My CV

Alicia R. Martin, PhD


ADDRESS CONTACT
Massachusetts General Hospital
Richard B. Simches Building
185 Cambridge St, CPZN 6818
Boston, MA 02113
Email: armartin [at] broadinstitute.org
Website: www.aliciarmartin.com
Twitter: @genetisaur
Education & Training Massachusetts General Hospital & Broad Institute, Research Fellow (2/2015 – Present)
Postdoctoral Advisor: Mark J. Daly, Analytic and Translational Genetics Unit

Stanford University, PhD Student (9/2010 – 1/2015)
Doctor of Philosophy, Genetics, 4/2015
Master of Science, Biomedical Informatics, 6/2013
Thesis Advisor: Carlos D. Bustamante
Dissertation Title: Genetic and Regulatory Variation Across Diverse Human Populations

University of Washington, Undergraduate Student (9/2006 – 6/2010)
Bachelor of Science, 6/2010
Major: Bioengineering, ABET accredited
Departmental Honors
Thesis Advisor: Celeste Berg
Dissertation Title: Developing Drosophila melanogaster as a Model for Aminoglycoside Antibiotic Toxicity

Publications See Google scholar page

Martin, A. R., Gignoux, C. R., Walters, R., Wojcik, G. L., Gravel, S., Daly, M. J., Bustamante, C. D., Kenny, E. E. (2017). Human demographic history impacts genetic risk prediction across diverse populations. American Journal of Human Genetics. 100, 635-649. [Featured article]

Duncan, L. E., Ratanatharathorn, A., Aiello, A. E., Almli, L. M., Amstadter, A. B., Ashley-Koch, A. E., Baker, D. G., Beckham, J. C., Bierut, L. J., Bisson, J., Bradley-Davino, B., Chen, C., Dalvie, S., Farrer, L. A., Galea, S., Garrett, M. E., Gelernter, J. E., Guffanti, G., Hauser, M. A., Johnson, E. O., Kessler, R. C., Kimbrel, N. A., King, A., Koen, N., Kranzler, H. R., Logue, M. W., Maihofer, A. X., Martin, A. R., Miller, M. W., Morey, R. A., Nugent, N. R., Rice, J. P., Ripke, S., Roberts, A. L., Saccone, N. L., Smoller, J. W., Stein, D. J., Stein, M. B., Sumner, J. A., Uddin, M., Ursano, R. J., Wildman, D. E., Yehuda, R., Zhao, H. Y., Daly, M. J., Liberzon, I., Ressler, K. J., Nievergelt, C. M., Koenen, K. C. (2017). Largest GWAS of PTSD (N=20,070) Yields Genetic Overlap with Schizophrenia and Sex Differences in Heritability. Molecular Psychiatry. [In Press]

Uren, C., Kim, M., Martin, A. R., Granka, J. M., Werely, C. J., Kidd, J. M., Bobo, D., Gignoux, C. R., Behr, A., Ramachandran, S., van Helden, P., Möller, M., Hoal, E. G., Henn, B. M. (2016). Fine-scale population structure in southern Africa reflects ecological boundaries. Genetics. 204, 303-314. [Online]

Henn, B. M.*, Botigué, L. R.*, Peishl, S.*, Dupanloup, I., Lipatov, M., Maples, B. K., Martin, A. R., Musharoff, S., Yee, MC, Cann, H. M., Snyder, M., Excoffier, L., Kidd, J. M., Bustamante, C. D. (2016). Distance from Sub-Saharan Africa Predicts Mutational Load in Diverse Human Genomes. PNAS. 113, E440-E449. [Online]

The 1000 Genomes Project Consortium. (2015). A global reference for human genetic variation. Nature. 526. 68-74. [Online] [In the news]

Grubert, F.*, Zaugg, J. B.*, Kasowski, M.*, Ursu, O.*, Spacek, D. V., Martin, A. R., Greenside, P., Srivas, R., Phanstiel, D., Pekowska, A., Pritchard, J. K., Bustamante, C. D., Steinmetz, L. M., Kundaje, A., Snyder, M. (2015). Genetic Control of Chromatin States and Gene Expression in Humans Involves Local and Distal Chromosomal Interactions. Cell. 162, 1051-1065. [Online] [In the news]

Martin, A. R.*, Costa, H. A.*, Lappalainen, T., Henn, B. M., Kidd, J. M., Yee, M. C., Grubert, F., Cann, H.M., Snyder, M., Montgomery, S. B., Bustamante, C.D. (2014). Transcriptome Sequencing from Diverse Human Populations Reveals Differentiated Regulatory Architecture. PLoS Genetics. 10, e1004549. [Online] [In the news]

Martin, A.R., Tse, G., Bustamante, C. D., Kenny, E. E. (2014). Imputation-based Assessment of Next Generation Rare Exome Variant Arrays. Pacific Symposium for Biocomputing. 241-252. [Online]

Kidd, J. M.*, Sharpton, T. J.*, Bobo, D., Norman, P. J., Martin, A. R., Carpenter, M. L., Sikora, M., Gignoux, C. R., Nemat-Gorgani, N., Adams, A., Guadalupe, M., Guo, X., Feng, Q., Li, Y., Liu, X., Parham, P., Hoal, E. G., Feldman, M. W., Pollard, K. S., Wall, J. D., Bustamante, C. D., Henn, B. M. (2014). Exome Capture from Saliva Produces High Quality Genomic and Metagenomic Data. BMC Genomics. 15, 262. [Online] [In the news]

Karczewski, K. J., Fernald, G. H., Martin, A. R., Snyder, M., Tatonetti, N. P., Dudley, J. T. (2014). STORMSeq: An Open-Source, User-Friendly Pipeline for Processing Personal Genomics Data in the Cloud. PLoS One. 9, e84860. [Online]

Martin, A. R. (2011) Developing Drosophila melanogaster as a Model for Aminoglycoside Antibiotic Toxicity. The McNair Scholars Journal. 10, 135-148. [Online]

Meeting Organizer American Society of Human Genetics Meeting (2016)
Vancouver, Canada, Co-moderator: “Studies of ancestry, migration, and admixture” session

Genome Informatics Meeting (2016)
Cambridge, United Kingdom, Co-chair: “Comparative, evolutionary and metagenomics” session

Big Data in Biomedicine Conference (2013)
Stanford University, Volunteer

12th Annual Biomedical Computation at Stanford (BCATS) Symposium (2011)
Stanford University, Organizer

Invited Talks Demographic history impacts polygenic risk across diverse populations. Society for Molecular Biology and Evolution Conference. Austin, TX. July 3, 2017.

Fine-scale identity-by-descent and birth records in Finland provide insights into recent population history. Department of Epidemiology and Biostatistics, Karolinska Institutet. Stockholm, Sweden. May 30, 2016.

Identity-by-descent (IBD) mapping as an alternative to single variant GWAS. BroadE Statistical Genetics Workshop. Cambridge, MA. April 8, 2016.

1000 Genomes Admixture Tutorial. American Society of Human Genetics. Baltimore, MD. October 8, 2015

Population Stratification. BroadE Statistical Genetics Workshop. Cambridge, MA. June 8, 2015.

The Genetic Architecture of Skin Pigmentation in the Southern African ‡Khomani San. Evolgenome. Stanford, CA. September 24, 2014

Transcriptome variation in the Human Genome Diversity Project & the genetic architecture of skin pigmentation in Southern Africa. Whole Genome Sequencing Seminar. Stanford, CA. March 14, 2013

Understanding genetic and transcriptome variation in diverse human populations. Mount Sinai School of Medicine Biobank Seminar. New York, NY. August 15, 2013

Conference Talks Martin, A.R., Gignoux, C. R., Walters, R., Wojcik, G. L., Gravel, S., Daly, M. J., Bustamante, C. D., Kenny, E. E. Human demographic history impacts genetic risk prediction across diverse populations. Center for Genomic Medicine Series, Massachusetts General Hospital. Boston, MA. March 29, 2017.

Martin, A.R., Kerminen, S., Sarin, AP., Palotie, A., Ripatti, S., Pirinen, M., Daly, MJ. Fine-scale identity-by-descent and birth records in Finland provide insights into recent population history. Society for Molecular Biology and Evolution (SMBE). Gold Coast, Australia. July 6, 2016.

Martin, A.R., Bustamante, C. D., Kenny, E. E. The history of admixture in the 1000 Genomes Project. Society for Molecular Biology and Evolution (SMBE) Genetics of Admixed People satellite meeting. San Antonio, TX. May 18, 2016.

Martin, A.R., Tse, G., Bustamante, C. D., Kenny, E. E. Imputation-based Assessment of Next Generation Rare Exome Variant Arrays. Pacific Symposium for Biocomputing. Kohala Coast, HI. January 3, 2014

Martin, A. R., Costa, H. A., Kidd, J. M., Henn, B. M., Yee, M. C., Grubert, F., Montgomery, S. B., Cann, H. M., Snyder, M., Bustamante, C. D. Characterizing gene expression variation across seven diverse human populations.

  • American Society of Human Genetics Conference. San Francisco, CA. November 9, 2012
  • Biomedical Computation at Stanford Symposium. Stanford, CA. October 30, 2012

Martin, A. R., Berg, C. A. Developing Drosophila melanogaster as a Model for Aminoglycoside Antibiotic Toxicity.

  • UW Undergraduate Research Symposium. Seattle, WA. May 21, 2010
  • Annual Pacific Northwest McNair/EIP Conference. Seattle, WA. April 30, 2010
Conference Posters Martin, A. R., Bertalan, M., Rosengren, A., Buil, A., Thygesen, J. H., Thompson, W., Sparsø, T. H., Als, T., Howrigan, D. P., Mortensen, P. B., Neale, B. M., Werge, T., Daly, M. J., iPSYCH-SSI-Broad collaboration. Population-level identity-by-descent haplotype sharing provides insight into demographic history and autism spectrum disorder. American Society of Human Genetics Conference. Baltimore, MD. October 9, 2015

Tse, G., Bustamante, C. D., Kenny, E. E. Imputation-based Assessment of Next Generation Rare Exome Variant Arrays. Bio-X Poster Session. Stanford, CA. March 3, 2014

Martin, A. R., Tse, G., Bustamante, C. D., Kenny, E. E. Imputation-based Assessment of Next Generation Rare Exome Variant Arrays. Bio-X Poster Session. Stanford, CA. March 3, 2014

Martin, A. R., Granka, J. M., BGI, Gignoux, C. R., Möller, M., Werely, C. J., Kidd, J. M., Feldman, M. W., Hoal, E. G., Bustamante, C. D., Henn, B. M. The Genetic Architecture Of Skin Pigmentation In Southern Africa.

  • 23rd Annual Society for Molecular Biology and Evolution Conference. Vienna, Austria. July 12 – 16, 2015
  • 26th Annual Biology of Genomes Conference. Cold Spring Harbor, NY. May 7 – 11, 2013
  • 2nd Annual Conference to Eliminate Health Disparities in Genomic Medicine. San Francisco, CA. May 29 – 31, 2013
  • American Society of Human Genetics Conference. Boston, MA. October 23, 2013

Martin, A. R., Costa, H. A., Kidd, J. M., Henn, B. M., Yee, M. C., Montgomery, S. B., Cann, H. M., Snyder, M., Bustamante, C. D. Characterizing gene expression variation across seven diverse human populations.

  • 20th Annual Society for Molecular Biology and Evolution Conference. Dublin, Ireland. June 23 – 26, 2012
  • 2nd Annual Stanford Biosciences Student Association Poster Session. Stanford, CA. February 11, 2013

Martin, A. R., Berg, C. A. Developing Drosophila melanogaster as a Model for Aminoglycoside Antibiotic Toxicity. 51st Annual Drosophila Research Conference. Washington, DC. April 8 – 10, 2010.

Martin, A. R., Berg, C. A. Investigating Cellular Interactions that Occur During Tube Formation.

  • 18th Annual National McNair Conference. Delavan, WI. November 7, 2009
  • UW-HHMI Biology Undergraduate Research Symposium. Seattle, WA. October 16, 2009
  • Office of Research and Educational Opportunities for Students (OREOS) Undergraduate Research Symposium. Missoula, MT. August 5, 2009
Journal Referee PLoS Genetics, Human Heredity, Human Molecular Genetics, EJHG, Axios
Honors & Awards “Best Talk” Gordon Research Seminar – Human Genetics and Genomics, 2017
Center for Genomic Medicine (CGM) Late-Breaking Abstract Winner, 2017
Society for Molecular Biology and Evolution (SMBE) 2014 Graduate Student Award
Stanford University Center for Computational, Evolutionary, and Human Genomics Trainee Research Grant, 2013-2014
“Honorable Mention” National Science Foundation (NSF) Graduate Research Fellowship, 2011
“Honorable Mention” 51st Annual Drosophila Research Conference Poster Presentation, 2010
Washington Research Foundation Fellowship, 2009-2010
Boeing/Office of Minority Affairs Research Scholarship, 2009-2010
Ronald E. McNair Program Scholar, 2009-2010
“Best Poster” UW-HHMI Biology Undergraduate Research Symposium Poster Presentation, 2009
Howard Hughes Medical Institute Integrative Research Internship
Four Marine Corps Scholarship Foundation Scholarships, 2006-2010
Potlatch Scholarship Foundation Scholarship, 2006-2010
Washington State PTA Scholarship, 2006-2007
Windermere Scholarship, 2006-2007
East Spokane Kiwanis Scholarship, 2006-2007
Elk’s Lodge Scholarship, 2006-2007
Teaching Experience Stanford at the Tech Participant, 2012 – 2013
The Tech Museum of Innovation, San Jose, CA

Head Teaching Assistant & Guest Lecturer, 2012 – 2012
Gene 210: Genomics and Personalized Medicine, Stanford, CA

  • Helped develop and maintain the Genotation (i.e. Interpretome) website for students to perform personal genome interpretation
  • Gave lectures on statistical genetics and linkage disequilibrium

SAT Tutor, 2010 – 2011
Boys & Girls Club, Redwood City, CA

  • Tutored low income and minority high school students for 6 months to prepare them in English and mathematics.
Work Experience Student Assistant/Stock Keeper, 2008 – 2010
Berg Lab/UW Genome Sciences, Seattle, WA

  • Selected and maintained healthiest Drosophila melanogaster stocks for the lab

Lab Coordinating Assistant, 2008
UW Department of Biology, Seattle, WA

  • Planned and expanded Drosophila melanogaster stocks according to the life cycle of P1, F1, and F2 crosses
  • Provided F2 crosses to ~350 students to teach the principles of Mendelian genetics

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