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Items: 1 to 50 of 175

1.

Word and Sentence Embedding Tools to Measure Semantic Similarity of Gene Ontology Terms by Their Definitions.

Duong D, Ahmad WU, Eskin E, Chang KW, Li JJ.

J Comput Biol. 2018 Oct 31. doi: 10.1089/cmb.2018.0093. [Epub ahead of print]

PMID:
30383443
2.

Improving Imputation Accuracy by Inferring Causal Variants in Genetic Studies.

Wu Y, Hormozdiari F, Joo JWJ, Eskin E.

J Comput Biol. 2018 Oct 1. doi: 10.1089/cmb.2018.0139. [Epub ahead of print]

PMID:
30272994
3.

BayesCCE: a Bayesian framework for estimating cell-type composition from DNA methylation without the need for methylation reference.

Rahmani E, Schweiger R, Shenhav L, Wingert T, Hofer I, Gabel E, Eskin E, Halperin E.

Genome Biol. 2018 Sep 21;19(1):141. doi: 10.1186/s13059-018-1513-2.

4.

Using an atlas of gene regulation across 44 human tissues to inform complex disease- and trait-associated variation.

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.

Nat Genet. 2018 Jul;50(7):956-967. doi: 10.1038/s41588-018-0154-4. Epub 2018 Jun 28.

PMID:
29955180
5.

Finding associated variants in genome-wide association studies on multiple traits.

Gai L, Eskin E.

Bioinformatics. 2018 Jul 1;34(13):i467-i474. doi: 10.1093/bioinformatics/bty249.

6.

Leveraging molecular quantitative trait loci to understand the genetic architecture of diseases and complex traits.

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.

Nat Genet. 2018 Jul;50(7):1041-1047. doi: 10.1038/s41588-018-0148-2. Epub 2018 Jun 25.

PMID:
29942083
7.

An integrated -omics analysis of the epigenetic landscape of gene expression in human blood cells.

Kennedy EM, Goehring GN, Nichols MH, Robins C, Mehta D, Klengel T, Eskin E, Smith AK, Conneely KN.

BMC Genomics. 2018 Jun 19;19(1):476. doi: 10.1186/s12864-018-4842-3.

8.

An Association Mapping Framework To Account for Potential Sex Difference in Genetic Architectures.

Kang EY, Lee CH, Furlotte NA, Joo JWJ, Kostem E, Zaitlen N, Eskin E, Han B.

Genetics. 2018 Jul;209(3):685-698. doi: 10.1534/genetics.117.300501. Epub 2018 May 11.

PMID:
29752291
9.

Transcriptome analysis in whole blood reveals increased microbial diversity in schizophrenia.

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.

Transl Psychiatry. 2018 May 10;8(1):96. doi: 10.1038/s41398-018-0107-9.

10.

Involving undergraduates in genomics research to narrow the education-research gap.

Mangul S, Martin LS, Eskin E.

Nat Biotechnol. 2018 Apr 5;36(4):369-371. doi: 10.1038/nbt.4113. No abstract available.

PMID:
29621227
11.

ROP: dumpster diving in RNA-sequencing to find the source of 1 trillion reads across diverse adult human tissues.

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.

Genome Biol. 2018 Feb 15;19(1):36. doi: 10.1186/s13059-018-1403-7.

12.

An ancestry-based approach for detecting interactions.

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.

Genet Epidemiol. 2018 Feb;42(1):49-63. doi: 10.1002/gepi.22087. Epub 2017 Nov 8.

PMID:
29114909
13.

Genetic variation and gene expression across multiple tissues and developmental stages in a nonhuman primate.

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.

Nat Genet. 2017 Dec;49(12):1714-1721. doi: 10.1038/ng.3959. Epub 2017 Oct 30.

14.

Loci associated with skin pigmentation identified in African populations.

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.

Science. 2017 Nov 17;358(6365). pii: eaan8433. doi: 10.1126/science.aan8433. Epub 2017 Oct 12.

15.

Incorporation of Biological Knowledge Into the Study of Gene-Environment Interactions.

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.

Am J Epidemiol. 2017 Oct 1;186(7):771-777. doi: 10.1093/aje/kwx229.

16.

Increasing the power of meta-analysis of genome-wide association studies to detect heterogeneous effects.

Lee CH, Eskin E, Han B.

Bioinformatics. 2017 Jul 15;33(14):i379-i388. doi: 10.1093/bioinformatics/btx242.

17.

Applying meta-analysis to genotype-tissue expression data from multiple tissues to identify eQTLs and increase the number of eGenes.

Duong D, Gai L, Snir S, Kang EY, Han B, Sul JH, Eskin E.

Bioinformatics. 2017 Jul 15;33(14):i67-i74. doi: 10.1093/bioinformatics/btx227.

18.

Addressing the Digital Divide in Contemporary Biology: Lessons from Teaching UNIX.

Mangul S, Martin LS, Hoffmann A, Pellegrini M, Eskin E.

Trends Biotechnol. 2017 Oct;35(10):901-903. doi: 10.1016/j.tibtech.2017.06.007. Epub 2017 Jul 15.

PMID:
28720283
19.

Widespread Allelic Heterogeneity in Complex Traits.

Hormozdiari F, Zhu A, Kichaev G, Ju CJ, Segrè AV, Joo JWJ, Won H, Sankararaman S, Pasaniuc B, Shifman S, Eskin E.

Am J Hum Genet. 2017 May 4;100(5):789-802. doi: 10.1016/j.ajhg.2017.04.005.

20.

IPED2: Inheritance Path Based Pedigree Reconstruction Algorithm for Complicated Pedigrees.

He D, Wang Z, Parida L, Eskin E.

IEEE/ACM Trans Comput Biol Bioinform. 2017 Sep-Oct;14(5):1094-1103. doi: 10.1109/TCBB.2017.2688439. Epub 2017 Mar 28.

PMID:
28368828
21.

Selection in Europeans on Fatty Acid Desaturases Associated with Dietary Changes.

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.

Mol Biol Evol. 2017 Jun 1;34(6):1307-1318. doi: 10.1093/molbev/msx103.

22.

HapIso: An Accurate Method for the Haplotype- Specific Isoforms Reconstruction From Long Single-Molecule Reads.

Mangul S, Yang TH, Hormozdiari F, Dainis AM, Tseng E, Ashley EA, Zelikovsky A, Eskin E.

IEEE Trans Nanobioscience. 2017 Mar;16(2):108-115. doi: 10.1109/TNB.2017.2675981. Epub 2017 Mar 17.

PMID:
28328508
23.

Correcting for cell-type heterogeneity in DNA methylation: a comprehensive evaluation.

Rahmani E, Zaitlen N, Baran Y, Eng C, Hu D, Galanter J, Oh S, Burchard EG, Eskin E, Zou J, Halperin E.

Nat Methods. 2017 Feb 28;14(3):218-219. doi: 10.1038/nmeth.4190. No abstract available.

24.

Simultaneous Modeling of Disease Status and Clinical Phenotypes To Increase Power in Genome-Wide Association Studies.

Bilow M, Crespo F, Pan Z, Eskin E, Eyheramendy S.

Genetics. 2017 Mar;205(3):1041-1047. doi: 10.1534/genetics.116.198473. Epub 2017 Jan 27.

25.

Long Single-Molecule Reads Can Resolve the Complexity of the Influenza Virus Composed of Rare, Closely Related Mutant Variants.

Artyomenko A, Wu NC, Mangul S, Eskin E, Sun R, Zelikovsky A.

J Comput Biol. 2017 Jun;24(6):558-570. doi: 10.1089/cmb.2016.0146. Epub 2016 Nov 30.

26.

Colocalization of GWAS and eQTL Signals Detects Target Genes.

Hormozdiari F, van de Bunt M, Segrè AV, Li X, Joo JWJ, Bilow M, Sul JH, Sankararaman S, Pasaniuc B, Eskin E.

Am J Hum Genet. 2016 Dec 1;99(6):1245-1260. doi: 10.1016/j.ajhg.2016.10.003. Epub 2016 Nov 17.

27.

Improved methods for multi-trait fine mapping of pleiotropic risk loci.

Kichaev G, Roytman M, Johnson R, Eskin E, Lindström S, Kraft P, Pasaniuc B.

Bioinformatics. 2017 Jan 15;33(2):248-255. doi: 10.1093/bioinformatics/btw615. Epub 2016 Sep 22.

28.

Chromosome conformation elucidates regulatory relationships in developing human brain.

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.

Nature. 2016 Oct 27;538(7626):523-527. doi: 10.1038/nature19847. Epub 2016 Oct 19.

29.

Efficient and Accurate Multiple-Phenotype Regression Method for High Dimensional Data Considering Population Structure.

Joo JW, Kang EY, Org E, Furlotte N, Parks B, Hormozdiari F, Lusis AJ, Eskin E.

Genetics. 2016 Dec;204(4):1379-1390. Epub 2016 Oct 21.

30.

Discovering Single Nucleotide Polymorphisms Regulating Human Gene Expression Using Allele Specific Expression from RNA-seq Data.

Kang EY, Martin LJ, Mangul S, Isvilanonda W, Zou J, Ben-David E, Han B, Lusis AJ, Shifman S, Eskin E.

Genetics. 2016 Nov;204(3):1057-1064. doi: 10.1534/genetics.115.177246. Epub 2016 Oct 7.

31.

The Genetic Basis of Host Preference and Resting Behavior in the Major African Malaria Vector, Anopheles arabiensis.

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.

PLoS Genet. 2016 Sep 15;12(9):e1006303. doi: 10.1371/journal.pgen.1006303. eCollection 2016 Sep.

32.

Hypothalamic transcriptomes of 99 mouse strains reveal trans eQTL hotspots, splicing QTLs and novel non-coding genes.

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.

Elife. 2016 Sep 13;5. pii: e15614. doi: 10.7554/eLife.15614.

33.

The Genetic Architecture of Noise-Induced Hearing Loss: Evidence for a Gene-by-Environment Interaction.

Lavinsky J, Ge M, Crow AL, Pan C, Wang J, Salehi P, Myint A, Eskin E, Allayee H, Lusis AJ, Friedman RA.

G3 (Bethesda). 2016 Oct 13;6(10):3219-3228. doi: 10.1534/g3.116.032516.

34.

Using genomic annotations increases statistical power to detect eGenes.

Duong D, Zou J, Hormozdiari F, Sul JH, Ernst J, Han B, Eskin E.

Bioinformatics. 2016 Jun 15;32(12):i156-i163. doi: 10.1093/bioinformatics/btw272.

35.

Imputing Phenotypes for Genome-wide Association Studies.

Hormozdiari F, Kang EY, Bilow M, Ben-David E, Vulpe C, McLachlan S, Lusis AJ, Han B, Eskin E.

Am J Hum Genet. 2016 Jul 7;99(1):89-103. doi: 10.1016/j.ajhg.2016.04.013. Epub 2016 Jun 9.

36.

Fast and Accurate Construction of Confidence Intervals for Heritability.

Schweiger R, Kaufman S, Laaksonen R, Kleber ME, März W, Eskin E, Rosset S, Halperin E.

Am J Hum Genet. 2016 Jun 2;98(6):1181-1192. doi: 10.1016/j.ajhg.2016.04.016.

37.

ForestPMPlot: A Flexible Tool for Visualizing Heterogeneity Between Studies in Meta-analysis.

Kang EY, Park Y, Li X, Segrè AV, Han B, Eskin E.

G3 (Bethesda). 2016 Jul 7;6(7):1793-8. doi: 10.1534/g3.116.029439.

38.

Characterization of Expression Quantitative Trait Loci in Pedigrees from Colombia and Costa Rica Ascertained for Bipolar Disorder.

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.

PLoS Genet. 2016 May 13;12(5):e1006046. doi: 10.1371/journal.pgen.1006046. eCollection 2016 May.

39.

The Hybrid Mouse Diversity Panel: a resource for systems genetics analyses of metabolic and cardiovascular traits.

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.

J Lipid Res. 2016 Jun;57(6):925-42. doi: 10.1194/jlr.R066944. Epub 2016 Apr 19. Review.

40.

Multiple testing correction in linear mixed models.

Joo JW, Hormozdiari F, Han B, Eskin E.

Genome Biol. 2016 Apr 1;17:62. doi: 10.1186/s13059-016-0903-6.

41.

Sparse PCA corrects for cell type heterogeneity in epigenome-wide association studies.

Rahmani E, Zaitlen N, Baran Y, Eng C, Hu D, Galanter J, Oh S, Burchard EG, Eskin E, Zou J, Halperin E.

Nat Methods. 2016 May;13(5):443-5. doi: 10.1038/nmeth.3809. Epub 2016 Mar 28.

42.

Accounting for Population Structure in Gene-by-Environment Interactions in Genome-Wide Association Studies Using Mixed Models.

Sul JH, Bilow M, Yang WY, Kostem E, Furlotte N, He D, Eskin E.

PLoS Genet. 2016 Mar 4;12(3):e1005849. doi: 10.1371/journal.pgen.1005849. eCollection 2016 Mar.

43.

Correction: Genetic Architecture of Atherosclerosis in Mice: A Systems Genetics Analysis of Common Inbred Strains.

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.

PLoS Genet. 2016 Mar 2;12(3):e1005913. doi: 10.1371/journal.pgen.1005913. eCollection 2016 Mar. No abstract available.

44.

A general framework for meta-analyzing dependent studies with overlapping subjects in association mapping.

Han B, Duong D, Sul JH, de Bakker PI, Eskin E, Raychaudhuri S.

Hum Mol Genet. 2016 May 1;25(9):1857-66. doi: 10.1093/hmg/ddw049. Epub 2016 Feb 21.

45.

Genetic Architecture of Atherosclerosis in Mice: A Systems Genetics Analysis of Common Inbred Strains.

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.

PLoS Genet. 2015 Dec 22;11(12):e1005711. doi: 10.1371/journal.pgen.1005711. eCollection 2015 Dec. Erratum in: PLoS Genet. 2016 Mar;12(3):e1005913.

46.

The Genetic Architecture of Hearing Impairment in Mice: Evidence for Frequency-Specific Genetic Determinants.

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.

G3 (Bethesda). 2015 Sep 4;5(11):2329-39. doi: 10.1534/g3.115.021592.

47.

Genetic and environmental control of host-gut microbiota interactions.

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.

Genome Res. 2015 Oct;25(10):1558-69. doi: 10.1101/gr.194118.115. Epub 2015 Aug 10.

48.

High-Density Genotypes of Inbred Mouse Strains: Improved Power and Precision of Association Mapping.

Rau CD, Parks B, Wang Y, Eskin E, Simecek P, Churchill GA, Lusis AJ.

G3 (Bethesda). 2015 Jul 28;5(10):2021-6. doi: 10.1534/g3.115.020784.

49.

Quantitative analysis of 3-dimensional facial soft tissue photographic images: technical methods and clinical application.

Nanda V, Gutman B, Bar E, Alghamdi S, Tetradis S, Lusis AJ, Eskin E, Moon W.

Prog Orthod. 2015;16:21. doi: 10.1186/s40510-015-0082-0. Epub 2015 Jul 2.

50.

Identification of causal genes for complex traits.

Hormozdiari F, Kichaev G, Yang WY, Pasaniuc B, Eskin E.

Bioinformatics. 2015 Jun 15;31(12):i206-13. doi: 10.1093/bioinformatics/btv240.

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