Harmit S. Malik

Appointments and Affiliations

Howard Hughes Medical Institute
Fred Hutchinson Cancer Research Center
Early Career Scientist, Appointed: 2009
Fred Hutchinson Cancer Research Center
Basic Sciences
Member, Appointed: 2010
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Degrees

Ph.D., University of Rochester, Biology, 1999.
B.Tech., Indian Institute of Technology, Bombay, Chemical Engineering, 1993.

Research Interests

Genetic Conflict

Our genomes are a tenuous conglomerate of different genetic entities, each trying to maximize their own evolutionary success, often at great cost to their genomic neighbors. As expected, this conflict can create problems for the host organism. My lab is interested in evolutionary studies of genetic conflict to gain insight into their mechanisms and consequences.We focus on conflicts that are both extrinsic (between different genetic entities) and intrinsic (between components of the same genome).

As an example of intrinsic conflicts, we study the rapid evolution of centromeres and centromeric proteins. Centromeres are crucial for the faithful segregation of genetic information in eukaryotes, but they remain the most mysterious part of our genomes. In both animal and plant meiosis, in the process of forming an egg, of four meiotic products, only one becomes the egg, while the other three are evolutionary dead-ends. There is intense competition between various chromosomes, likely through their centromeres for success into the egg. Our hypothesis is that this results in the rapid gain of centromeric satellites often with deleterious consequences to the host. For instance, in humans, Robertsonian fusions (chromosomes fused at their centromeres) are transmitted more frequently in women, but male carriers of these fusions are partially to completely sterile. We study the rapid evolution of centromeric components to gain a better understanding of aneuploidy events (commonly observed in cancer cells) and to answer one of the long-standing questions in biology: how do two species evolve from one?

Examples of extrinsic conflicts include innate immunity genes in primates that are directly implicated in host-pathogen interactions. In collaboration with the Emerman and Geballe labs, we are characterizing the driving forces and functional consequences of primate antiviral genes that act against retroviruses and large double-stranded DNA viruses.

Prospective graduate students are encouraged to apply to the MCB program at the University of Washington. Graduate students from the Genome Sciences Department at the University of Washington are also eligible to join my lab.

Additional Experience

Phylogenomics
Identification of novel domains by remote homology searches

Future Research

Impact of transposable elements on eukaryotic genomes and gene repertoires
Centromere complexity and its evolutionary origins

Memberships

American Society for Virology
American Society for Microbiology
Genetics Society of America
Society for Molecular Biology and Evolution

Honors and Awards

2010, Vilcek Prize for Creative Promise in Biomedical Research, Vilcek Foundation
2009, Presidential Early Career Award in Science and Engineering (PECASE), National Science Foundation (NSF)
2009-2015, Early Career Scientist Award, Howard Hughes Medical Institute, HHMI
2008-2013, CAREER Award, National Science Foundation (NSF)
2007-2012, Investigator in the Pathogenesis of Infectious Disease, Burroughs Wellcome Fund
2005-2008, Searle Scholar Award, Kinship Foundation
2004-2006, Sloan Research Fellowships, Alfred P. Sloan Foundation
2004-2006, Kimmel Scholars Award, Sidney Kimmel Foundation, Cancer Research
2002, Best Postdoctoral Research Poster, Gordon Conference on Molecular Evolution
1999-2003, Postdoctoral Fellowship, Helen Hay Whitney Foundation
1995, The Edward Peck Curtis Teaching Award, University of Rochester
1995, Graduate Student Teaching Award, Department of Biology, University of Rochester
1993-1995, Sproull Fellowhip, University of Rochester

Previous Positions

2007-2010, Associate Member, Basic Sciences, Fred Hutchinson Cancer Research Center
2003-2007, Assistant Member, Basic Sciences, Fred Hutchinson Cancer Research Center
1999-2003, Postdoctoral Fellow, Henikoff Lab, Basic Sciences, Fred Hutchinson Cancer Research Center
1993-1999, Graduate Student, University of Rochester, Biology

Current Funding

  • Harold E. and Leila Y. Mathers Foundation: Research Grant, 2012 to 2015
  • National Science Foundation (NSF): NSF (CAREER) award, 2008 to 2013
  • National Institutes of Health (NIAID) R21, 2012 to 2014
  • National Institutes of Health (NIGMS) R01, 2005 to 2014
  • Lupus Research Institute Pilot Grant, 2012 to 2015
  • Howard Hughes Medical Institute, 2009 to 2015

Recent Publications

2014
2013
Malfavon-Borja, R, Wu LI, Emerman M, Malik HS.  2013.  Birth, decay, and reconstruction of an ancient TRIMCyp gene fusion in primate genomes.. Proceedings of the National Academy of Sciences of the United States of America. 110(7):E583-92. Abstract
Compton, AA, Malik HS, Emerman M.  2013.  Host gene evolution traces the evolutionary history of ancient primate lentiviruses.. Philosophical transactions of the Royal Society of London. Series B, Biological sciences. 368(1626):20120496. Abstract
2012
Malik, HS.  2012.  Retroviruses push the envelope for mammalian placentation.. Proceedings of the National Academy of Sciences of the United States of America. 109(7):2184-5.
2011
2010