Plotkin Research Group

Overview

We use mathematics and computation to study questions in evolutionary biology and ecology. Research in the group is concerned primarily with adaptation in populations. Related interests include the evolution of robustness and adaptability, the evolutionary ecology of viral populations, the evolution of cooperation, conflict, coalitions, and group decision-making.


Evolutionary population genetics

We are broadly interested in molecular evolution and population-genetic theory. A primary goal is the development of statistical methods for inferring the action of natural selection from intra-specific polymorphism data and from inter-specific sequence variation. Of particular interest are methods to infer the distribution of selection pressures across sites, the recombination rate amoung sites, and the structure of epistatic interactions among sites.


Robustness and Adaptation

How do organisms ensure robustness against genetic and environmental perturbations? How do organisms simultaneously achieve sufficient plasticity to adapt to changing environments?

These questions are particularly puzzling in the context of viral populations. Viruses are bound by the same constraints that shape the evolution of higher organisms: the need to replicate with fidelity and adapt to local environments. Viral proteins are governed by the same physical laws that determine folding and functionality in higher organisms. But viruses are often subject to genetic mutations and environmental changes at rates that vastly exceed those of all other living organisms. As a result, the persistence of viruses presents an enigma: How can a viral population achieve both sufficient robustness against high mutation rates, as well as sufficient plasticity to adapt to rapidly changing environments? On the one hand, a viral population must purge itself of deleterious mutants; but at the same time it must be prepared to leverage genetic diversity in order to escape a host's immune system.

We are exploring the counterpoised requirements for robustness and adaptability by developing mathematical models of viral evolution. Models are complemented and parameterized by statistical inference techniques applied to empirical sequence data.


Viral Evolution

Influenza viruses offer an extraordinary opportunity for improving our understanding of molecular evolution. Roughly 30% of sites in Influenza's primary surface antigen have undergone amino-acid substitutions over the past four decades -- the equivalent of millions of years of protein evolution in mammals. Influenza's remarkable evolutionary rate is driven by selection for novel antigenic variants that evade antibodies in the host population.

We are leveraging the vast quantity of available viral sequence data to quantify the nature of selection pressures on influenza proteins. We are particularly interested in the differences between diversifying and directional positive selection, temporal changes in selective regimes, the identification of selectively neutral networks, and the structure of epistatic relations between sites.

Related projects include the modeling and inference of influenza epidemic fluctuations.

Social Evolution

What conditions foster the emergence of cooperation, conflict, or coalitions in populations? What governs the dynamics of ideological polarization, social norms, the evolution of communication systems, and the spread of (mis)information in human societies? We address these questions at a theoretical level, often applying evolutionary game theory; as well as empirically, through analysis of time series data on human cultural traits, or manipulative experiments on group behavior.



Joshua Plotkin is the Walter H. and Leonore C. Annenberg Professor of Natural Sciences. [CV]




Dan Cooney completed his PhD in Applied Mathematics at Princeton University. Dan is a Simons Fellow at the Penn Center for Mathematical Biology.




Alex McAvoy completed his PhD in Mathematics at the University of British Columbia.




Alfredo González-Espinoza (left) completed his PhD in Physics of complex systems, at U. Autónoma del Estado de Morelos.




Debora Princepe completed her PhD in Physics at Universidade Estadual de Campinas. Visiting Penn for a year she is pursuing research on mito-nuclear co-evolution.




Hiroake Okabe completed his Bachelor of Laws at Keio University before serving in Japan's Ministry of Economy, Trade and Industry. Now a PhD student in Penn's Applied Math and Computational Science, Hiro is pursuing research at the intersection of evolutionary theory and law.




Taylor Kessinger completed his PhD in computational biology at the Eberhard Karls University of Tübingen, on methods for detecting selection in rapidly adapting populations.




Qi Su completed his PhD in Mechanical Systems and Control at Peking University. He is a Simons Fellow at Penn jointly supervised by Yoichiro Mori.




Colin Twomey completed his PhD in Ecology and Evolutionary Biology at Princeton.





Alumni




Oana Carja is an Assistant Professor at Carnegie Mellon School of Computer Science.




Andrew Tilman is a research scientists with the US Forest Service.




Mitchell Newberry is a fellow of the Michigan Society of Fellows and Assistant Professor of Complex Systems at the University of Michigan.




Arunas Radzvilavicius is an Editor at Nature Human Behaviour.




Jakub Otwinowski is a research fellow at Max Plank Institute, Gottingen.




Davorka Gulisija is an Assitant Professor of Biology at the University of New Mexico.




David McCandlish is an Assistant Professor of Quantiative Biology at Cold Spring Harbor Labs.




Premal Shah is an Assistant Professor of Genetics at Rutgers University.



Grzegorz Kudla is a senior scientist in the MRC Human Genetics Group, at the University of Edinburgh.




Yang Ding is a post-doc in the Palsson lab at UCSD.




Helene Morlon is a permanent scientist of the CNRS, at École Normale Supérieure.




Michael Levy is an Associate Professor in the Biostatistics Department at the University of Pennsylvania.




Todd Parsons is a permanent scientist of the CNRS, at Université Pierre et Marie Curie.




Alex Stewart is an Assistant Professor at University of Houston.




Sergey Kryazhimskiy is an Assistant Professor of Biology at UCSD.




Alison Feder is an Assistant Professor in the Department of Genome Sciences (Summer 2021).




Jeremy Draghi is an Assistant Professor of Biology at Virgnia Tech.




Ricky Der completed his PhD in Mathematics at Penn, on generalized Markov models in population genetics.




Etienne Rajon is an Assistant Professor at University of Lyon.




Anchal Vishnoi is a lecturer at JNU, Delhi.




Sebastian Akle is a graduate student in Organismal and Evolutionary Biology at Harvard.




David Bostick completed his PhD in Physics at UNC, on molecular dynamics simulations of biomembranes.




Gasper Tkacik is an Assistant Professor at the Institute of Science and Technology, Austria.




Serena Rezny received her Master's in Applied Math at Penn, and is a PhD student in Statistics at Univeristy of Chicago.




Daril Vilhena recently received his PhD in Biology from the University of Washington.


Postdocs

Several postdoctoral fellowships (2-3 years) are available in the mathematical biology group of Joshua Plotkin at the University of Pennsylvania. The specific research project is flexible and can be tailored to the interests of the individual, but it will fall under the broad purview of evolutionary and ecological theory. Areas of interest in the Plotkin lab include theoretical population genetics, the evolutionary ecology of viral populations, the evolution of robustness and adaptability, and the evolution of cooperation, social norms, and decision-making.

Requirements for the position include: a record of self-motivated research; a PhD in mathematics, statistics, physics, biology or related area; strong communication and writing skills. The ideal candidate should also be familiar with scientific programming.

The postdoctoral fellowships provides a competitive annual stipend plus benefits and health insurance. Start date and term are negotiable. Highly motivated applicants, of any nationality, are encouraged to email a statement of research interests, CV, and contact details for three references to jplotkin (at) sas.upenn.edu. Informal inquiries are also welcomed. Applications from under-represented groups are especially encouraged.


Graduate Students

Students interested in graduate study in evolutionary and ecological theory are encouraged to contact Dr. Plotkin. Students may matriculate through one of several Penn graduate groups: Biology Department, Genomics & Computational Biology, Computer Science, or Applied Mathematics. Please email your CV to Dr. Plotkin, along with a cover letter explaining why you want to join the group.


Undergraduate Students

Students with a quantitative background and an interest in evolution or ecology are encouraged to contact Dr. Plotkin regarding the possibility of term or summer projects. Send an email explaining what you hope to get out of research with our lab, along with CV, to jplotkin (at) sas.upenn.edu.


Contact

Dr. Joshua B. Plotkin
Penn Department of Biology
219 Lynch Labs
433 S. University Ave
Philadelphia, PA 19104

jplotkin (at) sas.upenn.edu


News

  • July 2019: Davorka Gulisija accepts a position as Assistant Professor of Biology at the University of New Mexico, starting January 2020.

  • May 2018: Oana Carja accepts a position as Assistant Professor in the Carnegie Mellon School of Computer Science, starting January 2019.

  • May 2018: Mitchell Newberry defends his PhD thesis and accepts a position in the Michigan Society of Fellows as Assistant Professor of Complex Systems.

  • May 2018: Colin Twomey is selected as an inaugural MindCORE Fellow at the University of Pennsylvania.

  • December 2016: David McCandlish accepts a position as an Assistant Professor of Quantiative Biology at Cold Spring Harbor Labs, starting January 2017.

  • July 2015: Alex Stewart accepts a position at University College London, as a Royal Society University Research Fellow, starting October 2015.

  • May 2015: Premal Shah accepts a position as Assistant Professor of Genetics at Rutgers University, starting January 2016.

  • May 2015: Sergey Kryazhimskiy accepts a position as Assistant Professor of Biology at UCSD, starting January 2016.

  • May 2015: Jeremy Draghi accepts a position as Assistant Professor of Biology at CUNY Brooklyn College, starting August 2015.

  • August 2013: Todd Parsons assumes a permanent position with the CNRS, at Université Pierre et Marie Curie.

  • June 2013: Etienne Rajon starts a position as Assistant Professor of Biology at University of Lyon.

  • June 2012: Alison Feder is headed to Oxford for a year, followed by graduate school at Stanford Biology.

  • September 2011: Gasper Tkacik starts a position as Assistant Professor at the Institute of Science and Technology, Austria.

  • October 2010: Helene Morlon assumes a permanent position with the CNRS, now at École Normale Supérieure.

  • September 2010: Grzegorz Kudla assumes a position as Group Leader in the MRC Human Genetics Unit, at the University of Edinburgh.

  • September 2009: Michael Levy starts a position as Assistant Professor of Epidemiology and Biostatistics at UPenn.


Publications

Google Scholar
  • Kessinger T, Plotkin JB. Indirect reciprocity in populations with group structure. arXiv 2204.10811 [preprint]

  • Princepe D, de Aguiar M, Plotkin JB. Mito-nuclear selection induces a trade-off between species ecological dominance and evolutionary lifespan. arXiv 2111.04866 [preprint]

  • McAvoy A, Mori Y, Plotkin JB. Selfish optimization and collective learning in populations. Physica D 439: 133426 (2022) [pdf]

  • Tilman A, Vasconcelos V, Akcay E, Plotkin JB. The evolution of forecasting for decision making in dynamic environments. arXiv 2108.00047 [preprint]

  • Stewart A, Arechar A, Rand D, Plotkin JB. The coercive logic of fake news. arXiv 2108.13687 [preprint]

  • Kim H, Mori Y, Plotkin JB. Optimality of intercellular signaling: direct transport versus diffusion. arXiv 2204.09768 [preprint]

  • Ventura R, Plotkin JB, Roberts G. Drift as a driver of language change: an artificial language experiment. Cognitive Science (in press) [preprint]

  • Newberry M, Plotkin JB. Measuring frequency-dependent selection in culture. Nature Human Behaviour (2022) [pdf]

  • Su Q, McAvoy A, Plotkin JB. Evolution of cooperation with contextualized behavior. Science Advances 8:6066 (2022) [pdf]

  • Su Q, McAvoy A, Mori Y, Plotkin JB. Evolution of prosocial behavior in multilayer populations. Nature Human Behaviour (2022) [pdf]

  • Su Q, Allen B, Plotkin JB. Evolution of cooperation with asymmetric social interactions. PNAS 119:2113468118 (2021) [pdf]

  • Stewart A, Plotkin JB, McCarty N. Inequality, identity, and partisanship: how redistribution can stem the tide of mass polarization. PNAS 118:2102140118 (2021) [pdf]

  • Twomey C, Roberts G, Brainard D, Plotkin JB. What we talk about when we talk about colors. PNAS 118:2109237118 (2021) [pdf]

  • Hirshleifer D, Plotkin JB. Moonshots, investment booms, and selection bias in the transmission of cultural traits. PNAS 118:2015571118 (2021) [pdf]

  • Radzvilavicius A, Kessinger T, Plotkin JB. Adherence to public institutions that foster cooperation. Nature Communications 12: 3567 (2021) [pdf]

  • Stewart A, Plotkin JB. The natural selection of good science. Nature Human Behaviour (2021) [pdf]

  • Morris D, Rossine F, Plotkin JB, Levin SA. Optimal, near-optimal, and robust epidemic control. Communications Physics 4: 78 (2021) [pdf]

  • Jones JM, Foster W, Twomey C, Burdge J, Ahmed O, Talmo P, Wojick J, Corder G, Plotkin JB, Abdus-Saboor I. A machine-vision approach for automated pain measurement at millisecond timescales. eLife 9:57258 (2020) [pdf]

  • Tilman A, Plotkin JB, Akcay E. Evolutionary games with environmental feedbacks. Nature Communications 11: 915 (2020) [pdf]

  • Mosleh M, Stewart A, Plotkin JB, Rand D. Prosociality in the economic Dictator Game is associated with less parochialism and greater willingness to vote for intergroup compromise. Judgement and Decision Making 15: 1-6 (2020) [pdf]

  • Plotkin JB. Ancel (2000) on the Baldwin effect. Theoretical Population Biology 133:35 (2020) [pdf]

  • Stewart A, Mosleh M, Diakonova M, Arechar A, Rand D, Plotkin JB. Information gerrymandering and undemocratic decisions. Nature 583: 117-121 (2019) [pdf]

  • Radzvilavicius A, Stewart A, Plotkin JB. Evolution of empathetic moral evaluation. eLife 8: 44269 (2019) [pdf]

  • Carja O, Plotkin JB. Evolutionary rescue through partly heritable phenotypic variability. Genetics 211: 977-988 (2019) [pdf]

  • Otwinowski J, McCandlish D, Plotkin JB. Inferring the shape of global epistasis. PNAS 115: 7550-7558 (2018) [pdf]

  • Mittal P, Brindle J, Stephen J, Plotkin JB, Kudla G. Codon usage influences fitness through RNA toxicity. PNAS 115: 8639-8644 (2018) [pdf]

  • Posfai A, Zhou J, Plotkin JB, Kinney JB, McCandlish DM. Selection for protein stability enriches for epistatic interactions. Genes 9: 423 (2018) [pdf]

  • Newberry MG, Ahern C, Clark R, Plotkin JB. Detecting evolutionary forces in language change. Nature 551: 223-226 (2017) [pdf]

  • Gulisija D, Plotkin JB. Phenotypic plasticity promotes recombination and gene clustering in periodic environments. Nature Communications 8: 2041 (2017) [pdf]

  • Plotkin JB. No escape from the tangled bank. Nature 551: 42-43 (2017) [pdf]

  • Carja O, Xing T, Wallace EW, Plotkin JB, Shah P. riboviz: analysis and visualization of ribosome profiling datasets. BMC Bioinformatics 10.1186/s12859-017-1873-8 (2017) [pdf]

  • Carja O, Plotkin JB. The evolutionary advantage of heritable phenotypic heterogeneity. Scientific Reports 7: 5090 (2017) [pdf]

  • Stewart A, Parsons T, Plotkin JB. Evolutionary consequences of behavioral diversity. PNAS 113: 7003-7009 (2016) [pdf]

  • Newberry M, McCandlish D, Plotkin JB. Assortative mating can impede or facilitate fixation of underdominant alleles. Theoretical Population Biology 112: 14-21 (2016) [pdf]

  • Nourmohammad A, Otwinowski J, Plotkin JB. Host-pathogen co-evolution and the emergence of broadly neutralizing antibodies in chronic infections. PLOS Genetics 12: 1006171 (2016) [pdf]

  • Stewart A, Plotkin JB. Small groups and long memories promote cooperation. Scientific Reports 6: 26899 (2016) [pdf]

  • McCandlish D, Shah P, Plotkin JB. Epistasis and the dynamics of reversion in molecular evolution. Genetics 203: 1335-1351 (2016) [pdf]

  • McCandlish D, Plotkin JB. Transcriptional errors and the drift barrier. PNAS 113: 3136-3138 (2016) [pdf]

  • Gulisija D, Kim Y, Plotkin JB. Phenotypic plasticity promotes balanced polymorphism in periodic environments by a genomic storage effect. Genetics 202: 1437-1448 (2016) [pdf]

  • Weinberg DE, Shah P, Eichhorn SW, Hussmann JA, Plotkin JB, Bartel DP. Improved ribosome-footprint and mRNA measurements provide insights into dynamics and regulation of yeast translation. Cell Reports 14: 1-13 (2016) [pdf]

  • McCandlish M, Otwinowski J, Plotkin JB. Detecting epistasis from an ensemble of adapting populations. Evolution 69: 2359-2380 (2015) [pdf]

  • Kumar S, Plotkin JB, Hannenhalli S. Regulated CRISPR modules exploit a dual defense strategy of restriction and abortive infection in a model of prokaryote-phage coevolution. PLOS Computational Biology 11: 1004603 (2015) [pdf]

  • Neverov AD, Kryazhimskiy S, Plotkin JB, Bazykin GA. Coordinated evolution of Influenza A surface proteins. PLOS Genetics 11: 1005404 (2015) [pdf]

  • Stewart A, Plotkin JB. The evolvability of cooperation under local and non-local mutations. Games 6: 231-250 (2015) [pdf]

  • Shah P, McCandlish M, Plotkin JB. Contingency and entrenchment in protein evolution under purifying selection. PNAS 112: 3226–3235 (2015) [pdf]

  • Schulte MB, Draghi JA, Plotkin JB, Andino R. Experimentally guided models reveal replication principles that shape the mutation distribution of RNA viruses. eLife 4: 3753 (2015) [pdf]

  • McCandlish D, Epstein C, Plotkin JB. Formal properties of the probability of fixation: identities, inequalities and approximations. Theoretical Population Biology 99: 98-113 (2015) [pdf]

  • Stewart A, Plotkin JB. Collapse of cooperation in evolving games. PNAS 111: 17558-17563 (2014) [pdf]

  • Otwinowski J, Plotkin JB. Inferring fitness landscapes by regression produces biased estimates of epistasis. PNAS 111: 2301-2309 (2014) [pdf]

  • Der R, Plotkin JB. The equilibrium allele frequency distribution for a population with reproductive skew. Genetics 196: 1199-1216 (2014) [pdf]

  • McCandlish D, Epstein C, Plotkin JB. The inevitability of unconditionally deleterious substitutions during adaptation. Evolution 68: 1351-1365 (2014) [pdf]

  • Feder A, Kryazhimskiy S, Plotkin JB. Identifying signatures of selection in genetic time series. Genetics 196: 509-522 (2014) [pdf]

  • Draghi J, Plotkin JB. Selection biases the prevalence and type of epistasis along adaptive trajectories. Evolution 67: 3120–3131 (2013) [pdf]

  • Stewart A, Plotkin JB. From extortion to generosity, evolution in the Iterated Prisoner's Dilemma. PNAS 110: 15348-15353 (2013) [pdf]

  • Lipsitch M, Fisman D, Plotkin JB, Simonsen L. Ferret H7N9 flu model questioned. Nature 501: 33 (2013) [pdf]

  • Shah P, Ding Y, Niemczyk M, Kudla G, Plotkin JB. Rate-limiting steps in yeast protein translation. Cell 153: 1589-1601 (2013) [pdf]

  • McCandlish D, Rajon E, Shah P, Ding Y, Plotkin JB. The role of epistasis in protein evolution. Nature 497:E1-E2 (2013) [pdf]

  • Rajon E, Plotkin JB. The evolution of genetic architectures underlying quantitative traits. Proceedings of The Royal Society B 280: 20131552 (2013) [pdf]

  • Stewart A, Plotkin JB. The evolution of complex gene regulation by low-specificity binding sites. Proceedings of The Royal Society B 280: 20131313 (2013) [pdf]

  • Li Y, Bostick D, Sullivan C, Myers J, Griesemer S, St. George K, Plotkin JB, Hensley S. Single Hemagglutinin mutations that alter both antigenicity and receptor-binding avidity. Journal of Virology 87: 9904-9910 (2103) [pdf]

  • Li Y, Myers J, Bostick D, et al. Immune history shapes specificity of pandemic H1N1 Influenza antibody responses. Journal of Experimental Medicine 210: 1493-1500 (2013) [pdf]

  • Harrison RD, Tan S, Plotkin JB, Slik F, Detto M, Brenes T, Itoh A, Davis SJ. Consequences of defaunation for a tropical tree community. Ecology Letters 16: 687–694 (2013) [pdf]

  • Stewart A, Seymour R, Pomiankowski A, Plotkin JB. The population genetics of cooperative gene regulation. BMC Evolutionary Biology 12: 173 (2012) [pdf]

  • Stewart A, Hannenhalli S, Plotkin JB. Why transcription factor binding sites are ten nucleotides long. Genetics 192: 973-985 (2012) [pdf]

  • Ding Y, Shah P, Plotkin JB. Weak 5' mRNA structure in short eukaryotic genes. Genome Biology and Evolution 4: 1046-1053 (2012) [pdf]

  • Der R, Epstein C, Plotkin JB. The dynamics of neutral and selected alleles when the offspring distribution is skewed. Genetics 191: 1331-1344 (2012) [pdf]

  • Morlon H, Kemps B, Plotkin JB, Brisson D. Explosive radiation of a bacterial species group. Evolution 66: 2577-2586 (2012) [pdf]

  • Lipsitch M, Plotkin JB, Simonsen L, Bloom B. Evolution, safety, and highly pathogenic Influenza viruses. Science 336: 1529-1531 (2012) [pdf]

  • Stewart A, Plotkin JB. Extortion and cooperation in the Prisoner's Dilemma. PNAS 109: 10134-10135 (2012) [pdf]

  • Stewart A, Parsons T, Plotkin JB. Environmental robustness and the adaptability of populations. Evolution 66: 1598-1612 (2012) [pdf]

  • Toll-Riera M, Bostick D, Alba M, Plotkin JB. Structure and age jointly influence rates of protein evolution. PLOS Computational Biology 8: 1002542 (2012) [pdf]

  • Walczak AM, Nicolaisen LE, Plotkin JB, Desai MM. The structure of genealogies in the presence of purifying selection: a fitness-class coalescent. Genetics 190: 753-779 (2012) [pdf]

  • Desai MM, Nicolaisen LE, Walczak AM, Plotkin JB. The structure of allelic diversity in the presence of purifying selection. Theoretical Population Biology 8: 144-157 (2012) [pdf]

  • Draghi J, Plotkin JB. A network of paths toward innovation. Bioessays 34: 518–520 (2012) [pdf]

  • Morlon H, Parsons T, Plotkin JB. Reconciling molecular phylogenies with the fossil record. PNAS 108: 16327-16332 (2011) [pdf] [cover]

  • Der R, Epstein C, Plotkin JB. Generalized population models and the nature of genetic drift. Theoretical Population Biology 80: 80-99 (2011) [pdf]

  • Vishnoi A, Sethupathy P, Simola D, Plotkin JB, Hannenhalli S. Genome-wide survey of natural selection on functional, structural, and network properties of polymorphic sites in Saccharomyces paradoxus. Molecular Biology and Evolution 28: 2615-2627 (2011) [pdf]

  • Levy M, Small D, Vilhena D, Bowman N, Kawai V, del Carpio J, Codova E, Gilman R, Plotkin JB. Retracing micro-epidemics of Chagas disease using epicenter regression. PLOS Computational Biology 7: 1002146 (2011) [pdf]

  • Kryazhimskiy S, Draghi J, Plotkin JB. In evolution, the sum is less than its parts. Science 332: 1160-1161 (2011) [pdf]

  • Draghi J, Plotkin JB. Molecular evolution:Hidden diversity sparks adaptation. Nature 474: 45-46 (2011) [pdf]

  • Draghi J, Parsons TL, Plotkin JB. Epistasis increases the rate of conditionally neutral substitution in an adapting population. Genetics 187: 1139–1152 (2011) [pdf]

  • Toole J, Eagle N, Plotkin JB. Spatiotemporal Correlations in Criminal Offense Records. ACM Transactions on Intelligent Systems and Technology 2: 38 (2011) [pdf]

  • Kryazhimskiy S, Dushoff J, Bazykin G, Plotkin JB. Prevalence of epistasis in the evolution of influenza A surface proteins. PLOS Genetics 7: 1001301 (2011) [pdf]

  • Plotkin JB, Kudla G. Synonymous but not the same: the causes and consequences of codon bias. Nature Reviews Genetics 12: 32-42 (2011) [pdf]

  • Plotkin JB. The lives of proteins. Science 331: 683-684 (2011) [pdf]

  • Draghi J, Parsons TL, Wagner G, Plotkin JB. Mutational robustness can facilitate adaptation. Nature 426: 353-355 (2010) [pdf]

  • Morlon H, Potts M, Plotkin JB. Inferring the dynamics of diversification: a coalescent approach. PLOS Biology 8: 1000493 (2010) [pdf]

  • Plotkin JB. Transcriptional regulation is only half the story. Molecular Systems Biology 6: 204 (2010) [pdf]

  • Parsons TL, Quince C, Plotkin JB. Some consequences of demographic stochasticity in population genetics. Genetics 185: 1345-1354 (2010) [pdf]

  • Vishnoi A, Kryazhimskiy S, Bazykin G, Hannenhalli S, Plotkin JB. Young proteins experience more variable selection pressures than old proteins. Genome Research 20: 1574-1581 (2010) [pdf]

  • Salguero–Gomez R, Plotkin JB. The effects of dimensionality on demographic studies using projection matrices. The American Naturalist 176: 710-712 (2010) [pdf]

  • Levy MZ, Chavez F, Cornejo del Carpio JG, Vilhena D, McKenzie FE, Plotkin JB. Rational strategies for eliminating a Chagas disease vector. Proceedings of the Royal Society Interface (2010) [pdf]

  • Kudla G, Murray AW, Tollervey D, Plotkin JB. Coding-sequence determinants of gene expression in Escherichia coli. Science 324: 255-258 (2009) [pdf]

  • Kryazhimskiy S, Tkacik G, Plotkin JB. The dynamics of adaptation on correlated fitness landscapes. PNAS 106: 18638-18643 (2009) [pdf]

  • Goldstein E, Dushoff J, Ma J, Plotkin JB, Earn DJ, Lipsitch M. Reconstructing influenza incidence by deconvolution of daily mortality time series. PNAS 106: 21825–21829 (2009) [pdf]

  • Ndifon W, Plotkin JB, Dushoff J. Environmental impact on the evolutionary accessibility of adaptive phenotypes of a bacterial metabolic network. PLOS Computational Biology 5: 1000472 (2009) [pdf]

  • Roy S, Vandenberghe L, Kryazhimskiy S, Grant R, Calcedo R, Yuan X, Keough M, Sandhu A, Wang Q, Medina-Jaszek C, Plotkin JB, Wilson JM. Isolation and characterization of Adenoviruses persistently shed from the gastrointestinal tract of non-human primates. PLOS Pathogens 5: 1000503 (2009) [pdf]

  • Levy M, Bowman N, Kawai V, Plotkin JB et al. Spatial patterns in discordant diagnostic test results for Chagas disease: links to transmission hotspots. Clinical Infectious Diseases 48: 1104-1106 (2009).

  • Kryazhimskiy S, Plotkin JB. The population genetics of dN/dS. PLOS Genetics 4: 1000304 (2008) [pdf]

  • Desai MM, Plotkin JB. The polymorphism frequency spectrum of finitely many sites under selection. Genetics 180: 2175-2191 (2008) [pdf]

  • Parsons TL, Quince C, Plotkin JB. Absorption and fixation times for neutral and quasi-neutral populations with density dependence. Theoretical Population Biology 74: 302-310 (2008) [pdf]

  • Kryazhimskiy S, Basykin GA, Plotkin JB, Dushoff J. Directionality in the evolution of influenza A hemagglutinin. Proceedings of the Royal Society B 275: 2455-2464 (2008) [pdf]

  • Sethupathy P, Giang H, Plotkin JB, Hannenhalii S. Genome-wide analysis of natural selection on human cis-elements. PLOS One 3: 3137 (2008) [pdf]

  • Lucks JB, Nelson DR, Kudla G, Plotkin JB. Genome landscapes and bacteriophage codon usage. PLOS Computational Biology 4: 1 (2008) [pdf]

  • Wu M, Li J, Engleka K, Zhou B, Lu M, Plotkin JB, Epstein JA. Persistent expression of Pax3 in neural crest causes cleft palate and defective osteogenesis. Journal of Clinical Investigation 118: 2076-2078 (2008)

  • Chen-Plotkin AS, Geser F, Plotkin JB, Clark CM, Kwong LK,Yuan W, Grossman M, VanDeerlin V, Trojanowski JQ, Lee VM. Variations in the progranulin gene affect global gene expression in frontotemporal lobar degeneration. Human Molecular Genetics 17 : 1349-1362 (2008)

  • Fraser HB, Plotkin JB. Using protein complexes to predict phenotypic effects of gene mutation. Genome Biology 8: 252 (2007) [pdf]

  • Green JL, Plotkin JB. A statistical theory for sampling species abundances. Ecology Letters 10: 1037-1045 (2007) [pdf]

  • Plotkin JB, Fraser HB. Assessing the determinants of evolutionary rates in the presence of noise. Molecular Biology and Evolution 24: 1113-1121 (2007) [pdf]

  • Dushoff J, Plotkin JB, Viboud C, Simonesen L, Miller M. Vaccinating to protect a vulnerable subpopulation. PLOS Medicine 4: 174 (2007) [pdf]

  • Plotkin JB, Dushoff J, Desai MM, Fraser HB. Codon usage and selection on proteins. Journal of Molecular Evolution 63: 635-553 (2006) [pdf]

  • Plotkin JB, Dushoff J, Desai MM, Fraser HB. Estimating selection pressures from limited comparative data. Molecular Biology and Evolution 23: 1457-1459 (2006) [pdf]

  • Dushoff J, Plotkin JB, Viboud C, Earn JD, Simonsen L. Mortality due to influenza in the US -- an annualized approach to estimation using multiple-cause mortality data. American Journal of Epidemiology 163: 181-187 (2006) [pdf]

  • Seidler T, Plotkin JB. Seed dispersal and spatial pattern in tropical trees. PLOS Biology 4: 344- (2006) [pdf]

  • Ng K, Soon LL, Saw LG, Plotkin JB, Koh CL. Spatial structure and genetic diversity of three tropical tree species with different habitat preferences within a natural forest. Tree Genetics and Genomes 2: 121-131 (2006) [pdf]

  • HB Fraser, P Khaitovich, JB Plotkin, S Paabo, MB Eisen. Aging and gene expression in the primate brain. PLOS Biology 3: 274- (2005) [pdf]

  • Lukhtanov V, Kandul N, Plotkin JB, Dantchenko A, Haig D, Pierce N. Reinforcement of pre-zygotic isolation and karyotype evolution in Agrodiaetus butterflies. Nature 436: 385-389 (2005) [pdf]

  • Plotkin JB, Dushoff J, Fraser HB. Codon bias and selection on single genomes -- reply. Nature 433 E7-E8 (2005) [pdf]

  • Dushoff J, Plotkin JB, Levin SA, Earn DE. Dynamic resonance can explain the seasonality of influenza incidence. PNAS 101: 16915-16916 (2004) [pdf]

  • Plotkin JB, Robins H, Levine A. Tissue specific codon usage and the expression of human genes. PNAS 101: 12588-12591 (2004) [pdf]

  • Plotkin JB, Dushoff J, Fraser HB. Detecting selection using a single genome sequence of M. tuberculosis and P. falciparum. Nature 428: 942-945 (2004) [pdf]

  • Levin SA, Dushoff J, Plotkin JB. Evolution and persistence of Influenza A and other diseases. Mathematical Biosciences 188: 12-28 (2004) [pdf]

  • Plotkin JB, Dushoff J. Codon bias and frequency-dependent selection on the hemagglutinin epitopes of Influenza A virus. PNAS 100: 7152-7157 (2003) [pdf]

  • Plotkin JB, Dushoff J, Levin SA. Hemagglutinin sequence clusters and the antigenic evolution of Influenza A virus. PNAS 99: 6263-6268 (2002) [pdf]

  • Plotkin JB, Nowak MA. The different effects of apoptosis and DNA repair on tumorigenesis. Journal of Theoretical Biology 214: 453-467 (2002) [pdf]

  • Krakauer D, Plotkin JB. Redundancy, anti-redundancy, and the stability of genomes. PNAS 99: 1405-1409 (2002) [pdf]

  • Krakauer D, Plotkin JB. Principles and parameters of molecular robustness. In Robust Design, ed. Erica Jen, Santa Fe Press (2002) [pdf]

  • Plotkin JB, Muller-Landau H. Sampling the species composition of a landscape. Ecology 83: 3344-3356 (2002) [pdf]

  • Plotkin JB, Chave J, Ashton PS. Cluster analysis of spatial patterns in Malaysian tree species. The American Naturalist 160: 629-644 (2002) [pdf]

  • Potts MD, Ashton PS, Kaufman LS, Plotkin JB. Habitat patterns in tropical rain forests: a comparison of 105 plots in Northwest Borneo. Ecology 83: 2782?2797 (2002) [pdf]

  • Plotkin JB, Levin SA. The spatial distribution and abundances of species:Lessons from tropical forests. Comments on Theoretical Biology 6: 251-278 (2001) [pdf]

  • Plotkin JB, Nowak MA. Major transitions in language evolution. Entropy 4: 227-246 (2001)

  • Potts MD, Plotkin JB, Lee HS, Manokaran N. Sampling biodiversity: effects of plot shape. The Malaysian Forester 64: 29-34 (2001)

  • Plotkin JB, Potts M, Yu D, Bunyavejchewin S, Condit R, Foster R, Hubbell S, LaFrankie J, Manokaran N, Seng L, Sukumar R, Nowak MA, Ashton PS. Predicting species diversity in tropical forests. PNAS 97: 10850-10854 (2000) [pdf]

  • Nowak M, Plotkin JB, Jansen V. The evolution of syntactic communication. Nature 404: 495-498 (2000) [pdf]

  • Plotkin JB, Nowak MA. Language evolution and information theory. Journal of Theoretical Biology 205: 147-159 (2000) [pdf]

  • Plotkin JB, Potts M, Leslie N, Manokaran N, LaFrankie J, Ashton P. Species-area curves, spatial aggregation, and habitat specialization in tropical forests. Journal of Theoretical Biology 207: 81-99 (2000) [pdf]

  • Nowak MA, Plotkin JB, Krakauer D. The evolutionary language game. Journal of Theoretical Biology 200: 147-162 (1999) [pdf]

    Funding

    We gratefully acknowledge funding from:

    • U.S. National Institute of General Medical Sciences (NIGMS)
    • U.S. National Institute of Allergy and Infectious Diseases (NIAID)
    • U.S. Defense Advanced Research Projects Agency (DARPA)
    • U.S. Army Research Office
    • Alfred P. Sloan Foundation
    • Burroughs Wellcome Fund
    • James S. McDonnell Foundation
    • National Academies Keck Futures Initiative
    • United Nations Development Program
    • David & Lucile Packard Foundation
    • National Philanthropic Trust
    We are especially grateful for the generosity of Margy Meyerson, who established the Martin Meyerson Chair in Interdisciplinary Studies at the University of Pennsylvania; and also to Walter and Leonore Annenberg who established the Walter H. and Leonore C. Annenberg Chair in Natural Sciences at the University of Pennsylvania.
We use mathematics and computation to study questions in evolutionary biology and ecology. (read more)