Stephen Montgomery

Stephen is now at Stanford University School of Medicine. Visit him here.

Publication list

Montgomery, S.B., Lappalainen, T., Gutierrez-Arcelus, Dermitzakis, E.T. (2011) Rare and common regulatory variation in population-scale sequenced human genomes (accepted)

Montgomery, S.B., Dermitzakis, E.T. (2011) From Expression QTLs to Personalized Transcriptomics. Nature Reviews Genetics March 9 (AOP)

Nica, A.C., Parts., L., Glass, D., Nisbett, J., Barrett, A., Sekowska, M., Travers, M., Potter, S., Grundberg, E., Small, K., Hedma, A., Bataille, V., Bell, J.T., Surdulescu, G., Dimas, A.S., Ingle, C., Nestle, F.O., di Meglio, P., Min, J.L, Wilk, A., Hammond, C.J., Hassanali, N., Yang, T., Montgomery, S.B., O’Rahilly, S., Lindgren, C.M., Zondervan, K.T., Soranzo, N., Barroso, I., Durbin, R., Ahmadi, K., Deloukas, P., Dermitzakis, E.T., Spector, T.D. The Architecture of Gene Regulatory Variation across Multiple Human Tissues: the MuTHER Study. PLoS Genetics 7(2): e1002003

Borel, C., Deutsch, S., Letourneau, A., Migliavacca, E., Montgomery, S.B., Dimas, A.S., Vejnar, C.E., Attar, H., Gagnebin, M., Gehrig, C., Falconnet, E., Dupré, Y., Dermitzakis, E.T. and Antonarakis, S.E. (2011) Identification of cis- and trans- regulatory variation modulating microRNA expression levels in human fibroblasts Genome Research 21(1):68-73

Ning, Z., Montgomery, S.B., (2010) Out of the sequencer and into the wiki as we face new challenges in genome informatics. Genome Biology 11:308

1000 Genomes Project Consortium, Durbin, R.M., Abecasis, G.R., Altshuler, D.L., Auton, A., Brooks, L.D., Durbin, R.M., Gibbs, R.A., Hurles, M.E., McVean, G.A. (2010) A map of human genome variation from population-scale sequencing Nature 467(7319):1061-73.

Montgomery, S.B., Kasaian, K., Jones, S.J.M., Griffith, O.L. (2010) Annotating the Regulatory Genome (Chapter 20). Computational Biology of Transcription Factor Binding. Methods Mol Biol. 2010;674:313-49.

The International HapMap 3 Consortium (2010) Integrating common and rare genetic variation in diverse human populations. Nature 467(7311):52-58.

Yang, T.P., Beazley, C., Montgomery, S.B., Dimas, A.S., Gutierrez-Arcelus, M., Stranger, B.E., Deloukas, P., Dermitzakis, E.T., (2010) Genevar: a database and Java application for the analysis and visualization of SNP-gene associations in eQTL studies. Bioinformatics 26(19):2474-6

Nica, A.C., Montgomery, S.B., Dimas, A.S., Stranger, B.E., Beazley, C., Barroso, I., Dermitzakis, E.T., (2010) Candidate causal regulatory effects by integration of expression QTLs with complex trait genetic associations. PLoS Genetics 6(4): e1000895. doi:10.1371/journal.pgen.1000895

Montgomery, S.B., Sammeth, M., Gutierrez-Arcelus, M., Lach, R.P., Ingle, C., Nisbett, J., Guigo, R., Dermitzakis, E.T. (2010) Transcriptome genetics using second generation sequencing in a Caucasian population. Nature 464(7289):773-7 (also mentioned in Nature Reviews Genetics profile “Seq-ing regulatory variants and on Genome Web News “RNA Sequencing Studies Provide Insights into Expression in African, European Populations”)

Montgomery, S.B., Dermitzakis, E.T. (2009) The resolution of the genetics of gene expression. Human Molecular Genetics R(2):R211-5

Southam, L., Soranzo, N., Montgomery, S.B., Frayling, T.M., McCarthy, M.I., Barroso, I., Zeggini, E. (2009) Is the thrifty genotype hypothesis supported by evidence based on confirmed type 2 diabetes- and obesity-susceptibility variants? Diabetologia. 52(9) :1846-51

Dimas, A.S.*, Deutsch, S.*, Stranger, B.E.*, Montgomery, S.B.*, Borel, C., Attar-Cohen, H., Ingle, C., Beazley, C., Gutierrez-Arcelus, M., Sekowska, M., Gagnebin, M., Nisbett, J., Deloukas, P., Dermitzakis, E.T., Antonarakis, S.E. (2009) Common regulatory variation impacts gene expression in a tissue-dependent manner. Science 325(5945) :1246-50 *joint first authors.

Montgomery S.B. (2009) Current computational methods for prioritizing candidate regulatory polymorphisms. Methods in Molecular Medicine. Humana Press. 569 :89-114

Aerts, S., Haeussler, M., van Vooren, S., Griffith, O.L., Hulpiau, P., Jones, S.J.M., Montgomery, S.B., Bergman, C.M., The Open Regulatory Annotation Consortium (2008) Text-mining assisted regulatory annotation. Genome Biology. 9:R31

Griffith, O.L.*, Montgomery, S.B.*, Bernier, B., Chu, B., Aerts, S., Sleumer, M.C., Bilenky, M., Haeussler, M., Griffith, M., Gallo, S.M., Giardine, B., Mahony, S., Hooghe, S., Van Loo, P., Blanco, E., Ticoll, A., Lithwick, S., Portales-Casamar, E., Donaldson, I.J., Robertson, A.G., Wadelius, C., De Bleser, P., Vlieghe, D., Halfon, M.S., Wasserman, W.W., Hardison, R., Bergman, C.M., Jones, S.J.M. The Open Regulatory Annotation Consortium (2008) ORegAnno: an open-access community-driven resource for regulatory annotation. Nucleic Acids Research. Nov. 15th *joint first authors.

Stranger, B.E., Nica, A.C., Forrest, M.S., Dimas, A., Bird, C.P., Beazley, C., Ingle, C.E., Dunning, M., Flicek, P., Koller, D., Montgomery, S.B., Tavare, S., Deloukas, P. and Dermitzakis, E.T. (2007) Population genomics of human gene expression. Nature Genetics. 39(10):1217-24

Montgomery, S.B., Griffith, O.L., Scheutz, J.M., Brooks-Wilson, A., Jones, S.J. (2007) A Survey of Genomic Properties for the Detection of Regulatory Polymorphisms. PLoS Computational Biology 8;3(6):e106

Montgomery, S.B.*, Griffith, O.L.*, Sleumer, M.C., Bergman, C.M., Bilenky, M., Pleasance, E.D., Prychyna, Y., Zhang, X., Jones, S.J. (2006) ORegAnno: an open access database and curation system for literature-derived promoters, transcription factor binding sites and regulatory variation. Bioinformatics 1;22(5):637-50 *joint first authors

Robertson, A.G., Bilenky, M., Lin, K., He, A., Yuen, W., Dagpinar, M., Varhol, R., Teague, K., Griffith, O.L., Zhang, X., Pan, Y., Hassel, M., Sleumer, M.C., Pan, W., Pleasance, E.D., Chuang, M., Hao H., Li, Y.Y., Robertson, N., Fjell, C., Li, B., Montgomery, S.B., Astakhova, T., Zhou, J., Sander, J., Siddiqui, A.S. and Jones, S.J. (2006) cisRED: A database system for genome scale computational discovery of regulatory elements. Nucleic Acids Research 1;34 (Database issue):D68-73.

Montgomery, S.B., Fu, T., Guan, J., Lin, K., Jones, S.J.M., (2005) An application of peer-to-peer technology to the discovery, use and assessment of bioinformatics programs. Nature Methods 2(8):563

Montgomery, S.B., Astakhova, T., Bilenky, M., Birney, E., Fu, T., Hassel, M., Melsopp, C., Rak, M., Robertson, A.G., Sleumer, M.C., Siddiqui, A.S., and Jones, S.J. (2004) Sockeye: A 3D Environment for Comparative Genomics. Genome Research 14:956-962 (Sockeye featured on the cover of Linux Journal)

Marra, M.A., Jones, S.J., Astell, C.R., Holt, R.A., Brooks-Wilson, A., Butterfield, Y.S., Khattra, J., Asano, J.K., Barber, S.A., Chan, S.Y., Cloutier, A., Coughlin, S.M., Freeman, D., Girn, N., Griffith, O.L., Leach, S.R., Mayo, M., McDonald, H., Montgomery, S.B., Pandoh, P.K., Petrescu, A.S., Robertson, A.G., Schein, J.E., Siddiqui, A.S., Smailus, D.E., Stott, J.M., Yang, G.S., Plummer, F., Andonov, A., Artsob, H., Bastien, N., Bernard, K., Booth, T.F., Bowness, D., Czub, M., Drebot, M., Fernando, L., Flick, R., Garbutt, M., Gray, M., Grolla, A., Jones, S., Feldmann, H., Meyers, A., Kabani, A., Li, Y., Normand, S., Stroher, U., Tipples, G.A., Tyler, S., Vogrig, R., Ward, D., Watson, B., Brunham, R.C., Krajden, M., Petric, M., Skowronski, D.M., Upton, C., Roper, R.L. (2003) The Genome sequence of the SARS associated coronavirus. Science 300(5624):1399-404