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«Daniel M. Weinreich Department of Ecology and Evolutionary Biology, 401/863-3937 (v) -2749 (lab) -2166 (f) and Center for Computational Molecular ...»

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Daniel M. Weinreich

Department of Ecology and Evolutionary Biology, 401/863-3937 (v) -2749 (lab) -2166 (f)

and Center for Computational Molecular Biology Daniel_Weinreich@Brown.edu

Brown University, Box G-W http://research.brown.edu/myresearch/

Providence, RI 02912 Daniel_Weinreich

EDUCATION

1998 Ph.D. in Population Genetics and Molecular Evolution (Richard Lewontin, advisor). Harvard University, Cambridge, Massachusetts.

1983 B.S. in Computer Science, with highest honors (John H. Holland, advisor).

University of Michigan, Ann Arbor, Michigan.

PROFESSIONAL EXPERIENCE

2007- Assistant Professor of Biology. Department of Ecology and Evolutionary Biology, and Center for Computational Molecular Biology, Brown University, Providence, RI.

2004 – 2006 Postdoctoral Research Associate with Daniel L. Hartl, Organismic and Evolutionary Biology Department, Harvard University, Cambridge, MA.

2000 – 2003 NIH National Research Service Award Postdoctoral Fellow. Sponsors: Dr. Lin Chao, Department of Ecology and Evolution, University of California at San Diego and Dr. Daniel L. Hartl, Organismic and Evolutionary Biology Department, Harvard University, Cambridge, MA.

1998 – 2000 Post-doctoral Research Associate with Dr. David Rand, Department of Ecology and Evolutionary Biology, Brown University, Providence, RI.

1992 – 1998 Ph.D. student, Organismic and Evolutionary Biology Department, Harvard University, Cambridge, MA.

1989 – 1992 Software Engineer, Proteon Corporation, Westborough, MA.

1983 – 1989 Software Engineer, Codex Corporation, Canton, MA.

CLASSROOM TEACHING EXPERIENCE

Fall 2011 BIOL 0380: “Ecology and Evolution of Infectious Disease,” Brown University.

Enrolment: 24.

BIOL 1950: “Directed Research/Independent Study,” Brown University.

Enrollment: 4.

BIOL 2980: “Graduate Independent Study,” Brown University. Enrollment: 1.

Spring 2011 BIOL 1960: “Directed Research/Independent Study,” Brown University.

Enrollment: 3.

Fall 2010 BIOL 0380: “Ecology and Evolution of Infectious Disease,” Brown University.

Enrollment: 23.

BIOL 1950: “Directed Research/Independent Study,” Brown University.

Enrollment: 1.

BIOL 2980: “Graduate Independent Study,” Brown University. Enrollment: 1.

Spring 2010 BIOL 1960: “Directed Research/Independent Study,” Brown University.

Enrollment: 1.

BIOL 2980: “Graduate Independent Study,” Brown University. Enrollment: 2.

WEINREICH CV December 11, 2011 Fall 2009 BIOL 0380: “Ecology and Evolution of Infectious Disease,” Brown University.

Enrollment 21.

BIOL 1950: “Directed Research/Independent Study,” Brown University.

Enrollment: 1.

BIOL 2980: “Graduate Independent Study,” Brown University. Enrollment: 2.

Spring 2009 BIOL 1430: “Computational Theory of Molecular Evolution,” Brown University.

Enrollment 35.

BIOL 1960: “Directed Research/Independent Study,” Brown University.

Enrollment: 1.

BIOL 2980: “Graduate Independent Study,” Brown University. Enrollment: 1.

Fall 2008 BIOL 0380: “Ecology and Evolution of Infectious Disease,” Brown University.

Enrollment: 23 BIOL 1950: “Directed Research/Independent Study,” Brown University.

Enrollment: 3.

BIOL 2980: “Graduate Independent Study,” Brown University. Enrollment: 1.

Spring 2008 BIO 1960: “Directed Research/Independent Study,” Brown University.

Enrollment: 6.

Fall 2007 BIO 1950: “Directed Research/Independent Study,” Brown University.

Enrollment: 4.

“Minicourse: Genetic Interactions: Principles, Measurement and Interpretation”, Department of Integrative Developmental Biology, Harvard Medical School.

Participants: 40.

Spring 2007 BI 0143: “Computational Theory of Molecular Evolution,” Brown University.

Enrollment: 30.

Fall 2003 Teaching Fellow, BS50 “Genetics and Genomics (W. Gelbart and W. Fixsen), Harvard University.

Fall 1997 Teaching Fellow, Bio 153 “Population Genetics” (R.C. Lewontin, D. L. Hartl), Harvard University. Developed and taught independent syllabus on molecular population genetics.

Spring 1997 Teaching Fellow, BS14 “Genetics” (D. L. Hartl), Harvard University.

Fall 1992 Teaching Fellow, “Introduction to Organismic and Evolutionary Biology” (K.

Liem), Harvard University.

Fall 1979 Teaching Assistant, “Physics II (E&M),” University of Michigan.

–  –  –

Alan Bergland (Brown EEB) 2007 - 2010 Robert Haney (Brown EEB) 2007 Martine Zilversmit (Harvard University, Organismal and Evolutionary Biology) 2007 Sarah Pacocha Preheim (MIT, Civil and Environmental Engineering) 2006 - 2009 Masters Students Robin Zelman 2009 – 2010.

Undergraduate Theses Supervised Jeffrey Yuan 2011 Stephanie Spielman 2010 Robin Zelman 2009 Glenn Scheinberg 2008 Rohan Maddamsetti 2008 Funded Undergraduate Summer Research Assistantships Supervised Nichole Damari (Brown Undergraduate Teaching and Research Award) 2011 Ayoosh Pareek (Brown Undergraduate Teaching and Research Award) 2011 Jonathan Kang (Brown Undergraduate Teaching and Research Award) 2011 Matthew Weisberg (Brown Undergraduate Applied Math/Biology Award) 2011 Hans Gao (Program in Liberal Medical Education Summer Research Assistantship) 2011 Jeffrey Yuan (Brown Undergraduate Applied Math/Biology Award) 2010 Stephanie Spielman (Brown Undergraduate Teaching and Research Award) 2009 Max Abrahams (Brown Undergraduate Applied Math/Biology Award) 2009 Jamieson Mellor (EPSCoR SURF Award) 2009 Jacob Johnson (Brown Undergraduate Teaching and Research Award) 2008 Alex Franks (Brown Undergraduate Teaching and Research Award) 2007 Undergraduate Advising Sophomores (5) 2011 – 2012 First-Years (4) 2011 – 2012 First-Years (5) 2010 - 2011

RESEARCH INTERESTS





I employ population genetics, computational, molecular, microbial and protein biology to explicate the Darwinian paradigm in its most fundamental, mechanistic terms. In particular, I am interested in the theoretical and empirical nature of genetic constraint on evolution by natural selection imposed by functional interactions between mutations within loci and between loci within genomes. Additionally, in order to understand the mechanistic basis of such interactions, I seek to dissect the fitness consequences of individual mutations as a causal chain of effects at the molecular, biochemical, biophysical, cellular and physiological levels. My experimental work has employed natural populations of microbes, including bacteriophage, human pathogens and marine bacteria.

CURRENT RESEARCH AWARDS

NSF Emerging Frontiers Award 1038657. Inferring Biological Mechanism from Mutational Interactions. Sept 15, 2010 – Aug 31, 2013. $259,079.

–  –  –

COMPLETED RESEARCH AWARDS

Brown University Salomon Faculty Research Award The genetic basis of adaptation to novel environments in laboratory microbial populations. Feb 1, 2008 – June 30, 2009.

$16,000.

NSF Population Biology DEB Award 0343598. Molecular evolvability in theory and in a bacterial drug-resistance gene. Author and Co-investigator, PI: Dr. Daniel L. Hartl. Feb 1, 2004 – Jan 31, 2007. $236,000.

NIH National Research Service Award F32 GM20736. Molecular evolution in the bacteriophage φ6 Aug 1, 2000 – Jul 31, 2003. $109,164 NSF Population Biology DEB Award 9981497. Recombination, dominance, and selection on amino acid mutations. Co-investigator, PI: Dr. David Rand. Mar 1, 2000 – Feb 28, 2002. $172,367 NIH National Research Service Award Animal mtDNA and a novel model of molecular evolution. Awarded Jul 1998; declined. $79,312.

NSF Doctoral Dissertation Improvement Grant Award DEB-97000982. $7,940.

Harvard University Department of Organismic and Evolutionary Biology Departmental Student Research Grant. Jan 1, 1997. $3,500.

NIH Genetics Training Grant GM07620. PI: Nancy Kleckner. Sept 1, 1992 – Aug 31, 1997.

PEER REVIEWED JOURNAL ARTICLES

Knies Jennifer L, Angus Angermeyer and Daniel M. Weinreich (in prep for PLoS Genetics). The environmental dependence of epistasis: higher temperatures increase epistatic interactions between antibiotic resistance mutations Knies, Jennifer L., Fei Cai, Mark A. DePristo and Daniel M. Weinreich (in prep for Genetics).

Dissecting epistasis for fitness: Epistasis for kinetics and thermostability in an antibiotic resistance enzyme Weinreich, Daniel M., Suzanne Sindi and Richard Watson (submitted December 7, 2011 to the Journal of Statistical Mechanics). Finding the Boundary between Evolutionary Basins of Attraction and Implications for Wright’s Fitness Landscape Analogy.

Weinreich, Daniel M. and Jennifer L. Knies (Submitted to Evolution, Oct 1, 2011). Fisher’s Geometric Model of Adaptation Meets the Functional Synthesis: Data on Pairwise Epistasis for Fitness Yields Insights into the Shape and Size of Phenotype Space.

Watson, Richard A., Daniel M. Weinreich and John Wakeley (2010). Genome Structure and the Benefit of Sex. Evolution 65:523 – 536.

Rand, David M., Daniel M. Weinreich, Daniel Lerman, Donna Folk and George Gilchrist (2010). Three selections are better than one: clinal variation of thermal QTL from independent selection experiments in Drosophila. Evolution 64:2921 – 2934.

Christin, Pascal-Antoine, Daniel M. Weinreich and Guillaume Besnard (2010). The Causes and Evolutionary Significance of Genetic Convergence. Trends in Genetics 26:400-405.

O’Keefe, Kara J., Olin K. Silander, Helen McCreery, Daniel M. Weinreich, Kevin M. Wright, Lin Chao, Scott V. Edwards and Paul E. Turner. (2010) Biogeography of sexual reassortment in RNA phages. Evolution 64:3010-3023.

Brown, Kyle M., Mark A. DePristo, Daniel M. Weinreich and Daniel Hartl (2009). Temporal constraints on the incorporation of regulatory mutants in evolutionary pathways.

Molecular Biology and Evolution 26:2455-2462.

WEINREICH CV December 11, 2011 Lozovsky, Elena, Thanat Chookajorn, Kyle Brown, Mallika Imwong, Philip J. Shaw, Sumalee, Kamchonwongpaisan, Daniel E. Neafsey, Daniel M. Weinreich and Daniel Hartl (2009). Stepwise acquisition of pyrimethamine resistance in the malaria parasite.

PNAS 106:12015 – 12030.

DePristo, Mark A., Daniel L. Hartl and Daniel M. Weinreich (2007). Mutational reversions during adaptive protein evolution. Molecular Biology and Evolution 8:1608-1610.

Poelwijk, Frank J., Daniel J. Kivet, Daniel M. Weinreich and Sander J. Tans (2007) Empirical fitness landscapes reveal accessible paths. Nature 445:383-386.

Polz, Martin, Dana E. Hunt, Sarah P. Preheim and Daniel M. Weinreich (2006) Patterns and mechanisms of genetic and phenotypic differentiation in marine microbes. Phil. Trans.

Roy. Soc. B 361:2009-2021 doi 10.1098/rstb.2006.1928 Watson, Richard A., Daniel M. Weinreich, and John Wakeley (2006) Effects of Intra-gene Epistasis on the Benefit of Sexual Recombination. Biochemical Society Transactions 34:560-561.

Weinreich, Daniel M., Nigel Delaney, Mark A. DePristo and Daniel L. Hartl (2006).

Darwinian evolution can follow only very few mutational paths to fitter proteins.

Science 312:111-114.

Silander, Olin*, Daniel M. Weinreich*, Kevin Wright, Kara O’Keefe, Camilla U. Rang, Paul Turner and Lin Chao (2005). Widespread genetic exchange among terrestrial bacteriophage. Proc. Nat. Acad. Sci. USA 102:19009-19014.

*These authors contributed equally to this work.

Weinreich, Daniel M. (2005). The Rank Ordering of Genotypic Fitness Values Predicts Genetic Constraint on Natural Selection on Landscapes Lacking Sign Epistasis.

Genetics 171(3): 1397-1405.

DePristo, Mark A, Daniel M. Weinreich and Daniel L. Hartl (2005). Missense meanderings through sequence space: a biophysical perspective on protein evolution. Nature Reviews Genetics 6(8):678-687.

Weinreich, Daniel M., Richard A. Watson and Lin Chao (2005). Perspectives: Sign epistasis and constraint on evolutionary trajectories. (Cover article) Evolution 59:1165-1174.

Weinreich, Daniel M. and Lin Chao (2005). Rapid evolutionary escape by large populations from local peaks is likely in nature. Evolution: 59:1175-1182.

Sheldahl, Lea, Daniel M. Weinreich and David M. Rand. (2003). Recombination, dominance and selection on amino acid polymorphism in the Drosophila genome: Contrasting patterns on the X and fourth chromosomes. Genetics 165: 1195-1208.

Lake-Bakaar, Gerrond, Linda Ruffini and Daniel M. Weinreich. (2002). Ultra-rapid molecular evolution of hepatitis C virus E2-HRV1 sequences after interferon and ribavirin.

Gastroenterology 122: 473Suppl.

Rand, David M, Daniel M. Weinreich and Brent O. Cezairliyan (2001). Neutrality tests of conservative-radical amino acid changes in nuclear- and mitochondrially-encoded proteins. Gene 261: 115-125.

Weinreich, Daniel M. (2001). The rates of molecular evolution in rodent and primate mitochondrial DNA. J Molecular Evolution 52: 40-50.

Weinreich, Daniel M. and David M. Rand (2000). Contrasting patterns of non-neutral

evolution in proteins encoded in nuclear and mitochondrial genomes. Genetics 156:

385-399.

WEINREICH CV December 11, 2011 Nielson, Rasmus and Daniel M. Weinreich (1999). The age of nonsynonymous and synonymous mutations in animal mtDNA and implications for the mildly deleterious theory. Genetics 153: 497-506

NON-PEER REVIEWED JOURNAL ARTICLES

Weinreich, Daniel M. (2011) High-throughput identification of genetic interactions in HIV-1.

Nature Genetics 43: 398-400.

PEER REVIEWED BOOK CHAPTERS

Cruzan, Mitchell and Daniel M. Weinreich. Adaptive Landscapes (submitted September 25, 2011 to Brenner’s Encyclopedia of Genetics, Elsevier Publishers, Amsterdam).

Weinreich, Daniel M. (2010) Predicting molecular evolutionary trajectories in principle and in practice. Encyclopedia of Life Sciences, John Wiley and Sons, Ltd: Chichester.

INVITED CONFERENCE LECTURES

European Society of Evolutionary Biologists Annual Meeting, Tübingen, Germany. August 21 – 25, 2011.



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