High-throughput characterization of mutations in genes that drive clonal evolution using multiplex adaptome capture sequencing

The evolutionary dynamics and fitness landscape of clonal hematopoiesis

(2020) Caroline J. Watson et al.   SCIENCE

Causal mutations from adaptive laboratory evolution are outlined by multiple scales of genome annotations and condition-specificity

(2020) Patrick V. Phaneuf et al.   BMC GENOMICS

Patterns and Mechanisms of Diminishing Returns from Beneficial Mutations

(2019) Xinzhu Wei et al.   MOLECULAR BIOLOGY AND EVOLUTION

Bacterial genome architecture shapes global transcriptional regulation by DNA supercoiling

(2019) Bilal El Houdaigui et al.   NUCLEIC ACIDS RESEARCH

Microbial Experimental Evolution – a proving ground for evolutionary theory and a tool for discovery

(2019) Michael J McDonald   EMBO REPORTS

Overcoming genetic heterogeneity in industrial fermentations

(2019) Peter Rugbjerg et al.   NATURE BIOTECHNOLOGY

Toward prediction and control of antibiotic-resistance evolution

(2018) Chikara Furusawa et al.   CURRENT OPINION IN BIOTECHNOLOGY

Experimental Studies of Evolutionary Dynamics in Microbes

(2018) Ivana Cvijović et al.   TRENDS IN GENETICS

Diverse genetic error modes constrain large-scale bio-based production

(2018) Peter Rugbjerg et al.   Nature Communications

An incoherent feedforward loop facilitates adaptive tuning of gene expression

(2018) Jungeui Hong et al.   eLife

Relevance of multidrug-resistant Pseudomonas aeruginosa infections in cystic fibrosis

(2017) S. Stefani et al.   INTERNATIONAL JOURNAL OF MEDICAL MICROBIOLOGY

Multilocus amplicon sequencing of Pseudomonas aeruginosa cystic fibrosis airways isolates collected prior to and after early antipseudomonal chemotherapy

(2017) Sebastian Fischer et al.   Journal of Cystic Fibrosis

Effects of Beneficial Mutations in pykF Gene Vary over Time and across Replicate Populations in a Long-Term Experiment with Bacteria

(2017) Fen Peng et al.   MOLECULAR BIOLOGY AND EVOLUTION

The dynamics of molecular evolution over 60,000 generations

(2017) Benjamin H. Good et al.   NATURE

Specificity of genome evolution in experimental populations ofEscherichia colievolved at different temperatures

(2017) Daniel E. Deatherage et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Engineering Cellular Metabolism

(2016) Jens Nielsen et al.   CELL

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

(2016) Sandeep Venkataram et al.   CELL

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

(2016) Olivier Tenaillon et al.   NATURE

Genome-wide mapping of mutations at single-nucleotide resolution for protein, metabolic and genome engineering

(2016) Andrew D Garst et al.   NATURE BIOTECHNOLOGY

Integrated digital error suppression for improved detection of circulating tumor DNA

(2016) Aaron M Newman et al.   NATURE BIOTECHNOLOGY

Spatiotemporal microbial evolution on antibiotic landscapes

(2016) M. Baym et al.   SCIENCE

Pseudomonas aeruginosa Evolutionary Adaptation and Diversification in Cystic Fibrosis Chronic Lung Infections

(2016) Craig Winstanley et al.   TRENDS IN MICROBIOLOGY

Grappling with anisotropic data, pseudo-merohedral twinning and pseudo-translational noncrystallographic symmetry: a case study involving pyruvate kinase

(2016) Katherine A. Donovan et al.   Acta Crystallographica Section D-Structural Biology

Adaptation, Clonal Interference, and Frequency-Dependent Interactions in a Long-Term Evolution Experiment with Escherichia coli

(2015) Rohan Maddamsetti et al.   GENETICS

Quantitative evolutionary dynamics using high-resolution lineage tracking

(2015) Sasha F. Levy et al.   NATURE

Systems strategies for developing industrial microbial strains

(2015) Sang Yup Lee et al.   NATURE BIOTECHNOLOGY

Structural basis for suppression of hypernegative DNA supercoiling byE. colitopoisomerase I

(2015) Kemin Tan et al.   NUCLEIC ACIDS RESEARCH

Crowded growth leads to the spontaneous evolution of semistable coexistence in laboratory yeast populations

(2015) Evgeni M. Frenkel et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Experimental evolution reveals hidden diversity in evolutionary pathways

(2015) Peter A Lind et al.   eLife

Adaptation, Clonal Interference, and Frequency-Dependent Interactions in a Long-Term Evolution Experiment with Escherichia coli

(2015) Rohan Maddamsetti et al.   GENETICS

Identifying structural variation in haploid microbial genomes from short-read resequencing data using breseq

(2014) Jeffrey E Barrick et al.   BMC GENOMICS

The enduring utility of continuous culturing in experimental evolution

(2014) David Gresham et al.   GENOMICS

Beyond genome sequencing: Lineage tracking with barcodes to study the dynamics of evolution, infection, and cancer

(2014) Jamie R. Blundell et al.   GENOMICS

Use of pantothenate as a metabolic switch increases the genetic stability of farnesene producing Saccharomyces cerevisiae

(2014) Celeste M. Sandoval et al.   METABOLIC ENGINEERING

Engineering reduced evolutionary potential for synthetic biology

(2014) Brian A. Renda et al.   Molecular BioSystems

Convergent evolution and adaptation of Pseudomonas aeruginosa within patients with cystic fibrosis

(2014) Rasmus Lykke Marvig et al.   NATURE GENETICS

An ultrasensitive method for quantitating circulating tumor DNA with broad patient coverage

(2014) Aaron M Newman et al.   NATURE MEDICINE

Deep mutational scanning: a new style of protein science

(2014) Douglas M Fowler et al.   NATURE METHODS

Clonal Hematopoiesis and Blood-Cancer Risk Inferred from Blood DNA Sequence

(2014) Giulio Genovese et al.   NEW ENGLAND JOURNAL OF MEDICINE

Global epistasis makes adaptation predictable despite sequence-level stochasticity

(2014) S. Kryazhimskiy et al.   SCIENCE

Large Chromosomal Rearrangements during a Long-Term Evolution Experiment with Escherichia coli

(2014) C. Raeside et al.   mBio

Evolution and Impact of Subclonal Mutations in Chronic Lymphocytic Leukemia

(2013) Dan A. Landau et al.   CELL

Stacks: an analysis tool set for population genomics

(2013) Julian Catchen et al.   MOLECULAR ECOLOGY

Pervasive genetic hitchhiking and clonal interference in forty evolving yeast populations

(2013) Gregory I. Lang et al.   NATURE

Genome dynamics during experimental evolution

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

Transposon insertion sequencing: a new tool for systems-level analysis of microorganisms

(2013) Tim van Opijnen et al.   NATURE REVIEWS MICROBIOLOGY

Functioning of a metabolic flux sensor in Escherichia coli

(2013) K. Kochanowski et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Long-Term Dynamics of Adaptation in Asexual Populations

(2013) M. J. Wiser et al.   SCIENCE

Genetic Diversity and the Structure of Genealogies in Rapidly Adapting Populations

(2012) M. M. Desai et al.   GENETICS

Culture History and Population Heterogeneity as Determinants of Bacterial Adaptation: the Adaptomics of a Single Environmental Transition

(2012) B. Ryall et al.   MICROBIOLOGY AND MOLECULAR BIOLOGY REVIEWS

Clonal evolution in relapsed acute myeloid leukaemia revealed by whole-genome sequencing

(2012) Li Ding et al.   NATURE

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

FREQ-Seq: A Rapid, Cost-Effective, Sequencing-Based Method to Determine Allele Frequencies Directly from Mixed Populations

(2012) Lon M. Chubiz et al.   PLoS One

Detection of ultra-rare mutations by next-generation sequencing

(2012) M. W. Schmitt et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Tangled bank of experimentally evolved Burkholderia biofilms reflects selection during chronic infections

(2012) C. C. Traverse et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The Molecular Diversity of Adaptive Convergence

(2012) O. Tenaillon et al.   SCIENCE

Counting absolute numbers of molecules using unique molecular identifiers

(2011) Teemu Kivioja et al.   NATURE METHODS

Negative Epistasis Between Beneficial Mutations in an Evolving Bacterial Population

(2011) A. I. Khan et al.   SCIENCE

Diminishing Returns Epistasis Among Beneficial Mutations Decelerates Adaptation

(2011) H.-H. Chou et al.   SCIENCE

Second-Order Selection for Evolvability in a Large Escherichia coli Population

(2011) R. J. Woods et al.   SCIENCE

A Comprehensive Survey of Clonal Diversity Measures in Barrett's Esophagus as Biomarkers of Progression to Esophageal Adenocarcinoma

(2010) L. M. F. Merlo et al.   Cancer Prevention Research

Parallel Genetic and Phenotypic Evolution of DNA Superhelicity in Experimental Populations of Escherichia coli

(2010) E. Crozat et al.   MOLECULAR BIOLOGY AND EVOLUTION

Whole exome capture in solution with 3 Gbp of data

(2010) Matthew N Bainbridge et al.   GENOME BIOLOGY

BLAST+: architecture and applications

(2009) Christiam Camacho et al.   BMC BIOINFORMATICS

Genome Sequences of Escherichia coli B strains REL606 and BL21(DE3)

(2009) Haeyoung Jeong et al.   JOURNAL OF MOLECULAR BIOLOGY

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

(2009) Jeffrey E. Barrick et al.   NATURE