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PHILIP J.

GERRISH
Center for Evolutionary and Theoretical Immunology Department of Biology 230 Castetter Hall, MS03-2020 1 University of New Mexico Albuquerque, NM 87131 USA (505) 349-5671 Theoretical Biology & Biophysics Los Alamos National Lab, MS-K710 Los Alamos, NM 87545 USA (505) 663-6014

https://www.researchgate.net/profile/Philip_Gerrish/ https://www.vizify.com/philip-gerrish AREA AND MAIN CONTRIBUTIONS My work has focused on mathematical population biology and evolutionary genetics, with application to infectious diseases and cancer. My three main contributions to these areas have been: 1) to conjecture and mathematically formalize the phenomenon of clonal interference, which can strongly inuence adaptive trajectories of microbes and somatic tissue, 2) to co-discover that clonality as an evolutionary system is fundamentally awed because of unavoidable mutation rate instability, and 3) to derive a general statistical characterization of adaptation that shares some common ground with Fishers fundamental theorem of natural selection and the Price equation; it gives rise to a novel and robust method for forecasting the near-future course of evolution. EDUCATION PhD in Zoology, 1998. Michigan State University, East Lansing, Michigan, USA. Emphasis on population genetics and microbial evolution. Masters in Mathematics, pending qualifying exam. Michigan State University, East Lansing, Michigan, USA. Masters in BioSystems Engineering, 1993. Michigan State University, East Lansing, Michigan, USA. Emphasis on numerical methods. Bachelor of Science in Physics, 1988. Hope College, Holland, Michigan, USA. Bachelor of Arts in Philosophy, 1988. Hope College, Holland, Michigan, USA. EMPLOYMENT AND AFFILIATIONS University of New Mexico, Department of Biology, Albuquerque, USA. Res. Assoc. Prof., 2008 - present. University of Lisbon, Department of Mathematics, Lisbon, Portugal. Research Aliate, 2008 - present. Instituto Gulbenkian de Cincia, Oeiras, Portugal. Research Associate, 2007.

Philip J. Gerrish Santa Fe Institute, Santa Fe, New Mexico, USA. Research Associate, 2006.

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Los Alamos National Laboratory, Theoretical biology & Biophysics, Los Alamos, New Mexico, USA. Research Associate, 2002 - 2006; Research Aliate, 2006 - present. Los Alamos National Laboratory, Theoretical biology & Biophysics, Los Alamos, New Mexico, USA. Postdoctoral Fellow, 1999-2002. Centers for Disease Control, Retrovirology Branch, Atlanta, Georgia, USA. Postdoctoral Fellow, 1997-1999. Center for Microbial Ecology, Michigan State University. Research Assistant, 199597. Mathematics Department, Michigan State University. Teaching Assistant, 1994-95. School of Veterinary Medicine, Michigan State University. Teacher, summer 1994. BioSystems Engineering Department, Michigan State University. Research Assistant, 1992-94. Colegio Internacional (private college-prep school), Tegucigalpa, Honduras. Teacher, 1988-92. AWARDS Directors Fellowship, 2000-02. Los Alamos National Laboratory. Fellowship, 1997-99. Oak Ridge Institute for Science and Education. Assistantship, 1995-97. Center for Microbial Ecology, Michigan State Univerisity. Scholarship, 1995. U.S. National Science Foundation. Research Fellowship, 1994. Department of BioSystems Engineering, Michigan State University. Humanities Colloquium Student Speaker, 1988. Hope College. GRANTS

Awarded:
Principal Investigator on Research Grant, 2008-2012. US National Institutes of Health R01. Title: Mutation rate catastrophe: testing a novel theory for extinction of clonal organisms.

Philip J. Gerrish

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co-Principal Investigator on Research Grant (one of several PIs), 2009-2014. European Commission. Title: EPIWORK. Principal Investigator on Supplemental Research Grant, 2010-2012. US National Institutes of Health ARRA program. Title: Mutation rate catastrophe: testing a novel theory for extinction of clonal organisms. Principal Investigator on Seed Grant, 2011-2013. US National Institutes of Health, through CETI program at the University of New Mexico. Title: Assessing a novel hypothesis that B-cell error catastrophe can cause germinal center termination.

Recently submitted applications:


Principal Investigator on 5-year Research Grant application (new). US National Institutes of Health R01. Title: Predicting evolution: a novel theory and experimental approaches. Principal Investigator on 5-year Research Grant application (renewal). US National Institutes of Health R01. Title: Mutation rate catastrophe: testing a novel theory for extinction of clonal organisms. Principal Investigator on 2-year Research Grant application (new). US National Science Foundation. Title: Mutation rate the maintenance of cooperation. Principal Investigator on Research Grant application (new). Templeton Foundation. Title: Evolutionary interplay between tness and mutation rate in nite populations. Principal Investigator on Visitors Research Grant application (new). National Counsel of Technological and Scientic Development (Brazil). Host: Alexandre Colato. Title: Error-error catastrophe: when replication/repair genes undergo informational collapse.

Applications in preparation:
co-Director on COBRE center grant application (new). US National Institutes of Health COBRE program. Title: Center for Predictive Evolutionary Biology. CONFERENCES AND INVITED TALKS Workshop on Cancer as an Evolutionary Process (Invited Talk). April 2012. Institut des Sciences de lEvolution, Montpellier, France.

Philip J. Gerrish

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Department of Microbiology and Immunology seminar series (Invited Talk). April 2012. Institut Jean Roget, Grenoble, France. Center for Evolutionary and Theoretical Immunology seminar series (Invited Talk). Jan 2012. University of New Mexico, Albuquerque, New Mexico, USA. 9th International Conference on Numerical Analysis and Applied Mathematics (American Institute of Physics) (Invited Talk). Sept 2011. Thessoliniki, Greece. Instituto Gulbenkian de Ciencias (Invited Talk). Sept 2011. Oeiras, Portugal. 8th European Conference on Mathematical and Theoretical Biology (Invited Talk). June 2011. Jagiellonian University, Krakow, Poland. Bacterial and Viral Evolution Kavli Institute for Theoretical Physics (Invited Talk & Stay). Feb - March 2011. University of California Santa Barbara, USA. Mathematical Methods Conference (10th CMMSE) (Presentation). June 2010. Almeria, Andalucia, Spain. NIH National IDeA Symposium of Biomedical Research Excellence (Invited Talk). June 2010. Bethesda, Maryland, USA. Mutagenesis and Infectious Disease Population Dynamics, NIH PI Conference (Organizer & Speaker). March 2010. Atlantic City, New Jersey USA. Microbial Community Diversity and Next Generation Sequence Data lecture series (Invited Talk). February 2010. University of Idaho, USA. Dynamical Systems applied to Biology (Invited Talk & Session Chair). February 2010. Universidade de Lisboa, Portugal. Populations, Evolution, and Physics (Invited Talk). January 2010. Aspen Center for Physics, Colorado USA. The Mathematics of Darwins Legacy (Invited Talk & Session Chair). November 2009. University of Lisbon, Portugal. NIH Western Region COBRE-INBRE Scientic Conference (Poster). September 2009. University of Montana, USA. Understanding emergence of infectious diseases: New Experimental and Theoretical Approaches to Virus Evolution (Invited Talk). September 2009. Rosco, Brittany, France. 7th International Conference of Numerical Analysis and Applied Mathematics 2009 (American Institute of Physics) (Invited Talk). September 2009. Rethymno, Crete, Greece.

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Molecular Basis of Evolutionary Innovations (Invited Talk & Visit). May 2009. University of Cologne, Germany. Darwin Commemoration Celebration (Invited Public Lecture). May 2009. University of Lisbon, Portugal. Instituto Gulbenkian de Cincias (Invited Talk). May 2009. Oeiras, Portugal. Institut des Sciences de lEvolution (Invited Talk & Visit). April 2009. Montpellier, France. Population Genetics and Genomics Kavli Institute for Theoretical Physics (Invited Talk). November 2008. University of California Santa Barbara, USA. Physics of Biological Systems: From Genes to Societies (Invited Talk). October 2008. University of Lisbon, Portugal. Instituto de Ecologia (Invited Talk & Visit). August 2008. Xalapa, Mexico. Instituto Gulbenkian de Cincias (Invited Talk). February 2008. Oeiras, Portugal. Center for Applied Mathematics (CIMAT) (Invited Talk). October 2006. Guanajuato, Mexico. Center for Evolutionary and Theoretical Immunology (Invited Talk). September 2006. University of New Mexico, Albuquerque, New Mexico. Theoretical Biology & Biophysics (Invited Talk). July 2006. Los Alamos National Lab, Los Alamos, New Mexico. Ecology Institute, Universidad Nacional Autonoma de Mexico (Invited Talk). April 2006. Mexico City, Mexico. Annual Meeting of the American Physical Society, Evolution Symposium (Invited Talk). March 2006. Baltimore, Maryland. Collectives Formation and Specialization in Biological and Social Systems (Participant). April 2005. Center for Non-Linear Studies, Santa Fe, New Mexico. Statistical Physics of Macromolecules: from Electronic Structure to Fluid Dynamics (Participant). May 2004. Santa Fe, New Mexico. Robustness and Evolvability of Specialists and Generalists (Participant). October 2003. Santa Fe Institute, New Mexico. Congreso Latinoamericano de Biomatematicas (Organizer & Session Chair). November 2002. Guanajuato, Mexico.

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Gordon Conference on Microbial Population Biology (Participant). August 2001. Tilton, New Hampshire, USA. American Mathematical Society-Sociedad Mexicana de Matemticas: V Joint Meeting (Invited Speaker). May 2001. Morelia, Mexico. Universidad Autnoma Metropolitana: BioMathematics Lecture Series (Invited Speaker). November 2000. Mexico City, Mexico. Evolution: from Molecules to Ecosystems (Participant). November 2000. Valencia, Spain. Gordon Conference on Theoretical Biology (Presenter). June 2000. Tilton, New Hampshire, USA. Keystone Symposium on Emerging Viral Diseases (Participant). January 2000. Taos, New Mexico, USA. Evolution and Ecology of Inuenza Virus (Participant). January 2000. Santa Fe Institute, New Mexico, USA. Keystone Symposium on AIDS Pathogenesis (Presenter). January 1999. Keystone, Colorado, USA. 6th Annual International Conference on HIV Dynamics and Evolution (Organizer & Presenter). March 1999. Atlanta, Georgia, USA. International Conference on Mathematical Biology (Participant). April 1998. Mexico City, Mexico. Gordon Conference on Microbial Ecology (Presenter). July 1997. New Hampshire, USA. Annual Meeting of the Environmental Mutagen Society (Presenter). April 1997. Minneapolis, Minnesota, USA. Microbial Ecology Forum (Presenter). September 1996. Michigan State University, East Lansing, USA. NSF Special Year in Mathematical Biology (Participant). Fall 1995. Department of Mathematics, University of Utah, Salt Lake City, USA. Symposium on Territoriality (Participant). Nov 1995. Departments of Biology and Mathematics, University of Utah, Salt Lake City, USA.

Philip J. Gerrish RELEVANT PUBLICATIONS (total citations: 2037, h-index: 22)

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Penisson S, Sniegowski PD, Colato A, Gerrish PJ (2013) Lineage dynamics and mutationselection balance in non-adapting asexual populations. Journal of Statistical Mechanics P01013 doi:10.1088/1742-5468/2013/01/P01013. Sprouske K, Merlo LMF, Gerrish PJ, Maley CC, Sniegowski PD, (2012) Cancer in light of experimental evolution. Current Biology 22: R762-R771, doi: 10.1016/j.cub.2012.06.065. Gerrish PJ, Sniegowski, PD (2012) Real time forecasting of near-future evolution. Royal Society Interface, doi: 10.1098/rsif.2012.0119. de la Iglesia F, Martinez F, Hillung J, Cuevas JM, Gerrish PJ, Daros JA, Elena SF (2012) Luria-Delbruck Estimation of Turnip mosaic virus Mutation Rate in vivo. Journal of Virology, 86: 3386-3388. Gentile CF, Yu S-C, Serrano SA, Gerrish PJ, Sniegowski PD (2011) Competition between high- and higher-mutating strains of Escherichia coli. Biol. Lett. 7: 422-424. Gerrish PJ, Sniegowski PD (2011). Adding dynamical suciency to Fishers fundamental theorem of natural selection. In Numerical Analysis and Applied Mathematics ICNAAM 2011, Volume 1389, T. Simos, G. Psihoyios, C. Tsitouras and Z. Anastassi, eds. (New York: American Institute of Physics), pp. 1260-1262. Sniegowski PD, Gerrish PJ (2010) Benecial mutations and the dynamics of adaptation. Phil. Trans. R. Soc. B 365: 1255-1263. Gerrish PJ (2010) Mutation rate and the maintenance of cooperation: a parsimonious model of somatic evolution and oncogenic transitions. In Proceedings of Computational and Mathematical Methods in Science and Engineering, pp. 1129-1132. Gerrish PJ (2009). Some observations about the nearest-neighbor model of the error threshold. In Numerical Analysis and Applied Mathematics ICNAAM 2009, T. Simos, G. Psihoyios and C. Tsitouras, eds. (New York: American Institute of Physics), pp. 1564-1568. Gerrish PJ (2008) A simple formula for obtaining remarkably improved mutation rate estimates. Genetics 180: 1773-1778. Gerrish PJ, Colato A, Perelson AS, Sniegowski PD (2007) Complete genetic linkage can subvert natural selection. PNAS 104: 6266-6271. Burr TL, Gatticker JR, Gerrish PJ (2003) An investigation of error sources and their impact in estimating the time to the most recent ancestor of spatially and temporally distributed HIV sequences. Statistics in Medicine 22:1495-1516. Gerrish PJ, Garcia Lerma JG (2003) Mutation rate and the ecacy of anti-microbial drug treatment. The Lancet Infectious Diseases 3:28-32.

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Kalish ML, Korber BT, Pillai S, Robbins KE, Leo YS, Saekhou A, Verghese I, Gerrish P, Goh CL, Lupo D, Tan BH, Brown TM, Chan R (2003) The sequential introduction of HIV-1 subtype B and CRF01_AE in Singapore by sexual transmission: Accelerated V3 region evolution in a subpopulation of Asian CRF01 viruses. Virology 304:311-329. Gerrish PJ (2002) Evolution plays dice. Nature (News & Views) 420:756-757. Rozen D, de Visser JAGM, Gerrish PJ (2002) Fitness eects of xed benecial mutations in microbial populations. Current Biology 12:1040-1045 Johnson T, Gerrish PJ (2002) The probability of xation of a benecial mutation in populations that are dividing by binary ssion. Genetica 115:283-287. Wahl LM, Gerrish PJ, Saika-Voivod I (2002) Evaluating the eects of population bottlenecks in experimental evolution. Genetics 162:961-971. Wahl LM, Gerrish PJ (2001) The probability that benecial mutations are lost in populations with periodic bottlenecks. Evolution 55:2606-2610. Gerrish PJ (2001) The rhythm of microbial adaptation. Nature 413:299-302. Webby RJ, Swenson SL, Goyal SM, Krauss SL, Gerrish PJ, Webster RG (2000) Evolution of swine H3N2 Inuenza viruses in the United States. Journal of Virology 74:8243-8251. Garcia Lerma JG, Gerrish PJ, Wright AC, Qari SH, Heneine W (2000) Acquisition of the Q151M mutation may occur through a Q151L intermediate but requires the presence of specic polymorphisms (S68G) in HIV-1 reverse transcriptase. Journal of Virology 74:9339-9346. Sniegowski PD, Gerrish PJ, Johnson T, Shaver A (2000) The evolution of mutation rates: separating causes and consequences. BioEssays 22:1057-1066. Miralles R, Gerrish PJ, Moya A, Elena SF (1999) Clonal interference and the evolution of RNA viruses. Science 285:1745-1747. De Visser JAGM, Zeyl CW, Gerrish PJ, Blanchard JL, Lenski RE (1999) Diminishing returns from mutation supply rate in asexual populations. Science 283:404-407. Gerrish PJ, Lenski RE (1998) The fate of competing benecial mutations in an asexual population. Genetica 102/103:127-144. Sniegowski PD, Gerrish PJ, Lenski RE (1997) Evolution of high mutation rates in experimental populations of Escherichia coli. Nature 387:703-705. Lenski RE, Mongold JA, Sniegowski PD, Travisano M, Vasi F, Gerrish PJ, Scmidt TM (1996) Evolution of competitive tness in experimental populations of Escherichia coli: what makes one genotype a better competitor than another? Antonie von Leeuwenhoek 73:35-47.

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Submitted:
Gerrish PJ, Colato A, Sniegowski PD (2012) Genomic mutation rates that neutralize adaptive evolution and natural selection. Royal Society Interface (in 2nd round of review). Presently on arXiv:1211.0974 Gerrish PJ (2012) Mutant lineage dynamics under regular population bottlenecks. Genetics (accepted pending minor revisions). Balk DS, Gentile CF, Raynes Y, Gerrish PJ, Sniegowski PD (2012) Evolutionary responses of high- and low-mutating Escherichia coli populations to strong chemical mutagenesis. Evolution (submitted). Gerrish PJ, Ferreira CP, Pacheco JM, Perelson AS (2012). Mutation rate and the maintenance of cooperation. PLoS Biology (submitted).

Invited manuscripts in preparation:


Gerrish PJ, Sniegowski PD (2013) Recombination and mutation rate stability. Bioessays (in prep). PUBLICLY AVAILABLE SOFTWARE SeqWiz a hub for sequence analysis and phylogenetic reconstruction programs; used at the Centers for Disease Control in Atlanta. (PC) Mutation Rate Calculator - for estimating mutation rates using the Jones protocol (a signicant improvement over the traditional uctuation assay); this software implements new theory developed in: Gerrish PJ (2008) Genetics 180: 1773-1778. (Mac, PC and Linux) PROFESSIONAL ACTIVITIES

Regular reviewer for professional journals:


Science, Nature, PNAS, Physical Review Letters, Physical Review E, The Lancet Infectious Disease, Journal of Virology, PLoS Computational Biology, PLoS Biology, Journal of Theoretical Biology, Theoretical Population Biology, Mathematical Biosciences, Journal of Mathematical Biology, Evolution, BMC Evolutionary Biology, Genetics, Genetica, Genetics Research, among others.

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Program committee for professional conferences:


National Institutes of Health PI Conference (March 2010) Atlantic City, New Jersey USA. Spearheaded workshop: Mutagenesis and Infectious Disease Population Dynamics Evolution in Health and Disease (September 2008) Instituto Gulbenkian de Ciencias, Lisbon, Portugal. Program committee member, session chair, and presider of closing. Congreso Latinoamericano de Biomatematicas (November 2002) Centro de Investigacion en Matematicas, Guanajuato, Mexico. Program committee member and session chair. 6th Annual International Conference on HIV Dynamics and Evolution (March 1999) Centers for Disease Control and Prevention, Atlanta, Georgia, USA. Program committee member. LANGUAGES English, native Spanish, uent Portuguese, read/write/understand French, rusty OTHER ACTIVITIES

Music:
Jackson Symphony Orchestra (Michigan), Grand Rapids Symphony Orchestra (Michigan), Cafe con Leche String Quartet (Honduras; played for two Latin-American summits), Los Catrachos (Honduras), Assistant Professor of Music (Universidad Nacional Autonoma de Honduras), Vientos del Pueblo (Atlanta, Georgia), Studio Musician (Atlanta, Georgia), Los Alamos Symphony Orchestra (New Mexico), Hilltopper String Quartet (New Mexico), Volunteer with Los Alamos Summer Strings program.

Philip J. Gerrish REFERENCES

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Paul Sniegowski Department of Biology 213 Leidy Laboratories University of Pennsylvania Philadelphia, PA 19104 USA TEL: +1 215 573 4085 FAX: +1 215 898 8780 Email: paulsnie@sas.upenn.edu

Eric Loker Department of Biology MSC03-2020 1 University of New Mexico Albuquerque, NM 87131-0001 USA TEL: +1 505 277 2124 FAX: +1 505 277 0304 Email: esloker@unm.edu

Alan Perelson Theoretical Biology, MS-K710 Los Alamos National Laboratory Los Alamos, NM 87545 USA TEL: +1 505 667 6829 FAX: +1 505 665 3493 Email: asp@lanl.gov

Santiago Elena Instituto de Biologa Molecular y Celular de Plantas, CSIC-UPV Campus UPV, CPI 8E CL. Ingeniero Fausto Elio s/n 46022 Valencia, Spain TEL: +34 963 877 895 FAX: +34 963 877 859 Email: sfelena@ibmcp.upv.es

Gabriela Gomes Instituto Gulbenkian de Cincias P-2780-156 Oeiras, Portugal TEL: +351 21 446 4626 FAX: +351 21 440 7970 Email: ggomes@igc.gulbenkian.pt

Michael Lssig Institute of Theoretical Physics University of Cologne Zlpicher Str. 77 50937 Kln, Germany TEL: +49 221 470 3588 FAX: +49 221 470 7467 Email: lassig@thp.uni-koeln.de