Alex Platt

Alexander Platt

Sr. Research Scientist

Research Interest

Dr. Platt’s research focuses on the evolution of complex traits in structured populations. As such, it incorporates techniques from population genetics, ecology, and systems biology to describe how population variation and environmental heterogeneity act and interact to shape multi-factor traits such as disease and fitness. Modelling and simulation of the evolution of population-level variation supports theoretical and observational studies to discover the genetic architecture of traits of interest. Specific current projects include:

  • Modelling haplotype evolution for inference of demography and selection
  • Genetic and epigenetic architecture of adaptive evolution in natural populations
  • Effects of population structure on trait and genome architecture
  • Association mapping for polygenic and multi-factor quantitative traits and diseases

Education

1999 - 2005

 

1995 - 1999

Ph.D. Theoretical Population Genetics, Harvard University, Cambridge, MA
Advisor: John Wakeley, Ph.D.

B.S. University of Pennsylvania, Philadelphia, PA
Advisor: Warren Ewens, Ph.D.

Research Experience

2019 – Present

2014 – 2019



2011 – 2014

2008 - 2011

2009 - 2010

2007

2005 - 2008

2000

Senior Research Investigator
Department of Genetics, Perelman School of Medicine, University of Pennsylvania

Assistant Professor (Research)
Joint appointment in Center for Computational Genetics and Genomics and Institute for Genetic and Evolutionary Medicine
Temple University, Philadelphia PA

Assistant Researcher
Labs of John Novembre and Victoria Sork, University of California Los Angeles

Postdoctoral Research Asssociate
Lab of Magnus Nordborg, University of Southern California

Visiting Scholar
Gregor Mendel Institute for Plant Molecular Biology

Visiting Scholar
National Evolutionary Synthesis Center

Postdoctoral Research Associate Center of Excellence in Genome Science, University of Southern California

Graduate Research Assistant
Los Alamos National Laboratory. Advised by Alan Perelson

Publications & Manuscripts

McQuillan, Michael; Zhang, Chao; Tishkoff, Sarah; Platt, Alexander. In press 2020. The importance of including ethnically diverse populations in studies of quantitative trait evolution. Current Opinions in Genetics and Development.

Platt, Alexander; Pivirotto, Alyssa; Knoblauch, Jared; Hey, Jody. 2019. An estimator of first coalescent time reveals selection on young variants and large heterogeneity in rare allele ages among human populations. PLoS Genetics 15 (8), e1008340

Platt, Alexander Time-conditional properties of branches in coalescent gene trees. BioRxiv: 189209 [preprint] available here

Xiong, Zhi; Zhang, Qingrun; Platt, Alexander; Liao, Wenyuan; Xinghua, Shi; de los Campos, Gustavo; Long, Quan (2019) OCMA: Fast, Memory-Efficient Factorization of Prohibitively Large Relationship Matrices. G3: Genes, Genomes, Genetics 9(1),13-19.

Patel, Ravi; Scheinfeld, Laura; Lanham, Tamera; Tamura, Koichiro; Platt, Alexander; Glicksberg, Benjamin; Xu, Ke; Dudley, Joel; Kumar, Sudhir. 2018. Adaptive landscape of protein variation in human exomes. Molecular biology and evolution 35(8),2015-2025

Platt, Alexander;Weber, Claudia; Liberles, David. 2018. Protein evolution depends on multiple distinct population size parameters. BMC evolutionary biology 18.1 (2018): 17

Platt, Alexander; Gugger, Paul; Pellegrini, Matteo; Sork, Victoria. 2015. Genome-wide signature of local adaptation linked to variable CpG methylation in oak populations. Molecular Ecology24:3823-3830.

Brachi, Benjamin; Meyers, Christopher; Villoutreix, Romain; Platt, Alexander; Morton, Timothy; Roux, Fabrice; Bergelson, Joy. 2015. Co-selected genes determine adaptive variation in herbivore resistance throughout the native range of Arabidopsis thaliana. Proceedings of the National Academy of Sciences 112:4032-4037

Yang, Wen-Yun; Platt, Alexander; Wen-Kai Chiang, Charleston; Eskin, Eleazar; Novembre, John; Pasaniuc, Bogdan. 2014. Spatial localization of recent ancestors for admixed individuals. G3: Genes, Genomes, Genetics 4:2505-2518

Lovell, John; Juenger, Thomas; Michaels, Scott; Lasky, Jesse; Platt, Alexander; Richards, James; Yu, Xuhong; Easlon, Hsien; Sen, Saunak; McKay, John. 2013. Protagonistic pleiotropy of FRIGIDA promotes adaptation and positive assortative mating. Proceedings of the Royal Society B: Biological Sciences 280:20131043.

See full publication list here.

Book Review

David Reich. Who We Are and How We Got Here: Ancient DNA and the New Science of the Human Past. 2019 Evolutionary Studies in Imaginative Culture (3.2)

Teaching Experience

2020   Co-Instructor, University of Pennsylvania BIOL 522- Human Evolutionary Genomics.
2015-2019   Guest instructor, Temple University Biology 3211: Human Evolution.
2015-2019   Mentor, Temple University undergraduate independent study program.
2014-2015   Mentor, Temple University NIH Maximizing Access to Research Careers program.
2014   Guest lecturer, Temple University Biology 8003: Introduction to Graduate Research.
2012   Guest lecturer, UCLA EEB 135/235: Population Genetics.
2008   Guest lecturer, Keck School of Medicine at USC: Bayesian Computational Methods in Population Genetics.
2004   Teaching Fellow, Harvard University Organismic and Evolutionary Biology 275: Natural Selection at the Molecular Level.
2002   Teaching Fellow, Harvard University Core Curriculum 50: Evolution. A science class for non-scientist undergraduates.
2000   Teaching Fellow, Harvard University Biological Sciences 252: Coalescence Theory.
1999   Teaching Fellow, Harvard University Biological Sciences 2: Introduction to Organismic Biology.

Other Professional Activites

  • • 2019-present Associate Editor -- Journal of Molecular Evolution
  • • 2016-present Judge -- INFORMS Analytics Syngenta Crop Challenge Prize Committee