D. Petrov

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Illumina TruSeq synthetic long-reads empower de novo assembly and resolve complex, highly repetitive transposable elements

Rajiv C. McCoy, Dmitry Pushkarev, Ryan W Taylor, 2014 .

Evolution of gene function on the X chromosome versus the autosomes.

D. Petrov, N. Singh, Nadia D Singh, 2007, Genome dynamics.

Pervasive Natural Selection in the Drosophila Genome?

D. Petrov, G. Sella, P. Andolfatto, 2009, PLoS genetics.

Recent Selective Sweeps in North American Drosophila melanogaster Show Signatures of Soft Sweeps

Philipp W. Messer, D. Petrov, Nandita R. Garud, 2013, PLoS genetics.

Inferring the strength of selection in Drosophila under complex demographic models.

Philipp W. Messer, D. Petrov, J. M. Macpherson, 2008, Molecular biology and evolution.

High rate of DNA loss in the Drosophila melanogaster and Drosophila virilis species groups.

D. Petrov, D. Hartl, 1998, Molecular biology and evolution.

High intrinsic rate of DNA loss in Drosophila

D. Petrov, D. Hartl, E. Lozovskaya, 1996, Nature.

How intron splicing affects the deletion and insertion profile in Drosophila melanogaster.

D. Petrov, S. Ptak, 2002, Genetics.

The AMBRA1 E3 ligase adaptor regulates the stability of cyclin D

D. Petrov, N. Krogan, J. Demeter, 2021, Nature.

The clarifying role of time series data in the population genetics of HIV

D. Petrov, A. F. Feder, P. Pennings, 2018, bioRxiv.

T-lex: a program for fast and accurate assessment of transposable element presence using next-generation sequencing data

D. Petrov, Anna-Sophie Fiston-Lavier, Josefa González, 2010, Nucleic acids research.

T-lex2: genotyping, frequency estimation and re-annotation of transposable elements using single or pooled next-generation sequencing data

Maite G. Barrón, D. Petrov, Anna-Sophie Fiston-Lavier, 2014, bioRxiv.

Microbiome composition shapes rapid genomic adaptation of Drosophila melanogaster

Sharon I. Greenblum, John M. Chaston, D. Petrov, 2019, Proceedings of the National Academy of Sciences.

Illumina TruSeq Synthetic Long-Reads Empower De Novo Assembly and Resolve Complex, Highly-Repetitive Transposable Elements

Rajiv C. McCoy, Joanna L. Kelley, Dmitry Pushkarev, 2014, bioRxiv.

Imperfect drug penetration leads to spatial monotherapy and rapid evolution of multidrug resistance

Daniel I. S. Rosenbloom, M. Nowak, D. Petrov, 2014, Proceedings of the National Academy of Sciences.

Pervasive and Persistent Redundancy among Duplicated Genes in Yeast

Dmitri A. Petrov, Ronald W. Davis, G. McVean, 2008, PLoS genetics.

Preferential Duplication of Conserved Proteins in Eukaryotic Genomes

D. Petrov, J. Davis, 2004, PLoS biology.

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

Sasha F. Levy, G. Sherlock, D. Petrov, 2016, Cell.

Patterns of nucleotide substitution in Drosophila and mammalian genomes.

D. Petrov, D. Hartl, Dmitrii Petrov, 1999, Proceedings of the National Academy of Sciences of the United States of America.

Evolutionary Dynamics in Structured Populations Under Strong Population Genetic Forces

D. Petrov, J. Hermisson, A. F. Feder, 2019, G3: Genes, Genomes, Genetics.

Evidence That Mutation Is Universally Biased towards AT in Bacteria

D. Petrov, Ruth Hershberg, 2010, PLoS genetics.

Genomic Evidence of Rapid and Stable Adaptive Oscillations over Seasonal Time Scales in Drosophila

D. Petrov, P. Schmidt, K. O’Brien, 2013, PLoS genetics.

High Functional Diversity in Mycobacterium tuberculosis Driven by Genetic Drift and Human Demography

Stefan Niemann, Jared C Roach, Marcus W Feldman, 2008, PLoS biology.

Selection on codon bias.

Ruth Hershberg, Dmitri A Petrov, D. Petrov, 2008, Annual review of genetics.

Pervasive Hitchhiking at Coding and Regulatory Sites in Humans

Guy Sella, Dmitri A. Petrov, James J. Cai, 2009, PLoS genetics.

More effective drugs lead to harder selective sweeps in the evolution of drug resistance in HIV-1

D. Petrov, R. Shafer, S. Holmes, 2016, eLife.

Quantitative evolutionary dynamics using high-resolution lineage tracking

Gavin Sherlock, Sandeep Venkataram, Dmitri A. Petrov, 2015, Nature.

Viruses are a dominant driver of protein adaptation in mammals

D. Petrov, D. Enard, L. Cai, 2015, bioRxiv.

Strong Purifying Selection at Synonymous Sites in D. melanogaster

Philipp W. Messer, David S. Lawrie, D. Petrov, 2013, PLoS genetics.

Frequent adaptation and the McDonald–Kreitman test

Philipp W. Messer, D. Petrov, P. W. Messer, 2012, Proceedings of the National Academy of Sciences.

The McDonald-Kreitman Test and its Extensions under Frequent Adaptation: Problems and Solutions

Philipp W. Messer, D. Petrov, P. W. Messer, 2012, 1211.0060.

Evidence that Adaptation in Drosophila Is Not Limited by Mutation at Single Sites

Philipp W. Messer, Dmitri A. Petrov, D. Petrov, 2010, PLoS genetics.

The adaptive role of transposable elements in the Drosophila genome.

D. Petrov, Josefa González, 2009, Gene.

High Rate of Recent Transposable Element–Induced Adaptation in Drosophila melanogaster

Josefa González, Dmitri A Petrov, D. Petrov, 2008, PLoS biology.

High sensitivity to aligner and high rate of false positives in the estimates of positive selection in the 12 Drosophila genomes.

Dmitri Petrov, D. Petrov, P. Markova-Raina, 2011, Genome research.

Genome Patterns of Selection and Introgression of Haplotypes in Natural Populations of the House Mouse (Mus musculus)

Philipp W. Messer, Kun Tang, Dmitri A. Petrov, 2012, PLoS genetics.

Substantial Regional Variation in Substitution Rates in the Human Genome: Importance of GC Content, Gene Density, and Telomere-Specific Effects

Terence Hwa, Peter F. Arndt, Dmitri A. Petrov, 2005, Journal of Molecular Evolution.

Distinct changes of genomic biases in nucleotide substitution at the time of Mammalian radiation.

Terence Hwa, Dmitri A Petrov, D. Petrov, 2003, Molecular biology and evolution.

Soft selective sweeps in complex demographic scenarios

Philipp W. Messer, D. Petrov, B. A. Wilson, 2014, bioRxiv.

Reduced selection leads to accelerated gene loss in Shigella

Ruth Hershberg, Hua Tang, Dmitri A Petrov, 2007, Genome Biology.

Evidence for DNA loss as a determinant of genome size.

D. Petrov, D. Hartl, T. Sangster, 2000, Science.

Heterozygote advantage as a natural consequence of adaptation in diploids

Philipp W. Messer, D. Petrov, B. Callahan, 2011, Proceedings of the National Academy of Sciences.

High rate of adaptation of mammalian proteins that interact with Plasmodium and related parasites

D. Petrov, D. Enard, N. Telis, 2017, PLoS genetics.

Predictability of adaptive evolution under the successive fixation assumption

D. Petrov, Diamantis Sellis, S. Venkataram, 2015 .

Ploidy and the Predictability of Evolution in Fishers Geometric Model

D. Petrov, Diamantis Sellis, S. Venkataram, 2013 .

Title: Ploidy and the Predictability of Evolution in Fisher’s Geometric Model Running Title: Ploidy and the Predictability of Evolution First Author:

D. Petrov, Diamantis Sellis, S. Venkataram, 2013 .

Most cancers carry a substantial deleterious load due to Hill-Robertson interference

Christopher D. McFarland, D. Petrov, C. Curtis, 2019, bioRxiv.

Genetic determinants of EGFR-Driven Lung Cancer Growth and Therapeutic Response In Vivo

D. Petrov, H. Wakelee, M. Diehn, 2020, bioRxiv.

Population genomics of transposable elements in Drosophila.

Maite G. Barrón, D. Petrov, Anna-Sophie Fiston-Lavier, 2014, Annual review of genetics.

developmental loci in Drosophila melanogaster

D. Petrov, J. M. Macpherson, Josefa González, 2009 .

Rapid seasonal evolution in innate immunity of wild Drosophila melanogaster

D. Petrov, B. Lazzaro, M. Kapun, 2017, bioRxiv.

Entering the era of conservation genomics: Cost-effective assembly of the African wild dog genome using linked long reads

Ryan W Taylor, D. Petrov, J. Stuelpnagel, 2017, bioRxiv.

SNP genotyping to monitor wild tigers for conservation

Ryan W Taylor, D. Petrov, U. Ramakrishnan, 2017 .

Ancient RNA virus epidemics through the lens of recent adaptation in human genomes

D. Petrov, D. Enard, 2020, Philosophical Transactions of the Royal Society B.

Common host variation drives malaria parasite fitness in healthy human red cells

D. Petrov, E. Ebel, Carrie Lin, 2020, bioRxiv.

Tumor suppressor pathways shape EGFR-driven lung tumor progression and response to treatment

D. Petrov, K. Politi, Giorgia Foggetti, 2022, Molecular & cellular oncology.

Accurate allele frequencies from ultra-low coverage pool-seq samples in evolve-and-resequence experiments

Sharon I. Greenblum, D. Petrov, P. Schmidt, 2019, bioRxiv.

Accurate Allele Frequencies from Ultra-low Coverage Pool-Seq Samples in Evolve-and-Resequence Experiments

Sharon I. Greenblum, D. Petrov, P. Schmidt, 2019, G3: Genes, Genomes, Genetics.

High accuracy haplotype-derived allele frequencies from ultra-low coverage pool-seq samples

Sharon I. Greenblum, D. Petrov, P. Schmidt, 2018 .

Genetic Adaptation in New York City Rats

D. Petrov, N. Rosenberg, Nandita R. Garud, 2020, bioRxiv.

Detection of hard and soft selective sweeps from Drosophila melanogaster population genomic data

Philipp W. Messer, D. Petrov, Nandita R. Garud, 2020, bioRxiv.

Evolutionary Biology for the 21 st Century

S. J. Arnold, H. A. Orr, D. Petrov, 2012 .

Evolutionary Biology for the 21st Century The Harvard made this article Please share how this access benefits you. Your story matters

S. J. Arnold, H. A. Orr, D. Petrov, 2012 .

Malaria parasite fitness in healthy human red cells is driven by common host variation

D. Petrov, E. Ebel, E. Egan, 2020 .

Author ' s personal copy Drosophila melanogaster recombination rate calculator

D. Petrov, Anna-Sophie Fiston-Lavier, Nadia D. Singh, 2010 .

Tripolar chromosome segregation drives the association between maternal genotype at variants spanning PLK4 and aneuploidy in human preimplantation embryos

Omar E. Cornejo, Rajiv C. McCoy, D. Petrov, 2018, Human molecular genetics.

Tripolar mitosis drives the association between maternal genotypes of PLK4 and aneuploidy in human preimplantation embryos

Omar E. Cornejo, Rajiv C. McCoy, D. Petrov, 2017, bioRxiv.

Widespread introgression across a phylogeny of 155 Drosophila genomes

Aaron A. Comeault, Daniel R. Schrider, Bernard Y. Kim, 2020, Current Biology.

Genome-Wide Patterns of Adaptation to Temperate Environments Associated with Transposable Elements in Drosophila

Philipp W. Messer, D. Petrov, Josefa González, 2010, PLoS genetics.

Commentary: Raman nanospectroscopy of single DNA molecules

D. Petrov, 2010 .

The cis -regulatory of modern human-specific variants.

Hunter B. Fraser, D. Petrov, H. Fraser, 2021 .

LDx: Estimation of Linkage Disequilibrium from High-Throughput Pooled Resequencing Data

D. Petrov, A. Bergland, A. Feder, 2012, PloS one.

Cancers adapt to their mutational load by buffering protein misfolding stress

D. Petrov, C. Curtis, J. Frydman, 2022, bioRxiv.

On the Limitations of Using Ribosomal Genes as References for the Study of Codon Usage: A Rebuttal

D. Petrov, Ruth Hershberg, 2012, PloS one.

Genome report: chromosome-level draft assemblies of the snow leopard, African leopard, and tiger (Panthera uncia, Panthera pardus pardus, and Panthera tigris)

D. Petrov, O. Ryder, E. Hadly, 2022, bioRxiv.

Rates of DNA Duplication and Mitochondrial DNA Insertion in the Human Genome

M. Feldman, D. Petrov, D. Bensasson, 2004, Journal of Molecular Evolution.

Genomic inference accurately predicts the timing and severity of a recent bottleneck in a nonmodel insect population

Rajiv C. McCoy, Joanna L. Kelley, J. Kelley, 2014, Molecular ecology.

Historical trends and new surveillance of Plasmodium falciparum drug resistance markers in Angola

D. Petrov, S. Beleza, E. Ebel, 2021, Malaria journal.

Shifts in antimalarial drug policy since 2006 have rapidly selected P. falciparum resistance alleles in Angola

D. Petrov, S. Beleza, E. Ebel, 2020, bioRxiv.

Population genomics of transposable elements in Drosophila melanogaster.

D. Petrov, Anna-Sophie Fiston-Lavier, Josefa González, 2011, Molecular biology and evolution.

S14-03 From trait to base pairs: Parallel evolution of pelvic reduction in three-spined sticklebacks occurs by repeated deletion of a tissue-specific pelvic enhancer at Pitx1

D. Absher, D. Petrov, R. Myers, 2009, Mechanisms of Development.

Host Species and Environmental Effects on Bacterial Communities Associated with Drosophila in the Laboratory and in the Natural Environment

D. Petrov, E. Bik, S. Künzel, 2012, PloS one.

Adaptive Evolution of Pelvic Reduction in Sticklebacks by Recurrent Deletion of a Pitx1 Enhancer

Jeremy Schmutz, Jane Grimwood, Yingguang Frank Chan, 2010, Science.

Whole Genome Analysis of 132 Clinical Saccharomyces cerevisiae Strains Reveals Extensive Ploidy Variation

G. Sherlock, D. Petrov, Yuan O. Zhu, 2016, G3: Genes, Genomes, Genetics.

The large genome constraint hypothesis: evolution, ecology and phenotype.

D. Petrov, C. Knight, Nicole A. Molinari, 2005, Annals of botany.

Relaxed Purifying Selection and Possibly High Rate of Adaptation in Primate Lineage-Specific Genes

Dmitri A. Petrov, James J. Cai, D. Petrov, 2010, Genome biology and evolution.

A Patient-Derived Glioblastoma Organoid Model and Biobank Recapitulates Inter- and Intra-tumoral Heterogeneity

Zev A. Binder, D. Petrov, T. Lucas, 2019, Cell.

Revisiting the malaria hypothesis: accounting for polygenicity and pleiotropy.

Lawrence H. Uricchio, D. Petrov, E. Ebel, 2022, Trends in parasitology.

Effects of maternal age on euploidy rates in a large cohort of embryos analyzed with 24-chromosome single-nucleotide polymorphism-based preimplantation genetic screening.

Matthew Rabinowitz, Dmitri A Petrov, D. Petrov, 2016, Fertility and sterility.

A combined molecular and cytogenetic approach to genome evolution in Drosophila using large-fragment DNA cloning

D. Petrov, D. Hartl, E. Lozovskaya, 1993, Chromosoma.

Genome-wide signals of positive selection in human evolution

D. Petrov, D. Enard, P. W. Messer, 2014, Genome research.

Quantification of GC-biased gene conversion in the human genome

Philipp W. Messer, D. Petrov, L. Duret, 2014, bioRxiv.

Precise estimates of mutation rate and spectrum in yeast

David W. Hall, Dmitri A. Petrov, Mark L. Siegal, 2014, Proceedings of the National Academy of Sciences.

Soft Selective Sweeps in Complex Demographic Scenarios

Philipp W. Messer, D. Petrov, B. A. Wilson, 2014, Genetics.

Genome wide signals of pervasive positive selection in human evolution

D. Petrov, D. Enard, P. W. Messer, 2013, 1308.4951.

Mutational equilibrium model of genome size evolution.

Dmitri A Petrov, D. Petrov, 2002, Theoretical population biology.

Molecular evolution of the testis TAFs of Drosophila.

D. Petrov, V. Li, J. Davis, 2009, Molecular biology and evolution.

Human-chimpanzee fused cells reveal cis-regulatory divergence underlying skeletal evolution

Hunter B. Fraser, D. Petrov, H. Fraser, 2021, Nature Genetics.

Faster than Neutral Evolution of Constrained Sequences: The Complex Interplay of Mutational Biases and Weak Selection

Philipp W. Messer, David S. Lawrie, D. Petrov, 2011, Genome biology and evolution.

The cis-regulatory effects of modern human-specific variants

Hunter B. Fraser, D. Petrov, H. Fraser, 2020, bioRxiv.

Evolution of genome size: new approaches to an old problem.

D. Petrov, 2001, Trends in genetics : TIG.

Pseudogene evolution and natural selection for a compact genome.

D. Petrov, D. Hartl, D L Hartl, 2000, The Journal of heredity.

General Rules for Optimal Codon Choice

D. Petrov, Ruth Hershberg, 2009, PLoS genetics.

Minor shift in background substitutional patterns in the Drosophila saltans and willistoni lineages is insufficient to explain GC content of coding sequences.

D. Petrov, Nadia D. Singh, P. Arndt, 2006, BMC Biology.

X-Linked Genes Evolve Higher Codon Bias in Drosophila and Caenorhabditis

D. Petrov, Nadia D. Singh, J. Davis, 2005, Genetics.

Genomic Heterogeneity of Background Substitutional Patterns in Drosophila melanogaster

Dmitri A Petrov, D. Petrov, Nadia D. Singh, 2005, Genetics.

Common variants spanning PLK4 are associated with mitotic-origin aneuploidy in human embryos

Hunter B. Fraser, D. Petrov, H. Fraser, 2015, Science.

A quantitative and multiplexed approach to uncover the fitness landscape of tumor suppression in vivo

Christopher D. McFarland, D. Petrov, M. Winslow, 2017, Nature Methods.

Rong Chen, Elhanan Borenstein, Dmitri A. Petrov, 2009, Genome biology and evolution.

Protein Evolution in the Context of Drosophila Development

D. Petrov, Onn Brandman, J. Davis, 2005, Journal of Molecular Evolution.

Mapping the in vivo fitness landscape of lung adenocarcinoma tumor suppression in mice

Christopher D. McFarland, D. Petrov, C. Curtis, 2018, Nature Genetics.

Do disparate mechanisms of duplication add similar genes to the genome?

Dmitri A Petrov, D. Petrov, J. Davis, 2005, Trends in genetics : TIG.

Size matters: non-LTR retrotransposable elements and ectopic recombination in Drosophila.

A. E. Hirsh, D. Petrov, D. Bensasson, 2003, Molecular biology and evolution.

Reconsidering the management paradigm of fragmented populations

M. Feldman, Ryan W Taylor, D. Petrov, 2019, bioRxiv.

Exploiting selection at linked sites to infer the rate and strength of adaptation

Lawrence H. Uricchio, D. Petrov, D. Enard, 2018, Nature Ecology & Evolution.

Extremely Rare Polymorphisms in Saccharomyces cerevisiae Allow Inference of the Mutational Spectrum

G. Sherlock, D. Petrov, Yuan O. Zhu, 2017, PLoS genetics.

Pseudogene evolution in Drosophila suggests a high rate of DNA loss.

D. Petrov, D. Hartl, Y. Chao, 1998, Molecular biology and evolution.

Secondary contact and local adaptation contribute to genome‐wide patterns of clinal variation in Drosophila melanogaster

D. Petrov, P. Schmidt, Josefa González, 2016, Molecular ecology.

Secondary contact and local adaptation contribute to genome-wide patterns of clinal variation in Drosophila melanogaster

D. Petrov, P. Schmidt, Josefa González, 2014, bioRxiv.

Evolution of genome content: population dynamics of transposable elements in flies and humans.

D. Petrov, Josefa González, 2012, Methods in molecular biology.

Evolutionary Biology for the 21st Century

David P. Mindell, Gill Bejerano, Dmitri A. Petrov, 2013, PLoS biology.

DNA loss and evolution of genome size in Drosophila

Dmitri A. Petrov, D. Petrov, 2002, Genetica.

A recent adaptive transposable element insertion near highly conserved developmental loci in Drosophila melanogaster.

D. Petrov, J. M. Macpherson, Josefa González, 2009, Molecular biology and evolution.

Pervasive Strong Selection at the Level of Codon Usage Bias in Drosophila melanogaster

David S. Lawrie, D. Petrov, H. Machado, 2019, Genetics.

Comparative population genomics: power and principles for the inference of functionality.

David S. Lawrie, D. Petrov, David S Lawrie, 2014, Trends in genetics : TIG.

Drosophila melanogaster recombination rate calculator.

Anna-Sophie Fiston-Lavier, Dmitri A Petrov, D. Petrov, 2010, Gene.

Codon Bias and Noncoding GC Content Correlate Negatively with Recombination Rate on the Drosophila X Chromosome

D. Petrov, Nadia D. Singh, J. Davis, 2005, Journal of Molecular Evolution.

Long live the king: chromosome-level assembly of the lion (Panthera leo) using linked-read, Hi-C, and long-read data

Danny E. Miller, Ryan W Taylor, D. Petrov, 2019, BMC Biology.

Broad geographic sampling reveals predictable, pervasive, and strong seasonal adaptation in Drosophila

Bernard Y. Kim, Ryan W Taylor, D. Petrov, 2018, bioRxiv.

Heterozygote Advantage Is a Common Outcome of Adaptation in Saccharomyces cerevisiae

Daniel J. Kvitek, G. Sherlock, D. Petrov, 2016, Genetics.

Empirical evidence for heterozygote advantage in adapting diploid populations of Saccharomyces cerevisiae

Daniel J. Kvitek, G. Sherlock, D. Petrov, 2015, bioRxiv.

Rates of DNA Duplication and Mitochondrial DNA Insertion in the Human Genome

M. Feldman, D. Petrov, D. Bensasson, 2003, Journal of Molecular Evolution.

Genomic gigantism: DNA loss is slow in mountain grasshoppers.

D. Petrov, D. Hartl, D. Bensasson, 2001, Molecular biology and evolution.

Fully accessible fitness landscape of oncogene-negative lung adenocarcinoma

D. Petrov, Maryam Yousefi, G. Boross, 2023, bioRxiv.

Multiplexed screens identify RAS paralogues HRAS and NRAS as suppressors of KRAS-driven lung cancer growth

Min K. Tsai, D. Petrov, R. Dunbrack, 2023, Nature Cell Biology.

Combinatorial Inactivation of Tumor Suppressors Efficiently Initiates Lung Adenocarcinoma with Therapeutic Vulnerabilities.

Min K. Tsai, D. Petrov, C. Swanton, 2022, Cancer research.

Multiplexed identification of RAS paralog imbalance as a driver of lung cancer growth

Roland L. Dunbrack, Min K. Tsai, D. Petrov, 2021, bioRxiv.

A functional taxonomy of tumor suppression in oncogenic KRAS-driven lung cancer.

Christopher D. McFarland, Min K. Tsai, D. Petrov, 2021, Cancer discovery.

Fitness variation across subtle environmental perturbations reveals local modularity and global pleiotropy of adaptation

D. Petrov, K. Geiler-Samerotte, Grant Kinsler, 2020, eLife.

A genotype-phenotype-fitness map reveals local modularity and global pleiotropy of adaptation

D. Petrov, K. Geiler-Samerotte, Grant Kinsler, 2020, bioRxiv.

Multiplexed in vivo homology-directed repair and tumor barcoding enables parallel quantification of Kras variant oncogenicity

Christopher D. McFarland, D. Petrov, M. Kay, 2017, Nature Communications.

Transposable elements in clonal lineages: lethal hangover from sex

D. Petrov, S. Nuzhdin, 2003 .

Paucity of chimeric gene-transposable element transcripts in the Drosophila melanogaster genome

D. Petrov, C. Bergman, M. Lipatov, 2005, BMC Biology.

Genome size as a mutation-selection-drift process.

D. Petrov, D. Hartl, E. Lozovskaya, 1999, Genes & genetic systems.

Genome size and intron size in Drosophila.

D. Petrov, D. Hartl, E. Moriyama, 1998, Molecular biology and evolution.

Trash DNA is what gets thrown away: high rate of DNA loss in Drosophila.

D. Petrov, D. Hartl, 1997, Gene.

Genomewide Spatial Correspondence Between Nonsynonymous Divergence and Neutral Polymorphism Reveals Extensive Adaptation in Drosophila

D. Petrov, J. M. Macpherson, G. Sella, 2007, Genetics.

A Novel Method Distinguishes Between Mutation Rates and Fixation Biases in Patterns of Single-Nucleotide Substitution

D. Petrov, T. Hwa, P. Arndt, 2006, Journal of Molecular Evolution.

Strong selection at the level of codon usage bias: evidence against the Li-Bulmer model

David S. Lawrie, D. Petrov, H. Machado, 2017, bioRxiv.

Strong purifying selection on codon usage bias

David S. Lawrie, D. Petrov, H. Machado, 2017 .

D. Petrov, J. M. Macpherson, Nadia D. Singh, 2007, BMC Evolutionary Biology.

Elevated Linkage Disequilibrium and Signatures of Soft Sweeps Are Common in Drosophila melanogaster

D. Petrov, Nandita R. Garud, 2016, Genetics.

Elevation of linkage disequilibrium above neutral expectations in ancestral and derived populations of Drosophila melanogaster

D. Petrov, Nandita R. Garud, 2015, bioRxiv.

Recent selective sweeps in Drosophila were abundant and primarily soft

D. Petrov, Nandita R. Garud, P. W. Messer, 2013 .

Rapid sequence turnover at an intergenic locus in Drosophila.

D. Petrov, Nadia D. Singh, Nadia D Singh, 2004, Molecular biology and evolution.

Stress response, behavior, and development are shaped by transposable element-induced mutations in Drosophila

Maite G. Barrón, D. Petrov, Anna-Sophie Fiston-Lavier, 2018, bioRxiv.

T-lex 2 : genotyping , frequency estimation and re-annotation of transposable elements using single or pooled next-generation sequencing data

Dmitri A. Petrov, Anna-Sophie Fiston-Lavier, Maite G. Barrón, 2015 .

1 T-lex 2 : genotyping , frequency estimation and re-annotation of transposable elements using single or pooled next-generation sequencing data

Maite G. Barrón, D. Petrov, Anna-Sophie Fiston-Lavier, 2014 .

Population Genomics of Transposable Elements in Drosophila Maite

Maite G. Barrón, D. Petrov, Anna-Sophie Fiston-Lavier, 2014 .

Comparative population genomics of latitudinal variation in Drosophila simulans and Drosophila melanogaster

D. Petrov, P. Schmidt, E. Behrman, 2016, Molecular ecology.

Comparative Population Genomics of Latitudinal Variation in D. Simulans and D. Melanogaster

D. Petrov, P. Schmidt, K. O’Brien, 2022 .

Diverse transposable elements are mobilized in hybrid dysgenesis in Drosophila virilis.

D. Petrov, D. Hartl, E. Lozovskaya, 1995, Proceedings of the National Academy of Sciences of the United States of America.

Origins and rates of aneuploidy in human blastomeres.

D. Petrov, M. Rabinowitz, Z. Demko, 2012, Fertility and sterility.

Combinatorial tumor suppressor inactivation efficiently initiates lung adenocarcinoma with therapeutic vulnerabilities

Min K. Tsai, D. Petrov, C. Swanton, 2021, bioRxiv.

A repetitive DNA element, associated with telomeric sequences in Drosophila melanogaster, contains open reading frames

D. Petrov, D. Hartl, O. Danilevskaya, 1992, Chromosoma.

References and Notes Materials and Methods Tables S1 and S2 References and Notes Pesticide Resistance via Transposition-mediated Adaptive Gene Truncation in Drosophila

D. Petrov, J. M. Macpherson, M. Raath, 2022 .

Seeking Goldilocks During Evolution of Drug Resistance

G. Sherlock, D. Petrov, 2017, PLoS biology.

Population genomics of rapid adaptation by soft selective sweeps.

Philipp W. Messer, D. Petrov, P. W. Messer, 2013, Trends in ecology & evolution.

Elevated evolutionary rates in the laboratory strain of Saccharomyces cerevisiae.

Lars M Steinmetz, Ted Jones, Ronald W Davis, 2005, Proceedings of the National Academy of Sciences of the United States of America.

Empirical Validation of Pooled Whole Genome Population Re-Sequencing in Drosophila melanogaster

Dmitri A. Petrov, Josefa González, D. Petrov, 2012, PloS one.

Evidence of Selection against Complex Mitotic-Origin Aneuploidy during Preimplantation Development

D. Petrov, M. Rabinowitz, Z. Demko, 2015, PLoS genetics.

A spatio-temporal assessment of simian/human immunodeficiency virus (SHIV) evolution reveals a highly dynamic process within the host

D. Petrov, B. Keele, Shiu-Lok Hu, 2017, PLoS pathogens.

Spatiotemporal dynamics and genome‐wide association analysis of desiccation tolerance in Drosophila melanogaster

Subhash Rajpurohit, Paul S Schmidt, Dmitri A Petrov, 2018, Molecular ecology.

The mode and tempo of genome size evolution in eukaryotes.

D. Petrov, D. Ackerly, M. Oliver, 2007, Genome research.

Multiplexed in vivo homology-directed repair and tumor barcoding enables parallel quantification of Kras variant oncogenicity

Christopher D. McFarland, D. Petrov, M. Kay, 2017, Nature Communications.

An Intrinsically Disordered Region of the DNA Repair Protein Nbs1 Is a Species-Specific Barrier to Herpes Simplex Virus 1 in Primates.

Eui Tae Kim, M. Weitzman, D. Petrov, 2016, Cell host & microbe.

Adaptive dynamics of cuticular hydrocarbons in Drosophila

D. Petrov, P. Schmidt, R. Hanus, 2017, Journal of evolutionary biology.

The Tetragnatha kauaiensis Genome Sheds Light on the Origins of Genomic Novelty in Spiders

D. Petrov, J. Rozas, Bent Petersen, 2021, Genome biology and evolution.

Global Transcriptional Profiling of Diapause and Climatic Adaptation in Drosophila melanogaster

D. Petrov, B. Gregory, P. Schmidt, 2015, Molecular biology and evolution.

Broker Genes in Human Disease

Elhanan Borenstein, Dmitri A. Petrov, James J. Cai, 2010, Genome biology and evolution.

Functional biology in its natural context: A search for emergent simplicity

D. Petrov, Mikhail Tikhonov, J. Bergelson, 2021, eLife.

Deep sequencing of natural and experimental populations of Drosophila melanogaster reveals biases in the spectrum of new mutations

D. Petrov, M. Siegal, Z. Assaf, 2016, bioRxiv.

Cost-effective assembly of the African wild dog (Lycaon pictus) genome using linked reads

Ryan W Taylor, D. Petrov, J. Stuelpnagel, 2018, GigaScience.

Ancient RNA virus epidemics through the lens of recent adaptation in human genomes

D. Petrov, D. Enard, 2020, bioRxiv.

Genetic differences at four DNA typing loci in Finnish, Italian, and mixed Caucasian populations.

D. Petrov, D. Hartl, S. Sawyer, 1992, Proceedings of the National Academy of Sciences of the United States of America.

Evidence that RNA Viruses Drove Adaptive Introgression between Neanderthals and Modern Humans

D. Petrov, D. Enard, 2018, Cell.

Hidden Complexity of Yeast Adaptation under Simple Evolutionary Conditions

G. Sherlock, D. Petrov, B. Dunn, 2018, Current Biology.

Enhancer Choice in Cis and in Trans in Drosophila melanogaster

Dmitri A. Petrov, D. Petrov, James R. Morris, 2004, Genetics.

Reply to Chen and Zhang: On interpreting genome-wide trends from yeast mutation accumulation data

D. Petrov, M. Siegal, D. Hall, 2014, Proceedings of the National Academy of Sciences.

Nonadaptive explanations for signatures of partial selective sweeps in Drosophila.

A. E. Hirsh, D. Petrov, D. Witten, 2008, Molecular biology and evolution.

Soft selective sweeps are the primary mode of recent adaptation in Drosophila melanogaster

D. Petrov, Nandita R. Garud, P. W. Messer, 2013 .

Far From Home: Evolution of haploid and diploid populations reveals common, strong, and variable pleiotropic effects in non-home environments

Michael M. Desai, G. Sherlock, D. Petrov, 2023, bioRxiv.

Single nucleotide mapping of trait space reveals Pareto fronts that constrain adaptation

G. Sherlock, D. Petrov, Yuping Li, 2019, Nature Ecology & Evolution.

Single Nucleotide Mapping of the Locally Accessible Trait Space in Yeast Reveals Pareto Fronts that Constrain Initial Adaptation

Gavin Sherlock, Yuping Li, Dmitri A. Petrov, 2019, bioRxiv.

Highly contiguous assemblies of 101 drosophilid genomes

Aaron A. Comeault, Danny E. Miller, Bernard Y. Kim, 2020, bioRxiv.

Polymorphism and the Predictability of Evolution in Fisher?s Geometric Model

D. Petrov, Diamantis Sellis, S. Venkataram, 2013, 1312.0556.

Correction: More effective drugs lead to harder selective sweeps in the evolution of drug resistance in HIV-1

D. Petrov, R. Shafer, S. Holmes, 2017, eLife.

Tissue-specific cis-regulatory divergence implicates a fatty acid elongase necessary for inhibiting interspecies mating in Drosophila

Peter A. Combs, D. Petrov, H. Fraser, 2018, bioRxiv.

Direct observation of adaptive tracking on ecological time scales in Drosophila

Sharon I. Greenblum, D. Petrov, P. Schmidt, 2022, Science.

Direct observation of adaptive tracking on ecological timescales in Drosophila

Sharon I. Greenblum, D. Petrov, P. Schmidt, 2021, bioRxiv.

Tissue-Specific cis-Regulatory Divergence Implicates eloF in Inhibiting Interspecies Mating in Drosophila

Peter A. Combs, D. Petrov, H. Fraser, 2018, Current Biology.

Obstruction of adaptation in diploids by recessive, strongly deleterious alleles

D. Petrov, Z. Assaf, J. Blundell, 2015, Proceedings of the National Academy of Sciences.

Drosophila Evolution over Space and Time (DEST): A New Population Genomics Resource

D. Petrov, J. Parsch, S. Schaeffer, 2021, Molecular biology and evolution.

Drosophila Evolution over Space and Time (DEST) - A New Population Genomics Resource

D. Petrov, J. Parsch, S. Schaeffer, 2021, bioRxiv.

Title: Predictability of adaptive evolution under the successive fixation assumption

D. Petrov, Diamantis Sellis, S. Venkataram, 2015 .

Broad geographic sampling reveals the shared basis and environmental correlates of seasonal adaptation in Drosophila

Bernard Y. Kim, Ryan W Taylor, D. Petrov, 2021, eLife.

Evolutionary Dynamics in Structured Populations Under Strong Population Genetic Forces

D. Petrov, J. Hermisson, P. Pennings, 2019, G3: Genes, Genomes, Genetics.

High resolution spatio-temporal assessment of simian/human immunodeficiency virus (SHIV) evolution reveals a highly dynamic process within the host

D. Petrov, B. Keele, Shiu-Lok Hu, 2017, bioRxiv.

Soft Selective Sweeps in Evolutionary Rescue

Pleuni S Pennings, Dmitri A Petrov, D. Petrov, 2016, Genetics.

Recent Evolutionary History of Tigers Highlights Contrasting Roles of Genetic Drift and Selection

Ryan W Taylor, D. Petrov, L. Excoffier, 2019, bioRxiv.

Gene galaxies in the maize genome

D. Petrov, V. Walbot, 2001, Proceedings of the National Academy of Sciences of the United States of America.

Genomic regulation of transposable elements in Drosophila.

D. Petrov, D. Hartl, E. Lozovskaya, 1995, Current opinion in genetics & development.

RNA viruses drove adaptive introgressions between Neanderthals and modern humans

D. Petrov, D. Enard, 2017, bioRxiv.

Quantitative In Vivo Analyses Reveal a Complex Pharmacogenomic Landscape in Lung Adenocarcinoma

Christopher D. McFarland, D. Petrov, C. Rudin, 2020, Cancer Research.

More efficacious drugs lead to harder selective sweeps in the evolution of drug resistance in HIV-1

D. Petrov, R. Shafer, S. Rhee, 2015, bioRxiv.

Spatiotemporal patterns of desiccation tolerance in natural populations of Drosophila melanogaster

D. Petrov, P. Schmidt, A. Gibbs, 2016, bioRxiv.

Antigenic diversity in malaria parasites is maintained on extrachromosomal DNA

Bernard Y. Kim, D. Petrov, Marina McDew-White, 2023, bioRxiv.

Empowering conservation practice with efficient and economical genotyping from poor quality samples

Nathan K. Truelove, Ryan W Taylor, D. Petrov, 2019, Methods in ecology and evolution.

Empowering conservation practice with efficient and economical genotyping from poor quality samples using mPCRseq

Uma Ramakrishnan, Elizabeth A. Hadly, Meghana Natesh, 2018, bioRxiv.

A multiplexed in vivo approach to identify driver genes in small cell lung cancer

D. Petrov, M. van de Rijn, J. Sage, 2022, bioRxiv.

Decision letter: Global epistasis emerges from a generic model of a complex trait

Joachim Krug, Kristina Crona, Dmitri A Petrov, 2021 .

Unraveling the Genomic Diversity and Evolutionary History of Captive Tigers in the United States

Joseph K. Pickrell, Bernard Y. Kim, D. Petrov, 2023, bioRxiv.

Pervasive adaptation in Plasmodium-interacting proteins in mammals

D. Petrov, D. Enard, N. Telis, 2016, bioRxiv.

Exploiting selection at linked sites to infer the rate and strength of adaptation

Lawrence H. Uricchio, D. Petrov, D. Enard, 2018, bioRxiv.

Minor shift in background substitutional patterns in the Drosophila saltans and willistoni lineages is insufficient to explain GC content of coding sequences.

D. Petrov, E. Rugarli, P. Arndt, 2006, BMC biology.

Seasonally fluctuating selection can maintain polymorphism at many loci via segregation lift

Meike J. Wittmann, M. Feldman, D. Petrov, 2017, Proceedings of the National Academy of Sciences.

Cancers adapt to their mutational load by buffering protein misfolding stress

D. Petrov, C. Curtis, J. Frydman, 2023, bioRxiv.

Extreme Sensitivity of Fitness to Environmental Conditions: Lessons from #1BigBatch

D. Petrov, Grant Kinsler, Kara Schmidlin, 2022, bioRxiv.

Triple-ligation strategy with advantages over directional cloning.

D. Petrov, M. Siegal, D. De Aguiar, 1996, BioTechniques.

Correction: Highly contiguous assemblies of 101 drosophilid genomes

Danny E. Miller, Bernard Y. Kim, D. Petrov, 2022, eLife.

Characterization of bacteriophage P1 library containing inserts of Drosophila DNA of 75–100 kilobase pairs

D. Petrov, D. Hartl, D. Smoller, 1991, Chromosoma.

Minor shift in background substitutional patterns in the Drosophila saltans and willistoni lineages is insufficient to explain GC content of coding sequences

D. Petrov, P. Arndt, Nadia D Singh, 2006 .

In Vitro Reconstitution and Analysis of SARS-CoV-2/Host Protein–Protein Interactions

D. Petrov, Yuehua Wu, K. Alexandrov, 2023, ACS omega.

Dmitri Petrov genomes Drosophila estimates of positive selection in the 12 High sensitivity to aligner and high rate of false positives in the Material

D. Petrov, P. Markova-Raina, 2011 .

Seasonally fluctuating selection can maintain polymorphism at many loci via segregation lift

Meike J. Wittmann, M. Feldman, D. Petrov, 2017, Proceedings of the National Academy of Sciences.

Segregation lift: A general mechanism for the maintenance of polygenic variation under seasonally fluctuating selection

Meike J. Wittmann, M. Feldman, D. Petrov, 2017, bioRxiv.

Oncogenic context shapes the fitness landscape of tumor suppression

D. Petrov, K. Politi, A. Chenchik, 2022, bioRxiv.

Transposable elements in clonal lineages: lethal hangover from sex

D. Petrov, S. Nuzhdin, H. Loxdale, 2003 .

Publisher Correction: Human–chimpanzee fused cells reveal cis-regulatory divergence underlying skeletal evolution

Hunter B. Fraser, D. Petrov, N. Ahituv, 2021, Nature genetics.