Publications

Our group publishes papers presenting new methodologies, describing the results of studies that use our software, and reviewing current topics in the field of Bioinformatics. Scroll down or click here for a complete list of papers produced by our lab. Since 2013, we write blog posts summarizing new research papers and review articles:

GWAS

Mouse Genetics

Population Structure

Review Articles

Publications

186 entries « 2 of 4 »

2014

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

2013

Wang, Zhanyong; Hormozdiari, Farhad ; Yang, Wen-Yun Y; Halperin, Eran ; Eskin, Eleazar

CNVeM: Copy Number Variation Detection Using Uncertainty of Read Mapping. Journal Article

J Comput Biol, 2013, ISSN: 1557-8666.

Abstract | Links | BibTeX | Tags: Sequencing Next Generation, Structural Variation

Eskin, Itamar; Hormozdiari, Farhad ; Conde, Lucia ; Riby, Jacques ; Skibola, Chris ; Eskin, Eleazar ; Halperin, Eran

eALPS: Estimating Abundance Levels in Pooled Sequencing Using Available Genotyping Data Conference

Research in Computational Molecular Biology, Tel-Aviv University Springer Berlin Heidelberg, 2013.

Abstract | Links | BibTeX | Tags: Sequencing with Pools

Kostem, Emrah; Eskin, Eleazar

Efficiently Identifying Significant Associations in Genome-Wide Association Studies Conference

Research in Computational Molecular Biology, University of California Springer Berlin Heidelberg, 2013.

Abstract | Links | BibTeX | Tags: Association Study Methods, Expression QTLs

Leikauf, George D; Concel, Vincent J; Bein, Kiflai ; Liu, Pengyuan ; Berndt, Annerose ; Martin, Timothy M; Ganguly, Koustav ; Jang, An-Soo S; Brant, Kelly A; Jr, Richard Dopico A; Upadhyay, Swapna ; Cario, Clinton L; Di, Yp Peter ; Vuga, Louis J; Kostem, Emrah ; Eskin, Eleazar ; You, Ming ; Kaminski, Naftali ; Prows, Daniel R; Knoell, Daren L; Fabisiak, James P

Functional Genomic Assessment of Phosgene-induced Acute Lung Injury in Mice. Journal Article

Am J Respir Cell Mol Biol, 2013, ISSN: 1535-4989.

Abstract | Links | BibTeX | Tags: Mouse Genetics

Parks, Brian W; Nam, Elizabeth ; Org, Elin ; Kostem, Emrah ; Norheim, Frode ; Hui, Simon T; Pan, Calvin ; Civelek, Mete ; Rau, Christoph D; Bennett, Brian J; Mehrabian, Margarete ; Ursell, Luke K; He, Aiqing ; Castellani, Lawrence W; Zinker, Bradley ; Kirby, Mark ; Drake, Thomas A; Drevon, Christian A; Knight, Rob ; Gargalovic, Peter ; Kirchgessner, Todd ; Eskin, Eleazar ; Lusis, Aldons J

Genetic control of obesity and gut microbiota composition in response to high-fat, high-sucrose diet in mice. Journal Article

Cell Metab, 17 (1), pp. 141-52, 2013, ISSN: 1932-7420.

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

Parrish, Nathaniel; Sudakov, Benjamin ; Eskin, Eleazar

Genome reassembly with high-throughput sequencing data Journal Article

BMC Genomics, 14 (Suppl 1), pp. S8, 2013, ISSN: 1471-2164.

Abstract | Links | BibTeX | Tags: Sequence Assembly

He, Dan; Han, Buhm ; Eskin, Eleazar

Hap-seq: An Optimal Algorithm for Haplotype Phasing with Imputation Using Sequencing Data. Journal Article

J Comput Biol, 20 (2), pp. 80-92, 2013, ISSN: 1557-8666.

Abstract | Links | BibTeX | Tags: Haplotyping from Sequences, Imputation

Davis, Richard C; van Nas, Atila ; Bennett, Brian ; Orozco, Luz ; Pan, Calvin ; Rau, Christoph D; Eskin, Eleazar ; Lusis, Aldons J

Genome-wide association mapping of blood cell traits in mice. Journal Article

Mamm Genome, 2013, ISSN: 1432-1777.

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

Luykx, J J; Bakker, S C; Lentjes, E; Neeleman, M; Strengman, E; Mentink, L; Deyoung, J; de Jong, S; Sul, J H; Eskin, E; van Eijk, K; van Setten, J; Buizer-Voskamp, J E; Cantor, R M; Lu, A; van Amerongen, M; van Dongen, E P A; Keijzers, P; Kappen, T; Borgdorff, P; Bruins, P; Derks, E M; Kahn, R S; Ophoff, R A

Genome-wide association study of monoamine metabolite levels in human cerebrospinal fluid. Journal Article

Mol Psychiatry, 2013, ISSN: 1476-5578.

Abstract | Links | BibTeX | Tags:

Kostem, Emrah; Eskin, Eleazar

Improving the accuracy and efficiency of partitioning heritability into the contributions of genomic regions. Journal Article

Am J Hum Genet, 92 (4), pp. 558-64, 2013, ISSN: 1537-6605.

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

He, Dan; Wang, Zhanyong ; Han, Buhm ; Parida, Laxmi ; Eskin, Eleazar

IPED: Inheritance Path Based Pedigree Reconstruction Algorithm Using Genotype Data Conference

Research in Computational Molecular Biology, University of California Los Angeles Springer Berlin Heidelberg, 2013.

Abstract | Links | BibTeX | Tags: Pedigree Inference

Lagarrigue, Sandrine; Hormozdiari, Farhad ; Martin, Lisa Joy ; Lecerf, Frédéric ; Hasin, Yehudit ; Rau, Christoph ; Hagopian, Raffi ; Xiao, Yu ; Yan, Jun ; Drake, Thomas A; Ghazalpour, Anatole ; Eskin, Eleazar ; Lusis, Aldons J

Limited RNA Editing in Exons of Mouse Liver and Adipose Tissue. Journal Article

Genetics, 2013, ISSN: 1943-2631.

Abstract | Links | BibTeX | Tags: RNAseq

Sul, Jae Hoon; Eskin, Eleazar

Mixed models can correct for population structure for genomic regions under selection. Journal Article

Nat Rev Genet, 2013, ISSN: 1471-0064.

Links | BibTeX | Tags: Mixed Models, Population Structure Methods

Navon, Oron; Sul, Jae Hoon ; Han, Buhm ; Conde, Lucia ; Bracci, Paige ; Riby, Jacques ; Skibola, Christine F; Eskin, Eleazar ; Halperin, Eran

Rare Variant Association Testing Under Low-Coverage Sequencing. Journal Article

Genetics, 2013, ISSN: 1943-2631.

Abstract | Links | BibTeX | Tags: Rare Variants, Sequencing with Pools

Sul, Jae Hoon; Han, Buhm ; Ye, Chun ; Choi, Ted ; Eskin, Eleazar

Effectively Identifying eQTLs from Multiple Tissues by Combining Mixed Model and Meta-analytic Approaches Journal Article

PLoS Genet, 9 (6), pp. e1003491, 2013, ISSN: 1553-7404.

Abstract | Links | BibTeX | Tags: Expression QTLs, Meta-Analysis, Mixed Models, Multiple Phenotypes

Yang, Wen-Yun Y; Hormozdiari, Farhad ; Wang, Zhanyong ; He, Dan ; Pasaniuc, Bogdan ; Eskin, Eleazar

Leveraging Multi-SNP Reads from Sequencing Data for Haplotype Inference. Journal Article

Bioinformatics, 2013, ISSN: 1367-4811.

Abstract | Links | BibTeX | Tags: Haplotype Phasing, Haplotyping from Sequences, Imputation

Lagarrigue, Sandrine; Martin, Lisa J; Hormozdiari, Farhad; Roux, Pierre-François F; Pan, Calvin; van Nas, Atila; Demeure, Olivier; Cantor, Rita; Ghazalpour, Anatole; Eskin, Eleazar; Lusis, Aldons J

Analysis of Allele Specific Expression in Mouse Liver by RNA-Seq: A Comparison with Journal Article

Genetics, 2013, ISSN: 1943-2631.

Abstract | Links | BibTeX | Tags: Allele Specific Expression

Eskin, Itamar; Hormozdiari, Farhad; Conde, Lucia; Riby, Jacques; Skibola, Chris; Eskin, Eleazar; Halperin, Eran

eALPS: Estimating Abundance Levels in Pooled Sequencing Using Available Genotyping Data. Journal Article

J Comput Biol, 2013, ISSN: 1557-8666.

Abstract | Links | BibTeX | Tags: Sequencing with Pools

Kostem, Emrah; Eskin, Eleazar

Efficiently Identifying Significant Associations in Genome-wide Association Studies. Journal Article

J Comput Biol, 20 (10), pp. 817-30, 2013, ISSN: 1557-8666.

Abstract | Links | BibTeX | Tags: Association Study Methods, Expression QTLs

He, Dan; Wang, Zhanyong; Han, Buhm; Parida, Laxmi; Eskin, Eleazar

IPED: Inheritance Path-based Pedigree Reconstruction Algorithm Using Genotype Data. Journal Article

J Comput Biol, 20 (10), pp. 780-91, 2013, ISSN: 1557-8666.

Abstract | Links | BibTeX | Tags: Pedigree Inference

Marsden, Clare Diana; Lee, Yoosook; Kreppel, Katharina; Weakley, Allison; Cornel, Anthony; Ferguson, Heather M; Eskin, Eleazar; Lanzaro, Gregory C

Diversity, Differentiation and Linkage Disequilibrium: Prospects for Association Mapping in the Malaria Vector, Anopheles arabiensis. Journal Article

G3 (Bethesda), 2013, ISSN: 2160-1836.

Abstract | Links | BibTeX | Tags: association mapping, population structure

Han, Buhm; Kang, Eun Yong ; Raychaudhuri, Soumya ; de Bakker, Paul I W; Eskin, Eleazar

Fast Pairwise IBD Association Testing in Genome-wide Association Studies. Journal Article

Bioinformatics, 2013, ISSN: 1367-4811.

Abstract | Links | BibTeX | Tags: IBD Detection and Association

2012

He, Dan; Han, Buhm ; Eskin, Eleazar

Hap-seq: An Optimal Algorithm for Haplotype Phasing with Imputation Using Sequencing Data Conference

Research in Computational Molecular Biology, Univ. of California Springer Berlin Heidelberg, 2012.

Abstract | Links | BibTeX | Tags: Haplotyping from Sequences

Weiss, James N; Karma, Alain ; Maclellan, Robb W; Deng, Mario ; Rau, Christoph D; Rees, Colin M; Wang, Jessica ; Wisniewski, Nicholas ; Eskin, Eleazar ; Horvath, Steve ; Qu, Zhilin ; Wang, Yibin ; Lusis, Aldons J

"Good enough solutions" and the genetics of complex diseases. Journal Article

Circ Res, 111 (4), pp. 493-504, 2012, ISSN: 1524-4571.

Abstract | Links | BibTeX | Tags:

Yang, Wen-Yun Y; Novembre, John ; Eskin, Eleazar ; Halperin, Eran

A model-based approach for analysis of spatial structure in genetic data. Journal Article

Nat Genet, 44 (6), pp. 725-31, 2012, ISSN: 1546-1718.

Abstract | Links | BibTeX | Tags: Population Genetics, Population Structure Methods

Wang, Zhanyong; Hormozdiari, Farhad ; Yang, Wen-Yun - Y; Halperin, Eran ; Eskin, Eleazar

CNVeM: Copy Number Variation Detection Using Uncertainty of Read Mapping Conference

Research in Computational Molecular Biology, University of California Springer Berlin Heidelberg, 2012.

Abstract | Links | BibTeX | Tags: Structural Variation

Hormozdiariy, Farhad; Wang, Zhanyong ; Yang, Wen-Yun - Y; Eskin, Eleazar

Efficient genotyping of individuals using overlapping pool sequencing and imputation Conference

2012 Conference Record of the Forty Sixth Asilomar Conference on Signals, Systems and Computers (ASILOMAR), IEEE, 2012, ISBN: 978-1-4673-5051-8.

Abstract | Links | BibTeX | Tags: Sequencing with Pools

Flint, Jonathan; Eskin, Eleazar

Genome-wide association studies in mice Journal Article

Nature Reviews Genetics, 13 (11), pp. 807-17, 2012, ISSN: 1471-0064.

Abstract | Links | BibTeX | Tags: Mouse Genetics

Scharf, J M; Yu, D; Mathews, C A; Neale, B M; Stewart, S E; Fagerness, J A; Evans, P; Gamazon, E; Edlund, C K; Service, S K; Tikhomirov, A; Osiecki, L; Illmann, C; Pluzhnikov, A; Konkashbaev, A; Davis, L K; Han, B; Crane, J; Moorjani, P; Crenshaw, A T; Parkin, M A; Reus, V I; Lowe, T L; Rangel-Lugo, M; Chouinard, S; Dion, Y; Girard, S; Cath, D C; Smit, J H; King, R A; Fernandez, T V; Leckman, J F; Kidd, K K; Kidd, J R; Pakstis, A J; State, M W; Herrera, L D; Romero, R; Fournier, E; Sandor, P; Barr, C L; Phan, N; Gross-Tsur, V; Benarroc, F

Genome-wide association study of Tourette's syndrome. Journal Article

Mol Psychiatry, 2012, ISSN: 1476-5578.

Abstract | Links | BibTeX | Tags:

He, Dan; Eskin, Eleazar

Hap-seqX: Expedite Algorithm for Haplotype Phasing with Imputation using Sequence Data. Journal Article

Gene, 2012, ISSN: 1879-0038.

Abstract | Links | BibTeX | Tags: Haplotyping from Sequences, Imputation

Bennett, Brian J; Orozco, Luz ; Kostem, Emrah ; Erbilgin, Ayca ; Dallinga, Marchien ; Neuhaus, Isaac ; Guan, Bo ; Wang, Xuping ; Eskin, Eleazar ; Lusis, Aldons J

High-Resolution Association Mapping of Atherosclerosis Loci in Mice. Journal Article

Arterioscler Thromb Vasc Biol, 2012, ISSN: 1524-4636.

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

Friese, Ryan S; Ye, Chun ; Nievergelt, Caroline M; Schork, Andrew J; Mahapatra, Nitish R; Rao, Fangwen ; Napolitan, Philip S; Waalen, Jill ; Schmid-Schönbein, Geert W; Eskin, Eleazar ; O'Connor, Daniel T

Integrated Computational and Experimental Analysis of the Neuroendocrine Transcriptome in Genetic Hypertension Identifies Novel Control Points for the Cardio-Metabolic Syndrome. Journal Article

Circ Cardiovasc Genet, 2012, ISSN: 1942-3268.

Abstract | Links | BibTeX | Tags:

Ghazalpour, Anatole; Rau, Christoph D; Farber, Charles R; Bennett, Brian J; Orozco, Luz D; van Nas, Atila; Pan, Calvin; Allayee, Hooman; Beaven, Simon W; Civelek, Mete; Davis, Richard C; Drake, Thomas A; Friedman, Rick A; Furlotte, Nick; Hui, Simon T; Jentsch, David J; Kostem, Emrah; Kang, Hyun Min; Kang, Eun Yong; Joo, Jong Wha; Korshunov, Vyacheslav A; Laughlin, Rick E; Martin, Lisa J; Ohmen, Jeffrey D; Parks, Brian W; Pellegrini, Matteo; Reue, Karen; Smith, Desmond J; Tetradis, Sotirios; Wang, Jessica; Wang, Yibin; N, James

Hybrid mouse diversity panel: a panel of inbred mouse strains suitable for analysis of complex genetic traits. Journal Article

Mamm Genome, 2012, ISSN: 1432-1777.

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

Darnell, Gregory; Duong, Dat ; Han, Buhm ; Eskin, Eleazar

Incorporating prior information into association studies. Journal Article

Bioinformatics, 28 (12), pp. i147-i153, 2012, ISSN: 1367-4811.

Abstract | Links | BibTeX | Tags: Association Priors, Association Study Methods

Listgarten, Jennifer; Lippert, Christoph ; Kadie, Carl M; Davidson, Robert I; Eskin, Eleazar ; Heckerman, David

Improved linear mixed models for genome-wide association studies. Journal Article

Nat Methods, 9 (6), pp. 525-6, 2012, ISSN: 1548-7105.

Links | BibTeX | Tags: Mixed Models, Population Structure Methods

Hersch, Micha; Peter, Bastian ; Kang, Hyun Min ; Schüpfer, Fanny ; Abriel, Hugues ; Pedrazzini, Thierry ; Eskin, Eleazar ; Beckmann, Jacques S; Bergmann, Sven ; Maurer, Fabienne

Mapping genetic variants associated with Beta-adrenergic responses in inbred mice. Journal Article

PLoS One, 7 (7), pp. e41032, 2012, ISSN: 1932-6203.

Abstract | Links | BibTeX | Tags: Mouse Genetics

Calabrese, Gina; Bennett, Brian J; Orozco, Luz ; Kang, Hyun M; Eskin, Eleazar ; Dombret, Carlos ; Backer, Olivier De ; Lusis, Aldons J; Farber, Charles R

Systems genetic analysis of osteoblast-lineage cells. Journal Article

PLoS Genet, 8 (12), pp. e1003150, 2012, ISSN: 1553-7404.

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

Han, Buhm; Eskin, Eleazar

Interpreting meta-analyses of genome-wide association studies. Journal Article

PLoS Genet, 8 (3), pp. e1002555, 2012, ISSN: 1553-7404.

Abstract | Links | BibTeX | Tags: Meta-Analysis

Miller, Michael B; Basu, Saonli ; Cunningham, Julie ; Eskin, Eleazar ; Malone, Steven M; Oetting, William S; Schork, Nicholas ; Sul, Jae Hoon ; Iacono, William G; McGue, Matt

The Minnesota Center for Twin and Family Research genome-wide association study. Journal Article

Twin Res Hum Genet, 15 (6), pp. 767-74, 2012, ISSN: 1832-4274.

Abstract | Links | BibTeX | Tags:

Furlotte, Nicholas A; Kang, Eun Yong; Nas, Atila Van; Farber, Charles R; Lusis, Aldons J; Eskin, Eleazar

Increasing Association Mapping Power and Resolution in Mouse Genetic Studies Through the Use of Meta-analysis for Structured Populations. Journal Article

Genetics, 191 (3), pp. 959-67, 2012, ISSN: 1943-2631.

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

2011

He, Dan; Zaitlen, Noah ; Pasaniuc, Bogdan ; Eskin, Eleazar ; Halperin, Eran

Genotyping common and rare variation using overlapping pool sequencing. Journal Article

BMC Bioinformatics, 12 Suppl 6 , pp. S2, 2011, ISSN: 1471-2105.

Abstract | Links | BibTeX | Tags: Sequencing with Pools

Dan He Farhad Hormozdiari, Nicholas Furlotte ; Eskin, Eleazar

Efficient Algorithms for Tandem Copy Number Variation Reconstruction in Repeat-rich Regions. Journal Article

Bioinformatics, 2011, ISSN: 1367-4811.

Abstract | Links | BibTeX | Tags: Structural Variation

Parrish, Nathaniel; Hormozdiari, Farhad ; Eskin, Eleazar

Assembly of non-unique insertion content using next-generation sequencing. Journal Article

BMC Bioinformatics, 12 Suppl 6 , pp. S3, 2011, ISSN: 1471-2105.

Abstract | Links | BibTeX | Tags: Sequence Assembly, Structural Variation

Ghazalpour, Anatole; Bennett, Brian; Petyuk, Vladislav A; Orozco, Luz; Hagopian, Raffi; Mungrue, Imran N; Farber, Charles R; Sinsheimer, Janet; Kang, Hyun M; Furlotte, Nicholas; Park, Christopher C; Wen, Ping-Zi; Brewer, Heather; Weitz, Karl; Camp, David G; Pan, Calvin; Yordanova, Roumyana; Neuhaus, Isaac; Tilford, Charles; Siemers, Nathan; Gargalovic, Peter; Eskin, Eleazar; Kirchgessner, Todd; Smith, Desmond J; Smith, Richard D; Lusis, Aldons J

Comparative analysis of proteome and transcriptome variation in mouse. Journal Article

PLoS Genet, 7 (6), pp. e1001393, 2011, ISSN: 1553-7404.

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

Sul, Jae Hoon; Han, Buhm ; He, Dan ; Eskin, Eleazar

An Optimal Weighted Aggregated Association Test for Identification of Rare Variants Involved in Common Diseases. Journal Article

Genetics, 188 (1), pp. 181-188, 2011, ISSN: 1943-2631.

Abstract | Links | BibTeX | Tags: Rare Variants

Park, Christopher C; Gale, Greg D; de Jong, Simone ; Ghazalpour, Anatole ; Bennett, Brian J; Farber, Charles R; Langfelder, Peter ; Lin, Andy ; Khan, Arshad H; Eskin, Eleazar ; Horvath, Steve ; Lusis, Aldons J; Ophoff, Roel A; Smith, Desmond J

Gene networks associated with conditional fear in mice identified using a systems genetics approach. Journal Article

BMC Syst Biol, 5 , pp. 43, 2011, ISSN: 1752-0509.

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

186 entries « 2 of 4 »