Predicting evolution

[1]  D. Levey.  Recognition , 2017, The Harps that Once....

[2]  B. Grenfell,et al.  Forecasting Epidemiological and Evolutionary Dynamics of Infectious Diseases. , 2016, Trends in ecology & evolution.

[3]  Sasha F. Levy,et al.  Development of a Comprehensive Genotype-to-Fitness Map of Adaptation-Driving Mutations in Yeast , 2016, Cell.

[4]  J. Jensen,et al.  On the (un-)predictability of a large intragenic fitness landscape , 2016, bioRxiv.

[5]  Emanuel J. V. Gonçalves,et al.  A Landscape of Pharmacogenomic Interactions in Cancer , 2016, Cell.

[6]  Ville Mustonen,et al.  Background-dependent effects of selection on subclonal heterogeneity , 2016 .

[7]  I. Gordo,et al.  Macrophage adaptation leads to parallel evolution of genetically diverse Escherichia coli small‐colony variants with increased fitness in vivo and antibiotic collateral sensitivity , 2016, Evolutionary applications.

[8]  Sebastian Bonhoeffer,et al.  How Good Are Statistical Models at Approximating Complex Fitness Landscapes? , 2016, Molecular biology and evolution.

[9]  B. Walker,et al.  Relative rate and location of intra-host HIV evolution to evade cellular immunity are predictable , 2016, Nature Communications.

[10]  Thierry Mora,et al.  Quantifying lymphocyte receptor diversity , 2016, bioRxiv.

[11]  Michael E Hochberg,et al.  Evolutionary Rationale for Phages as Complements of Antibiotics. , 2016, Trends in microbiology.

[12]  Elena R. Lozovsky,et al.  Biophysical principles predict fitness landscapes of drug resistance , 2016, Proceedings of the National Academy of Sciences.

[13]  Richard E. Lenski,et al.  Tempo and mode of genome evolution in a 50,000-generation experiment , 2016, Nature.

[14]  Thierry Mora,et al.  Measuring the sequence-affinity landscape of antibodies with massively parallel titration curves , 2016, bioRxiv.

[15]  Andrea Sottoriva,et al.  Cancer Evolution and the Limits of Predictability in Precision Cancer Medicine , 2016, Trends in cancer.

[16]  J. Plotkin,et al.  Host-Pathogen Coevolution and the Emergence of Broadly Neutralizing Antibodies in Chronic Infections , 2015, bioRxiv.

[17]  Thierry Mora,et al.  Diversity of immune strategies explained by adaptation to pathogen statistics , 2015, Proceedings of the National Academy of Sciences.

[18]  Trevor Bedford,et al.  Prediction, dynamics, and visualization of antigenic phenotypes of seasonal influenza viruses , 2015, Proceedings of the National Academy of Sciences.

[19]  E. Borenstein,et al.  Evolutionary assembly patterns of prokaryotic genomes , 2015, bioRxiv.

[20]  V. Orgogozo,et al.  Replaying the tape of life in the twenty-first century , 2015, Interface Focus.

[21]  J. Gern,et al.  Antibody Landscapes After Influenza Virus Infection or Vaccination , 2015, Pediatrics.

[22]  Isabel Gordo,et al.  Adaptive immunity increases the pace and predictability of evolutionary change in commensal gut bacteria , 2015, Nature Communications.

[23]  M. Laub,et al.  Evolving New Protein-Protein Interaction Specificity through Promiscuous Intermediates , 2015, Cell.

[24]  A. Long,et al.  Elucidating the molecular architecture of adaptation via evolve and resequence experiments , 2015, Nature Reviews Genetics.

[25]  Jacob G. Scott,et al.  Passenger DNA alterations reduce cancer fitness in cell culture and mouse models , 2015, bioRxiv.

[26]  Astrid Gall,et al.  Dynamics of immunoglobulin sequence diversity in HIV-1 infected individuals , 2015, Philosophical Transactions of the Royal Society B: Biological Sciences.

[27]  Martin A. Nowak,et al.  Mutations driving CLL and their evolution in progression and relapse , 2015, Nature.

[28]  Mel Greaves,et al.  Evolutionary determinants of cancer. , 2015, Cancer discovery.

[29]  David A. Rasmussen,et al.  Author response: The effects of a deleterious mutation load on patterns of influenza A/H3N2's antigenic evolution in humans , 2015 .

[30]  Diarmaid Hughes,et al.  Evolutionary consequences of drug resistance: shared principles across diverse targets and organisms , 2015, Nature Reviews Genetics.

[31]  Michael S. Seaman,et al.  Viraemia suppressed in HIV-1-infected humans by broadly neutralizing antibody 3BNC117 , 2015, Nature.

[32]  T. Schumacher,et al.  Neoantigens in cancer immunotherapy , 2015, Science.

[33]  Gavin Sherlock,et al.  Quantitative evolutionary dynamics using high-resolution lineage tracking , 2015, Nature.

[34]  O. Tenaillon,et al.  The rule of declining adaptability in microbial evolution experiments , 2015, Front. Genet..

[35]  Shane Legg,et al.  Human-level control through deep reinforcement learning , 2015, Nature.

[36]  T. Mora,et al.  Inferring processes underlying B-cell repertoire diversity , 2015, bioRxiv.

[37]  Mehran Kardar,et al.  Manipulating the selection forces during affinity maturation to generate cross-reactive HIV antibodies , 2015, Cell.

[38]  P. Campbell,et al.  Combining gene mutation with gene expression data improves outcome prediction in myelodysplastic syndromes , 2015, Nature Communications.

[39]  R. MacLean,et al.  The genetic basis of the fitness costs of antimicrobial resistance: a meta-analysis approach , 2014, Evolutionary applications.

[40]  Ville Mustonen,et al.  The value of monitoring to control evolving populations , 2014, Proceedings of the National Academy of Sciences.

[41]  Fyodor A Kondrashov,et al.  Topological features of rugged fitness landscapes in sequence space. , 2015, Trends in genetics : TIG.

[42]  Michael M. Desai,et al.  The spectrum of adaptive mutations in experimental evolution. , 2014, Genomics.

[43]  A. Long,et al.  Standing genetic variation drives repeatable experimental evolution in outcrossing populations of Saccharomyces cerevisiae. , 2014, Molecular biology and evolution.

[44]  Christian Munck,et al.  Prediction of resistance development against drug combinations by collateral responses to component drugs , 2014, Science Translational Medicine.

[45]  E. Ortlund,et al.  Evolution of DNA Specificity in a Transcription Factor Family Produced a New Gene Regulatory Module , 2014, Cell.

[46]  Asif U. Tamuri,et al.  Genome sequencing of normal cells reveals developmental lineages and mutational processes , 2014, Nature.

[47]  John Shawe-Taylor,et al.  Tracking global changes induced in the CD4 T-cell receptor repertoire by immunization with a complex antigen using short stretches of CDR3 protein sequence , 2014, bioRxiv.

[48]  Jesse D Bloom,et al.  The inherent mutational tolerance and antigenic evolvability of influenza hemagglutinin , 2014, bioRxiv.

[49]  J. Krug,et al.  Empirical fitness landscapes and the predictability of evolution , 2014, Nature Reviews Genetics.

[50]  Colin A Russell,et al.  Predicting evolution from the shape of genealogical trees , 2014, eLife.

[51]  Adrian W. R. Serohijos,et al.  Merging molecular mechanism and evolution: theory and computation at the interface of biophysics and evolutionary population genetics. , 2014, Current opinion in structural biology.

[52]  Christopher J. R. Illingworth,et al.  High-Definition Reconstruction of Clonal Composition in Cancer , 2014, Cell reports.

[53]  Mark M. Davis,et al.  Deconstructing the Peptide-MHC Specificity of T Cell Recognition , 2014, Cell.

[54]  Peter Ankomah,et al.  Exploring the collaboration between antibiotics and the immune response in the treatment of acute, self-limiting infections , 2014, Proceedings of the National Academy of Sciences.

[55]  M. Lässig,et al.  A predictive fitness model for influenza , 2014, Nature.

[56]  Leonid A. Mirny,et al.  Tug-of-war between driver and passenger mutations in cancer and other adaptive processes , 2014, Proceedings of the National Academy of Sciences.

[57]  D. Sobral,et al.  The First Steps of Adaptation of Escherichia coli to the Gut Are Dominated by Soft Sweeps , 2013, PLoS genetics.

[58]  Trevor Bedford,et al.  Integrating influenza antigenic dynamics with molecular evolution , 2013, eLife.

[59]  Olivier Tenaillon,et al.  The reproducibility of adaptation in the light of experimental evolution with whole genome sequencing. , 2014, Advances in experimental medicine and biology.

[60]  Robert B. Heckendorn,et al.  Should evolutionary geneticists worry about higher-order epistasis? , 2013, Current opinion in genetics & development.

[61]  Daniel J. Kvitek,et al.  Whole Genome, Whole Population Sequencing Reveals That Loss of Signaling Networks Is the Major Adaptive Strategy in a Constant Environment , 2013, PLoS genetics.

[62]  Jeffrey E. Barrick,et al.  Genome dynamics during experimental evolution , 2013, Nature Reviews Genetics.

[63]  Benjamin J. Raphael,et al.  Mutational landscape and significance across 12 major cancer types , 2013, Nature.

[64]  Michael Lässig,et al.  Universality and predictability in molecular quantitative genetics , 2013, bioRxiv.

[65]  J. Poulain,et al.  Capturing the mutational landscape of the beta-lactamase TEM-1 , 2013, Proceedings of the National Academy of Sciences.

[66]  Arup K Chakraborty,et al.  Quorum sensing allows T cells to discriminate between self and nonself , 2013, Proceedings of the National Academy of Sciences.

[67]  Martin J. Lercher,et al.  Predicting C4 Photosynthesis Evolution: Modular, Individually Adaptive Steps on a Mount Fuji Fitness Landscape , 2013, Cell.

[68]  Marc A Suchard,et al.  Stability-mediated epistasis constrains the evolution of an influenza protein , 2013, eLife.

[69]  Chaim A. Schramm,et al.  Co-evolution of a broadly neutralizing HIV-1 antibody and founder virus , 2013, Nature.

[70]  J. D. de Visser,et al.  Predicting the evolution of antibiotic resistance , 2013, BMC Biology.

[71]  Roy Kishony,et al.  Understanding, predicting and manipulating the genotypic evolution of antibiotic resistance , 2013, Nature Reviews Genetics.

[72]  Mark M. Davis,et al.  Lineage Structure of the Human Antibody Repertoire in Response to Influenza Vaccination , 2013, Science Translational Medicine.

[73]  R. Neher.  Genetic Draft, Selective Interference, and Population Genetics of Rapid Adaptation , 2013, 1302.1148.

[74]  W. Sellers,et al.  Modelling vemurafenib resistance in melanoma reveals a strategy to forestall drug resistance , 2013, Nature.

[75]  O. Tenaillon,et al.  Evolution of Escherichia coli rifampicin resistance in an antibiotic-free environment during thermal stress , 2013, BMC Evolutionary Biology.

[76]  A. Sousa,et al.  ANTIBIOTIC RESISTANCE AND STRESS IN THE LIGHT OF FISHER'S MODEL , 2012, Evolution; international journal of organic evolution.

[77]  Christopher J. R. Illingworth,et al.  Components of Selection in the Evolution of the Influenza Virus: Linkage Effects Beat Inherent Selection , 2012, PLoS pathogens.

[78]  Jenny Taylor,et al.  Monitoring chronic lymphocytic leukemia progression by whole genome sequencing reveals heterogeneous clonal evolution patterns. , 2012, Blood.

[79]  M. Lässig,et al.  Clonal Interference in the Evolution of Influenza , 2012, Genetics.

[80]  Eugene V. Koonin,et al.  Replaying the Tape of Life: Quantification of the Predictability of Evolution , 2012, Front. Gene..

[81]  T. Hwa,et al.  On the rapidity of antibiotic resistance evolution facilitated by a concentration gradient , 2012, Proceedings of the National Academy of Sciences.

[82]  Lucy J. Colwell,et al.  The interface of protein structure, protein biophysics, and molecular evolution , 2012, Protein science : a publication of the Protein Society.

[83]  Sebastian Bonhoeffer,et al.  Exploring the Complexity of the HIV-1 Fitness Landscape , 2012, PLoS genetics.

[84]  Benjamin H. Good,et al.  Distribution of fixed beneficial mutations and the rate of adaptation in asexual populations , 2012, Proceedings of the National Academy of Sciences.

[85]  B. Waclaw,et al.  Mutational pathway determines whether drug gradients accelerate evolution of drug-resistant cells. , 2012, Physical review letters.

[86]  A. F. Bennett,et al.  The Molecular Diversity of Adaptive Convergence , 2012, Science.

[87]  Remy Chait,et al.  Evolutionary paths to antibiotic resistance under dynamically sustained drug selection , 2011, Nature Genetics.

[88]  A. Sousa,et al.  Cost of Antibiotic Resistance and the Geometry of Adaptation , 2011, Molecular biology and evolution.

[89]  T. Eberlein,et al.  Improved Survival with Vemurafenib in Melanoma with BRAF V600E Mutation , 2012 .

[90]  M. Roizen,et al.  Hallmarks of Cancer: The Next Generation , 2012 .

[91]  Gergely J. Szöllősi,et al.  Emergent Neutrality in Adaptive Asexual Evolution , 2011, Genetics.

[92]  Joanna B. Goldberg,et al.  Parallel bacterial evolution within multiple patients identifies candidate pathogenicity genes , 2011, Nature Genetics.

[93]  Balázs Papp,et al.  Systems-biology approaches for predicting genomic evolution , 2011, Nature Reviews Genetics.

[94]  Michael M. Desai,et al.  Genetic Variation and the Fate of Beneficial Mutations in Asexual Populations , 2011, Genetics.

[95]  M. Lässig,et al.  Nonlinear Fitness Landscape of a Molecular Pathway , 2011, PLoS genetics.

[96]  Troy Day,et al.  The evolution of drug resistance and the curious orthodoxy of aggressive chemotherapy , 2011, Proceedings of the National Academy of Sciences.

[97]  Eugene I Shakhnovich,et al.  A biophysical protein folding model accounts for most mutational fitness effects in viruses , 2011, Proceedings of the National Academy of Sciences.

[98]  Pia Abel zur Wiesch,et al.  Population biological principles of drug-resistance evolution in infectious diseases. , 2011, The Lancet. Infectious diseases.

[99]  Dan S. Tawfik,et al.  Initial Mutations Direct Alternative Pathways of Protein Evolution , 2011, PLoS genetics.

[100]  Daniel C Douek,et al.  Bias in the αβ T‐cell repertoire: implications for disease pathogenesis and vaccination , 2011, Immunology and cell biology.

[101]  Stefan Niemann,et al.  Whole-genome sequencing of rifampicin-resistant Mycobacterium tuberculosis strains identifies compensatory mutations in RNA polymerase genes , 2011 .

[102]  D. Weinreich,et al.  Causes and evolutionary significance of genetic convergence. , 2010, Trends in genetics : TIG.

[103]  Alex R. Hall,et al.  The population genetics of antibiotic resistance: integrating molecular mechanisms and treatment contexts , 2010, Nature Reviews Genetics.

[104]  J. Kinney,et al.  Using deep sequencing to characterize the biophysical mechanism of a transcriptional regulatory sequence , 2010, Proceedings of the National Academy of Sciences.

[105]  Diarmaid Hughes,et al.  Antibiotic resistance and its cost: is it possible to reverse resistance? , 2010, Nature Reviews Microbiology.

[106]  M. Lässig,et al.  Fitness flux and ubiquity of adaptive evolution , 2010, Proceedings of the National Academy of Sciences.

[107]  M. DePristo,et al.  Temporal constraints on the incorporation of regulatory mutants in evolutionary pathways. , 2009, Molecular biology and evolution.

[108]  Jeffrey E. Barrick,et al.  Genome evolution and adaptation in a long-term experiment with Escherichia coli , 2009, Nature.

[109]  Andrew R. Francis,et al.  The epidemiological fitness cost of drug resistance in Mycobacterium tuberculosis , 2009, Proceedings of the National Academy of Sciences.

[110]  D. Hughes,et al.  Interplay in the Selection of Fluoroquinolone Resistance and Bacterial Fitness , 2009, PLoS pathogens.

[111]  M. Stratton,et al.  The cancer genome , 2009, Nature.

[112]  A. Betancourt.  Genomewide Patterns of Substitution in Adaptively Evolving Populations of the RNA Bacteriophage MS2 , 2009, Genetics.

[113]  M. Lässig,et al.  From fitness landscapes to seascapes: non-equilibrium dynamics of selection and adaptation. , 2009, Trends in genetics : TIG.

[114]  Ville Mustonen,et al.  Energy-dependent fitness: A quantitative model for the evolution of yeast transcription factor binding sites , 2008, Proceedings of the National Academy of Sciences.

[115]  J. Altman,et al.  Human effector and memory CD8+ T cell responses to smallpox and yellow fever vaccines. , 2008, Immunity.

[116]  J. Bull,et al.  Predicting evolution from genomics: experimental evolution of bacteriophage T7 , 2008, Heredity.

[117]  D. Price,et al.  The molecular basis for public T-cell responses? , 2008, Nature Reviews Immunology.

[118]  D. Nelson,et al.  Genetic drift at expanding frontiers promotes gene segregation , 2007, Proceedings of the National Academy of Sciences.

[119]  Michael Lässig,et al.  From biophysics to evolutionary genetics: statistical aspects of gene regulation , 2007, BMC Bioinformatics.

[120]  Eugene I. Shakhnovich,et al.  Protein stability imposes limits on organism complexity and speed of molecular evolution , 2007, Proceedings of the National Academy of Sciences.

[121]  D. J. Kiviet,et al.  Empirical fitness landscapes reveal accessible evolutionary paths , 2007, Nature.

[122]  S. Quake,et al.  A Systems Approach to Measuring the Binding Energy Landscapes of Transcription Factors , 2007, Science.

[123]  Martha L Bulyk,et al.  DNA microarray technologies for measuring protein-DNA interactions. , 2006, Current opinion in biotechnology.

[124]  Nigel F. Delaney,et al.  Darwinian Evolution Can Follow Only Very Few Mutational Paths to Fitter Proteins , 2006, Science.

[125]  Art Poon,et al.  The Rate of Compensatory Mutation in the DNA Bacteriophage φX174 , 2005, Genetics.

[126]  Alan M. Moses,et al.  MONKEY: identifying conserved transcription-factor binding sites in multiple alignments using a binding site-specific evolutionary model , 2004, Genome Biology.

[127]  A. Lapedes,et al.  Mapping the Antigenic and Genetic Evolution of Influenza Virus , 2004, Science.

[128]  Johannes Berg,et al.  Adaptive evolution of transcription factor binding sites , 2003, BMC Evolutionary Biology.

[129]  R. Lenski,et al.  The fate of competing beneficial mutations in an asexual population , 2004, Genetica.

[130]  R. Lenski,et al.  Microbial genetics: Evolution experiments with microorganisms: the dynamics and genetic bases of adaptation , 2003, Nature Reviews Genetics.

[131]  Lars Liljas,et al.  Compensatory adaptation to the deleterious effect of antibiotic resistance in Salmonella typhimurium , 2002, Molecular microbiology.

[132]  Terence Hwa,et al.  On the Selection and Evolution of Regulatory DNA Motifs , 2001, Journal of Molecular Evolution.

[133]  A. U.S.,et al.  Predictability , Complexity , and Learning , 2002 .

[134]  M G Reynolds,et al.  Compensatory evolution in rifampin-resistant Escherichia coli. , 2000, Genetics.

[135]  B. Levin,et al.  Compensatory mutations, antibiotic resistance and the population genetics of adaptive evolution in bacteria. , 2000, Genetics.

[136]  S. Elena,et al.  Clonal interference and the evolution of RNA viruses. , 1999, Science.

[137]  Hervé Le Nagard,et al.  Mutators, population size, adaptive landscape and the adaptation of asexual populations of bacteria. , 1999, Genetics.

[138]  A. Halpern,et al.  Evolutionary distances for protein-coding sequences: modeling site-specific residue frequencies. , 1998, Molecular biology and evolution.

[139]  J. Altman,et al.  Counting antigen-specific CD8 T cells: a reevaluation of bystander activation during viral infection. , 1998, Immunity.

[140]  A. Perelson,et al.  HIV-1 Dynamics in Vivo: Virion Clearance Rate, Infected Cell Life-Span, and Viral Generation Time , 1996, Science.

[141]  J. Hailman.  Wonderful Life: The Burgess Shale and the Nature of History, Stephen Jay Gould. W. W. Norton, New York (1989), 347, Price $19.95 (U.S.A.), $27.95 (Canada) , 1991 .

[142]  R. Punnett,et al.  The Genetical Theory of Natural Selection , 1930, Nature.