Publications

Since 2013, we write summaries of new research papers and review articles. Scroll down or click here for a complete list of papers produced by our lab.

GWAS

Mouse Genetics

Population Structure

Review Articles

Publications

182 entries « 1 of 4 »

2016

Mangul, Serghei; Loohuis, Loes Olde M; Ori, Anil; Jospin, Guillaume; Koslicki, David; Yang, Harry Taegyun; Wu, Timothy; Boks, Marco P; Lomen-Hoerth, Catherine; Wiedau-Pazos, Martina; Cantor, Rita; de Vos, Willem M; Kahn, Rene S; Eskin, Eleazar; Ophoff, Roel A

Total RNA Sequencing reveals microbial communities in human blood and disease specific effects. Journal Article

BioRxiv, (057570), 2016.

Abstract | Links | BibTeX | Tags: blood microbiome, RNA sequencing, schizophrenia, unmapped reads

Mangul, Serghei; Yang, Harry Taegyun; Strauli, Nicolas; Gruhl, Franziska; Daley, Timothy; Christenson, Stephanie; Andersen, Agata Wesolowska; Spreafico, Roberto; Rios, Cydney; Eng, Celeste; Smith, Andrew D; Hernandez, Ryan D; Ophoff, Roel A; Santana, Jose Rodriguez; Woodruff, Prescott G; Burchard, Esteban; Seibold, Max A; Shifman, Sagiv; Eskin, Eleazar; Zaitlen, Noah

Dumpster diving in RNA-sequencing to find the source of every last read. Journal Article

BioRxiv, 2016.

Links | BibTeX | Tags: read origin protocol, RNA sequencing, unmapped reads

Han, Buhm; Duong, Dat; Sul, Jae Hoon; de Bakker, Paul I W; Eskin, Eleazar; Raychaudhuri, Soumya

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

Hum Mol Genet, 2016, ISSN: 1460-2083.

Abstract | Links | BibTeX | Tags: eQTL, genome-wide association studies, Meta-Analysis

Sul, Jae Hoon; Bilow, Michael; Yang, Wen-Yun Y; Kostem, Emrah; Furlotte, Nick; He, Dan; Eskin, Eleazar

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

PLoS Genet, 12 (3), pp. e1005849, 2016, ISSN: 1553-7404.

Abstract | Links | BibTeX | Tags: gene-by-environment interactions, genome-wide association studies, Mixed Models

Joo, Jong Wha J; Hormozdiari, Farhad; Han, Buhm; Eskin, Eleazar

Multiple testing correction in linear mixed models. Journal Article

Genome Biol, 17 (1), pp. 62, 2016, ISSN: 1474-760X.

Abstract | Links | BibTeX | Tags: genome-wide association studies, Mixed Models, Multiple Testing

Lusis, Aldons J; Seldin, Marcus; Allayee, Hooman; Bennett, Brian J; Civelek, Mete; Davis, Richard C; Eskin, Eleazar; Farber, Charles; Hui, Simon T; Mehrabian, Margarete; Norheim, Frode; Pan, Calvin; Parks, Brian; Rau, Christoph; Smith, Desmond J; Vallim, Thomas; Wang, Yibin; Wang, Jessica

The Hybrid Mouse Diversity Panel: A Resource for Systems Genetics Analyses of Metabolic and Cardiovascular Traits. Journal Article

J Lipid Res, 2016, ISSN: 1539-7262.

Abstract | Links | BibTeX | Tags: genome-wide association studies, Hybrid Mouse Diversity Panel, Mouse Genetics

Mangul, Serghei ; Yang, Harry ; Hormozdiari, Farhad ; Tseng, Elizabeth ; Zelikovsky, Alex ; Eskin, Eleazar

HapIso: An Accurate Method for the Haplotype-Specific Isoforms Reconstruction from Long Single-Molecule Reads Book Chapter

Bioinformatics Research and Applications, pp. 80-92, Springer International Publishing, 2016.

Links | BibTeX | Tags: RNAseq;Haplotyping from Sequences

Hormozdiari, Farhad ; Kang, Eun Yong ; Bilow, Michael ; Ben-David, Eyal ; Vulpe, Chris ; McLachlan, Stela ; Lusis, Aldons J; Han, Buhm ; Eskin, Eleazar

Imputing Phenotypes for Genome-wide Association Studies. Journal Article

Am J Hum Genet, 99 (1), pp. 89-103, 2016, ISSN: 1537-6605.

Abstract | Links | BibTeX | Tags: Multiple Phenotypes;Imputation

Duong, Dat ; Zou, Jennifer ; Hormozdiari, Farhad ; Sul, Jae Hoon ; Ernst, Jason ; Han, Buhm ; Eskin, Eleazar

Using genomic annotations increases statistical power to detect eGenes. Journal Article

Bioinformatics, 32 (12), pp. i156-i163, 2016, ISSN: 1367-4811.

Abstract | Links | BibTeX | Tags: Expression QTLs

Kang, Eun Yong; Park, Yurang; Li, Xiao; Segrè, Ayellet V; Han, Buhm; Eskin, Eleazar

ForestPMPlot: A Flexible Tool for Visualizing Heterogeneity between Studies in Meta-analysis. Journal Article

G3 (Bethesda), 6 (7), pp. 1793-8, 2016, ISSN: 2160-1836.

Abstract | Links | BibTeX | Tags: Expression QTLs;Meta-Analysis

Won, Hyejung; de la Torre-Ubieta, Luis; Stein, Jason L; Parikshak, Neelroop N; Huang, Jerry; Opland, Carli K; Gandal, Michael J; Sutton, Gavin J; Hormozdiari, Farhad; Lu, Daning; Lee, Changhoon; Eskin, Eleazar; Voineagu, Irina; Ernst, Jason; Geschwind, Daniel H

Chromosome conformation elucidates regulatory relationships in developing human brain. Journal Article

Nature, 538 (7626), pp. 523-527, 2016, ISSN: 1476-4687.

Abstract | Links | BibTeX | Tags: Fine Mapping

Kang, Eun Yong; Martin, Lisa; Mangul, Serghei; Isvilanonda, Warin; Zou, Jennifer; Ben-David, Eyal; Han, Buhm; Lusis, Aldons J; Shifman, Sagiv; Eskin, Eleazar

Discovering SNPs Regulating Human Gene Expression Using Allele Specific Expression from RNA-Seq Data. Journal Article

Genetics, 2016, ISSN: 1943-2631.

Abstract | Links | BibTeX | Tags: Allele Specific Expression, Expression QTLs

Artyomenko, Alexander; Wu, Nicholas C; Mangul, Serghei; Eskin, Eleazar; Sun, Ren; Zelikovsky, Alex

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

Research in Computational Molecular Biology, pp. 164-175, Springer International Publishing, 2016.

Links | BibTeX | Tags: Virus Genomics;Virus Assembly

Hormozdiari, Farhad; van de Bunt, Martijn; Segrè, Ayellet V; Li, Xiao; Joo, Jong Wha J; Bilow, Michael; Sul, Jae Hoon; Sankararaman, Sriram; Pasaniuc, Bogdan; Eskin, Eleazar

Colocalization of GWAS and eQTL Signals Detects Target Genes. Journal Article

Am J Hum Genet, 2016, ISSN: 1537-6605.

Abstract | Links | BibTeX | Tags: Expression QTLs, Fine Mapping

Joo, Jong Wha J; Kang, Eun Yong; Org, Elin; Furlotte, Nick; Parks, Brian; Hormozdiari, Farhad; Lusis, Aldons J; Eskin, Eleazar

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

Genetics, 204 (4), pp. 1379-1390, 2016, ISSN: 1943-2631.

Abstract | Links | BibTeX | Tags: Mixed Models, Multiple Phenotypes

2015

Eskin, Eleazar

Discovering Genes Involved in Disease and the Mystery of Missing Heritability Journal Article

Commun. ACM, 58 (10), pp. 80-87, 2015, ISSN: 0001-0782.

Abstract | Links | BibTeX | Tags: Association Study Methods, Heritability, Review

Lavinsky, Joel; Crow, Amanda L; Pan, Calvin; Wang, Juemei; Aaron, Ksenia A; Ho, Maria K; Li, Qingzhong; Salehide, Pehzman; Myint, Anthony; Monges-Hernadez, Maya; Eskin, Eleazar; Allayee, Hooman; Lusis, Aldons J; Friedman, Rick A

Genome-wide association study identifies nox3 as a critical gene for susceptibility to noise-induced hearing loss. Journal Article

11 (6), pp. e1005293, 2015, ISSN: 1553-7404.

Links | BibTeX | Tags: cochlear function, genome-wide association studies

Sul, Jae Hoon; Raj, Towfique; de Jong, Simone; de Bakker, Paul I W; Raychaudhuri, Soumya; Ophoff, Roel A; Stranger, Barbara E; Eskin, Eleazar; Han, Buhm

Accurate and Fast Multiple-Testing Correction in eQTL Studies. Journal Article

Am J Hum Genet, 96 (6), pp. 857-68, 2015, ISSN: 1537-6605.

Abstract | Links | BibTeX | Tags: Expression QTLs, Multiple Testing

Joo, Jong Wha J; Kang, Eun Yong; Org, Elin; Furlotte, Nick; Parks, Brian; Lusis, Aldons J; Eskin, Eleazar

Efficient and Accurate Multiple-Phenotypes Regression Method for High Dimensional Data Considering Population Structure Book Chapter

Research in Computational Molecular Biology, pp. 136-153, Springer International Publishing, 2015.

Abstract | Links | BibTeX | Tags: GAMMA, genome-wide association studies, microbiome

Furlotte, Nicholas A; Eskin, Eleazar

Efficient Multiple Trait Association and Estimation of Genetic Correlation Using the Matrix-Variate Linear Mixed-Model. Journal Article

Genetics, 200 (1), pp. 59-68, 2015, ISSN: 1943-2631.

Abstract | Links | BibTeX | Tags: Heritability, Mixed Models, Multiple Phenotypes

Wang, Zhanyong; Sul, Jae Hoon; Snir, Sagi; Lozano, Jose A; Eskin, Eleazar

Gene-Gene Interactions Detection Using a Two-stage Model. Journal Article

J Comput Biol, 22 (6), pp. 563-76, 2015, ISSN: 1557-8666.

Abstract | Links | BibTeX | Tags: genome-wide association studies, Threshold-based Efficient Pairwise Association Approach

Org, Elin; Parks, Brian W W; Joo, Jong Wha J; Emert, Benjamin; Schwartzman, William; Kang, Eun Yong; Mehrabian, Margarete; Pan, Calvin; Knight, Rob; Gunsalus, Robert; Drake, Thomas A; Eskin, Eleazar; Lusis, Aldons J

Genetic and environmental control of host-gut microbiota interactions. Journal Article

Genome Res, 2015, ISSN: 1549-5469.

Abstract | Links | BibTeX | Tags: Mouse Genetics. HDMAP, RNA sequencing

Luykx, J J; Bakker, S C; Visser, W F; Verhoeven-Duif, N; Buizer-Voskamp, J E; den Heijer, J M; Boks, M P M; Sul, J H; Eskin, E; Ori, A P; Cantor, R M; Vorstman, J; Strengman, E; DeYoung, J; Kappen, T H; Pariama, E; van Dongen, E P A; Borgdorff, P; Bruins, P; de Koning, T J; Kahn, R S; Ophoff, R A

Genome-wide association study of NMDA receptor coagonists in human cerebrospinal fluid and plasma. Journal Article

Mol Psychiatry, 2015, ISSN: 1476-5578.

Abstract | Links | BibTeX | Tags: genome-wide association studies, NMDAR, schizophrenia

Hiyari, S; Atti, E; Camargo, P M; Eskin, E; Lusis, A J; Tetradis, S; Pirih, F Q

Heritability of periodontal bone loss in mice. Journal Article

J Periodontal Res, 2015, ISSN: 1600-0765.

Abstract | Links | BibTeX | Tags: Periodontitis

Rau, Christoph D; Parks, Brian; Wang, Yibin; Eskin, Eleazar; Simecek, Petr; Churchill, Gary A; Lusis, Aldons J

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

G3 (Bethesda), 5 (10), pp. 2021-6, 2015, ISSN: 2160-1836.

Abstract | Links | BibTeX | Tags: HMDP, Mouse Genetics

Hormozdiari, Farhad; Kichaev, Gleb; Yang, Wen-Yun Y; Pasaniuc, Bogdan; Eskin, Eleazar

Identification of causal genes for complex traits. Journal Article

Bioinformatics, 31 (12), pp. i206-i213, 2015, ISSN: 1367-4811.

Abstract | Links | BibTeX | Tags: Fine Mapping

Crow, Amanda L; Ohmen, Jeffrey; Wang, Juemei; Lavinsky, Joel; Hartiala, Jaana; Li, Qingzhong; Li, Xin; Salehide, Pezhman; Eskin, Eleazar; Pan, Calvin; Lusis, Aldons J; Allayee, Hooman; Friedman, Rick A

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

G3 (Bethesda), 2015, ISSN: 2160-1836.

Abstract | Links | BibTeX | Tags: cochlear function, genome-wide association studies, phenotypic heterogeneity

Zhou, Xiaoying; Crow, Amanda L; Hartiala, Jaana; Spindler, Tassja J; Ghazalpour, Anatole; Barsky, Lora W; Bennett, Brian J; Parks, Brian W; Eskin, Eleazar; Jain, Rajan; Epstein, Jonathan A; Lusis, Aldons J; Adams, Gregor B; Allayee, Hooman

The Genetic Landscape of Hematopoietic Stem Cell Frequency in Mice. Journal Article

Stem Cell Reports, 5 (1), pp. 125-38, 2015, ISSN: 2213-6711.

Abstract | Links | BibTeX | Tags: HMDP

Patananan, Alexander Nikolich; Budenholzer, Lauren Michelle; Eskin, Ascia; Torres, Eric Rommel; Clarke, Steven Gerard

Ethanol-induced differential gene expression and acetyl-CoA metabolism in a longevity model of the nematode Caenorhabditis elegans. Journal Article

Exp Gerontol, 61 , pp. 20-30, 2015, ISSN: 1873-6815.

Abstract | Links | BibTeX | Tags: Caenorhabditis, ethanol, RNA sequencing

Baxter, Ruth M; Arboleda, Valerie A; Lee, Hane; Barseghyan, Hayk; Adam, Margaret P; Fechner, Patricia Y; Bargman, Renee; Keegan, Catherine; Travers, Sharon; Schelley, Susan; Hudgins, Louanne; Mathew, Revi P; Stalker, Heather J; Zori, Roberto; Gordon, Ora K; Ramos-Platt, Leigh; Pawlikowska-Haddal, Anna; Eskin, Ascia; Nelson, Stanley F; Délot, Emmanuèle; Vilain, Eric

Exome sequencing for the diagnosis of 46,XY disorders of sex development. Journal Article

J Clin Endocrinol Metab, 100 (2), pp. E333-44, 2015, ISSN: 1945-7197.

Abstract | Links | BibTeX | Tags: Disorders of sex development, exome sequencing

Bennett, Brian J; Davis, Richard C; Civelek, Mete; Orozco, Luz; Wu, Judy; Qi, Hannah; Pan, Calvin; Packard, René Sevag R; Eskin, Eleazar; Yan, Mujing; Kirchgessner, Todd; Wang, Zeneng; Li, Xinmin; Gregory, Jill C; Hazen, Stanley L; Gargalovic, Peter S; JLusis, Aldons

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

PLoS Genet, 11 (12), pp. e1005711, 2015, ISSN: 1553-7404.

Abstract | Links | BibTeX | Tags: atherosclerosis, genome-wide association studies, HMDP

Hormozdiari, Farhad; Kichaev, Gleb; Yang, Wen-Yun Y; Pasaniuc, Bogdan; Eskin, Eleazar

Identification of causal genes for complex traits. Journal Article

Bioinformatics, 31 (12), pp. i206-i213, 2015, ISSN: 1367-4811.

Abstract | Links | BibTeX | Tags: Fine Mapping

Brown, Robert; Lee, Hane; Eskin, Ascia; Kichaev, Gleb; Lohmueller, Kirk E; Reversade, Bruno; Nelson, Stanley F; Pasaniuc, Bogdan

Leveraging ancestry to improve causal variant identification in exome sequencing for monogenic disorders. Journal Article

Eur J Hum Genet, 24 (1), pp. 113-9, 2015, ISSN: 1476-5438.

Abstract | Links | BibTeX | Tags: Causal Inference, exome sequencing, monogenic disorders

Ng, Calista K L; Shboul, Mohammad; Taverniti, Valerio; Bonnard, Carine; Lee, Hane; Eskin, Ascia; Nelson, Stanley F; Al-Raqad, Mohammed; Altawalbeh, Samah; Séraphin, Bertrand; Reversade, Bruno

Loss of the scavenger mRNA decapping enzyme DCPS causes syndromic intellectual disability with neuromuscular defects. Journal Article

Hum Mol Genet, 24 (11), pp. 3163-71, 2015, ISSN: 1460-2083.

Abstract | Links | BibTeX | Tags: DCPS, mRNA

Nanda, Vikrum; Gutman, Boris; Bar, Ehab; Alghamdi, Suha; Tetradis, Sotirios; Lusis, Aldons J; Eskin, Eleazar; Moon, Won

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

Prog Orthod, 16 , pp. 21, 2015, ISSN: 2196-1042.

Abstract | Links | BibTeX | Tags: 3D photography, anthropomorphics

2014

He, Dan; Eskin, Eleazar

IPED2X: a robust pedigree reconstruction algorithm for complicated pedigrees. Journal Article

Journal of Bioinformatics and Computational Biology, 12 , 2014.

Abstract | Links | BibTeX | Tags: IPED2X, pedigree reconstruction

Kang, Eun Yong; Han, Buhm; Furlotte, Nicholas; Joo, Jong Wha J; Shih, Diana; Davis, Richard C; Lusis, Aldons J; Eskin, Eleazar

Meta-Analysis Identifies Gene-by-Environment Interactions as Demonstrated in a Study of 4,965 Mice Journal Article

PLoS Genet, 10 (1), pp. e1004022, 2014, ISSN: 1553-7404.

Abstract | Links | BibTeX | Tags: Genes By Environment, Meta-Analysis, Mouse Genetics

He, Dan; Furlotte, Nicholas A; Hormozdiari, Farhad ; Joo, Jong Wha J; Wadia, Akshay ; Ostrovsky, Rafail ; Sahai, Amit ; Eskin, Eleazar

Identifying genetic relatives without compromising privacy. Journal Article

Genome Res, 2014, ISSN: 1549-5469.

Abstract | Links | BibTeX | Tags: Genomic Privacy

Mangul, Serghei; Wu, Nicholas C; Mancuso, Nicholas; Zelikovsky, Alex; Sun, Ren; Eskin, Eleazar

Accurate viral population assembly from ultra-deep sequencing data. Journal Article

Bioinformatics, 30 (12), pp. i329-i337, 2014, ISSN: 1367-4811.

Abstract | Links | BibTeX | Tags: Virus Assembly

Yang, Wen-Yun - Y; Hormozdiari, Farhad ; Eskin, Eleazar ; Pasaniuc, Bogdan

A Spatial-Aware Haplotype Copying Model with Applications to Genotype Imputation Book Chapter

Research in Computational Molecular Biology, pp. 371-384, Springer International Publishing, 2014.

Abstract | Links | BibTeX | Tags: Spatial Population Structure

Hasin-Brumshtein, Yehudit; Hormozdiari, Farhad ; Martin, Lisa ; van Nas, Atila ; Eskin, Eleazar ; Lusis, Aldons J; Drake, Thomas A

Allele-specific expression and eQTL analysis in mouse adipose tissue. Journal Article

BMC Genomics, 15 (1), pp. 471, 2014, ISSN: 1471-2164.

Abstract | Links | BibTeX | Tags: Allele Specific Expression

Joo, Jong Wha J; Sul, Jae Hoon ; Han, Buhm ; Ye, Chun ; Eskin, Eleazar

Effectively identifying regulatory hotspots while capturing expression heterogeneity in gene expression studies. Journal Article

Genome Biol, 15 (4), pp. R61, 2014, ISSN: 1465-6914.

Abstract | Links | BibTeX | Tags: Confounding, eQTL Confounding, Expression QTLs

Wang, Zhanyong; Sul, Jae Hoon ; Snir, Sagi ; Lozano, Jose A; Eskin, Eleazar

Gene-Gene Interactions Detection Using a Two-Stage Model Book Chapter

Research in Computational Molecular Biology, pp. 340-355, Springer International Publishing, 2014.

Abstract | Links | BibTeX | Tags: Gene-Gene Interactions

Zhang, Kuixing; Huentelman, Matthew J; Rao, Fangwen; Sun, Eric I; Corneveaux, Jason J; Schork, Andrew J; Wei, Zhiyun; Waalen, Jill; Miramontes-Gonzalez, Jose Pablo; Hightower, Makena C; Maihofer, Adam X; Mahata, Manjula; Pastinen, Tomi; Ehret, Georg B; Schork, Nicholas J; Eskin, Eleazar; Nievergelt, Caroline M; Saier, Milton H; O'Connor, Daniel T

Genetic implication of a novel thiamine transporter in human hypertension. Journal Article

J Am Coll Cardiol, 2014, ISSN: 1558-3597.

Abstract | Links | BibTeX | Tags: genome-wide pooling, trait extremes

Ohmen, Jeffrey; Kang, Eun Yong ; Li, Xin ; Joo, Jong Wha ; Hormozdiari, Farhad ; Zheng, Qing Yin ; Davis, Richard C; Lusis, Aldons J; Eskin, Eleazar ; Friedman, Rick A

Genome-Wide Association Study for Age-Related Hearing Loss (AHL) in the Mouse: A Meta-Analysis. Journal Article

J Assoc Res Otolaryngol, 15 (3), pp. 335-52, 2014, ISSN: 1438-7573.

Abstract | Links | BibTeX | Tags: HMDP, Meta-Analysis, Mouse Genetics

Hormozdiari, Farhad; Joo, Jong Wha J; Wadia, Akshay ; Guan, Feng ; Ostrosky, Rafail ; Sahai, Amit ; Eskin, Eleazar

Privacy preserving protocol for detecting genetic relatives using rare variants. Journal Article

Bioinformatics, 30 (12), pp. i204-i211, 2014, ISSN: 1367-4811.

Abstract | Links | BibTeX | Tags: Genomic Privacy

Hormozdiari, Farhad; Kostem, Emrah ; Kang, Eun Yong ; Pasaniuc, Bogdan ; Eskin, Eleazar

Identifying causal variants at Loci with multiple signals of association. Journal Article

Genetics, 198 (2), pp. 497-508, 2014, ISSN: 1943-2631.

Abstract | Links | BibTeX | Tags: Fine Mapping

Kichaev, Gleb; Yang, Wen-Yun Y; Lindstrom, Sara ; Hormozdiari, Farhad ; Eskin, Eleazar ; Price, Alkes L; Kraft, Peter ; Pasaniuc, Bogdan

Integrating functional data to prioritize causal variants in statistical fine-mapping studies. Journal Article

PLoS Genet, 10 (10), pp. e1004722, 2014, ISSN: 1553-7404.

Abstract | Links | BibTeX | Tags: Fine Mapping

Hormozdiari, Farhad; Eskin, Eleazar

Memory efficient assembly of human genome. Journal Article

J Bioinform Comput Biol, pp. 1550008, 2014, ISSN: 1757-6334.

Abstract | Links | BibTeX | Tags: Sequence Assembly

Yang, Wen-Yun Y; Platt, Alexander; Chiang, Charleston Wen-Kai; Eskin, Eleazar; Novembre, John; Pasaniuc, Bogdan

Spatial localization of recent ancestors for admixed individuals. Journal Article

G3 (Bethesda), 4 (12), pp. 2505-18, 2014, ISSN: 2160-1836.

Abstract | Links | BibTeX | Tags: Spatial Population Structure

182 entries « 1 of 4 »