Cote A, Sullivan A, Stamatoyannopoulos JA, Raj A. ClampFISH detects individual nucleic acid molecules using click chemistry-based amplification. Nat Biotechnol. 2018 Nov 12. doi: 10.1038/nbt.4286. PMCID: PMC6511493. [Pubmed]

  • Lin N, Shay JES, Xie H, Lee DSM, Skuli N, Tang Q, Zhou Z, Azzam A, Meng H, Wang H, FitzGerald GA, Simon MC. Myeloid Cell Hypoxia-Inducible Factors Promote Resolution of Inflammation in Experimental Colitis. Front Immunol. 2018 Nov 5;9:2565. doi: 10.3389/fimmu.2018.02565. eCollection 2018. PMCID: PMC6230677. [Pubmed]

  • Mishra R*, Hodge KM*, Cousminer DL, Leslie RD, Grant SFA. A Global Perspective of Latent Autoimmune Diabetes in Adults. Trends Endocrinol Metab. 2018 Sep;29(9):638-650. doi: 10.1016/j.tem.2018.07.001. Epub 2018 Jul 23. Review. [Pubmed]

  • Sun JH, Zhou L, Emerson DJ, Phyo SA, Titus KR, Gong W, Gilgenast TG, Beagan JA, Davidson BL, Tassone F, Phillips-Cremins JE. Disease-Associated Short Tandem  Repeats Co-localize with Chromatin Domain Boundaries. Cell. 2018 Sep 20;175(1):224-238.e15. doi: 10.1016/j.cell.2018.08.005. Epub 2018 Aug 30. PMCID: PMC6175607. [Pubmed]

  • Sun JH, Zhou L, Emerson DJ, Phyo SA, Titus KR, Gong W, Gilgenast TG, Beagan JA, Davidson BL, Tassone F, Phillips-Cremins JE. Disease-Associated Short Tandem  Repeats Co-localize with Chromatin Domain Boundaries. Cell. 2018 Sep 20;175(1):224-238.e15. doi: 10.1016/j.cell.2018.08.005. Epub 2018 Aug 30. PMCID: PMC6175607. [Pubmed]

  • Amlie-Wolf A, Tang M, Mlynarski EE, Kuksa PP, Valladares O, Katanic Z, Tsuang D, Brown CD, Schellenberg GD, Wang LS. INFERNO: inferring the molecular mechanisms of noncoding genetic variants. Nucleic Acids Res. 2018 Aug 3. doi: 10.1093/nar/gky686. [Pubmed]

  • Mishra R*, Hodge KM*, Cousminer DL, Leslie RD, Grant SFA. A Global Perspective of Latent Autoimmune Diabetes in Adults. Trends Endocrinol Metab. 2018 Sep;29(9):638-650. doi: 10.1016/j.tem.2018.07.001. Epub 2018 Jul 23. Review. [Pubmed]

  • Weiner AK, Sidoli S, Diskin SJ, Garcia BA. Graphical Interpretation and Analysis of Proteins and their Ontologies (GiaPronto): A One-Click Graph Visualization Software for Proteomics Data Sets. Mol Cell Proteomics. 2018 Jul;17(7):1426-1431. doi: 10.1074/mcp.TIR117.000438 PMCID: PMC6030729. [Pubmed]

  • Zhou Z, Wang W, Wang LS, Zhang NR. Integrative DNA copy number detection and genotyping from sequencing and array-based platforms. Bioinformatics. 2018 Jul 15;34(14):2349-2355. doi: 10.1093/bioinformatics/bty104. PMCID: PMC6041760 [Pubmed]

  • Zheng Q, Bartow-McKenney C, Meisel JS, Grice EA. HmmUFOtu: An HMM and phylogenetic placement based ultra-fast taxonomic assignment and OTU picking tool for microbiome amplicon sequencing studies. Genome Biol. 2018 Jun 27;19(1):82. doi: 10.1186/s13059-018-1450-0. [Pubmed]

  • Shields EJ, Sheng L, Weiner AK, Garcia BA, Bonasio R. High-Quality Genome Assemblies Reveal Long Non-coding RNAs Expressed in Ant Brains. Cell Rep. 2018 Jun 5;23(10):3078-3090. doi: 10.1016/j.celrep.2018.05.014. PMCID: PMC6023404. [Pubmed]

  • Hill DA, Lim HW, Kim YH, Ho WY, Foong YH, Nelson VL, Nguyen HCB, Chegireddy K, Kim J, Habertheuer A, Vallabhajosyula P, Kambayashi T, Won KJ, Lazar MA. Distinct macrophage populations direct inflammatory versus physiological changes in adipose tissue. Proc Natl Acad Sci U S A. 2018 May 29;115(22):E5096-E5105. doi: 10.1073/pnas.1802611115. PMC5984532. [Pubmed]

  • Bartow-McKenney C, Hannigan GD, Horwinski J, Hesketh P, Horan AD, Mehta S, Grice EA. The microbiota of traumatic, open fracture wounds is associated with mechanism of injury. Wound Repair Regen. 2018 May 26. doi: 10.1111/wrr.12642. [Pubmed]

  • Kuksa PP, Amlie-Wolf A, Katanic Ž, Valladares O, Wang LS, Leung YY. SPAR: small RNA-seq portal for analysis of sequencing experiments. Nucleic Acids Res. 2018 May 4. doi: 10.1093/nar/gky330. [Pubmed]

  • Nativio R, Donahue G, Berson A, Lan Y, Amlie-Wolf A, Tuzer F, Toledo JB, Gosai SJ, Gregory BD, Torres C, Trojanowski JQ, Wang LS, Johnson FB, Bonini NM, Berger SL. Dysregulation of the epigenetic landscape of normal aging in Alzheimer's disease. Nat Neurosci. 2018 Apr;21(4):497-505. doi: 10.1038/s41593-018-0101-9. Epub 2018 Mar 5. Erratum in: Nat Neurosci. 2018 Mar 19,. [Pubmed]

  • Verma SS, Lucas A, Zhang X, Veturi Y, Dudek S, Li B, Li R, Urbanowicz R, Moore JH, Kim D, Ritchie MD. Collective feature selection to identify crucial epistatic variants. BioData Min. 2018 Apr 19;11:5. doi: 10.1186/s13040-018-0168-6. eCollection 2018. PMCID: PMC5907720. [Pubmed]

  • Way GP, Sanchez-Vega F, La K, Armenia J, Chatila WK, Luna A, Sander C, Cherniack AD, Mina M, Ciriello G, Schultz N; Cancer Genome Atlas Research Network, Sanchez Y, Greene CS. Machine Learning Detects Pan-cancer Ras Pathway Activation in The Cancer Genome Atlas. Cell Rep. 2018 Apr 3;23(1):172-180.e3. doi: 10.1016/j.celrep.2018.03.046.PMCID: PMC5918694. [Pubmed]

  • Kuehn MH, Mishra R, Deonovic BE, Miller KN, McCormack SE, Liu GT, Kupersmith MJ, Wall M; NORDIC IIHTT Study Group. Genetic Survey of Adult-Onset Idiopathic Intracranial Hypertension. J Neuroophthalmol. 2018 Mar 30. doi: 10.1097/WNO.0000000000000648. [Pubmed]

  • Nativio R, Donahue G, Berson A, Lan Y, Amlie-Wolf A, Tuzer F, Toledo JB, Gosai SJ, Gregory BD, Torres C, Trojanowski JQ, Wang LS, Johnson FB, Bonini NM, Berger SL. Dysregulation of the epigenetic landscape of normal aging in Alzheimer's disease. Nat Neurosci. 2018 Apr;21(4):497-505. doi: 10.1038/s41593-018-0101-9. Epub 2018 Mar 5. Erratum in: Nat Neurosci. 2018 Mar 19,. [Pubmed]

  • Urrutia E, Chen H, Zhou Z, Zhang NR, Jiang Y. Integrative pipeline for profiling DNA copy number and inferring tumor phylogeny. Bioinformatics. 2018 Feb 5. doi: 10.1093/bioinformatics/bty057. [Pubmed]

  • Zhu Q, Fisher SA, Dueck H, Middleton S, Khaladkar M, Kim J. PIVOT: platform for interactive analysis and visualization of transcriptomics data. BMC Bioinformatics. 2018 Jan 5;19(1):6. doi: 10.1186/s12859-017-1994-0. PMCID: PMC5756333. [Pubmed]

2017
  • Norton S, Vaquero-Garcia J, Lahens NF, Grant GR, Barash Y. Outlier detection for improved differential splicing quantification from RNA-Seq experiments with replicates. Bioinformatics. 2017 Dec 11. doi: 10.1093/bioinformatics/btx790. [Pubmed]

  • Agarwal D, Nowak C, Zhang NR, Pusztai L, Hatzis C. Functional germline variants as potential co-oncogenes. NPJ Breast Cancer. 2017 Nov 22;3:46. doi: 10.1038/s41523-017-0051-5. eCollection 2017. Review. PMCID: PMC5700137. [Pubmed]

  • Crawford NG, Kelly DE, Hansen MEB, Beltrame MH, Fan S, Bowman SL, Jewett E, Ranciaro A, Thompson S, Lo Y, Pfeifer SP, Jensen JD, Campbell MC, Beggs W, Hormozdiari F, Mpoloka SW, Mokone GG, Nyambo T, Meskel DW, Belay G, Haut J; NISC Comparative Sequencing Program, Rothschild H, Zon L, Zhou Y, Kovacs MA, Xu M, Zhang T, Bishop K, Sinclair J, Rivas C, Elliot E, Choi J, Li SA, Hicks B, Burgess S, Abnet C, Watkins-Chow DE, Oceana E, Song YS, Eskin E, Brown KM, Marks MS, Loftus SK, Pavan WJ, Yeager M, Chanock S, Tishkoff SA. Loci associated with skin pigmentation identified in African populations. Science. 2017 Nov 17;358(6365). pii: eaan8433. doi: 10.1126/science.aan8433. PMCID: PMC5759959. [Pubmed]

  • Jia C, Hu Y, Kelly D, Kim J, Li M, Zhang NR. Accounting for technical noise in differential expression analysis of single-cell RNA sequencing data. Nucleic Acids Res. 2017 Nov 2;45(19):10978-10988. doi: 10.1093/nar/gkx754. PMCID: PMC5737676. [Pubmed]

  • Titus AJ, Way GP, Johnson KC, Christensen BC. Deconvolution of DNA methylation identifies differentially methylated gene regions on 1p36 across breast cancer subtypes. Sci Rep. 2017 Sep 14;7(1):11594. doi: 10.1038/s41598-017-10199-z. PMC5599639. [Pubmed]

  • Clarke EL, Lauder AP, Hofstaedter CE, Hwang Y, Fitzgerald AS, Imai I, Biernat W, Rękawiecki B, Majewska H, Dubaniewicz A, Litzky LA, Feldman MD, Bittinger K, Rossman MD, Patterson KC, Bushman FD, Collman RG. Microbial Lineages in Sarcoidosis: A Metagenomic Analysis Tailored for Low Microbial Content Samples. Am J Respir Crit Care Med. 2017 Aug 28. doi: 10.1164/rccm.201705-0891OC. [Pubmed]

  • Xiao J, Jin R, Yu X, Shen M, Wagner JD, Pai A, Song C, Zhuang M, Klasfeld S, He C, Santos AM, Helliwell C, Pruneda-Paz JL, Kay SA, Lin X, Cui S, Garcia MF, Clarenz O, Goodrich J, Zhang X, Austin RS, Bonasio R, Wagner D. Cis and trans determinants of epigenetic silencing by Polycomb repressive complex 2 in Arabidopsis. Nat Genet. 2017 Aug 21. doi: 10.1038/ng.3937. [Pubmed]

  • Gospocic J, Shields EJ, Glastad KM, Lin Y, Penick CA, Yan H, Mikheyev AS, Linksvayer TA, Garcia BA, Berger SL, Liebig J, Reinberg D, Bonasio R. The Neuropeptide Corazonin Controls Social Behavior and Caste Identity in Ants. Cell. 2017 Aug 10;170(4):748-759.e12. doi: 10.1016/j.cell.2017.07.014. PMCID: PMC5564227. [Pubmed]

  • Way GP, Youngstrom DW, Hankenson KD, Greene CS, Grant SF. Implicating candidate genes at GWAS signals by leveraging topologically associating domains. Eur J Hum Genet. 2017 Aug 9. doi: 10.1038/ejhg.2017.108. [Pubmed]

  • Beagan JA, Duong MT, Titus KR, Zhou L, Cao Z, Ma J, Lachanski CV, Gillis DR, Phillips-Cremins JE. YY1 and CTCF orchestrate a 3D chromatin looping switch during early neural lineage commitment. Genome Res. 2017 Jul;27(7):1139-1152. doi: 10.1101/gr.215160.116. PMCID: PMC5495066. [Pubmed]

  • Siewert KM, Voight BF. Detecting Long-Term Balancing Selection Using Allele Frequency Correlation. Mol Biol Evol. 2017 Jul 21. doi: 10.1093/molbev/msx209. [Epub ahead of print] [Pubmed]

  • Mellis IA, Gupte R, Raj A, Rouhanifard SH. Visualizing adenosine-to-inosine RNA editing in single mammalian cells. Nat Methods. 2017 Jun 12. doi: 10.1038/nmeth.4332. [Pubmed]

  • Mishra R*, Chesi A*, Cousminer DL*, Hawa MI, Bradfield JP, Hodge KM, Guy VC, Hakonarson H; Bone Mineral Density in Childhood Study., Mauricio D, Schloot NC, Yderstræde KB, Voight BF, Schwartz S, Boehm BO, Leslie RD, Grant SFA. Relative contribution of type 1 and type 2 diabetes loci to the genetic etiology of adult-onset, non-insulin-requiring autoimmune diabetes. BMC Med. 2017 Apr 25;15(1):88. doi: 10.1186/s12916-017-0846-0. PMCID: PMC5404312. [Pubmed]

  • Middleton SA, Illuminati J, Kim J. Complete fold annotation of the human proteome using a novel structural feature space. Sci Rep. 2017 Apr 13;7:46321. doi: 10.1038/srep46321. PMCID: PMC5390313. [Pubmed]

  • Kim H, Walsh MC, Takegahara N, Middleton SA, Shin HI, Kim J, Choi Y. The purinergic receptor P2X5 regulates inflammasome activity and hyper-multinucleation of murine osteoclasts. Sci Rep. 2017 Mar 15;7(1):196. doi: 10.1038/s41598-017-00139-2. [Pubmed]

  • Clarke EL, Sundararaman SA, Seifert SN, Bushman FD, Hahn BH, Brisson D. swga: A primer design toolkit for selective whole genome amplification. Bioinformatics. 2017 Feb 27. doi: 10.1093/bioinformatics/btx118. [Pubmed]

  • Hannigan GD, Zheng Q, Meisel JS, Minot SS, Bushman FD, Grice EA. Evolutionary and functional implications of hypervariable loci within the skin virome. PeerJ. 2017 Feb 7;5:e2959. doi: 10.7717/peerj.2959. PMCID: PMC5299996. [Pubmed]

  • Way GP, Allaway RJ, Bouley SJ, Fadul CE, Sanchez Y, Greene CS. A machine learning classifier trained on cancer transcriptomes detects NF1 inactivation signal in glioblastoma. BMC Genomics. 2017 Feb 6;18(1):127. doi: 10.1186/s12864-017-3519-7. PMCID: PMC5292791. [Pubmed]

  • Kelly DE, Hansen M, Tishkoff SA. Global variation in gene expression and the value of diverse sampling. Current Opinion in Systems Biology, 1 (2017), pp. 102-108. [link to paper]

  • Meisel JS and Grice EA, Chapter 4 - The Human Microbiome, In Genomic and Precision Medicine (Third Edition), edited by Geoffrey S. Ginsburg and Huntington F. Willard, Academic Press, Boston, 2017, Pages 63-77, ISBN 9780128006818, [link to chapter]

  • Beaulieu-Jones BK, Moore JH. Missing Data Imputation in the Electronic Health Record using Deeply Learned Autoencoders. Pac Symp Biocomput. 2017;22:207-218. PMCID: PMC5144587. [Pubmed]

2016
  •  Ji X, Kember RL, Brown CD, Bućan M. Increased burden of deleterious variants in essential genes in autism spectrum disorder. Proc Natl Acad Sci U S A. 2016 Dec 27;113(52):15054-15059. doi: 10.1073/pnas.1613195113. PMCID: PMC5206557. [Pubmed]
  • Yin P, Anttila V, Siewert KM, Palotie A, Davey Smith G, Voight BF. Serum calcium and risk of migraine: a Mendelian randomization study. Hum Mol Genet. 2016 Dec 26. pii: ddw416. doi: 10.1093/hmg/ddw416. [Epub ahead of print] [Pubmed]

  • Way GP, Rudd J, Wang C, Hamidi H, Fridley BL, Konecny GE, Goode EL, Greene CS, Doherty JA. Comprehensive Cross-Population Analysis of High-Grade Serous Ovarian Cancer Supports No More Than Three Subtypes. G3 (Bethesda). 2016 Dec 7;6(12):4097-4103. PMCID: PMC5144978 [Pubmed]

  • Beaulieu-Jones BK, Greene CS; Pooled Resource Open-Access ALS Clinical Trials Consortium. Semi-supervised learning of the electronic health record for phenotype stratification. J Biomed Inform. 2016 Dec;64:168-178. doi: 10.1016/j.jbi.2016.10.007. [Pubmed]

  • Brzezinski JD, Modi A, Liu M, Roth MJ. Repression of the Chromatin-Tethering Domain of Murine Leukemia Virus p12. J Virol. 2016 Nov 28;90(24):11197-11207. Print 2016 Dec 15. PMC5126376. [Pubmed]

  • Brzezinski JD, Felkner R, Modi A, Liu M, Roth MJ. Phosphorylation Requirement of Murine Leukemia Virus p12. J Virol. 2016 Nov 28;90(24):11208-11219. Print 2016 Dec 15. PMC5126377. [Pubmed]

  • Dickinson ME*, Flenniken AM*, Ji X*, Teboul L*, Wong MD*, et al. High-throughput discovery of novel developmental phenotypes. Nature. 2016 Sep14;537(7621):508-514. *contributed equally [Pubmed]

  • Jiang Y, Qiu Y, Minn AJ, Zhang NR. Assessing intratumor heterogeneity and tracking longitudinal and spatial clonal evolutionary history by next-generation sequencing. Proc Natl Acad Sci U S A. 2016 Sep 13;113(37):E5528-37. [Pubmed]

  • Brauer PM, Pessach IM, Clarke E, Rowe JH, Ott de Bruin L, Lee YN, Dominguez-Brauer C, Comeau AM, Awong G, Felgentreff K, Zhang YH, Bredemeyer A, Al-Herz W, Du L, Ververs F, Kennedy M, Giliani S, Keller G, Sleckman BP, Schatz DG, Bushman FD, Notarangelo LD, Zúñiga-Pflücker JC. Modeling altered T-cell development with induced pluripotent stem cells from patients with RAG1-dependent immune deficiencies. Blood. 2016 Aug 11;128(6):783-93. PMCID: PMC4982452. [Pubmed]

  • Berkowitz ND, Silverman IM, Childress DM, Kazan H, Wang LS, Gregory BD. A comprehensive database of high-throughput sequencing-based RNA secondary structure probing data (Structure Surfer). BMC Bioinformatics. 2016 May 17;17(1):215. doi: 10.1186/s12859-016-1071-0. PMCID: PMC4869249. [Pubmed]

  •  Meisel JS, Hannigan GD, Tyldsley AS, SanMiguel AJ, Hodkinson BP, Zheng Q, Grice EA. Skin Microbiome Surveys Are Strongly Influenced by Experimental Design. J Invest Dermatol. 2016 May;136(5):947-56. PMCID: PMC4842136.  [Pubmed]

  • Paul MR, Levitt NP, Moore DE, Watson PM, Wilson RC, Denlinger CE, Watson DK, Anderson PE. Multivariate models from RNA-Seq SNVs yield candidate molecular targets for biomarker discovery: SNV-DA. BMC Genomics. 2016 Mar 31;17(1):263. [Pubmed]

  • Berlyand Y, Weintraub D, Xie SX, Mellis IA, Doshi J, Rick J, McBride J, Davatzikos C, Shaw LM, Hurtig H, Trojanowski JQ, Chen-Plotkin AS. An Alzheimer's Disease-Derived Biomarker Signature Identifies Parkinson's Disease Patients with Dementia. PLoS One. 2016 Jan 26;11(1):e0147319. [Pubmed]

  • Leung YY, Kuksa PP, Amlie-Wolf A, Valladares O, Ungar LH, Kannan S, Gregory BD, Wang LS. DASHR: database of small human noncoding RNAs. Nucleic Acids Res. 2016 Jan 4;44(D1):D216-22. [Pubmed]

  • Silverman IM, Berkowitz ND, Gosai SJ, Gregory BD. Genome-Wide Approaches for RNA Structure Probing. Adv Exp Med Biol. 2016;907:29-59. doi: 10.1007/978-3-319-29073-7_2. [Pubmed]

2015
  • Amlie-Wolf A, Ryvkin P, Tong R, Dragomir I, Suh E, Xu Y, Van Deerlin VM, Gregory BD, Kwong LK, Trojanowski JQ, Lee VM, Wang LS, Lee EB. Transcriptomic Changes Due to Cytoplasmic TDP-43 Expression Reveal Dysregulation of Histone Transcripts and Nuclear Chromatin. PLoS One. 2015 Oct 28;10(10):e0141836. [Pubmed]

  • Mellis IA, Raj A. Half dozen of one, six billion of the other: What can small-and large-scale molecular systems biology learn from one another? Genome Res. 2015 Oct;25(10):1466-72. [Pubmed]

  • Hannigan GD, Meisel JS, Tyldsley AS, Zheng Q, Hodkinson BP, SanMiguel AJ, Minot S, Bushman FD, Grice EA. The human skin double-stranded DNA virome: topographical and temporal diversity, genetic enrichment, and dynamic associations with the host microbiome. MBio. 2015 Oct 20;6(5):e01578-15. [Pubmed]

  • Gao F, Chang D, Biddanda A, Ma L, Guo Y, Zhou Z, Keinan A. XWAS: A Software Toolset for Genetic Data Analysis and Association Studies of the X Chromosome. J Hered. 2015 Sep-Oct;106(5):666-71. [Pubmed]

  • Jiang Y, Oldridge DA, Diskin SJ, Zhang NR. CODEX: a normalization and copy number variation detection method for whole exome sequencing. Nucleic Acids Res. 2015 Mar 31;43(6):e39. [Pubmed]