Tools and databases

ANT-seq Ancestry inference through microfluidic multiplex PCR and targeted sequencing

EAGLE Detection of GxE interactions in transcriptome data

EigenMT An efficient multiple hypothesis testing correction for eQTLs

IPF Gene Explorer A web server for investigating differential expression and splicing in idiopathic pulmonary fibrosis lung tissue.

mmPCR-Seq Primer Design scripts

ORegAnno: Open Regulatory Annotation Database A database of literature curated gene regulatory elements and regulatory variants.

Path-scan A reporting tool for identifying clinically actionable variants.

Sardinia eQTL browser Browse Sardinian eQTLs from Pala, Zappala et al.

Sex-specific eQTL browser Browse sex-specific eQTLs from Kukurba et al.

Sockeye, Chinook and CHuM 3D genome visualization, peer-to-peer bioinformatics and machine-learning for regulatory variation (pre-2006).

SplicePlot A tool for visualizing splicing quantitative trait loci (sQTL).

Supplemental pages for manuscripts

Pala, Zappala et al, Nature Genetics, 2017 "Individual- and population-specific regulatory variation in Sardinia" - supplemental code/info page

Kukurba et al.,, PloS Genetics, 2013 "Allelic expression of deleterious protein-coding variants across human tissues" - supplemental info page

Montgomery et al., Nature, 2010 "Transcriptome genetics using second generation sequencing in a Caucasian sample" - supplemental info page


March 24th, 2017: Craig Smail joins the lab

Feb 10th, 2017: Zach Zappala passes Ph.D oral defense

Dec 15th, 2016: Montgomery lab joins MoTrPAC

Aug 30th, 2016: Abhiram Rao joins our lab and Ingelsson lab

July 1st, 2016: Mike Gloudemans and Nathan Abell join the lab

Apr 2nd, 2016: 'How genes define us' on Radio New Zealand

Jan 16th, 2016: Montgomery lab featured on BBC News

Oct 9th, 2015: Xin Li wins Cotterman award at ASHG meeting

Sept 14th, 2015: Bruna Balliu, Ph.D. joins the lab

May 27th, 2015: Kim Kukurba passes Ph.D. oral defense.

May 27th, 2015: Kim Kukurba wins CSH Biology of the Genomes poster competition

May 22nd, 2015: Laure Fresard wins CEHG Postdoctoral Fellowship

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.


Mar 27th-31st, 2017: Banff, Canada, BIRS

Oct 18th-22nd, 2016: Vancouver, Canada, ASHG

July 11th, 2016: Stanford, USA, GTEx Community Meeting

June 25-26th, 2016: Stanford, USA, BioC 2016 Meeting

June 20-24th, 2016: Sardinia, Italy 5th Sardinia Summer School 'From Gwas to Function'

Feb 8-10, 2016: Helsinki, Finland, FIMM Think Different Seminar

Jan 4-8, 2016: Holetown, Barbados, 2nd Barbados Workshop on Population Epigenomics

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

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


see Publications

Pala, M., Zappala, Z. et al. Population- and individual-specific regulatory variation in Sardinia, Nature Genetics, 2017

Chiang, C. et al. The impact of structural variation on human gene expression, Nature Genetics, 2017

Salsman, J. et al. PML nuclear bodies contribute to the basal expression of the mTOR inhibitor DDIT4, Sci Rep., 2017

Kernohan, K.D., Frésard, L., Zappala, Z. et al. Whole-transcriptome sequencing in blood provides a diagnosis of spinal muscular atrophy with progressive myoclonic epilepsy, Human Mutation, 2017

Tsang, E.K. et al. Small RNA sequencing in cells and exosomes identifies eQTLs and 14q32 as a region of active export, G3, 2017

Zappala, Z. and Montgomery, S.B. Non-Coding Loss-of-Function Variation in Human Genomes, Human Heredity, 2017

Sibilano, R. et al. A TNFRSF14-FceRI-mast cell pathway contributes to development of multiple features of asthma pathology in mice, Nature Communications, 2016

Hess, G.T. et al. Directed evolution using dCas9-targeted somatic hypermutation in mammalian cells, Nature Methods, 2016

Joshi, R.S., Garg, P. et al. DNA Methylation Profiling of Uniparental Disomy Subjects Provides a Map of Parental Epigenetic Bias in the Human Genome, AJHG, 2016

Miller, C.L. et al. Integrative functional genomics identifies regulatory mechanisms at coronary artery disease loci, Nature Communications, 2016

Kukurba, K. et al. Impact of the X Chromosome and sex on regulatory variation, Genome Research, 2016

Davis, J., Fresard, L. et al. An efficient multiple-testing adjustment for eQTL studies that accounts for linkage disequilibrium between variants, AJHG, 2016

Lesurf, R. et al ORegAnno 3.0: a community-driven resource for curated regulatory annotation, NAR, 2016

The Thousand Genomes Project Consortium A global reference for human genetic variation, Nature, 2015

Baran, Y. et al. The landscape of genomic imprinting across diverse adult human tissues Genome Research, 2015

Rivas, M. et al. Effect of predicted protein-truncating genetic variants on the human transcriptome Science, 2015

Kukurba, K. et al. RNA Sequencing and Analysis CSH Protocols

Babak, T. et al. Genetic conflict reflected in tissue-specific maps of genomic imprinting in human and mouse Nature Genetics, 2015

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