Publications

1. Alser M, Lawlor B, Abdill RJ, Waymost S, Ayyala R, Rajkumar N, LaPierre N, Brito J, Ribeiro-Dos-Santos AM, Almadhoun N, Sarwal V, Firtina C, Osinski T, Eskin E, Hu Q, Strong D, Kim BBD, Abedalthagafi MS, Mutlu O, Mangul S. Packaging and containerization of computational methods.. Nature protocols, 2024.
2. Fu M, Tran T, Eskin E, Lajonchere C, Pasaniuc B, Geschwind DH, Vossel K, Chang TS. Multi-class Modeling Identifies Shared Genetic Risk for Late-onset Epilepsy and Alzheimer's Disease.. medRxiv : the preprint server for health sciences, 2024.
3. Sathe LM, Khan NN, Williams JM, Saul R, Jajieh K, Sartippour MR, Young R, Xie J, Marquette DM, Duncan T, Eskin E, Arboleda VA. 3D Printing as an Effective Quality Assurance Implementation in Massive-Scale SARS-CoV-2 Testing at a SwabSeq Next-Generation Sequencing Laboratory.. Laboratory medicine, 2023.
4. Khan AH, Bagley JR, LaPierre N, Gonzalez-Figueroa C, Spencer TC, Choudhury M, Xiao X, Eskin E, Jentsch JD, Smith DJ. Genetic pathways regulating the longitudinal acquisition of cocaine self-administration in a panel of inbred and recombinant inbred mice.. Cell reports, 2023.
5. LaPierre N, Fu B, Turnbull S, Eskin E, Sankararaman S. Leveraging family data to design Mendelian randomization that is provably robust to population stratification.. Genome research, 2023.
6. Deshpande D, Chhugani K, Chang Y, Karlsberg A, Loeffler C, Zhang J, Muszynska A, Munteanu V, Yang H, Rotman J, Tao L, Balliu B, Tseng E, Eskin E, Zhao F, Mohammadi P, P Labaj P, Mangul S. RNA-seq data science: From raw data to effective interpretation.. Frontiers in genetics, 2023.
7. LaPierre N, Fu B, Turnbull S, Eskin E, Sankararaman S. Leveraging family data to design Mendelian Randomization that is provably robust to population stratification.. bioRxiv : the preprint server for biology, 2023.
8. Zou J, Zhou J, Faller S, Brown RP, Sankararaman SS, Eskin E. Accurate modeling of replication rates in genome-wide association studies by accounting for Winner's Curse and study-specific heterogeneity.. G3 (Bethesda, Md.), 2022.
9. Taraszka K, Zaitlen N, Eskin E. Leveraging pleiotropy for joint analysis of genome-wide association studies with per trait interpretations.. PLoS genetics, 2022.
10. Karlin J, Gai L, LaPierre N, Danesh K, Farajzadeh J, Palileo B, Taraszka K, Zheng J, Wang W, Eskin E, Rootman D. Ensemble neural network model for detecting thyroid eye disease using external photographs.. The British journal of ophthalmology, 2022.
11. Sarwal V, Niehus S, Ayyala R, Kim M, Sarkar A, Chang S, Lu A, Rajkumar N, Darfci-Maher N, Littman R, Chhugani K, Soylev A, Comarova Z, Wesel E, Castellanos J, Chikka R, Distler MG, Eskin E, Flint J, Mangul S. A comprehensive benchmarking of WGS-based deletion structural variant callers.. Briefings in bioinformatics, 2022.
12. Coller HA, Beggs S, Andrews S, Maloy J, Chiu A, Sankararaman S, Pellegrini M, Freimer N, Johnson T, Papp J, Eskin E, Hoffmann A. Bruins-in-Genomics: Evaluation of the impact of a UCLA undergraduate summer program in computational biology on participating students.. PloS one, 2022.
13. Meyer F, Fritz A, Deng ZL, Koslicki D, Lesker TR, Gurevich A, Robertson G, Alser M, Antipov D, Beghini F, Bertrand D, Brito JJ, Brown CT, Buchmann J, Buluç A, Chen B, Chikhi R, Clausen PTLC, Cristian A, Dabrowski PW, Darling AE, Egan R, Eskin E, Georganas E, Goltsman E, Gray MA, Hansen LH, Hofmeyr S, Huang P, Irber L, Jia H, Jørgensen TS, Kieser SD, Klemetsen T, Kola A, Kolmogorov M, Korobeynikov A, Kwan J, LaPierre N, Lemaitre C, Li C, Limasset A, Malcher-Miranda F, Mangul S, Marcelino VR, Marchet C, Marijon P, Meleshko D, Mende DR, Milanese A, Nagarajan N, Nissen J, Nurk S, Oliker L, Paoli L, Peterlongo P, Piro VC, Porter JS, Rasmussen S, Rees ER, Reinert K, Renard B, Robertsen EM, Rosen GL, Ruscheweyh HJ, Sarwal V, Segata N, Seiler E, Shi L, Sun F, Sunagawa S, Sørensen SJ, Thomas A, Tong C, Trajkovski M, Tremblay J, Uritskiy G, Vicedomini R, Wang Z, Wang Z, Wang Z, Warren A, Willassen NP, Yelick K, You R, Zeller G, Zhao Z, Zhu S, Zhu J, Garrido-Oter R, Gastmeier P, Hacquard S, Häußler S, Khaledi A, Maechler F, Mesny F, Radutoiu S, Schulze-Lefert P, Smit N, Strowig T, Bremges A, Sczyrba A, McHardy AC. Critical Assessment of Metagenome Interpretation: the second round of challenges.. Nature methods, 2022.
14. Guo L, Boocock J, Hilt EE, Chandrasekaran S, Zhang Y, Munugala C, Sathe L, Alexander N, Arboleda VA, Flint J, Eskin E, Luo C, Yang S, Garner OB, Yin Y, Bloom JS, Kruglyak L. Genomic epidemiology of the Los Angeles COVID-19 outbreak and the early history of the B.1.43 strain in the USA.. BMC genomics, 2022.
15. Cinelli C, LaPierre N, Hill BL, Sankararaman S, Eskin E. Robust Mendelian randomization in the presence of residual population stratification, batch effects and horizontal pleiotropy.. Nature communications, 2022.
16. LaPierre N, Taraszka K, Huang H, He R, Hormozdiari F, Eskin E. Identifying causal variants by fine mapping across multiple studies.. PLoS genetics, 2021.
17. Bloom JS, Sathe L, Munugala C, Jones EM, Gasperini M, Lubock NB, Yarza F, Thompson EM, Kovary KM, Park J, Marquette D, Kay S, Lucas M, Love T, Sina Booeshaghi A, Brandenberg OF, Guo L, Boocock J, Hochman M, Simpkins SW, Lin I, LaPierre N, Hong D, Zhang Y, Oland G, Choe BJ, Chandrasekaran S, Hilt EE, Butte MJ, Damoiseaux R, Kravit C, Cooper AR, Yin Y, Pachter L, Garner OB, Flint J, Eskin E, Luo C, Kosuri S, Kruglyak L, Arboleda VA. Massively scaled-up testing for SARS-CoV-2 RNA via next-generation sequencing of pooled and barcoded nasal and saliva samples.. Nature biomedical engineering, 2021.
18. Hormozdiari F, Jung J, Eskin E, J Joo JW. MARS: leveraging allelic heterogeneity to increase power of association testing.. Genome biology, 2021.
19. de Goede OM, Nachun DC, Ferraro NM, Gloudemans MJ, Rao AS, Smail C, Eulalio TY, Aguet F, Ng B, Xu J, Barbeira AN, Castel SE, Kim-Hellmuth S, Park Y, Scott AJ, Strober BJ, GTEx Consortium, Brown CD, Wen X, Hall IM, Battle A, Lappalainen T, Im HK, Ardlie KG, Mostafavi S, Quertermous T, Kirkegaard K, Montgomery SB. Population-scale tissue transcriptomics maps long non-coding RNAs to complex disease.. Cell, 2021.
20. Bloom JS, Sathe L, Munugala C, Jones EM, Gasperini M, Lubock NB, Yarza F, Thompson EM, Kovary KM, Park J, Marquette D, Kay S, Lucas M, Love T, Booeshaghi AS, Brandenberg OF, Guo L, Boocock J, Hochman M, Simpkins SW, Lin I, LaPierre N, Hong D, Zhang Y, Oland G, Choe BJ, Chandrasekaran S, Hilt EE, Butte MJ, Damoiseaux R, Kravit C, Cooper AR, Yin Y, Pachter L, Garner OB, Flint J, Eskin E, Luo C, Kosuri S, Kruglyak L, Arboleda VA. Swab-Seq: A high-throughput platform for massively scaled up SARS-CoV-2 testing.. medRxiv : the preprint server for health sciences, 2021.
21. Chang TS, Ding Y, Freund MK, Johnson R, Schwarz T, Yabu JM, Hazlett C, Chiang JN, Wulf DA, UCLA Precision Health Data Discovery Repository Working Group, Geschwind DH, Butte MJ, Pasaniuc B. Pre-existing conditions in Hispanics/Latinxs that are COVID-19 risk factors.. iScience, 2021.
22. Lee CH, Shi H, Pasaniuc B, Eskin E, Han B. PLEIO: a method to map and interpret pleiotropic loci with GWAS summary statistics.. American journal of human genetics, 2020.
23. Bein K, Ganguly K, Martin TM, Concel VJ, Brant KA, Di YPP, Upadhyay S, Fabisiak JP, Vuga LJ, Kaminski N, Kostem E, Eskin E, Prows DR, Jang AS, Leikauf GD. Genetic determinants of ammonia-induced acute lung injury in mice.. American journal of physiology. Lung cellular and molecular physiology, 2020.
24. Goodman-Meza D, Rudas A, Chiang JN, Adamson PC, Ebinger J, Sun N, Botting P, Fulcher JA, Saab FG, Brook R, Eskin E, An U, Kordi M, Jew B, Balliu B, Chen Z, Hill BL, Rahmani E, Halperin E, Manuel V. A machine learning algorithm to increase COVID-19 inpatient diagnostic capacity.. PloS one, 2020.
25. Castel SE, Aguet F, Mohammadi P, GTEx Consortium, Ardlie KG, Lappalainen T. A vast resource of allelic expression data spanning human tissues.. Genome biology, 2020.
26. Kim-Hellmuth S, Aguet F, Oliva M, Muñoz-Aguirre M, Kasela S, Wucher V, Castel SE, Hamel AR, Viñuela A, Roberts AL, Mangul S, Wen X, Wang G, Barbeira AN, Garrido-Martín D, Nadel BB, Zou Y, Bonazzola R, Quan J, Brown A, Martinez-Perez A, Soria JM, GTEx Consortium, Getz G, Dermitzakis ET, Small KS, Stephens M, Xi HS, Im HK, Guigó R, Segrè AV, Stranger BE, Ardlie KG, Lappalainen T. Cell type-specific genetic regulation of gene expression across human tissues.. Science (New York, N.Y.), 2020.
27. Demanelis K, Jasmine F, Chen LS, Chernoff M, Tong L, Delgado D, Zhang C, Shinkle J, Sabarinathan M, Lin H, Ramirez E, Oliva M, Kim-Hellmuth S, Stranger BE, Lai TP, Aviv A, Ardlie KG, Aguet F, Ahsan H, GTEx Consortium, Doherty JA, Kibriya MG, Pierce BL. Determinants of telomere length across human tissues.. Science (New York, N.Y.), 2020.
28. GTEx Consortium. The GTEx Consortium atlas of genetic regulatory effects across human tissues.. Science (New York, N.Y.), 2020.
29. Oliva M, Muñoz-Aguirre M, Kim-Hellmuth S, Wucher V, Gewirtz ADH, Cotter DJ, Parsana P, Kasela S, Balliu B, Viñuela A, Castel SE, Mohammadi P, Aguet F, Zou Y, Khramtsova EA, Skol AD, Garrido-Martín D, Reverter F, Brown A, Evans P, Gamazon ER, Payne A, Bonazzola R, Barbeira AN, Hamel AR, Martinez-Perez A, Soria JM, GTEx Consortium, Pierce BL, Stephens M, Eskin E, Dermitzakis ET, Segrè AV, Im HK, Engelhardt BE, Ardlie KG, Montgomery SB, Battle AJ, Lappalainen T, Guigó R, Stranger BE. The impact of sex on gene expression across human tissues.. Science (New York, N.Y.), 2020.
30. Jiang L, Wang M, Lin S, Jian R, Li X, Chan J, Dong G, Fang H, Robinson AE, GTEx Consortium, Snyder MP. A Quantitative Proteome Map of the Human Body.. Cell, 2020.
31. LaPierre N, Alser M, Eskin E, Koslicki D, Mangul S. Metalign: efficient alignment-based metagenomic profiling via containment min hash.. Genome biology, 2020.
32. Ferraro NM, Strober BJ, Einson J, Abell NS, Aguet F, Barbeira AN, Brandt M, Bucan M, Castel SE, Davis JR, Greenwald E, Hess GT, Hilliard AT, Kember RL, Kotis B, Park Y, Peloso G, Ramdas S, Scott AJ, Smail C, Tsang EK, Zekavat SM, Ziosi M, TOPMed Lipids Working Group, Ardlie KG, Assimes TL, Bassik MC, Brown CD, Correa A, Hall I, Im HK, Li X, Natarajan P, GTEx Consortium, Lappalainen T, Mohammadi P, Montgomery SB, Battle A. Transcriptomic signatures across human tissues identify functional rare genetic variation.. Science (New York, N.Y.), 2020.
33. Mandric I, Rotman J, Yang HT, Strauli N, Montoya DJ, Van Der Wey W, Ronas JR, Statz B, Yao D, Petrova V, Zelikovsky A, Spreafico R, Shifman S, Zaitlen N, Rossetti M, Ansel KM, Eskin E, Mangul S. Author Correction: Profiling immunoglobulin repertoires across multiple human tissues using RNA sequencing.. Nature communications, 2020.
34. Loeffler C, Karlsberg A, Martin LS, Eskin E, Koslicki D, Mangul S. Correction to: Improving the usability and comprehensiveness of microbial databases.. BMC biology, 2020.
35. Mandric I, Rotman J, Yang HT, Strauli N, Montoya DJ, Van Der Wey W, Ronas JR, Statz B, Yao D, Petrova V, Zelikovsky A, Spreafico R, Shifman S, Zaitlen N, Rossetti M, Ansel KM, Eskin E, Mangul S. Profiling immunoglobulin repertoires across multiple human tissues using RNA sequencing.. Nature communications, 2020.
36. Han Y, Jia Q, Jahani PS, Hurrell BP, Pan C, Huang P, Gukasyan J, Woodward NC, Eskin E, Gilliland FD, Akbari O, Hartiala JA, Allayee H. Genome-wide analysis highlights contribution of immune system pathways to the genetic architecture of asthma.. Nature communications, 2020.
37. Loeffler C, Karlsberg A, Martin LS, Eskin E, Koslicki D, Mangul S. Improving the usability and comprehensiveness of microbial databases.. BMC biology, 2020.
38. Mitchell K, Brito JJ, Mandric I, Wu Q, Knyazev S, Chang S, Martin LS, Karlsberg A, Gerasimov E, Littman R, Hill BL, Wu NC, Yang HT, Hsieh K, Chen L, Littman E, Shabani T, Enik G, Yao D, Sun R, Schroeder J, Eskin E, Zelikovsky A, Skums P, Pop M, Mangul S. Benchmarking of computational error-correction methods for next-generation sequencing data.. Genome biology, 2020.
39. Wu Y, Eskin E, Sankararaman S. A Unifying Framework for Imputing Summary Statistics in Genome-Wide Association Studies.. Journal of computational biology : a journal of computational molecular cell biology, 2020.
40. Maazi H, Hartiala JA, Suzuki Y, Crow AL, Shafiei Jahani P, Lam J, Patel N, Rigas D, Han Y, Huang P, Eskin E, Lusis AJ, Gilliland FD, Akbari O, Allayee H. A GWAS approach identifies Dapp1 as a determinant of air pollution-induced airway hyperreactivity.. PLoS genetics, 2019.
41. Zou J, Hormozdiari F, Jew B, Castel SE, Lappalainen T, Ernst J, Sul JH, Eskin E. Leveraging allelic imbalance to refine fine-mapping for eQTL studies.. PLoS genetics, 2019.
42. Kim K, Baik H, Jang CS, Roh JK, Eskin E, Han B. Genomic GPS: using genetic distance from individuals to public data for genomic analysis without disclosing personal genomes.. Genome biology, 2019.
43. Lee C, Kang EY, Gandal MJ, Eskin E, Geschwind DH. Profiling allele-specific gene expression in brains from individuals with autism spectrum disorder reveals preferential minor allele usage.. Nature neuroscience, 2019.
44. Yao DW, Balanis NG, Eskin E, Graeber TG. A linear mixed model approach to gene expression-tumor aneuploidy association studies.. Scientific reports, 2019.
45. Rahmani E, Schweiger R, Rhead B, Criswell LA, Barcellos LF, Eskin E, Rosset S, Sankararaman S, Halperin E. Cell-type-specific resolution epigenetics without the need for cell sorting or single-cell biology.. Nature communications, 2019.
46. Mangul S, Mosqueiro T, Abdill RJ, Duong D, Mitchell K, Sarwal V, Hill B, Brito J, Littman RJ, Statz B, Lam AK, Dayama G, Grieneisen L, Martin LS, Flint J, Eskin E, Blekhman R. Challenges and recommendations to improve the installability and archival stability of omics computational tools.. PLoS biology, 2019.
47. LaPierre N, Mangul S, Alser M, Mandric I, Wu NC, Koslicki D, Eskin E. MiCoP: microbial community profiling method for detecting viral and fungal organisms in metagenomic samples.. BMC genomics, 2019.
48. Mangul S, Martin LS, Hill BL, Lam AK, Distler MG, Zelikovsky A, Eskin E, Flint J. Systematic benchmarking of omics computational tools.. Nature communications, 2019.
49. Mangul S, Martin LS, Langmead B, Sanchez-Galan JE, Toma I, Hormozdiari F, Pevzner P, Eskin E. How bioinformatics and open data can boost basic science in countries and universities with limited resources.. Nature biotechnology, 2019.
50. Mangul S, Martin LS, Eskin E, Blekhman R. Improving the usability and archival stability of bioinformatics software.. Genome biology, 2019.
51. Sul JH, Martin LS, Eskin E. Population structure in genetic studies: Confounding factors and mixed models.. PLoS genetics, 2018.
52. Duong D, Ahmad WU, Eskin E, Chang KW, Li JJ. Word and Sentence Embedding Tools to Measure Semantic Similarity of Gene Ontology Terms by Their Definitions.. Journal of computational biology : a journal of computational molecular cell biology, 2018.
53. Wu Y, Hormozdiari F, Joo JWJ, Eskin E. Improving Imputation Accuracy by Inferring Causal Variants in Genetic Studies.. Journal of computational biology : a journal of computational molecular cell biology, 2018.
54. Rahmani E, Schweiger R, Shenhav L, Wingert T, Hofer I, Gabel E, Eskin E, Halperin E. BayesCCE: a Bayesian framework for estimating cell-type composition from DNA methylation without the need for methylation reference.. Genome biology, 2018.
55. Gai L, Eskin E. Finding associated variants in genome-wide association studies on multiple traits.. Bioinformatics (Oxford, England), 2018.
56. Gamazon ER, Segrè AV, van de Bunt M, Wen X, Xi HS, Hormozdiari F, Ongen H, Konkashbaev A, Derks EM, Aguet F, Quan J, GTEx Consortium, Nicolae DL, Eskin E, Kellis M, Getz G, McCarthy MI, Dermitzakis ET, Cox NJ, Ardlie KG. Using an atlas of gene regulation across 44 human tissues to inform complex disease- and trait-associated variation.. Nature genetics, 2018.
57. Hormozdiari F, Gazal S, van de Geijn B, Finucane HK, Ju CJ, Loh PR, Schoech A, Reshef Y, Liu X, O'Connor L, Gusev A, Eskin E, Price AL. Leveraging molecular quantitative trait loci to understand the genetic architecture of diseases and complex traits.. Nature genetics, 2018.
58. Kennedy EM, Goehring GN, Nichols MH, Robins C, Mehta D, Klengel T, Eskin E, Smith AK, Conneely KN. An integrated -omics analysis of the epigenetic landscape of gene expression in human blood cells.. BMC genomics, 2018.
59. Kang EY, Lee CH, Furlotte NA, Joo JWJ, Kostem E, Zaitlen N, Eskin E, Han B. An Association Mapping Framework To Account for Potential Sex Difference in Genetic Architectures.. Genetics, 2018.
60. Olde Loohuis LM, Mangul S, Ori APS, Jospin G, Koslicki D, Yang HT, Wu T, Boks MP, Lomen-Hoerth C, Wiedau-Pazos M, Cantor RM, de Vos WM, Kahn RS, Eskin E, Ophoff RA. Transcriptome analysis in whole blood reveals increased microbial diversity in schizophrenia.. Translational psychiatry, 2018.
61. Mangul S, Martin LS, Eskin E. Involving undergraduates in genomics research to narrow the education-research gap.. Nature biotechnology, 2018.
62. Mangul S, Yang HT, Strauli N, Gruhl F, Porath HT, Hsieh K, Chen L, Daley T, Christenson S, Wesolowska-Andersen A, Spreafico R, Rios C, Eng C, Smith AD, Hernandez RD, Ophoff RA, Santana JR, Levanon EY, Woodruff PG, Burchard E, Seibold MA, Shifman S, Eskin E, Zaitlen N. ROP: dumpster diving in RNA-sequencing to find the source of 1 trillion reads across diverse adult human tissues.. Genome biology, 2018.
63. Computational Pan-Genomics Consortium. Computational pan-genomics: status, promises and challenges.. Briefings in bioinformatics, 2018.
64. Park DS, Eskin I, Kang EY, Gamazon ER, Eng C, Gignoux CR, Galanter JM, Burchard E, Ye CJ, Aschard H, Eskin E, Halperin E, Zaitlen N. An ancestry-based approach for detecting interactions.. Genetic epidemiology, 2017.
65. Jasinska AJ, Zelaya I, Service SK, Peterson CB, Cantor RM, Choi OW, DeYoung J, Eskin E, Fairbanks LA, Fears S, Furterer AE, Huang YS, Ramensky V, Schmitt CA, Svardal H, Jorgensen MJ, Kaplan JR, Villar D, Aken BL, Flicek P, Nag R, Wong ES, Blangero J, Dyer TD, Bogomolov M, Benjamini Y, Weinstock GM, Dewar K, Sabatti C, Wilson RK, Jentsch JD, Warren W, Coppola G, Woods RP, Freimer NB. Genetic variation and gene expression across multiple tissues and developmental stages in a nonhuman primate.. Nature genetics, 2017.
66. 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 (New York, N.Y.), 2017.
67. Saha A, Kim Y, Gewirtz ADH, Jo B, Gao C, McDowell IC, GTEx Consortium, Engelhardt BE, Battle A. Co-expression networks reveal the tissue-specific regulation of transcription and splicing.. Genome research, 2017.
68. Tan MH, Li Q, Shanmugam R, Piskol R, Kohler J, Young AN, Liu KI, Zhang R, Ramaswami G, Ariyoshi K, Gupte A, Keegan LP, George CX, Ramu A, Huang N, Pollina EA, Leeman DS, Rustighi A, Goh YPS, GTEx Consortium, Laboratory, Data Analysis &Coordinating Center (LDACC)—Analysis Working Group, Statistical Methods groups—Analysis Working Group, Enhancing GTEx (eGTEx) groups, NIH Common Fund, NIH/NCI, NIH/NHGRI, NIH/NIMH, NIH/NIDA, Biospecimen Collection Source Site—NDRI, Biospecimen Collection Source Site—RPCI, Biospecimen Core Resource—VARI, Brain Bank Repository—University of Miami Brain Endowment Bank, Leidos Biomedical—Project Management, ELSI Study, Genome Browser Data Integration &Visualization—EBI, Genome Browser Data Integration &Visualization—UCSC Genomics Institute, University of California San, Chawla A, Del Sal G, Peltz G, Brunet A, Conrad DF, Samuel CE, O'Connell MA, Walkley CR, Nishikura K, Li JB. Dynamic landscape and regulation of RNA editing in mammals.. Nature, 2017.
69. GTEx Consortium, Laboratory, Data Analysis &Coordinating Center (LDACC)—Analysis Working Group, Statistical Methods groups—Analysis Working Group, Enhancing GTEx (eGTEx) groups, NIH Common Fund, NIH/NCI, NIH/NHGRI, NIH/NIMH, NIH/NIDA, Biospecimen Collection Source Site—NDRI, Biospecimen Collection Source Site—RPCI, Biospecimen Core Resource—VARI, Brain Bank Repository—University of Miami Brain Endowment Bank, Leidos Biomedical—Project Management, ELSI Study, Genome Browser Data Integration &Visualization—EBI, Genome Browser Data Integration &Visualization—UCSC Genomics Institute, University of California San, Lead analysts:, Laboratory, Data Analysis &Coordinating Center (LDACC):, NIH program management:, Biospecimen collection:, Pathology:, eQTL manuscript working group:, Battle A, Brown CD, Engelhardt BE, Montgomery SB. Genetic effects on gene expression across human tissues.. Nature, 2017.
70. Yang F, Wang J, GTEx Consortium, Pierce BL, Chen LS. Identifying cis-mediators for trans-eQTLs across many human tissues using genomic mediation analysis.. Genome research, 2017.
71. Tukiainen T, Villani AC, Yen A, Rivas MA, Marshall JL, Satija R, Aguirre M, Gauthier L, Fleharty M, Kirby A, Cummings BB, Castel SE, Karczewski KJ, Aguet F, Byrnes A, GTEx Consortium, Laboratory, Data Analysis &Coordinating Center (LDACC)—Analysis Working Group, Statistical Methods groups—Analysis Working Group, Enhancing GTEx (eGTEx) groups, NIH Common Fund, NIH/NCI, NIH/NHGRI, NIH/NIMH, NIH/NIDA, Biospecimen Collection Source Site—NDRI, Biospecimen Collection Source Site—RPCI, Biospecimen Core Resource—VARI, Brain Bank Repository—University of Miami Brain Endowment Bank, Leidos Biomedical—Project Management, ELSI Study, Genome Browser Data Integration &Visualization—EBI, Genome Browser Data Integration &Visualization—UCSC Genomics Institute, University of California San, Lappalainen T, Regev A, Ardlie KG, Hacohen N, MacArthur DG. Landscape of X chromosome inactivation across human tissues.. Nature, 2017.
72. Li X, Kim Y, Tsang EK, Davis JR, Damani FN, Chiang C, Hess GT, Zappala Z, Strober BJ, Scott AJ, Li A, Ganna A, Bassik MC, Merker JD, GTEx Consortium, Laboratory, Data Analysis &Coordinating Center (LDACC)—Analysis Working Group, Statistical Methods groups—Analysis Working Group, Enhancing GTEx (eGTEx) groups, NIH Common Fund, NIH/NCI, NIH/NHGRI, NIH/NIMH, NIH/NIDA, Biospecimen Collection Source Site—NDRI, Biospecimen Collection Source Site—RPCI, Biospecimen Core Resource—VARI, Brain Bank Repository—University of Miami Brain Endowment Bank, Leidos Biomedical—Project Management, ELSI Study, Genome Browser Data Integration &Visualization—EBI, Genome Browser Data Integration &Visualization—UCSC Genomics Institute, University of California San, Hall IM, Battle A, Montgomery SB. The impact of rare variation on gene expression across tissues.. Nature, 2017.
73. Ritchie MD, Davis JR, Aschard H, Battle A, Conti D, Du M, Eskin E, Fallin MD, Hsu L, Kraft P, Moore JH, Pierce BL, Bien SA, Thomas DC, Wei P, Montgomery SB. Incorporation of Biological Knowledge Into the Study of Gene-Environment Interactions.. American journal of epidemiology, 2017.
74. Mangul S, Martin LS, Hoffmann A, Pellegrini M, Eskin E. Addressing the Digital Divide in Contemporary Biology: Lessons from Teaching UNIX.. Trends in biotechnology, 2017.
75. Duong D, Gai L, Snir S, Kang EY, Han B, Sul JH, Eskin E. Applying meta-analysis to genotype-tissue expression data from multiple tissues to identify eQTLs and increase the number of eGenes.. Bioinformatics (Oxford, England), 2017.
76. Lee CH, Eskin E, Han B. Increasing the power of meta-analysis of genome-wide association studies to detect heterogeneous effects.. Bioinformatics (Oxford, England), 2017.
77. Buckley MT, Racimo F, Allentoft ME, Jensen MK, Jonsson A, Huang H, Hormozdiari F, Sikora M, Marnetto D, Eskin E, Jørgensen ME, Grarup N, Pedersen O, Hansen T, Kraft P, Willerslev E, Nielsen R. Selection in Europeans on Fatty Acid Desaturases Associated with Dietary Changes.. Molecular biology and evolution, 2017.
78. Hormozdiari F, Zhu A, Kichaev G, Ju CJ, Segrè AV, Joo JWJ, Won H, Sankararaman S, Pasaniuc B, Shifman S, Eskin E. Widespread Allelic Heterogeneity in Complex Traits.. American journal of human genetics, 2017.
79. He D, Wang Z, Parida L, Eskin E. IPED2: Inheritance Path Based Pedigree Reconstruction Algorithm for Complicated Pedigrees.. IEEE/ACM transactions on computational biology and bioinformatics, 2017.
80. Mangul S, Yang TH, Hormozdiari F, Dainis AM, Tseng E, Ashley EA, Zelikovsky A, Eskin E. HapIso: An Accurate Method for the Haplotype- Specific Isoforms Reconstruction From Long Single-Molecule Reads.. IEEE transactions on nanobioscience, 2017.
81. Rahmani E, Zaitlen N, Baran Y, Eng C, Hu D, Galanter J, Oh S, Burchard EG, Eskin E, Zou J, Halperin E. Correcting for cell-type heterogeneity in DNA methylation: a comprehensive evaluation.. Nature methods, 2017.
82. Bilow M, Crespo F, Pan Z, Eskin E, Eyheramendy S. Simultaneous Modeling of Disease Status and Clinical Phenotypes To Increase Power in Genome-Wide Association Studies.. Genetics, 2017.
83. Artyomenko A, Wu NC, Mangul S, Eskin E, Sun R, Zelikovsky A. Long Single-Molecule Reads Can Resolve the Complexity of the Influenza Virus Composed of Rare, Closely Related Mutant Variants.. Journal of computational biology : a journal of computational molecular cell biology, 2016.
84. Hormozdiari F, van de Bunt M, Segrè AV, Li X, Joo JWJ, Bilow M, Sul JH, Sankararaman S, Pasaniuc B, Eskin E. Colocalization of GWAS and eQTL Signals Detects Target Genes.. American journal of human genetics, 2016.
85. Joo JW, Kang EY, Org E, Furlotte N, Parks B, Hormozdiari F, Lusis AJ, Eskin E. Efficient and Accurate Multiple-Phenotype Regression Method for High Dimensional Data Considering Population Structure.. Genetics, 2016.
86. Won H, de la Torre-Ubieta L, Stein JL, Parikshak NN, Huang J, Opland CK, Gandal MJ, Sutton GJ, Hormozdiari F, Lu D, Lee C, Eskin E, Voineagu I, Ernst J, Geschwind DH. Chromosome conformation elucidates regulatory relationships in developing human brain.. Nature, 2016.
87. Lavinsky J, Ge M, Crow AL, Pan C, Wang J, Salehi P, Myint A, Eskin E, Allayee H, Lusis AJ, Friedman RA. The Genetic Architecture of Noise-Induced Hearing Loss: Evidence for a Gene-by-Environment Interaction.. G3 (Bethesda, Md.), 2016.
88. Kang EY, Martin LJ, Mangul S, Isvilanonda W, Zou J, Ben-David E, Han B, Lusis AJ, Shifman S, Eskin E. Discovering Single Nucleotide Polymorphisms Regulating Human Gene Expression Using Allele Specific Expression from RNA-seq Data.. Genetics, 2016.
89. Kichaev G, Roytman M, Johnson R, Eskin E, Lindström S, Kraft P, Pasaniuc B. Improved methods for multi-trait fine mapping of pleiotropic risk loci.. Bioinformatics (Oxford, England), 2016.
90. Main BJ, Lee Y, Ferguson HM, Kreppel KS, Kihonda A, Govella NJ, Collier TC, Cornel AJ, Eskin E, Kang EY, Nieman CC, Weakley AM, Lanzaro GC. The Genetic Basis of Host Preference and Resting Behavior in the Major African Malaria Vector, Anopheles arabiensis.. PLoS genetics, 2016.
91. Hasin-Brumshtein Y, Khan AH, Hormozdiari F, Pan C, Parks BW, Petyuk VA, Piehowski PD, Brümmer A, Pellegrini M, Xiao X, Eskin E, Smith RD, Lusis AJ, Smith DJ. Hypothalamic transcriptomes of 99 mouse strains reveal trans eQTL hotspots, splicing QTLs and novel non-coding genes.. eLife, 2016.
92. Kang EY, Park Y, Li X, Segrè AV, Han B, Eskin E. ForestPMPlot: A Flexible Tool for Visualizing Heterogeneity Between Studies in Meta-analysis.. G3 (Bethesda, Md.), 2016.
93. Duong D, Zou J, Hormozdiari F, Sul JH, Ernst J, Han B, Eskin E. Using genomic annotations increases statistical power to detect eGenes.. Bioinformatics (Oxford, England), 2016.
94. Hormozdiari F, Kang EY, Bilow M, Ben-David E, Vulpe C, McLachlan S, Lusis AJ, Han B, Eskin E. Imputing Phenotypes for Genome-wide Association Studies.. American journal of human genetics, 2016.
95. Schweiger R, Kaufman S, Laaksonen R, Kleber ME, März W, Eskin E, Rosset S, Halperin E. Fast and Accurate Construction of Confidence Intervals for Heritability.. American journal of human genetics, 2016.
96. Peterson CB, Service SK, Jasinska AJ, Gao F, Zelaya I, Teshiba TM, Bearden CE, Cantor RM, Reus VI, Macaya G, López-Jaramillo C, Bogomolov M, Benjamini Y, Eskin E, Coppola G, Freimer NB, Sabatti C. Characterization of Expression Quantitative Trait Loci in Pedigrees from Colombia and Costa Rica Ascertained for Bipolar Disorder.. PLoS genetics, 2016.
97. Lusis AJ, Seldin MM, Allayee H, Bennett BJ, Civelek M, Davis RC, Eskin E, Farber CR, Hui S, Mehrabian M, Norheim F, Pan C, Parks B, Rau CD, Smith DJ, Vallim T, Wang Y, Wang J. The Hybrid Mouse Diversity Panel: a resource for systems genetics analyses of metabolic and cardiovascular traits.. Journal of lipid research, 2016.
98. Joo JW, Hormozdiari F, Han B, Eskin E. Multiple testing correction in linear mixed models.. Genome biology, 2016.
99. Rahmani E, Zaitlen N, Baran Y, Eng C, Hu D, Galanter J, Oh S, Burchard EG, Eskin E, Zou J, Halperin E. Sparse PCA corrects for cell type heterogeneity in epigenome-wide association studies.. Nature methods, 2016.
100. Sul JH, Bilow M, Yang WY, Kostem E, Furlotte N, He D, Eskin E. Accounting for Population Structure in Gene-by-Environment Interactions in Genome-Wide Association Studies Using Mixed Models.. PLoS genetics, 2016.
101. Bennett BJ, Davis RC, Civelek M, Orozco L, Wu J, Qi H, Pan C, Sevag Packard RR, Eskin E, Yan M, Kirchgessner T, Wang Z, Li X, Gregory JC, Hazen SL, Gargalovic PS, Lusis AJ. Correction: Genetic Architecture of Atherosclerosis in Mice: A Systems Genetics Analysis of Common Inbred Strains.. PLoS genetics, 2016.
102. Han B, Duong D, Sul JH, de Bakker PI, Eskin E, Raychaudhuri S. A general framework for meta-analyzing dependent studies with overlapping subjects in association mapping.. Human molecular genetics, 2016.
103. Bennett BJ, Davis RC, Civelek M, Orozco L, Wu J, Qi H, Pan C, Packard RR, Eskin E, Yan M, Kirchgessner T, Wang Z, Li X, Gregory JC, Hazen SL, Gargalovic PS, Lusis AJ. Genetic Architecture of Atherosclerosis in Mice: A Systems Genetics Analysis of Common Inbred Strains.. PLoS genetics, 2015.
104. Crow AL, Ohmen J, Wang J, Lavinsky J, Hartiala J, Li Q, Li X, Salehide P, Eskin E, Pan C, Lusis AJ, Allayee H, Friedman RA. The Genetic Architecture of Hearing Impairment in Mice: Evidence for Frequency-Specific Genetic Determinants.. G3 (Bethesda, Md.), 2015.
105. Org E, Parks BW, Joo JW, Emert B, Schwartzman W, Kang EY, Mehrabian M, Pan C, Knight R, Gunsalus R, Drake TA, Eskin E, Lusis AJ. Genetic and environmental control of host-gut microbiota interactions.. Genome research, 2015.
106. Rau CD, Parks B, Wang Y, Eskin E, Simecek P, Churchill GA, Lusis AJ. High-Density Genotypes of Inbred Mouse Strains: Improved Power and Precision of Association Mapping.. G3 (Bethesda, Md.), 2015.
107. Nanda V, Gutman B, Bar E, Alghamdi S, Tetradis S, Lusis AJ, Eskin E, Moon W. Quantitative analysis of 3-dimensional facial soft tissue photographic images: technical methods and clinical application.. Progress in orthodontics, 2015.
108. Hormozdiari F, Kichaev G, Yang WY, Pasaniuc B, Eskin E. Identification of causal genes for complex traits.. Bioinformatics (Oxford, England), 2015.
109. Lavinsky J, Crow AL, Pan C, Wang J, Aaron KA, Ho MK, Li Q, Salehide P, Myint A, Monges-Hernadez M, Eskin E, Allayee H, Lusis AJ, Friedman RA. Correction: Genome-Wide Association Study Identifies Nox3 as a Critical Gene for Susceptibility to Noise-Induced Hearing Loss.. PLoS genetics, 2015.
110. Zhou X, Crow AL, Hartiala J, Spindler TJ, Ghazalpour A, Barsky LW, Bennett BJ, Parks BW, Eskin E, Jain R, Epstein JA, Lusis AJ, Adams GB, Allayee H. The Genetic Landscape of Hematopoietic Stem Cell Frequency in Mice.. Stem cell reports, 2015.
111. Sul JH, Raj T, de Jong S, de Bakker PI, Raychaudhuri S, Ophoff RA, Stranger BE, Eskin E, Han B. Accurate and fast multiple-testing correction in eQTL studies.. American journal of human genetics, 2015.
112. Lavinsky J, Crow AL, Pan C, Wang J, Aaron KA, Ho MK, Li Q, Salehide P, Myint A, Monges-Hernadez M, Eskin E, Allayee H, Lusis AJ, Friedman RA. Genome-wide association study identifies nox3 as a critical gene for susceptibility to noise-induced hearing loss.. PLoS genetics, 2015.
113. Wang Z, Sul JH, Snir S, Lozano JA, Eskin E. Gene-Gene Interactions Detection Using a Two-stage Model.. Journal of computational biology : a journal of computational molecular cell biology, 2015.
114. Furlotte NA, Eskin E. Efficient multiple-trait association and estimation of genetic correlation using the matrix-variate linear mixed model.. Genetics, 2015.
115. Luykx JJ, Bakker SC, Visser WF, Verhoeven-Duif N, Buizer-Voskamp JE, den Heijer JM, Boks MP, Sul JH, Eskin E, Ori AP, Cantor RM, Vorstman J, Strengman E, DeYoung J, Kappen TH, Pariama E, van Dongen EP, Borgdorff P, Bruins P, de Koning TJ, Kahn RS, Ophoff RA. Genome-wide association study of NMDA receptor coagonists in human cerebrospinal fluid and plasma.. Molecular psychiatry, 2015.
116. Hiyari S, Atti E, Camargo PM, Eskin E, Lusis AJ, Tetradis S, Pirih FQ. Heritability of periodontal bone loss in mice.. Journal of periodontal research, 2015.
117. Yang WY, Hormozdiari F, Eskin E, Pasaniuc B. A spatial haplotype copying model with applications to genotype imputation.. Journal of computational biology : a journal of computational molecular cell biology, 2014.
118. Hormozdiari F, Eskin E. Memory efficient assembly of human genome.. Journal of bioinformatics and computational biology, 2014.
119. He D, Eskin E. IPED2X: a robust pedigree reconstruction algorithm for complicated pedigrees.. Journal of bioinformatics and computational biology, 2014.
120. Yang WY, Platt A, Chiang CW, Eskin E, Novembre J, Pasaniuc B. Spatial localization of recent ancestors for admixed individuals.. G3 (Bethesda, Md.), 2014.
121. Kichaev G, Yang WY, Lindstrom S, Hormozdiari F, Eskin E, Price AL, Kraft P, Pasaniuc B. Integrating functional data to prioritize causal variants in statistical fine-mapping studies.. PLoS genetics, 2014.
122. Hormozdiari F, Kostem E, Kang EY, Pasaniuc B, Eskin E. Identifying causal variants at loci with multiple signals of association.. Genetics, 2014.
123. Mangul S, Wu NC, Mancuso N, Zelikovsky A, Sun R, Eskin E. Accurate viral population assembly from ultra-deep sequencing data.. Bioinformatics (Oxford, England), 2014.
124. Hormozdiari F, Joo JW, Wadia A, Guan F, Ostrosky R, Sahai A, Eskin E. Privacy preserving protocol for detecting genetic relatives using rare variants.. Bioinformatics (Oxford, England), 2014.
125. Hasin-Brumshtein Y, Hormozdiari F, Martin L, van Nas A, Eskin E, Lusis AJ, Drake TA. Allele-specific expression and eQTL analysis in mouse adipose tissue.. BMC genomics, 2014.
126. Joo JW, Sul JH, Han B, Ye C, Eskin E. Effectively identifying regulatory hotspots while capturing expression heterogeneity in gene expression studies.. Genome biology, 2014.
127. He D, Furlotte NA, Hormozdiari F, Joo JW, Wadia A, Ostrovsky R, Sahai A, Eskin E. Identifying genetic relatives without compromising privacy.. Genome research, 2014.
128. Ohmen J, Kang EY, Li X, Joo JW, Hormozdiari F, Zheng QY, Davis RC, Lusis AJ, Eskin E, Friedman RA. Genome-wide association study for age-related hearing loss (AHL) in the mouse: a meta-analysis.. Journal of the Association for Research in Otolaryngology : JARO, 2014.
129. Zhang K, Huentelman MJ, Rao F, Sun EI, Corneveaux JJ, Schork AJ, Wei Z, Waalen J, Miramontes-Gonzalez JP, Hightower CM, Maihofer AX, Mahata M, Pastinen T, Ehret GB, International Consortium for Blood Pressure Genome-Wide Association Studies, Schork NJ, Eskin E, Nievergelt CM, Saier MH, O'Connor DT. Genetic implication of a novel thiamine transporter in human hypertension.. Journal of the American College of Cardiology, 2014.
130. Marsden CD, Lee Y, Kreppel K, Weakley A, Cornel A, Ferguson HM, Eskin E, Lanzaro GC. Diversity, differentiation, and linkage disequilibrium: prospects for association mapping in the malaria vector Anopheles arabiensis.. G3 (Bethesda, Md.), 2014.
131. Kang EY, Han B, Furlotte N, Joo JW, Shih D, Davis RC, Lusis AJ, Eskin E. Meta-analysis identifies gene-by-environment interactions as demonstrated in a study of 4,965 mice.. PLoS genetics, 2014.
132. Han B, Kang EY, Raychaudhuri S, de Bakker PI, Eskin E. Fast pairwise IBD association testing in genome-wide association studies.. Bioinformatics (Oxford, England), 2013.
133. Eskin I, Hormozdiari F, Conde L, Riby J, Skibola CF, Eskin E, Halperin E. eALPS: estimating abundance levels in pooled sequencing using available genotyping data.. Journal of computational biology : a journal of computational molecular cell biology, 2013.
134. He D, Wang Z, Han B, Parida L, Eskin E. IPED: inheritance path-based pedigree reconstruction algorithm using genotype data.. Journal of computational biology : a journal of computational molecular cell biology, 2013.
135. Kostem E, Eskin E. Efficiently identifying significant associations in genome-wide association studies.. Journal of computational biology : a journal of computational molecular cell biology, 2013.
136. Lagarrigue S, Martin L, Hormozdiari F, Roux PF, Pan C, van Nas A, Demeure O, Cantor R, Ghazalpour A, Eskin E, Lusis AJ. Analysis of allele-specific expression in mouse liver by RNA-Seq: a comparison with Cis-eQTL identified using genetic linkage.. Genetics, 2013.
137. Leikauf GD, Concel VJ, Bein K, Liu P, Berndt A, Martin TM, Ganguly K, Jang AS, Brant KA, Dopico RA, Upadhyay S, Cario C, Di YP, Vuga LJ, Kostem E, Eskin E, You M, Kaminski N, Prows DR, Knoell DL, Fabisiak JP. Functional genomic assessment of phosgene-induced acute lung injury in mice.. American journal of respiratory cell and molecular biology, 2013.
138. Yang WY, Hormozdiari F, Wang Z, He D, Pasaniuc B, Eskin E. Leveraging reads that span multiple single nucleotide polymorphisms for haplotype inference from sequencing data.. Bioinformatics (Oxford, England), 2013.
139. Sul JH, Han B, Ye C, Choi T, Eskin E. Effectively identifying eQTLs from multiple tissues by combining mixed model and meta-analytic approaches.. PLoS genetics, 2013.
140. Navon O, Sul JH, Han B, Conde L, Bracci PM, Riby J, Skibola CF, Eskin E, Halperin E. Rare variant association testing under low-coverage sequencing.. Genetics, 2013.
141. Kostem E, Eskin E. Improving the accuracy and efficiency of partitioning heritability into the contributions of genomic regions.. American journal of human genetics, 2013.
142. Sul JH, Eskin E. Mixed models can correct for population structure for genomic regions under selection.. Nature reviews. Genetics, 2013.
143. Wang Z, Hormozdiari F, Yang WY, Halperin E, Eskin E. CNVeM: copy number variation detection using uncertainty of read mapping.. Journal of computational biology : a journal of computational molecular cell biology, 2013.
144. Davis RC, van Nas A, Bennett B, Orozco L, Pan C, Rau CD, Eskin E, Lusis AJ. Genome-wide association mapping of blood cell traits in mice.. Mammalian genome : official journal of the International Mammalian Genome Society, 2013.
145. Lagarrigue S, Hormozdiari F, Martin LJ, Lecerf F, Hasin Y, Rau C, Hagopian R, Xiao Y, Yan J, Drake TA, Ghazalpour A, Eskin E, Lusis AJ. Limited RNA editing in exons of mouse liver and adipose.. Genetics, 2013.
146. He D, Han B, Eskin E. Hap-seq: an optimal algorithm for haplotype phasing with imputation using sequencing data.. Journal of computational biology : a journal of computational molecular cell biology, 2013.
147. Parrish N, Sudakov B, Eskin E. Genome reassembly with high-throughput sequencing data.. BMC genomics, 2013.
148. Luykx JJ, Bakker SC, Lentjes E, Neeleman M, Strengman E, Mentink L, DeYoung J, de Jong S, Sul JH, Eskin E, van Eijk K, van Setten J, Buizer-Voskamp JE, Cantor RM, Lu A, van Amerongen M, van Dongen EP, Keijzers P, Kappen T, Borgdorff P, Bruins P, Derks EM, Kahn RS, Ophoff RA. Genome-wide association study of monoamine metabolite levels in human cerebrospinal fluid.. Molecular psychiatry, 2013.
149. Parks BW, Nam E, Org E, Kostem E, Norheim F, Hui ST, Pan C, Civelek M, Rau CD, Bennett BJ, Mehrabian M, Ursell LK, He A, Castellani LW, Zinker B, Kirby M, Drake TA, Drevon CA, Knight R, Gargalovic P, Kirchgessner T, Eskin E, Lusis AJ. Genetic control of obesity and gut microbiota composition in response to high-fat, high-sucrose diet in mice.. Cell metabolism, 2013.
150. Calabrese G, Bennett BJ, Orozco L, Kang HM, Eskin E, Dombret C, De Backer O, Lusis AJ, Farber CR. Systems genetic analysis of osteoblast-lineage cells.. PLoS genetics, 2012.
151. He D, Eskin E. Hap-seqX: expedite algorithm for haplotype phasing with imputation using sequence data.. Gene, 2012.
152. Miller MB, Basu S, Cunningham J, Eskin E, Malone SM, Oetting WS, Schork N, Sul JH, Iacono WG, McGue M. The Minnesota Center for Twin and Family Research genome-wide association study.. Twin research and human genetics : the official journal of the International Society for Twin Studies, 2012.
153. Flint J, Eskin E. Genome-wide association studies in mice.. Nature reviews. Genetics, 2012.
154. Ghazalpour A, Rau CD, Farber CR, Bennett BJ, Orozco LD, van Nas A, Pan C, Allayee H, Beaven SW, Civelek M, Davis RC, Drake TA, Friedman RA, Furlotte N, Hui ST, Jentsch JD, Kostem E, Kang HM, Kang EY, Joo JW, Korshunov VA, Laughlin RE, Martin LJ, Ohmen JD, Parks BW, Pellegrini M, Reue K, Smith DJ, Tetradis S, Wang J, Wang Y, Weiss JN, Kirchgessner T, Gargalovic PS, Eskin E, Lusis AJ, LeBoeuf RC. Hybrid mouse diversity panel: a panel of inbred mouse strains suitable for analysis of complex genetic traits.. Mammalian genome : official journal of the International Mammalian Genome Society, 2012.
155. Scharf JM, Yu D, Mathews CA, Neale BM, Stewart SE, Fagerness JA, Evans P, Gamazon E, Edlund CK, Service SK, Tikhomirov A, Osiecki L, Illmann C, Pluzhnikov A, Konkashbaev A, Davis LK, Han B, Crane J, Moorjani P, Crenshaw AT, Parkin MA, Reus VI, Lowe TL, Rangel-Lugo M, Chouinard S, Dion Y, Girard S, Cath DC, Smit JH, King RA, Fernandez TV, Leckman JF, Kidd KK, Kidd JR, Pakstis AJ, State MW, Herrera LD, Romero R, Fournier E, Sandor P, Barr CL, Phan N, Gross-Tsur V, Benarroch F, Pollak Y, Budman CL, Bruun RD, Erenberg G, Naarden AL, Lee PC, Weiss N, Kremeyer B, Berrío GB, Campbell DD, Cardona Silgado JC, Ochoa WC, Mesa Restrepo SC, Muller H, Valencia Duarte AV, Lyon GJ, Leppert M, Morgan J, Weiss R, Grados MA, Anderson K, Davarya S, Singer H, Walkup J, Jankovic J, Tischfield JA, Heiman GA, Gilbert DL, Hoekstra PJ, Robertson MM, Kurlan R, Liu C, Gibbs JR, Singleton A, North American Brain Expression Consortium, Hardy J, UK Human Brain Expression Database, Strengman E, Ophoff RA, Wagner M, Moessner R, Mirel DB, Posthuma D, Sabatti C, Eskin E, Conti DV, Knowles JA, Ruiz-Linares A, Rouleau GA, Purcell S, Heutink P, Oostra BA, McMahon WM, Freimer NB, Cox NJ, Pauls DL. Genome-wide association study of Tourette's syndrome.. Molecular psychiatry, 2012.
156. Weiss JN, Karma A, MacLellan WR, Deng M, Rau CD, Rees CM, Wang J, Wisniewski N, Eskin E, Horvath S, Qu Z, Wang Y, Lusis AJ. "Good enough solutions" and the genetics of complex diseases.. Circulation research, 2012.
157. Hersch M, Peter B, Kang HM, Schüpfer F, Abriel H, Pedrazzini T, Eskin E, Beckmann JS, Bergmann S, Maurer F. Mapping genetic variants associated with beta-adrenergic responses in inbred mice.. PloS one, 2012.
158. Bennett BJ, Orozco L, Kostem E, Erbilgin A, Dallinga M, Neuhaus I, Guan B, Wang X, Eskin E, Lusis AJ. High-resolution association mapping of atherosclerosis loci in mice.. Arteriosclerosis, thrombosis, and vascular biology, 2012.
159. Darnell G, Duong D, Han B, Eskin E. Incorporating prior information into association studies.. Bioinformatics (Oxford, England), 2012.
160. Friese RS, Ye C, Nievergelt CM, Schork AJ, Mahapatra NR, Rao F, Napolitan PS, Waalen J, Ehret GB, Munroe PB, Schmid-Schönbein GW, Eskin E, O'Connor DT. Integrated computational and experimental analysis of the neuroendocrine transcriptome in genetic hypertension identifies novel control points for the cardiometabolic syndrome.. Circulation. Cardiovascular genetics, 2012.
161. Listgarten J, Lippert C, Kadie CM, Davidson RI, Eskin E, Heckerman D. Improved linear mixed models for genome-wide association studies.. Nature methods, 2012.
162. Yang WY, Novembre J, Eskin E, Halperin E. A model-based approach for analysis of spatial structure in genetic data.. Nature genetics, 2012.
163. Furlotte NA, Eskin E, Eyheramendy S. Genome-wide association mapping with longitudinal data.. Genetic epidemiology, 2012.
164. Furlotte NA, Kang EY, Van Nas A, Farber CR, Lusis AJ, Eskin E. Increasing association mapping power and resolution in mouse genetic studies through the use of meta-analysis for structured populations.. Genetics, 2012.
165. Han B, Eskin E. Interpreting meta-analyses of genome-wide association studies.. PLoS genetics, 2012.
166. Lerman SE, Eskin E, Flower DJ, George EC, Gerson B, Hartenbaum N, Hursh SR, Moore-Ede M, American College of Occupational and Environmental Medicine Presidential Task Force on Fatigue Risk . Fatigue risk management in the workplace.. Journal of occupational and environmental medicine, 2012.
167. Sul JH, Han B, Eskin E. Increasing power of groupwise association test with likelihood ratio test.. Journal of computational biology : a journal of computational molecular cell biology, 2011.
168. Keane TM, Goodstadt L, Danecek P, White MA, Wong K, Yalcin B, Heger A, Agam A, Slater G, Goodson M, Furlotte NA, Eskin E, Nellåker C, Whitley H, Cleak J, Janowitz D, Hernandez-Pliego P, Edwards A, Belgard TG, Oliver PL, McIntyre RE, Bhomra A, Nicod J, Gan X, Yuan W, van der Weyden L, Steward CA, Bala S, Stalker J, Mott R, Durbin R, Jackson IJ, Czechanski A, Guerra-Assunção JA, Donahue LR, Reinholdt LG, Payseur BA, Ponting CP, Birney E, Flint J, Adams DJ. Mouse genomic variation and its effect on phenotypes and gene regulation.. Nature, 2011.
169. Parrish N, Hormozdiari F, Eskin E. Assembly of non-unique insertion content using next-generation sequencing.. BMC bioinformatics, 2011.
170. He D, Zaitlen N, Pasaniuc B, Eskin E, Halperin E. Genotyping common and rare variation using overlapping pool sequencing.. BMC bioinformatics, 2011.
171. Furlotte NA, Kang HM, Ye C, Eskin E. Mixed-model coexpression: calculating gene coexpression while accounting for expression heterogeneity.. Bioinformatics (Oxford, England), 2011.
172. Ghazalpour A, Bennett B, Petyuk VA, Orozco L, Hagopian R, Mungrue IN, Farber CR, Sinsheimer J, Kang HM, Furlotte N, Park CC, Wen PZ, Brewer H, Weitz K, Camp DG, Pan C, Yordanova R, Neuhaus I, Tilford C, Siemers N, Gargalovic P, Eskin E, Kirchgessner T, Smith DJ, Smith RD, Lusis AJ. Comparative analysis of proteome and transcriptome variation in mouse.. PLoS genetics, 2011.
173. Han B, Eskin E. Random-effects model aimed at discovering associations in meta-analysis of genome-wide association studies.. American journal of human genetics, 2011.
174. Van Tyne D, Park DJ, Schaffner SF, Neafsey DE, Angelino E, Cortese JF, Barnes KG, Rosen DM, Lukens AK, Daniels RF, Milner DA, Johnson CA, Shlyakhter I, Grossman SR, Becker JS, Yamins D, Karlsson EK, Ndiaye D, Sarr O, Mboup S, Happi C, Furlotte NA, Eskin E, Kang HM, Hartl DL, Birren BW, Wiegand RC, Lander ES, Wirth DF, Volkman SK, Sabeti PC. Identification and functional validation of the novel antimalarial resistance locus PF10_0355 in Plasmodium falciparum.. PLoS genetics, 2011.
175. He D, Hormozdiari F, Furlotte N, Eskin E. Efficient algorithms for tandem copy number variation reconstruction in repeat-rich regions.. Bioinformatics (Oxford, England), 2011.
176. Farber CR, Bennett BJ, Orozco L, Zou W, Lira A, Kostem E, Kang HM, Furlotte N, Berberyan A, Ghazalpour A, Suwanwela J, Drake TA, Eskin E, Wang QT, Teitelbaum SL, Lusis AJ. Mouse genome-wide association and systems genetics identify Asxl2 as a regulator of bone mineral density and osteoclastogenesis.. PLoS genetics, 2011.
177. Kostem E, Lozano JA, Eskin E. Increasing power of genome-wide association studies by collecting additional single-nucleotide polymorphisms.. Genetics, 2011.
178. Park CC, Gale GD, de Jong S, Ghazalpour A, Bennett BJ, Farber CR, Langfelder P, Lin A, Khan AH, Eskin E, Horvath S, Lusis AJ, Ophoff RA, Smith DJ. Gene networks associated with conditional fear in mice identified using a systems genetics approach.. BMC systems biology, 2011.
179. Sul JH, Han B, He D, Eskin E. An optimal weighted aggregated association test for identification of rare variants involved in common diseases.. Genetics, 2011.
180. Han B, Hackel BM, Eskin E. Postassociation cleaning using linkage disequilibrium information.. Genetic epidemiology, 2011.
181. He D, Furlotte N, Eskin E. Detection and reconstruction of tandemly organized de novo copy number variations.. BMC bioinformatics, 2010.
182. Kenny EE, Kim M, Gusev A, Lowe JK, Salit J, Smith JG, Kovvali S, Kang HM, Newton-Cheh C, Daly MJ, Stoffel M, Altshuler DM, Friedman JM, Eskin E, Breslow JL, Pe'er I. Increased power of mixed models facilitates association mapping of 10 loci for metabolic traits in an isolated population.. Human molecular genetics, 2010.
183. McLachlan S, Lee SM, Steele TM, Hawthorne PL, Zapala MA, Eskin E, Schork NJ, Anderson GJ, Vulpe CD. In silico QTL mapping of basal liver iron levels in inbred mouse strains.. Physiological genomics, 2010.
184. Zaitlen N, Eskin E. Imputation aware meta-analysis of genome-wide association studies.. Genetic epidemiology, 2010.
185. Santana R, Mendiburu A, Zaitlen N, Eskin E, Lozano JA. Multi-marker tagging single nucleotide polymorphism selection using estimation of distribution algorithms.. Artificial intelligence in medicine, 2010.
186. He D, Choi A, Pipatsrisawat K, Darwiche A, Eskin E. Optimal algorithms for haplotype assembly from whole-genome sequence data.. Bioinformatics (Oxford, England), 2010.
187. Zhang K, Weder AB, Eskin E, O'Connor DT. Genome-wide case/control studies in hypertension: only the 'tip of the iceberg'.. Journal of hypertension, 2010.
188. Kirby A, Kang HM, Wade CM, Cotsapas C, Kostem E, Han B, Furlotte N, Kang EY, Rivas M, Bogue MA, Frazer KA, Johnson FM, Beilharz EJ, Cox DR, Eskin E, Daly MJ. Fine mapping in 94 inbred mouse strains using a high-density haplotype resource.. Genetics, 2010.
189. Kang HM, Sul JH, Service SK, Zaitlen NA, Kong SY, Freimer NB, Sabatti C, Eskin E. Variance component model to account for sample structure in genome-wide association studies.. Nature genetics, 2010.
190. Kang EY, Ye C, Shpitser I, Eskin E. Detecting the presence and absence of causal relationships between expression of yeast genes with very few samples.. Journal of computational biology : a journal of computational molecular cell biology, 2010.
191. Kang HM, Zaitlen NA, Eskin E. EMINIM: an adaptive and memory-efficient algorithm for genotype imputation.. Journal of computational biology : a journal of computational molecular cell biology, 2010.
192. Stein JL, Hua X, Morra JH, Lee S, Hibar DP, Ho AJ, Leow AD, Toga AW, Sul JH, Kang HM, Eskin E, Saykin AJ, Shen L, Foroud T, Pankratz N, Huentelman MJ, Craig DW, Gerber JD, Allen AN, Corneveaux JJ, Stephan DA, Webster J, DeChairo BM, Potkin SG, Jack CR, Weiner MW, Thompson PM, Alzheimer's Disease Neuroimaging Initiative. Genome-wide analysis reveals novel genes influencing temporal lobe structure with relevance to neurodegeneration in Alzheimer's disease.. NeuroImage, 2010.
193. Bennett BJ, Farber CR, Orozco L, Kang HM, Ghazalpour A, Siemers N, Neubauer M, Neuhaus I, Yordanova R, Guan B, Truong A, Yang WP, He A, Kayne P, Gargalovic P, Kirchgessner T, Pan C, Castellani LW, Kostem E, Furlotte N, Drake TA, Eskin E, Lusis AJ. A high-resolution association mapping panel for the dissection of complex traits in mice.. Genome research, 2010.
194. Yang IV, Wade CM, Kang HM, Alper S, Rutledge H, Lackford B, Eskin E, Daly MJ, Schwartz DA. Identification of novel genes that mediate innate immunity using inbred mice.. Genetics, 2009.
195. Rana BK, Wessel J, Mahboubi V, Rao F, Haeller J, Gayen JR, Eskin E, Valle AM, Das M, Mahata SK, Taupenot L, Stridsberg M, Talley TT, Ziegler MG, Smith DW, Schork NJ, O'Connor DT, Taylor P. Natural variation within the neuronal nicotinic acetylcholine receptor cluster on human chromosome 15q24: influence on heritable autonomic traits in twin pairs.. The Journal of pharmacology and experimental therapeutics, 2009.
196. Smith EN, Bloss CS, Badner JA, Barrett T, Belmonte PL, Berrettini W, Byerley W, Coryell W, Craig D, Edenberg HJ, Eskin E, Foroud T, Gershon E, Greenwood TA, Hipolito M, Koller DL, Lawson WB, Liu C, Lohoff F, McInnis MG, McMahon FJ, Mirel DB, Murray SS, Nievergelt C, Nurnberger J, Nwulia EA, Paschall J, Potash JB, Rice J, Schulze TG, Scheftner W, Panganiban C, Zaitlen N, Zandi PP, Zöllner S, Schork NJ, Kelsoe JR. Genome-wide association study of bipolar disorder in European American and African American individuals.. Molecular psychiatry, 2009.
197. Han B, Kang HM, Eskin E. Rapid and accurate multiple testing correction and power estimation for millions of correlated markers.. PLoS genetics, 2009.
198. Zaitlen N, Kang HM, Eskin E. Linkage effects and analysis of finite sample errors in the HapMap.. Human heredity, 2009.
199. Ye C, Galbraith SJ, Liao JC, Eskin E. Using network component analysis to dissect regulatory networks mediated by transcription factors in yeast.. PLoS computational biology, 2009.
200. Kang HM, Ye C, Eskin E. Accurate discovery of expression quantitative trait loci under confounding from spurious and genuine regulatory hotspots.. Genetics, 2008.
201. Han B, Kang HM, Seo MS, Zaitlen N, Eskin E. Efficient association study design via power-optimized tag SNP selection.. Annals of human genetics, 2008.
202. Ghazalpour A, Doss S, Kang H, Farber C, Wen PZ, Brozell A, Castellanos R, Eskin E, Smith DJ, Drake TA, Lusis AJ. High-resolution mapping of gene expression using association in an outbred mouse stock.. PLoS genetics, 2008.
203. Eskin E. Increasing power in association studies by using linkage disequilibrium structure and molecular function as prior information.. Genome research, 2008.
204. Kang HM, Zaitlen NA, Wade CM, Kirby A, Heckerman D, Daly MJ, Eskin E. Efficient control of population structure in model organism association mapping.. Genetics, 2008.
205. Olshen AB, Gold B, Lohmueller KE, Struewing JP, Satagopan J, Stefanov SA, Eskin E, Kirchhoff T, Lautenberger JA, Klein RJ, Friedman E, Norton L, Ellis NA, Viale A, Lee CS, Borgen PI, Clark AG, Offit K, Boyd J. Analysis of genetic variation in Ashkenazi Jews by high density SNP genotyping.. BMC genetics, 2008.
206. Barrett TB, Emberton JE, Nievergelt CM, Liang SG, Hauger RL, Eskin E, Schork NJ, Kelsoe JR. Further evidence for association of GRK3 to bipolar disorder suggests a second disease mutation.. Psychiatric genetics, 2007.
207. Frazer KA, Eskin E, Kang HM, Bogue MA, Hinds DA, Beilharz EJ, Gupta RV, Montgomery J, Morenzoni MM, Nilsen GB, Pethiyagoda CL, Stuve LL, Johnson FM, Daly MJ, Wade CM, Cox DR. A sequence-based variation map of 8.27 million SNPs in inbred mouse strains.. Nature, 2007.
208. Eskin E, Snir S. Incorporating homologues into sequence embeddings for protein analysis.. Journal of bioinformatics and computational biology, 2007.
209. Rao F, Wen G, Gayen JR, Das M, Vaingankar SM, Rana BK, Mahata M, Kennedy BP, Salem RM, Stridsberg M, Abel K, Smith DW, Eskin E, Schork NJ, Hamilton BA, Ziegler MG, Mahata SK, O'Connor DT. Catecholamine release-inhibitory peptide catestatin (chromogranin A(352-372)): naturally occurring amino acid variant Gly364Ser causes profound changes in human autonomic activity and alters risk for hypertension.. Circulation, 2007.
210. Zaitlen N, Kang HM, Eskin E, Halperin E. Leveraging the HapMap correlation structure in association studies.. American journal of human genetics, 2007.
211. Ye C, Eskin E. Discovering tightly regulated and differentially expressed gene sets in whole genome expression data.. Bioinformatics (Oxford, England), 2007.
212. Eskin E, Sharan R, Halperin E. A note on phasing long genomic regions using local haplotype predictions.. Journal of bioinformatics and computational biology, 2006.
213. O'Rourke S, Chechik G, Friedman R, Eskin E. Discrete profile comparison using information bottleneck.. BMC bioinformatics, 2006.
214. Greenwood TA, Schork NJ, Eskin E, Kelsoe JR. Identification of additional variants within the human dopamine transporter gene provides further evidence for an association with bipolar disorder in two independent samples.. Molecular psychiatry, 2006.
215. Marchini J, Cutler D, Patterson N, Stephens M, Eskin E, Halperin E, Lin S, Qin ZS, Munro HM, Abecasis GR, Donnelly P, International HapMap Consortium. A comparison of phasing algorithms for trios and unrelated individuals.. American journal of human genetics, 2006.
216. Riddle EL, Rana BK, Murthy KK, Rao F, Eskin E, O'Connor DT, Insel PA. Polymorphisms and haplotypes of the regulator of G protein signaling-2 gene in normotensives and hypertensives.. Hypertension (Dallas, Tex. : 1979), 2006.
217. Zaitlen NA, Kang HM, Feolo ML, Sherry ST, Halperin E, Eskin E. Inference and analysis of haplotypes from combined genotyping studies deposited in dbSNP.. Genome research, 2005.
218. Zhang S, Haas B, Eskin E, Bafna V. Searching genomes for noncoding RNA using FastR.. IEEE/ACM transactions on computational biology and bioinformatics, 2005.
219. Hinds DA, Stuve LL, Nilsen GB, Halperin E, Eskin E, Ballinger DG, Frazer KA, Cox DR. Whole-genome patterns of common DNA variation in three human populations.. Science (New York, N.Y.), 2005.
220. Tompa M, Li N, Bailey TL, Church GM, De Moor B, Eskin E, Favorov AV, Frith MC, Fu Y, Kent WJ, Makeev VJ, Mironov AA, Noble WS, Pavesi G, Pesole G, Régnier M, Simonis N, Sinha S, Thijs G, van Helden J, Vandenbogaert M, Weng Z, Workman C, Ye C, Zhu Z. Assessing computational tools for the discovery of transcription factor binding sites.. Nature biotechnology, 2005.
221. Price AL, Eskin E, Pevzner PA. Whole-genome analysis of Alu repeat elements reveals complex evolutionary history.. Genome research, 2004.
222. Halperin E, Eskin E. Haplotype reconstruction from genotype data using Imperfect Phylogeny.. Bioinformatics (Oxford, England), 2004.
223. Leslie CS, Eskin E, Cohen A, Weston J, Noble WS. Mismatch string kernels for discriminative protein classification.. Bioinformatics (Oxford, England), 2004.
224. Eskin E, Agichtein E. Combining text mining and sequence analysis to discover protein functional regions.. Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing, 2004.
225. Eskin E, Halperin E, Karp RM. Efficient reconstruction of haplotype structure via perfect phylogeny.. Journal of bioinformatics and computational biology, 2003.
226. Eskin E, Keich U, Gelfand MS, Pevzner PA. Genome-wide analysis of bacterial promoter regions.. Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing, 2003.
227. Eskin E, Noble WS, Singer Y. Protein family classification using sparse markov transducers.. Journal of computational biology : a journal of computational molecular cell biology, 2003.
228. Eskin E, Pevzner PA. Finding composite regulatory patterns in DNA sequences.. Bioinformatics (Oxford, England), 2002.
229. Leslie C, Eskin E, Noble WS. The spectrum kernel: a string kernel for SVM protein classification.. Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing, 2002.
230. Eskin E, Noble WS, Singer Y. Using substitution matrices to estimate probability distributions for biological sequences.. Journal of computational biology : a journal of computational molecular cell biology, 2002.
231. Eskin E, Grundy WN, Singer Y. Using mixtures of common ancestors for estimating the probabilities of discrete events in biological sequences.. Bioinformatics (Oxford, England), 2001.
232. Eskin E, Grundy WN, Singer Y. Protein family classification using sparse Markov transducers.. Proceedings. International Conference on Intelligent Systems for Molecular Biology, 2000.
233. Kniskern JH, Eskin EM, Fletcher HS. Increasing accuracy in the diagnosis of acute appendicitis with modern diagnostic techniques.. The American surgeon, 1986.