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List of works by Matthew W Hahn

"Reverse ecology" and the power of population genomics

scientific article

A Three-Sample Test for Introgression

scientific article published on 01 December 2019

A complex suite of forces drives gene traffic from Drosophila X chromosomes.

scientific article

A multispecies coalescent model for quantitative traits

scientific article published on 14 August 2018

A new class of metrics for learning on real-valued and structured data

scientific article published in 2019

AGOUTI: improving genome assembly and annotation using transcriptome data

scientific article

Abundant genetic variation in transcript level during early Drosophila development

scientific article published on November 2008

Accelerated rate of gene gain and loss in primates

scientific article

Adaptive evolution of young gene duplicates in mammals.

scientific article published on May 2009

All human-specific gene losses are present in the genome as pseudogenes

scientific article

Ancient and recent positive selection transformed opioid cis-regulation in humans

scientific article

Association mapping desiccation resistance within chromosomal inversions in the African malaria vector Anopheles gambiae

scientific article published on 22 October 2018

Author Correction: Comparative and demographic analysis of orang-utan genomes

correction of a scholarly article

Bias in phylogenetic tree reconciliation methods: implications for vertebrate genome evolution

scientific article published on January 2007

CAFE 5 models variation in evolutionary rates among gene families

scientific article published on 16 December 2020

COMPUTATIONAL APPROACHES TO UNDERSTANDING THE EVOLUTION OF MOLECULAR FUNCTION.

scientific article published in January 2017

Clonal polymorphism and high heterozygosity in the celibate genome of the Amazon molly

scientific article published on 12 February 2018

Coding sequence divergence between two closely related plant species: Arabidopsis thaliana and Brassica rapa ssp. pekinensis

scientific article

Comparative analysis of the domestic cat genome reveals genetic signatures underlying feline biology and domestication

scientific article

Comparative and demographic analysis of orang-utan genomes

scientific article

Comparative genomics of centrality and essentiality in three eukaryotic protein-interaction networks

scientific article published on 22 December 2004

Convergent evolution of the genomes of marine mammals

scientific article published on 26 January 2015

Detecting highly differentiated copy-number variants from pooled population sequencing.

scientific article published on January 2013

Detecting natural selection on cis-regulatory DNA.

scientific article published on 6 September 2006

Detection and Polarization of Introgression in a Five-Taxon Phylogeny

scientific article published on 17 April 2015

Determining the Null Model for Detecting Adaptive Convergence from Genomic Data: A Case Study using Echolocating Mammals

scientific article

Determining the probability of hemiplasy in the presence of incomplete lineage sorting and introgression

scientific article published on 21 December 2020

Differential gene expression in incipient species of Anopheles gambiae

scientific article published on 21 April 2008

Discovery of functional elements in 12 Drosophila genomes using evolutionary signatures

scientific article

Disentangling the effects of demography and selection in human history

scientific article

Dissecting the basis of novel trait evolution in a radiation with widespread phylogenetic discordance

scientific article published on 28 June 2018

Distinguishing among evolutionary models for the maintenance of gene duplicates

scientific article

Distinguishing between selection and population expansion in an experimental lineage of bacteriophage T7.

scientific article

Divergent transcriptional response to thermal stress by Anopheles gambiae larvae carrying alternative arrangements of inversion 2La

scientific article published on 03 May 2011

Does a complex life cycle affect adaptation to environmental change? Genome-informed insights for characterizing selection across complex life cycle

scientific article published on 01 December 2021

Drift as a mechanism for cultural change: an example from baby names.

scientific article

Ecological genomics of Anopheles gambiae along a latitudinal cline: a population-resequencing approach

scientific article published on 29 December 2011

Erratum to: Genus-wide characterization of bumblebee genomes provides insights into their evolution and variation in ecological and behavioral traits

scientific article published on 20 May 2021

Estimating Gene Gain and Loss Rates in the Presence of Error in Genome Assembly and Annotation Using CAFE 3 ⬇️

scientific article published on May 24, 2013

Estimating the tempo and mode of gene family evolution from comparative genomic data

scientific article

Evaluating methods to visualize patterns of genetic differentiation on a landscape.

scientific article published on 28 December 2017

Evolution of genes and genomes on the Drosophila phylogeny

scientific article

Evolutionary and Biomedical Insights from the Rhesus Macaque Genome

scientific article

Evolutionary genomics: codon bias and selection on single genomes.

scientific article published in January 2005

Evolutionary superscaffolding and chromosome anchoring to improve Anopheles genome assemblies

scientific article published on 02 January 2020

Extensive error in the number of genes inferred from draft genome assemblies

scientific article

Female-biased gene expression in the malaria mosquito Anopheles gambiae

scientific article published in March 2005

Gain and loss of phosphorylation sites in human cancer

scientific article published in August 2008

Gene Tree Discordance Can Generate Patterns of Diminishing Convergence over Time

scientific article published on 15 September 2016

Gene Tree Discordance Causes Apparent Substitution Rate Variation

scientific article

Gene content evolution in the arthropods

scientific article published on 23 January 2020

Gene conversion among paralogs results in moderate false detection of positive selection using likelihood methods

scientific article published on 27 May 2009

Gene copy-number polymorphism caused by retrotransposition in humans

scientific article

Gene copy-number polymorphism in nature.

scientific article published on 30 June 2010

Gene expression divergence between malaria vector sibling species Anopheles gambiae and An. coluzzii from rural and urban Yaoundé Cameroon.

scientific article

Gene family evolution across 12 Drosophila genomes

scientific article

Gene-tree reconciliation with MUL-trees to resolve polyploidy events

scientific article published on 13 April 2017

Genome-Wide Estimates of Transposable Element Insertion and Deletion Rates in Drosophila Melanogaster

scientific article

Genome-wide analysis of retrogene polymorphisms in Drosophila melanogaster

scientific article published on December 2011

Genome-wide patterns of regulatory divergence revealed by introgression lines

scientific article published on 4 February 2016

Genomic evidence of gene flow during reinforcement in Texas Phlox.

scientific article published on 31 January 2017

Genomic islands of speciation in Anopheles gambiae

scientific article

Genomic islands of speciation or genomic islands and speciation?

scientific article published in March 2010

Genomic variation in natural populations of Drosophila melanogaster

scientific article published on 5 June 2012

Genus-wide characterization of bumblebee genomes provides insights into their evolution and variation in ecological and behavioral traits

scientific article published on 18 September 2020

Gibbon genome and the fast karyotype evolution of small apes

scientific article

How reticulated are species?

scientific article published on 28 December 2015

Identifying parent-daughter relationships among duplicated genes

scientific article published on 01 January 2009

Inferring the Genetic Basis of Sex Determination from the Genome of a Dioecious Nightshade

scientific article published on 01 June 2021

Inferring the History of Interchromosomal Gene Transposition in Drosophila Using n-Dimensional Parsimony ⬇️

scientific article published on November 17, 2011

Interlocus gene conversion events introduce deleterious mutations into at least 1% of human genes associated with inherited disease

scientific article published on 16 November 2011

Irrational exuberance for resolved species trees

scientific article published on 7 December 2015

Leveraging evolutionary relationships to improve Anopheles genome assemblies

Localization of candidate regions maintaining a common polymorphic inversion (2La) in Anopheles gambiae

scientific article

Locus- and population-specific selection and differentiation between incipient species of Anopheles gambiae

scientific article published on 17 July 2007

Lower linkage disequilibrium at CNVs is due to both recurrent mutation and transposing duplications

scientific article

Minimal effect of ectopic gene conversion among recent duplicates in four mammalian genomes.

scientific article published on 23 March 2009

Molecular evolution in large genetic networks: does connectivity equal constraint?

scientific article published in February 2004

Molecular mechanisms of postmating prezygotic reproductive isolation uncovered by transcriptome analysis

scientific article published on 2 May 2016

More accurate phylogenies inferred from low-recombination regions in the presence of incomplete lineage sorting

scientific article published on 19 April 2013

Mosquito genomics. Extensive introgression in a malaria vector species complex revealed by phylogenomics

scientific article

Mosquito genomics. Highly evolvable malaria vectors: the genomes of 16 Anopheles mosquitoes

scientific article published on 27 November 2014

Multinucleotide mutations cause false inferences of lineage-specific positive selection.

scientific article

Natural diversity of the malaria vector Anopheles gambiae

scholarly article by Alistair Miles et al published 22 December 2016 in bioRxiv

New Approaches for Inferring Phylogenies in the Presence of Paralogs

scientific article published on 10 September 2020

New methods to calculate concordance factors for phylogenomic datasets

article published in 2018

New methods to calculate concordance factors for phylogenomic datasets

scientific article published on 04 May 2020

No evidence for biased co-transmission of speciation islands in Anopheles gambiae.

scientific article published on February 2012

No excess gene movement is detected off the avian or lepidopteran Z chromosome

scientific article published on 24 October 2011

Nonallelic gene conversion in the genus Drosophila

scientific article

Noncoding sequences near duplicated genes evolve rapidly

scientific article

Origins and long-term patterns of copy-number variation in rhesus macaques

scientific article published on 23 November 2020

Parallel Evolution of Copy-Number Variation across Continents in Drosophila melanogaster

scientific article published on 25 January 2016

Paternal age in rhesus macaques is positively associated with germline mutation accumulation but not with measures of offspring sociability

scientific article published on 27 May 2020

Patterns of transposable element variation and clinality in Drosophila

scientific article published on 11 January 2019

Pervasive Multinucleotide Mutational Events in Eukaryotes ⬇️

scientific article published on June 21, 2011

Phylogenomics Reveals Three Sources of Adaptive Variation during a Rapid Radiation

scientific article

Population genetic and phylogenetic evidence for positive selection on regulatory mutations at the factor VII locus in humans

scientific article

Population genomics: whole-genome analysis of polymorphism and divergence in Drosophila simulans

scientific article

Positive Selection on a Human-Specific Transcription Factor Binding Site Regulating IL4 Expression

scientific article published on 01 December 2003

Positive selection on MMP3 regulation has shaped heart disease risk

scientific article

Powerful methods for detecting introgressed regions from population genomic data

scientific article

Primate phylogenomics uncovers multiple rapid radiations and ancient interspecific introgression

scientific article published on 03 December 2020

Proceedings of the SMBE Tri-National Young Investigators' Workshop 2005. Accurate inference and estimation in population genomics

scientific article

Proteomic evidence for in-frame and out-of-frame alternatively spliced isoforms in human and mouse

scientific article published on 18 September 2015

Quantifying the risk of hemiplasy in phylogenetic inference

article published in the Proceedings of the National Academy of Sciences of the United States of America

Radiation with reticulation marks the origin of a major malaria vector

scientific article published on 01 December 2020

Radical remodeling of the Y chromosome in a recent radiation of malaria mosquitoes

scientific article published on 29 March 2016

Random drift and culture change

article

Random drift and large shifts in popularity of dog breeds

scientific article published in 2004

Rates and Genomic Consequences of Spontaneous Mutational Events inDrosophila melanogaster ⬇️

scientific article published on 03 June 2013

Reanalysis suggests that genomic islands of speciation are due to reduced diversity, not reduced gene flow

scientific article

Referee: Reference Assembly Quality Scores

scientific article published on 01 May 2019

Regular rates of popular culture change reflect random copying

article

Reproductive Longevity Predicts Mutation Rates in Primates

scientific article published on 27 September 2018

Reticulate evolutionary history and extensive introgression in mosquito species revealed by phylogenetic network analysis

scientific article published on 25 January 2016

Retrogenes reveal the direction of sex-chromosome evolution in mosquitoes

scientific article

Revisiting classic clines in Drosophila melanogaster in the age of genomics

scientific article published on 10 June 2015

Sequencing, assembling, and correcting draft genomes using recombinant populations

scientific article

Sex chromosomes evolved from independent ancestral linkage groups in winged insects

scientific article published on 16 January 2012

Sex determination: why so many ways of doing it?

scientific article

Similar Efficacies of Selection Shape Mitochondrial and Nuclear Genes in Both Drosophila melanogaster and Homo sapiens

scientific article

Soft shoulders ahead: spurious signatures of soft and partial selective sweeps result from linked hard sweeps

scientific article published on 25 February 2015

Sooty mangabey genome sequence provides insight into AIDS resistance in a natural SIV host

scientific article published in January 2018

Speciation as a sieve for ancestral polymorphism.

scientific article

Speciation genes are more likely to have discordant gene trees

article

Systems genetic analysis of inversion polymorphisms in the malaria mosquito

article published in the Proceedings of the National Academy of Sciences of the United States of America

Testing the Ortholog Conjecture with Comparative Functional Genomic Data from Mammals ⬇️

scientific article published on June 9, 2011

The Effects of Increasing the Number of Taxa on Inferences of Molecular Convergence

scientific article published on 04 January 2017

The Genomic Basis of Arthropod Diversity

article published in 2018

The Neutral Theory in Light of Natural Selection

scientific article published on 01 June 2018

The Potential for a Released Autosomal X-Shredder Becoming a Driving-Y Chromosome and Invasively Suppressing Wild Populations of Malaria Mosquitoes

scientific article published on 03 December 2021

The Timing and Direction of Introgression Under the Multispecies Network Coalescent

scientific article published on 22 January 2019

The comparative genomics and complex population history of baboons

scientific article published on 30 January 2019

The contribution of gene movement to the "two rules of speciation".

scientific article

The effects of introgression across thousands of quantitative traits revealed by gene expression in wild tomatoes

scientific article published in 2021

The effects of selection against spurious transcription factor binding sites

scientific article published on 25 April 2003

The evolution of mammalian gene families

scientific article published in 2006

The evolution of the Anopheles 16 genomes project

scientific article published on 08 July 2013

The evolution of transcriptional regulation in eukaryotes

scientific article (publication date: September 2003)

The fixation of malaria refractoriness in mosquitoes

scientific article published in April 2004

The g-value paradox

scientific article published on 01 March 2002

The genome of the vervet (Chlorocebus aethiops sabaeus)

scientific article published on 16 September 2015

The human mutation rate is increasing, even as it slows

scientific article published on 6 November 2013

The life and death of gene families

scientific article

The limited contribution of reciprocal gene loss to increased speciation rates following whole-genome duplication.

scientific article

The ortholog conjecture revisited: the value of orthologs and paralogs in function prediction

scientific article published on 01 July 2020

The perils of intralocus recombination for inferences of molecular convergence

scientific article published on 03 June 2019

The sequencing and interpretation of the genome obtained from a Serbian individual

scientific article published in PLoS ONE

The strength of transcription-factor binding modulates co-variation in transcriptional networks

scientific article

Three new genome assemblies support a rapid radiation in Musa acuminata (wild banana)

article

Toward a selection theory of molecular evolution

scientific article

Transcriptomic analysis links gene expression to unilateral pollen-pistil reproductive barriers

scientific article

Very Few RNA and DNA Sequence Differences in the Human Transcriptome ⬇️

scientific article published on October 12, 2011

Very low rate of gene conversion in the yeast genome

scientific article published on 27 July 2012

Why Concatenation Fails Near the Anomaly Zone

scientific article

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