Publications

Utilizing state-of-the-art computational methodologies, we explore the intricate ways sex influences the genetic architecture of complex traits and diseases. By integrating multi-omics data, we aim to pinpoint causal genes and pathways, enhancing our understanding of disease biology and identifying therapeutic targets within a ‘sex-aware’ framework. Our research capitalizes on our deep expertise in statistical genetics, genomics, machine learning, and sex differences, pushing the boundaries of precision medicine to improve health outcomes for all.

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2023

Toward a deeper understanding of gene-by-sex interaction models

Ekaterina A. Khramtsova, Stacey J. Winham, Lea K. Davis, Barbara E. Stranger, Melissa A. Wilson

Cell Genomics  ·  01 May 2023  ·  doi:10.1016/j.xgen.2023.100324

Quality control and analytic best practices for testing genetic models of sex differences in large populations

Ekaterina A. Khramtsova, Melissa A. Wilson, Joanna Martin, Stacey J. Winham, Karen Y. He, Lea K. Davis, Barbara E. Stranger

Cell  ·  01 May 2023  ·  doi:10.1016/j.cell.2023.04.014

Deciphering genetic causes for sex differences in human health through drug metabolism and transporter genes

Yingbo Huang, Yuting Shan, Weijie Zhang, Adam M. Lee, Feng Li, Barbara E. Stranger, R. Stephanie Huang

Nature Communications  ·  12 Jan 2023  ·  doi:10.1038/s41467-023-35808-6

2021

Systematic evaluation of transcriptomics-based deconvolution methods and references using thousands of clinical samples

Brian B. Nadel, Meritxell Oliva, Benjamin L. Shou, Keith Mitchell, Feiyang Ma, …, Alice Mouton, Sarah Kim-Hellmuth, Barbara E. Stranger, Matteo Pellegrini, Serghei Mangul

Cold Spring Harbor Laboratory  ·  10 Mar 2021  ·  doi:10.1101/2021.03.09.434660

2019

ImmGen report: sexual dimorphism in the immune system transcriptome

Shani Talia Gal-Oz, Barbara Maier, Hideyuki Yoshida, Kumba Seddu, Nitzan Elbaz, Charles Czysz, Or Zuk, Barbara E. Stranger, Hadas Ner-Gaon, Tal Shay

Nature Communications  ·  20 Sep 2019  ·  doi:10.1038/s41467-019-12348-6

2018

The role of sex in the genomics of human complex traits

Ekaterina A. Khramtsova, Lea K. Davis, Barbara E. Stranger

Nature Reviews Genetics  ·  23 Dec 2018  ·  doi:10.1038/s41576-018-0083-1

2017

Sex differences in the genetic architecture of obsessive-compulsive disorder

Ekaterina A. Khramtsova, Raphael Heldman, Eske M. Derks, Dongmei Yu, Lea K. Davis, Barbara E. Stranger

Cold Spring Harbor Laboratory  ·  21 Nov 2017  ·  doi:10.1101/219170

Enhancing GTEx by bridging the gaps between genotype, gene expression, and disease

Nature Genetics  ·  11 Oct 2017  ·  doi:10.1038/ng.3969

Neuroblastoma survivors are at increased risk for second malignancies: A report from the International Neuroblastoma Risk Group Project

Mark A. Applebaum, Zalman Vaksman, Sang Mee Lee, Eric A. Hungate, Tara O. Henderson, …, Barbara Hero, Andrew D. Pearson, Barbara E. Stranger, Susan L. Cohn, Sharon J. Diskin

European Journal of Cancer  ·  01 Feb 2017  ·  doi:10.1016/j.ejca.2016.11.022

2016

Integrative genomics reveals hypoxia inducible genes that are associated with a poor prognosis in neuroblastoma patients

Mark A. Applebaum, Aashish R. Jha, Clara Kao, Kyle M. Hernandez, Gillian DeWane, …, Lucy A. Godley, Nanduri Prabhakar, Kevin White, Barbara E. Stranger, Susan L. Cohn

Oncotarget  ·  17 Oct 2016  ·  doi:10.18632/oncotarget.12713

Imputing Gene Expression in Uncollected Tissues Within and Beyond GTEx

Jiebiao Wang, Eric R. Gamazon, Brandon L. Pierce, Barbara E. Stranger, Hae Kyung Im, Robert D. Gibbons, Nancy J. Cox, Dan L. Nicolae, Lin S. Chen

The American Journal of Human Genetics  ·  01 Apr 2016  ·  doi:10.1016/j.ajhg.2016.02.020

2015

Design and Implementation of the International Genetics and Translational Research in Transplantation Network

Transplantation  ·  01 Nov 2015  ·  doi:10.1097/TP.0000000000000913

The transcriptional landscape of age in human peripheral blood

Marjolein J. Peters, Roby Joehanes, Luke C. Pilling, Claudia Schurmann, Karen N. Conneely, …, Luigi Ferrucci, Tonu Esko, Alexander Teumer, Joyce B. J. van Meurs, Andrew D. Johnson

Nature Communications  ·  22 Oct 2015  ·  doi:10.1038/ncomms9570

Expression Quantitative Trait Loci Information Improves Predictive Modeling of Disease Relevance of Non-Coding Genetic Variation

Damien C. Croteau-Chonka, Angela J. Rogers, Towfique Raj, Michael J. McGeachie, Weiliang Qiu, …, Robert F. Lemanske, Andrew H. Liu, Barbara E. Stranger, Vincent J. Carey, Benjamin A. Raby

PLOS ONE  ·  16 Oct 2015  ·  doi:10.1371/journal.pone.0140758

Disentangling the Effects of Colocalizing Genomic Annotations to Functionally Prioritize Non-coding Variants within Complex-Trait Loci

Gosia Trynka, Harm-Jan Westra, Kamil Slowikowski, Xinli Hu, Han Xu, Barbara E. Stranger, Robert J. Klein, Buhm Han, Soumya Raychaudhuri

The American Journal of Human Genetics  ·  01 Jul 2015  ·  doi:10.1016/j.ajhg.2015.05.016

Accurate and Fast Multiple-Testing Correction in eQTL Studies

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

The American Journal of Human Genetics  ·  01 Jun 2015  ·  doi:10.1016/j.ajhg.2015.04.012

Human HLA-G+ extravillous trophoblasts: Immune-activating cells that interact with decidual leukocytes

Tamara Tilburgs, Ângela C. Crespo, Anita van der Zwan, Basya Rybalov, Towfique Raj, Barbara Stranger, Lucy Gardner, Ashley Moffett, Jack L. Strominger

Proceedings of the National Academy of Sciences  ·  26 May 2015  ·  doi:10.1073/pnas.1507977112

The impact of human copy number variation on gene expression: Figure 1

Eric R. Gamazon, Barbara E. Stranger

Briefings in Functional Genomics  ·  27 Apr 2015  ·  doi:10.1093/bfgp/elv017

ImmVar project: Insights and design considerations for future studies of “healthy” immune variation

Philip L. De Jager, Nir Hacohen, Diane Mathis, Aviv Regev, Barbara E. Stranger, Christophe Benoist

Seminars in Immunology  ·  01 Feb 2015  ·  doi:10.1016/j.smim.2015.03.003

2014

Intersection of population variation and autoimmunity genetics in human T cell activation

Chun Jimmie Ye, Ting Feng, Ho-Keun Kwon, Towfique Raj, Michael T. Wilson, …, Barbara Stranger, Philip De Jager, Diane Mathis, Aviv Regev, Christophe Benoist

Science  ·  12 Sep 2014  ·  doi:10.1126/science.1254665

Regulation of Gene Expression in Autoimmune Disease Loci and the Genetic Basis of Proliferation in CD4+ Effector Memory T Cells

Xinli Hu, Hyun Kim, Towfique Raj, Patrick J. Brennan, Gosia Trynka, …, Philip L. De Jager, Stephen S. Rich, Barbara E. Stranger, Michael B. Brenner, Soumya Raychaudhuri

PLoS Genetics  ·  26 Jun 2014  ·  doi:10.1371/journal.pgen.1004404

Expression QTL-based analyses reveal candidate causal genes and loci across five tumor types

Qiyuan Li, Alexander Stram, Constance Chen, Siddhartha Kar, Simon Gayther, Paul Pharoah, Christopher Haiman, Barbara Stranger, Peter Kraft, Matthew L. Freedman

Human Molecular Genetics  ·  06 Jun 2014  ·  doi:10.1093/hmg/ddu228

Polarization of the Effects of Autoimmune and Neurodegenerative Risk Alleles in Leukocytes

Towfique Raj, Katie Rothamel, Sara Mostafavi, Chun Ye, Mark N. Lee, …, Nir Hacohen, Diane Mathis, Christophe Benoist, Barbara E. Stranger, Philip L. De Jager

Science  ·  02 May 2014  ·  doi:10.1126/science.1249547

Interindividual variation in human T regulatory cells

Alessandra Ferraro, Anna Morena D’Alise, Towfique Raj, Natasha Asinovski, Roxanne Phillips, …, Lori Laffel, Barbara E. Stranger, Philip L. De Jager, Diane Mathis, Christophe Benoist

Proceedings of the National Academy of Sciences  ·  07 Mar 2014  ·  doi:10.1073/pnas.1401343111

Common Genetic Variants Modulate Pathogen-Sensing Responses in Human Dendritic Cells

Mark N. Lee, Chun Ye, Alexandra-Chloé Villani, Towfique Raj, Weibo Li, …, Barbara E. Stranger, Christophe O. Benoist, Philip L. De Jager, Aviv Regev, Nir Hacohen

Science  ·  07 Mar 2014  ·  doi:10.1126/science.1246980

Genomics of alternative splicing: evolution, development and pathophysiology

Eric R. Gamazon, Barbara E. Stranger

Human Genetics  ·  01 Jan 2014  ·  doi:10.1007/s00439-013-1411-3

2013

CD33: increased inclusion of exon 2 implicates the Ig V-set domain in Alzheimer's disease susceptibility

T. Raj, K. J. Ryan, J. M. Replogle, L. B. Chibnik, L. Rosenkrantz, …, B. E. Stranger, D. A. Bennett, D. A. Evans, P. L. De Jager, E. M. Bradshaw

Human Molecular Genetics  ·  30 Dec 2013  ·  doi:10.1093/hmg/ddt666

Genetics of rheumatoid arthritis contributes to biology and drug discovery

Yukinori Okada, Di Wu, Gosia Trynka, Towfique Raj, Chikashi Terao, …, Katherine A. Siminovitch, Shigeki Momohara, Fumihiko Matsuda, Kazuhiko Yamamoto, Robert M. Plenge

Nature  ·  25 Dec 2013  ·  doi:10.1038/nature12873

Genetics of human gene expression

Barbara E Stranger, Towfique Raj

Current Opinion in Genetics & Development  ·  01 Dec 2013  ·  doi:10.1016/j.gde.2013.10.004

Fine-Mapping the Genetic Association of the Major Histocompatibility Complex in Multiple Sclerosis: HLA and Non-HLA Effects

Nikolaos A. Patsopoulos, Lisa F. Barcellos, Rogier Q. Hintzen, Catherine Schaefer, Cornelia M. van Duijn, …, Stephen Sawcer, David A. Hafler, Mary Carrington, Philip L. De Jager, Paul I. W. de Bakker

PLoS Genetics  ·  21 Nov 2013  ·  doi:10.1371/journal.pgen.1003926

Balancing Selection on a Regulatory Region Exhibiting Ancient Variation That Predates Human–Neandertal Divergence

Omer Gokcumen, Qihui Zhu, Lubbertus C. F. Mulder, Rebecca C. Iskow, Christian Austermann, …, Shamil Sunyaev, Alkes Price, Barbara Stranger, Viviana Simon, Charles Lee

PLoS Genetics  ·  11 Apr 2013  ·  doi:10.1371/journal.pgen.1003404

Common Risk Alleles for Inflammatory Diseases Are Targets of Recent Positive Selection

Towfique Raj, Manik Kuchroo, Joseph M. Replogle, Soumya Raychaudhuri, Barbara E. Stranger, Philip L. De Jager

The American Journal of Human Genetics  ·  01 Apr 2013  ·  doi:10.1016/j.ajhg.2013.03.001

Genome-Wide Association Study and Gene Expression Analysis Identifies CD84 as a Predictor of Response to Etanercept Therapy in Rheumatoid Arthritis

Jing Cui, Eli A. Stahl, Saedis Saevarsdottir, Corinne Miceli, Dorothee Diogo, …, Anne Barton, Leonid Padyukov, Marieke J. H. Coenen, Elizabeth W. Karlson, Robert M. Plenge

PLoS Genetics  ·  28 Mar 2013  ·  doi:10.1371/journal.pgen.1003394

Integrative eQTL-Based Analyses Reveal the Biology of Breast Cancer Risk Loci

Qiyuan Li, Ji-Heui Seo, Barbara Stranger, Aaron McKenna, Itsik Pe’er, Thomas LaFramboise, Myles Brown, Svitlana Tyekucheva, Matthew L. Freedman

Cell  ·  01 Jan 2013  ·  doi:10.1016/j.cell.2012.12.034

2012

Chromatin marks identify critical cell types for fine mapping complex trait variants

Gosia Trynka, Cynthia Sandor, Buhm Han, Han Xu, Barbara E Stranger, X Shirley Liu, Soumya Raychaudhuri

Nature Genetics  ·  23 Dec 2012  ·  doi:10.1038/ng.2504

Coordinating GWAS results with gene expression in a systems immunologic paradigm in autoimmunity

Barbara E Stranger, Phillip L De Jager

Current Opinion in Immunology  ·  01 Oct 2012  ·  doi:10.1016/j.coi.2012.09.002

Sex-biased genetic effects on gene regulation in humans

Antigone S. Dimas, Alexandra C. Nica, Stephen B. Montgomery, Barbara E. Stranger, Towfique Raj, …, Thomas Giger, Tuuli Lappalainen, Maria Gutierrez-Arcelus, Mark I. McCarthy, Emmanouil T. Dermitzakis

Genome Research  ·  07 Sep 2012  ·  doi:10.1101/gr.134981.111

Analysis of case–control association studies with known risk variants

Noah Zaitlen, Bogdan Paşaniuc, Nick Patterson, Samuela Pollack, Benjamin Voight, …, Christopher A. Haiman, Barbara E. Stranger, Emmanouil T. Dermitzakis, Peter Kraft, Alkes L. Price

Bioinformatics  ·  03 May 2012  ·  doi:10.1093/bioinformatics/bts259

Patterns of Cis Regulatory Variation in Diverse Human Populations

Barbara E. Stranger, Stephen B. Montgomery, Antigone S. Dimas, Leopold Parts, Oliver Stegle, …, Alexandra C. Nica, Claude Beazley, Richard Durbin, Panos Deloukas, Emmanouil T. Dermitzakis

PLoS Genetics  ·  19 Apr 2012  ·  doi:10.1371/journal.pgen.1002639

Alzheimer Disease Susceptibility Loci: Evidence for a Protein Network under Natural Selection

Towfique Raj, Joshua M. Shulman, Brendan T. Keenan, Lori B. Chibnik, Denis A. Evans, David A. Bennett, Barbara E. Stranger, Philip L. De Jager

The American Journal of Human Genetics  ·  01 Apr 2012  ·  doi:10.1016/j.ajhg.2012.02.022

Systems and genome-wide approaches unite to provide a route to personalized medicine

Barbara E Stranger, Johan Björkegren, M Eileen Dolan, Marylyn D Ritchie

Genome Medicine  ·  01 Jan 2012  ·  doi:10.1186/gm328

2011

Extensive genetic diversity and substructuring among zebrafish strains revealed through copy number variant analysis

Kim H. Brown, Kimberly P. Dobrinski, Arthur S. Lee, Omer Gokcumen, Ryan E. Mills, …, Barbara E. Stranger, Robin E. Williamson, Leonard I. Zon, Jennifer L. Freeman, Charles Lee

Proceedings of the National Academy of Sciences  ·  27 Dec 2011  ·  doi:10.1073/pnas.1112163109

Progress and Promise of Genome-Wide Association Studies for Human Complex Trait Genetics

Barbara E Stranger, Eli A Stahl, Towfique Raj

Genetics  ·  01 Feb 2011  ·  doi:10.1534/genetics.110.120907

2010

Genevar: a database and Java application for the analysis and visualization of SNP-gene associations in eQTL studies

Tsun-Po Yang, Claude Beazley, Stephen B. Montgomery, Antigone S. Dimas, Maria Gutierrez-Arcelus, Barbara E. Stranger, Panos Deloukas, Emmanouil T. Dermitzakis

Bioinformatics  ·  10 Aug 2010  ·  doi:10.1093/bioinformatics/btq452

IL12A, MPHOSPH9/CDK2AP1 and RGS1 are novel multiple sclerosis susceptibility loci

Genes & Immunity  ·  17 Jun 2010  ·  doi:10.1038/gene.2010.28

Candidate Causal Regulatory Effects by Integration of Expression QTLs with Complex Trait Genetic Associations

Alexandra C. Nica, Stephen B. Montgomery, Antigone S. Dimas, Barbara E. Stranger, Claude Beazley, Inês Barroso, Emmanouil T. Dermitzakis

PLoS Genetics  ·  01 Apr 2010  ·  doi:10.1371/journal.pgen.1000895

Independent and population-specific association of risk variants at the IRGM locus with Crohn's disease

Natalie J. Prescott, Katherine M. Dominy, Michiaki Kubo, Cathryn M. Lewis, Sheila A. Fisher, …, John C. Mansfield, Jeremy Sanderson, Matthew E. Hurles, Roland G. Roberts, Christopher G. Mathew

Human Molecular Genetics  ·  27 Jan 2010  ·  doi:10.1093/hmg/ddq041

2009

Common Regulatory Variation Impacts Gene Expression in a Cell Type–Dependent Manner

Antigone S. Dimas, Samuel Deutsch, Barbara E. Stranger, Stephen B. Montgomery, Christelle Borel, …, Marilyne Gagnebin, James Nisbett, Panos Deloukas, Emmanouil T. Dermitzakis, Stylianos E. Antonarakis

Science  ·  04 Sep 2009  ·  doi:10.1126/science.1174148

2008

Gene Expression Levels Are a Target of Recent Natural Selection in the Human Genome

S. Kudaravalli, J.-B. Veyrieras, B. E. Stranger, E. T. Dermitzakis, J. K. Pritchard

Molecular Biology and Evolution  ·  23 Dec 2008  ·  doi:10.1093/molbev/msn289

Modifier Effects between Regulatory and Protein-Coding Variation

Antigone S. Dimas, Barbara E. Stranger, Claude Beazley, Robert D. Finn, Catherine E. Ingle, Matthew S. Forrest, Matthew E. Ritchie, Panos Deloukas, Simon Tavaré, Emmanouil T. Dermitzakis

PLoS Genetics  ·  31 Oct 2008  ·  doi:10.1371/journal.pgen.1000244

Large-Scale Population Study of Human Cell Lines Indicates that Dosage Compensation Is Virtually Complete

Colette M Johnston, Frances L Lovell, Daniel A Leongamornlert, Barbara E Stranger, Emmanouil T Dermitzakis, Mark T Ross

PLoS Genetics  ·  18 Jan 2008  ·  doi:10.1371/journal.pgen.0040009

2007

Genome-wide detection and characterization of positive selection in human populations

Pardis C. Sabeti, Patrick Varilly, Ben Fry, Jason Lohmueller, Elizabeth Hostetter, …, Elizabeth H. Byrne, Steven A. McCarroll, Rachelle Gaudet, Stephen F. Schaffner, Eric S. Lander

Nature  ·  01 Oct 2007  ·  doi:10.1038/nature06250

A second generation human haplotype map of over 3.1 million SNPs

Nature  ·  01 Oct 2007  ·  doi:10.1038/nature06258

Population genomics of human gene expression

Barbara E Stranger, Alexandra C Nica, Matthew S Forrest, Antigone Dimas, Christine P Bird, …, Daphne Koller, Stephen Montgomery, Simon Tavaré, Panos Deloukas, Emmanouil T Dermitzakis

Nature Genetics  ·  16 Sep 2007  ·  doi:10.1038/ng2142

Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project

Nature  ·  01 Jun 2007  ·  doi:10.1038/nature05874

Relative Impact of Nucleotide and Copy Number Variation on Gene Expression Phenotypes

Barbara E. Stranger, Matthew S. Forrest, Mark Dunning, Catherine E. Ingle, Claude Beazley, …, Stephen W. Scherer, Simon Tavaré, Panagiotis Deloukas, Matthew E. Hurles, Emmanouil T. Dermitzakis

Science  ·  09 Feb 2007  ·  doi:10.1126/science.1136678

Fast-evolving noncoding sequences in the human genome

Christine P Bird, Barbara E Stranger, Maureen Liu, Daryl J Thomas, Catherine E Ingle, Claude Beazley, Webb Miller, Matthew E Hurles, Emmanouil T Dermitzakis

Genome Biology  ·  01 Jan 2007  ·  doi:10.1186/gb-2007-8-6-r118

Breaking the waves: improved detection of copy number variation from microarray-based comparative genomic hybridization

John C Marioni, Natalie P Thorne, Armand Valsesia, Tomas Fitzgerald, Richard Redon, …, Andrew G Lynch, Emmanouil T Dermitzakis, Nigel P Carter, Simon Tavaré, Matthew E Hurles

Genome Biology  ·  01 Jan 2007  ·  doi:10.1186/gb-2007-8-10-r228

2006

Functional variation and evolution of non-coding DNA

Christine P Bird, Barbara E Stranger, Emmanouil T Dermitzakis

Current Opinion in Genetics & Development  ·  01 Dec 2006  ·  doi:10.1016/j.gde.2006.10.003

Genetic variation in human gene expression

Emmanouil T. Dermitzakis, Barbara E. Stranger

Mammalian Genome  ·  01 Jun 2006  ·  doi:10.1007/s00335-006-0005-y

2005

Genome-Wide Associations of Gene Expression Variation in Humans

Barbara E Stranger, Matthew S Forrest, Andrew G Clark, Mark J Minichiello, Samuel Deutsch, …, Brenda Kahl, Stylianos E Antonarakis, Simon Tavaré, Panagiotis Deloukas, Emmanouil T Dermitzakis

PLoS Genetics  ·  16 Dec 2005  ·  doi:10.1371/journal.pgen.0010078

A haplotype map of the human genome

Nature  ·  01 Oct 2005  ·  doi:10.1038/nature04226

2004

Nucleotide variation at the myrosinase‐encoding locus, TGG1, and quantitative myrosinase enzyme activity variation in Arabidopsis thaliana

BARBARA E. STRANGER, THOMAS MITCHELL‐OLDS

Molecular Ecology  ·  07 Dec 2004  ·  doi:10.1111/j.1365-294X.2004.02403.x

Multilocus Analysis of Variation and Speciation in the Closely Related Species Arabidopsis halleri and A. lyrata

Sebastián E Ramos-Onsins, Barbara E Stranger, Thomas Mitchell-Olds, Montserrat Aguadé

Genetics  ·  01 Jan 2004  ·  doi:10.1534/genetics.166.1.373

2002

Primers for 22 candidate genes for ecological adaptations in Brassicaceae

H. Kuittinen, M. Aguadé, D. Charlesworth, A. D. E. Haan, B. Lauga, …, S. Oikarinen, S. Ramos‐Onsins, B. Stranger, P. Van Tienderen, O. Savolainen

Molecular Ecology Notes  ·  07 Aug 2002  ·  doi:10.1046/j.1471-8286.2002.00210.x