Predicting evolution

A Landscape of Pharmacogenomic Interactions in Cancer

(2016) Francesco Iorio et al.   CELL

Development of a Comprehensive Genotype-to-Fitness Map of Adaptation-Driving Mutations in Yeast

(2016) Sandeep Venkataram et al.   CELL

Macrophage adaptation leads to parallel evolution of genetically diverse Escherichia coli small-colony variants with increased fitness in vivo and antibiotic collateral sensitivity

(2016) Ricardo S. Ramiro et al.   Evolutionary Applications

Evolutionary assembly patterns of prokaryotic genomes

(2016) Maximilian O. Press et al.   GENOME RESEARCH

How Good Are Statistical Models at Approximating Complex Fitness Landscapes?

(2016) Louis du Plessis et al.   MOLECULAR BIOLOGY AND EVOLUTION

Tempo and mode of genome evolution in a 50,000-generation experiment

(2016) Olivier Tenaillon et al.   NATURE

Diversity of immune strategies explained by adaptation to pathogen statistics

(2016) Andreas Mayer et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Prediction, dynamics, and visualization of antigenic phenotypes of seasonal influenza viruses

(2016) Richard A. Neher et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

On the (un)predictability of a large intragenic fitness landscape

(2016) Claudia Bank et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Biophysical principles predict fitness landscapes of drug resistance

(2016) João V. Rodrigues et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Forecasting Epidemiological and Evolutionary Dynamics of Infectious Diseases

(2016) Sylvain Gandon et al.   TRENDS IN ECOLOGY & EVOLUTION

Evolutionary Rationale for Phages as Complements of Antibiotics

(2016) Clara Torres-Barceló et al.   TRENDS IN MICROBIOLOGY

Relative rate and location of intra-host HIV evolution to evade cellular immunity are predictable

(2016) John P. Barton et al.   Nature Communications

Host-Pathogen Coevolution and the Emergence of Broadly Neutralizing Antibodies in Chronic Infections

(2016) Armita Nourmohammad et al.   PLoS Genetics

Evolving New Protein-Protein Interaction Specificity through Promiscuous Intermediates

(2015) Christopher D. Aakre et al.   CELL

Manipulating the Selection Forces during Affinity Maturation to Generate Cross-Reactive HIV Antibodies

(2015) Shenshen Wang et al.   CELL

Viraemia suppressed in HIV-1-infected humans by broadly neutralizing antibody 3BNC117

(2015) Marina Caskey et al.   NATURE

Mutations driving CLL and their evolution in progression and relapse

(2015) Dan A. Landau et al.   NATURE

Quantitative evolutionary dynamics using high-resolution lineage tracking

(2015) Sasha F. Levy et al.   NATURE

Human-level control through deep reinforcement learning

(2015) Volodymyr Mnih et al.   NATURE

Evolutionary consequences of drug resistance: shared principles across diverse targets and organisms

(2015) Diarmaid Hughes et al.   NATURE REVIEWS GENETICS

Elucidating the molecular architecture of adaptation via evolve and resequence experiments

(2015) Anthony Long et al.   NATURE REVIEWS GENETICS

Dynamics of immunoglobulin sequence diversity in HIV-1 infected individuals

(2015) Kenneth B. Hoehn et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Inferring processes underlying B-cell repertoire diversity

(2015) Yuval Elhanati et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

The value of monitoring to control evolving populations

(2015) Andrej Fischer et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Neoantigens in cancer immunotherapy

(2015) T. N. Schumacher et al.   SCIENCE

Topological features of rugged fitness landscapes in sequence space

(2015) Dmitry A. Kondrashov et al.   TRENDS IN GENETICS

Adaptive immunity increases the pace and predictability of evolutionary change in commensal gut bacteria

(2015) João Barroso-Batista et al.   Nature Communications

Combining gene mutation with gene expression data improves outcome prediction in myelodysplastic syndromes

(2015) Moritz Gerstung et al.   Nature Communications

Evolutionary Determinants of Cancer

(2015) M. Greaves   Cancer Discovery

Replaying the tape of life in the twenty-first century

(2015) Virginie Orgogozo   Interface Focus

The effects of a deleterious mutation load on patterns of influenza A/H3N2's antigenic evolution in humans

(2015) Katia Koelle et al.   eLife

The rule of declining adaptability in microbial evolution experiments

(2015) Alejandro Couce et al.   Frontiers in Genetics

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) Niclas Thomas et al.   BIOINFORMATICS

Deconstructing the Peptide-MHC Specificity of T Cell Recognition

(2014) Michael E. Birnbaum et al.   CELL

Evolution of DNA Specificity in a Transcription Factor Family Produced a New Gene Regulatory Module

(2014) Alesia N. McKeown et al.   CELL

Merging molecular mechanism and evolution: theory and computation at the interface of biophysics and evolutionary population genetics

(2014) Adrian WR Serohijos et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

The genetic basis of the fitness costs of antimicrobial resistance: a meta-analysis approach

(2014) Tom Vogwill et al.   Evolutionary Applications

The spectrum of adaptive mutations in experimental evolution

(2014) Gregory I. Lang et al.   GENOMICS

Standing Genetic Variation Drives Repeatable Experimental Evolution in Outcrossing Populations of Saccharomyces cerevisiae

(2014) Molly K. Burke et al.   MOLECULAR BIOLOGY AND EVOLUTION

Genome sequencing of normal cells reveals developmental lineages and mutational processes

(2014) Sam Behjati et al.   NATURE

A predictive fitness model for influenza

(2014) Marta Łuksza et al.   NATURE

Empirical fitness landscapes and the predictability of evolution

(2014) J. Arjan G.M. de Visser et al.   NATURE REVIEWS GENETICS

Tug-of-war between driver and passenger mutations in cancer and other adaptive processes

(2014) Christopher D. McFarland et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Exploring the collaboration between antibiotics and the immune response in the treatment of acute, self-limiting infections

(2014) P. Ankomah et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Global epistasis makes adaptation predictable despite sequence-level stochasticity

(2014) S. Kryazhimskiy et al.   SCIENCE

Antibody landscapes after influenza virus infection or vaccination

(2014) J. M. Fonville et al.   SCIENCE

Prediction of resistance development against drug combinations by collateral responses to component drugs

(2014) C. Munck et al.   Science Translational Medicine

High-Definition Reconstruction of Clonal Composition in Cancer

(2014) Andrej Fischer et al.   Cell Reports

The First Steps of Adaptation of Escherichia coli to the Gut Are Dominated by Soft Sweeps

(2014) João Barroso-Batista et al.   PLoS Genetics

Integrating influenza antigenic dynamics with molecular evolution

(2014) Trevor Bedford et al.   eLife

The inherent mutational tolerance and antigenic evolvability of influenza hemagglutinin

(2014) Bargavi Thyagarajan et al.   eLife

Predicting evolution from the shape of genealogical trees

(2014) Richard A Neher et al.   eLife

Genetic Draft, Selective Interference, and Population Genetics of Rapid Adaptation

(2013) Richard A. Neher   Annual Review of Ecology Evolution and Systematics

Predicting the evolution of antibiotic resistance

(2013) Martijn F Schenk et al.   BMC BIOLOGY

Evolution of Escherichia coli rifampicin resistance in an antibiotic-free environment during thermal stress

(2013) Alejandra Rodríguez-Verdugo et al.   BMC EVOLUTIONARY BIOLOGY

Predicting C4 Photosynthesis Evolution: Modular, Individually Adaptive Steps on a Mount Fuji Fitness Landscape

(2013) David Heckmann et al.   CELL

Universality and predictability in molecular quantitative genetics

(2013) Armita Nourmohammad et al.   CURRENT OPINION IN GENETICS & DEVELOPMENT

Should evolutionary geneticists worry about higher-order epistasis?

(2013) Daniel M Weinreich et al.   CURRENT OPINION IN GENETICS & DEVELOPMENT

Mutational landscape and significance across 12 major cancer types

(2013) Cyriac Kandoth et al.   NATURE

Modelling vemurafenib resistance in melanoma reveals a strategy to forestall drug resistance

(2013) Meghna Das Thakur et al.   NATURE

Co-evolution of a broadly neutralizing HIV-1 antibody and founder virus

(2013) Hua-Xin Liao et al.   NATURE

Understanding, predicting and manipulating the genotypic evolution of antibiotic resistance

(2013) Adam C. Palmer et al.   NATURE REVIEWS GENETICS

Genome dynamics during experimental evolution

(2013) Jeffrey E. Barrick et al.   NATURE REVIEWS GENETICS

Capturing the mutational landscape of the beta-lactamase TEM-1

(2013) H. Jacquier et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Quorum sensing allows T cells to discriminate between self and nonself

(2013) T. C. Butler et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Lineage Structure of the Human Antibody Repertoire in Response to Influenza Vaccination

(2013) N. Jiang et al.   Science Translational Medicine

Whole Genome, Whole Population Sequencing Reveals That Loss of Signaling Networks Is the Major Adaptive Strategy in a Constant Environment

(2013) Daniel J. Kvitek et al.   PLoS Genetics

Components of Selection in the Evolution of the Influenza Virus: Linkage Effects Beat Inherent Selection

(2013) Christopher J. R. Illingworth et al.   PLoS Pathogens

Stability-mediated epistasis constrains the evolution of an influenza protein

(2013) Lizhi Ian Gong et al.   eLife

Monitoring chronic lymphocytic leukemia progression by whole genome sequencing reveals heterogeneous clonal evolution patterns

(2012) A. Schuh et al.   BLOOD

ANTIBIOTIC RESISTANCE AND STRESS IN THE LIGHT OF FISHER'S MODEL

(2012) Sandra Trindade et al.   EVOLUTION

Clonal Interference in the Evolution of Influenza

(2012) N. Strelkowa et al.   GENETICS

Mutational Pathway Determines Whether Drug Gradients Accelerate Evolution of Drug-Resistant Cells

(2012) Philip Greulich et al.   PHYSICAL REVIEW LETTERS

Distribution of fixed beneficial mutations and the rate of adaptation in asexual populations

(2012) B. H. Good et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

On the rapidity of antibiotic resistance evolution facilitated by a concentration gradient

(2012) R. Hermsen et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The interface of protein structure, protein biophysics, and molecular evolution

(2012) David A. Liberles et al.   PROTEIN SCIENCE

The Molecular Diversity of Adaptive Convergence

(2012) O. Tenaillon et al.   SCIENCE

Exploring the Complexity of the HIV-1 Fitness Landscape

(2012) Roger D. Kouyos et al.   PLoS Genetics

Replaying the Tape of Life: Quantification of the Predictability of Evolution

(2012) Alexander E. Lobkovsky et al.   Frontiers in Genetics

Hallmarks of Cancer: The Next Generation

(2011) Douglas Hanahan et al.   CELL

Emergent Neutrality in Adaptive Asexual Evolution

(2011) Stephan Schiffels et al.   GENETICS

Genetic Variation and the Fate of Beneficial Mutations in Asexual Populations

(2011) Gregory I. Lang et al.   GENETICS

Bias in the αβ T-cell repertoire: implications for disease pathogenesis and vaccination

(2011) John J Miles et al.   IMMUNOLOGY AND CELL BIOLOGY

Population biological principles of drug-resistance evolution in infectious diseases

(2011) Pia Abel zur Wiesch et al.   LANCET INFECTIOUS DISEASES

Cost of Antibiotic Resistance and the Geometry of Adaptation

(2011) Ana Sousa et al.   MOLECULAR BIOLOGY AND EVOLUTION

Parallel bacterial evolution within multiple patients identifies candidate pathogenicity genes

(2011) Tami D Lieberman et al.   NATURE GENETICS

Evolutionary paths to antibiotic resistance under dynamically sustained drug selection

(2011) Erdal Toprak et al.   NATURE GENETICS

Whole-genome sequencing of rifampicin-resistant Mycobacterium tuberculosis strains identifies compensatory mutations in RNA polymerase genes

(2011) Iñaki Comas et al.   NATURE GENETICS

Systems-biology approaches for predicting genomic evolution

(2011) Balázs Papp et al.   NATURE REVIEWS GENETICS

Improved Survival with Vemurafenib in Melanoma with BRAF V600E Mutation

(2011) Paul B. Chapman et al.   NEW ENGLAND JOURNAL OF MEDICINE

The evolution of drug resistance and the curious orthodoxy of aggressive chemotherapy

(2011) A. F. Read et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A biophysical protein folding model accounts for most mutational fitness effects in viruses

(2011) C. S. Wylie et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Nonlinear Fitness Landscape of a Molecular Pathway

(2011) Lilia Perfeito et al.   PLoS Genetics

Initial Mutations Direct Alternative Pathways of Protein Evolution

(2011) Merijn L. M. Salverda et al.   PLoS Genetics

The population genetics of antibiotic resistance: integrating molecular mechanisms and treatment contexts

(2010) R. Craig MacLean et al.   NATURE REVIEWS GENETICS

Fitness flux and ubiquity of adaptive evolution

(2010) V. Mustonen et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Using deep sequencing to characterize the biophysical mechanism of a transcriptional regulatory sequence

(2010) J. B. Kinney et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Causes and evolutionary significance of genetic convergence

(2010) Pascal-Antoine Christin et al.   TRENDS IN GENETICS

Genomewide Patterns of Substitution in Adaptively Evolving Populations of the RNA Bacteriophage MS2

(2009) A. J. Betancourt   GENETICS

Temporal Constraints on the Incorporation of Regulatory Mutants in Evolutionary Pathways

(2009) K. M. Brown et al.   MOLECULAR BIOLOGY AND EVOLUTION

Genome evolution and adaptation in a long-term experiment with Escherichia coli

(2009) Jeffrey E. Barrick et al.   NATURE

The cancer genome

(2009) Michael R. Stratton et al.   NATURE

The epidemiological fitness cost of drug resistance in Mycobacterium tuberculosis

(2009) F. Luciani et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

From fitness landscapes to seascapes: non-equilibrium dynamics of selection and adaptation

(2009) Ville Mustonen et al.   TRENDS IN GENETICS

Interplay in the Selection of Fluoroquinolone Resistance and Bacterial Fitness

(2009) Linda L. Marcusson et al.   PLoS Pathogens

Predicting evolution from genomics: experimental evolution of bacteriophage T7

(2008) J J Bull et al.   HEREDITY

Human Effector and Memory CD8+ T Cell Responses to Smallpox and Yellow Fever Vaccines

(2008) Joseph D. Miller et al.   IMMUNITY

Energy-dependent fitness: A quantitative model for the evolution of yeast transcription factor binding sites

(2008) V. Mustonen et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA