From genes to cells to diseases

Our lab studies genetic effects on gene regulation and gene expression to identify the molecular and cellular mechanisms which define human traits.

Read more about our research activities or visit our publications.


Jan 26th, 2014: Laure Fresard, Ph.D. joins the lab

June 10th, 2014: Bosh Liu joins the lab

May 19th, 2014: Inside Stanford Medicine highlights our multi-tissue allele-specific expression work

March 29th, 2014: Emily Tsang is awarded a Natural Sciences and Research Council of Canada (NSERC) doctoral fellowship

March 6th, 2014: Mauro Pala obtains his PhD

Dec 31st, 2013: Konrad Karczewski is off to Boston to postdoc with the Macarthur lab

June 24th, 2013: Emily Tsang, Hewlett-Packard Stanford Graduate Fellow, joins the lab

May 4th, 2013: Kim Kukurba wins Department of Pathology research award for her work on multi-tissue ASE

March 31, 2013: Marianne DeGorter named a Banting Fellow

March 14, 2013: Marianne DeGorter, Ph.D. joins the lab

August 31st, 2012: Tracy Nance, Ph.D. joins the lab

June 6th, 2012: Kim Kukurba awarded Ford Foundation Predoctoral Fellowship

April 18th, 2012: Kim Kukurba awarded a Dept of Defense Graduate Research Fellowship

April 16th, 2012: Mauro Pala joins the lab

April 2th, 2012: Mark Piercy joins the lab

Mar 30th, 2012: Kim Kukurba awarded an NSF Graduate Research Fellowship

Feb 8th, 2012: Our work gets featured in Nature.

Jan 3rd, 2012: Dr Xin Li joins the lab

Dec 1, 2011: Profiled by Genome Technology magazine.

Sept 23rd, 2011: Dr Kevin Smith joins the lab

July 1, 2011: The lab opens its doors in the Department of Pathology. Actively seeking postdoctoral researchers and graduate students.


Nov 16-19th, 2015: Heidelberg, Germany, EMBL|Stanford Conference: Personalised Health.

Oct 6-10th, 2015: Baltimore, USA, ASHG

Aug 2-7th, 2015: Banff, Canada, BIRS Statistical and Computational Challenges In Bridging Functional Genomics, Epigenomics, Molecular QTLs, and Disease Genetics

July 6-10th, 2015: Brisbane, Australia, 2015 Winter School in Mathematical and Computational Biology

June 22-26th, 2015: Pula, Sardinia, Italy, NGS and GWAS for Complex and Monogenic Disorders

May 29th, 2015: Philadelphia, USA, Symposium on Advances in Genomics, Epidemiology, and Statistics

Apr 16-17th, 2015: Montreal, Canada, Cohorts, Big Data and Personalized Medicine: Challenges and Solutions

Mar 13th, 2015: San Francisco, USA, UCSF Institute of Human Genetics


see Publications

Gutierrez-Arcelus, M. et al. Tissue-Specific Effects of Genetic and Epigenetic Variation on Gene Regulation and Splicing PLoS Genetics

Cho, H. et al. High-Resolution Transcriptome Analysis with Long-Read RNA Sequencing PLoS One

Li, X. et al. Transcriptome sequencing of a Large Human Family Identifies the Impact of Rare Noncoding Variants AJHG, 2014

Martin, A. et al. Transcriptome Sequencing from Diverse Human Populations Reveals Differentiated Regulatory Architecture PLoS Genetics, 2014

Bryois, J. et al. Cis and Trans Effects of Human Genomic Variants on Gene Expression PLoS Genetics, 2014

Kukurba, K. et al. Allelic Expression of Deleterious Protein-Coding Variants across Human Tissues PLoS Genetics, 2014

Battle, A. et al. Determining causality and consequence of expression quantitative trait loci Human Genetics, 2014

Nance, T. et al. Transcriptome Analysis Reveals Differential Splicing Events in IPF Tissue PLoS One, 2014

Miller, C.L. et al. Investigation of causal genetic mechanisms for coronary heart disease genome-wide associations Curr Atheroscler Rep, 2014

Wu, E. et al SplicePlot: a utility for visualizing splicing quantitative trait loci Bioinformatics, 2014

Karczewski, K., et al. Performance of genomic medicine Genome Biology, 2013

Mostafavi, S., et al. Type I interferon signaling genes in recurrent major depression: increased expression detected by whole-blood RNA sequencing Molecular Psychiatry, 2013

Daneshjou, R., Zappala, Z. et al. Path-scan: A reporting tool for identifying clinically actionable variants Pac Symp Biocomput, 2014

Zhang, R. et al. Quantifying RNA allelic ratios by microfluidic multiplex PCR and sequencing Nature Methods, 2013

Battle, A. et al. Characterizing the genetic basis of transcriptome diversity through RNA-sequencing of 922 individuals Genome Research, 2013

Lappalainen, T. et al. Transcriptome and genome sequencing uncovers functional variation in humans Nature, 2013

Mostafavi, S. et al. Normalizing RNA-Sequencing Data by Modeling Hidden Covariates with Prior Knowledge PLoS One, 2013

Gutierrez-Arcelus, M., et al. Passive and active DNA methylation and the interplay with genetic variation in gene regulation eLIFE, 2013

Karczewski, K.J., et al. Systematic functional regulatory assessment of disease-associated variants PNAS, 2013

Sweeney, R.T., et al. Desktop transcriptome sequencing from archival tissue to identify clinically relevant translocations. American Journal of Surgical Pathology, 2013

Li, X, et al. Detection and impact of rare regulatory variants in human disease Frontiers in Statistical Genetics and Methodology, 2013

Montgomery, S.B, et al. The origin, evolution and functional impact of short insertion-deletion variants identified in 179 human genomes Genome Research, 2013

Conde, L., et al. Integrating GWAS and Expression Data for Functional Characterization of Disease-Associated SNPs: An Application to Follicular Lymphoma AJHG, 2013

Granel, R., et al. Examination of the relationship between variation at 17q21 and childhood wheeze phenotypes J Allergy Clin Immunology, 2012

Dimas, A.S., et al. Sex-biased genetic effects on gene regulation in humans Genome Research, Sept 2012

Grundberg, E. et al. Mapping cis- and trans-regulatory effects across multiple tissues in twins. Nature Genetics, Sept 2012

Lefebvre, J.F. et al. Genotype-Based Test in Mapping Cis-Regulatory Variants from Allele-Specific Expression Data PLoS One, June 2012

Stranger, B.E., Montgomery, S.B., Dimas, A.S., et al. Patterns of Cis Regulatory Variation in Diverse Human Populations PLoS Genetics, Apr 2012

Macarthur et al. A Systematic Survey of Loss-of-Function Variants in Human Protein-Coding Genes Science, Feb 2012

Paternoster et al.Meta-analysis of genome-wide association studies identifies three new risk loci for atopic dermatitis. Nature Genetics, Dec 2011

Lappalainen et al. Epistatic Selection between Coding and Regulatory Variation in Human Evolution and Disease American Journal of Human Genetics, Sept 2011

Sharp et al. DNA methylation profiles of human active and inactive X chromosomes Genome Research, Aug 2011