Matthew W Hahn

Matthew W Hahn

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Matthew W Hahn

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A three-sample test for introgression.

Mol Biol Evol 2019 Aug 2. Epub 2019 Aug 2.

Department of Biology, Indiana University.

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http://dx.doi.org/10.1093/molbev/msz178DOI Listing
August 2019

The perils of intralocus recombination for inferences of molecular convergence.

Philos Trans R Soc Lond B Biol Sci 2019 Jul 3;374(1777):20180244. Epub 2019 Jun 3.

2 Department of Biology, Indiana University , Bloomington, IN 47405 , USA.

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http://dx.doi.org/10.1098/rstb.2018.0244DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6560264PMC
July 2019

Proteomic Evidence for In-Frame and Out-of-Frame Alternatively Spliced Isoforms in Human and Mouse.

IEEE/ACM Trans Comput Biol Bioinform 2018 Jul-Aug;15(4):1284-1289. Epub 2015 Sep 18.

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http://dx.doi.org/10.1109/TCBB.2015.2480068DOI Listing
May 2019

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

PLoS One 2018 19;13(12):e0208901. Epub 2018 Dec 19.

College of Computer and Information Science, Northeastern University, Boston, Massachusetts, United States of America.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0208901PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6300249PMC
May 2019

Referee: Reference Assembly Quality Scores.

Genome Biol Evol 2019 05;11(5):1483-1486

Department of Biology, Indiana University, Bloomington.

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http://dx.doi.org/10.1093/gbe/evz088DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6535810PMC
May 2019

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

Mol Ecol 2019 03 22;28(6):1333-1342. Epub 2018 Oct 22.

Eck Institute for Global Health and Department of Biological Sciences, University of Notre Dame, Notre Dame, Indiana.

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http://dx.doi.org/10.1111/mec.14880DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6433559PMC
March 2019

Patterns of transposable element variation and clinality in Drosophila.

Mol Ecol 2019 03 11;28(6):1523-1536. Epub 2019 Jan 11.

Department of Biology, Indiana University, Bloomington, Indiana.

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https://onlinelibrary.wiley.com/doi/abs/10.1111/mec.14961
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http://dx.doi.org/10.1111/mec.14961DOI Listing
March 2019

The Timing and Direction of Introgression Under the Multispecies Network Coalescent.

Genetics 2019 03 22;211(3):1059-1073. Epub 2019 Jan 22.

Department of Biology, Indiana University, Bloomington, Indiana 47405.

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http://dx.doi.org/10.1534/genetics.118.301831DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6404246PMC
March 2019

Quantifying the risk of hemiplasy in phylogenetic inference.

Proc Natl Acad Sci U S A 2018 12 27;115(50):12787-12792. Epub 2018 Nov 27.

Department of Biology, Indiana University, Bloomington, IN 47405.

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http://dx.doi.org/10.1073/pnas.1811268115DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6294915PMC
December 2018

Reproductive Longevity Predicts Mutation Rates in Primates.

Curr Biol 2018 10 27;28(19):3193-3197.e5. Epub 2018 Sep 27.

Department of Biology, Indiana University, 107 S. Indiana Avenue, Bloomington, IN 47405, USA; Department of Computer Science, Indiana University, 107 S. Indiana Avenue, Bloomington, IN 47405, USA. Electronic address:

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https://linkinghub.elsevier.com/retrieve/pii/S09609822183113
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http://dx.doi.org/10.1016/j.cub.2018.08.050DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6177314PMC
October 2018

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

Nat Ecol Evol 2018 08 2;2(8):1280-1288. Epub 2018 Jul 2.

Department of Human Genetics, University of Chicago, Chicago, IL, USA.

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http://dx.doi.org/10.1038/s41559-018-0584-5DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6093625PMC
August 2018

A multispecies coalescent model for quantitative traits.

Elife 2018 08 14;7. Epub 2018 Aug 14.

Department of Biology, Indiana University, Bloomington, United States.

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http://dx.doi.org/10.7554/eLife.36482DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6092125PMC
August 2018

Speciation genes are more likely to have discordant gene trees.

Evol Lett 2018 Aug 8;2(4):281-296. Epub 2018 Aug 8.

Department of Biology Indiana University Bloomington Indiana.

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http://dx.doi.org/10.1002/evl3.77DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6121824PMC
August 2018

Systems genetic analysis of inversion polymorphisms in the malaria mosquito .

Proc Natl Acad Sci U S A 2018 07 9;115(30):E7005-E7014. Epub 2018 Jul 9.

Eck Institute for Global Health, University of Notre Dame, Notre Dame, IN 46556;

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http://dx.doi.org/10.1073/pnas.1806760115DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6064990PMC
July 2018

The Neutral Theory in Light of Natural Selection.

Mol Biol Evol 2018 06;35(6):1366-1371

Department of Biology and Department of Computer Science, Indiana University Bloomington, IN.

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http://dx.doi.org/10.1093/molbev/msy092DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5967545PMC
June 2018

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

Mol Ecol 2018 Jun 28. Epub 2018 Jun 28.

Department of Biology, Indiana University, Bloomington, Indiana.

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http://dx.doi.org/10.1111/mec.14780DOI Listing
June 2018

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

Mol Ecol Resour 2018 May 18;18(3):448-460. Epub 2018 Jan 18.

Indiana University Bloomington, Bloomington, IN, USA.

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http://dx.doi.org/10.1111/1755-0998.12747DOI Listing
May 2018

Why Concatenation Fails Near the Anomaly Zone.

Syst Biol 2018 Jan;67(1):158-169

Department of Biology, Indiana University, Bloomington, IN 47405, USA.

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http://dx.doi.org/10.1093/sysbio/syx063DOI Listing
January 2018

Gene-Tree Reconciliation with MUL-Trees to Resolve Polyploidy Events.

Syst Biol 2017 Nov;66(6):1007-1018

Department of Biology and School of Informatics and Computing, Indiana University, Bloomington, IN 47405, USA.

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http://dx.doi.org/10.1093/sysbio/syx044DOI Listing
November 2017

Speciation as a sieve for ancestral polymorphism.

Mol Ecol 2017 Oct 8;26(20):5362-5368. Epub 2017 Sep 8.

Department of Biology, Indiana University, Bloomington, IN, USA.

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http://dx.doi.org/10.1111/mec.14290DOI Listing
October 2017

COMPUTATIONAL APPROACHES TO UNDERSTANDING THE EVOLUTION OF MOLECULAR FUNCTION.

Pac Symp Biocomput 2017 ;22:1-2

Department of Biochemistry and Microbiology, Rutgers University, New Brunswick, New Jersey, USA.

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http://dx.doi.org/10.1142/9789813207813_0001DOI Listing
July 2017

Genomic evidence of gene flow during reinforcement in Texas Phlox.

Mol Ecol 2017 Apr 6;26(8):2317-2330. Epub 2017 Mar 6.

Department of Organismic and Evolutionary Biology, The Arnold Arboretum of Harvard University, 1300 Centre Street, Boston, MA, 02131, USA.

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http://dx.doi.org/10.1111/mec.14041DOI Listing
April 2017

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

BMC Plant Biol 2017 04 24;17(1):81. Epub 2017 Apr 24.

Department of Biology, Colorado State University, Fort Collins, CO, 80523-1878, USA.

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http://dx.doi.org/10.1186/s12870-017-1032-4DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5402651PMC
April 2017

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

Genome Biol Evol 2017 01;9(1):213-221

Department of Life Science, Research Center for Biomolecules and Biosystems, Chung-Ang University, Seoul, Republic of Korea.

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http://dx.doi.org/10.1093/gbe/evw306DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5381636PMC
January 2017

Gene Tree Discordance Can Generate Patterns of Diminishing Convergence over Time.

Mol Biol Evol 2016 12 15;33(12):3299-3307. Epub 2016 Sep 15.

Department of Biology, Indiana University, Bloomington, IN.

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http://dx.doi.org/10.1093/molbev/msw197DOI Listing
December 2016

Gene Tree Discordance Causes Apparent Substitution Rate Variation.

Syst Biol 2016 Jul 28;65(4):711-21. Epub 2016 Feb 28.

Department of Biology and School of Informatics and Computing, Indiana University, Bloomington, IN 47405, USA.

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http://dx.doi.org/10.1093/sysbio/syw018DOI Listing
July 2016

AGOUTI: improving genome assembly and annotation using transcriptome data.

Gigascience 2016 07 19;5(1):31. Epub 2016 Jul 19.

School of Informatics and Computing, Indiana University, Bloomington, IN, 47405, USA.

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http://dx.doi.org/10.1186/s13742-016-0136-3DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4952227PMC
July 2016

Powerful methods for detecting introgressed regions from population genomic data.

Mol Ecol 2016 Jun 31;25(11):2387-97. Epub 2016 Mar 31.

School of Informatics and Computing, Indiana University, Bloomington, IN, 47405, USA.

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http://dx.doi.org/10.1111/mec.13610DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4899106PMC
June 2016

Molecular mechanisms of postmating prezygotic reproductive isolation uncovered by transcriptome analysis.

Mol Ecol 2016 Jun 30;25(11):2592-608. Epub 2016 May 30.

Department of Biology, Indiana University, 1001 East Third Street, Bloomington, IN, 47405, USA.

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http://dx.doi.org/10.1111/mec.13679DOI Listing
June 2016

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

Mol Biol Evol 2016 05 25;33(5):1308-16. Epub 2016 Jan 25.

Department of Evolution and Ecology, University of California, Davis.

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http://dx.doi.org/10.1093/molbev/msw014DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4909135PMC
May 2016

Genome-wide patterns of regulatory divergence revealed by introgression lines.

Evolution 2016 Mar 24;70(3):696-706. Epub 2016 Feb 24.

Department of Biology, Indiana University, Bloomington, Indiana, 47405.

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http://dx.doi.org/10.1111/evo.12875DOI Listing
March 2016

How reticulated are species?

Bioessays 2016 Feb 28;38(2):140-9. Epub 2015 Dec 28.

Department of Biology and School of Informatics and Computing, Indiana University, Bloomington, IN, USA.

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http://dx.doi.org/10.1002/bies.201500149DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4813508PMC
February 2016

Phylogenomics Reveals Three Sources of Adaptive Variation during a Rapid Radiation.

PLoS Biol 2016 02 12;14(2):e1002379. Epub 2016 Feb 12.

Department of Biology, Indiana University, Bloomington, Indiana, United States of America.

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http://dx.doi.org/10.1371/journal.pbio.1002379DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4752443PMC
February 2016

Irrational exuberance for resolved species trees.

Evolution 2016 Jan 17;70(1):7-17. Epub 2015 Dec 17.

Department of Computer Science, Rice University, Houston, Texas, 77005.

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http://dx.doi.org/10.1111/evo.12832DOI Listing
January 2016

Revisiting classic clines in Drosophila melanogaster in the age of genomics.

Trends Genet 2015 Aug 10;31(8):434-44. Epub 2015 Jun 10.

Center for Population Biology, University of California, Davis, CA 95616, USA; Department of Evolution and Ecology, University of California, Davis, CA 95616, USA. Electronic address:

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http://www.cell.com/trends/genetics/pdf/S0168-9525(15)00095-
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http://linkinghub.elsevier.com/retrieve/pii/S016895251500095
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http://dx.doi.org/10.1016/j.tig.2015.05.006DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4526433PMC
August 2015

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

G3 (Bethesda) 2015 Aug 21;5(10):2165-76. Epub 2015 Aug 21.

Department of Biology, Indiana University, Bloomington, Indiana 47405

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http://dx.doi.org/10.1534/g3.114.016493DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4592998PMC
August 2015

Detection and Polarization of Introgression in a Five-Taxon Phylogeny.

Syst Biol 2015 Jul 17;64(4):651-62. Epub 2015 Apr 17.

Department of Biology, Indiana University, 1001 E. Third St., Bloomington, IN 47405, USA and School of Informatics and Computing, Indiana University, Bloomington, IN 47405, USA Department of Biology, Indiana University, 1001 E. Third St., Bloomington, IN 47405, USA and School of Informatics and Computing, Indiana University, Bloomington, IN 47405, USA.

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http://dx.doi.org/10.1093/sysbio/syv023DOI Listing
July 2015

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

Mol Biol Evol 2015 May 27;32(5):1232-6. Epub 2015 Jan 27.

School of Informatics and Computing, Indiana University, Bloomington Department of Biology, Indiana University, Bloomington

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http://dx.doi.org/10.1093/molbev/msv013DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4408409PMC
May 2015

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

Genetics 2015 May 25;200(1):267-84. Epub 2015 Feb 25.

Department of Genetics, Rutgers University, Piscataway, New Jersey 08854 Human Genetics Institute of New Jersey, Piscataway, New Jersey 08854.

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http://www.genetics.org/cgi/doi/10.1534/genetics.115.174912
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http://dx.doi.org/10.1534/genetics.115.174912DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4423368PMC
May 2015

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

Authors:
Daniel E Neafsey Robert M Waterhouse Mohammad R Abai Sergey S Aganezov Max A Alekseyev James E Allen James Amon Bruno Arcà Peter Arensburger Gleb Artemov Lauren A Assour Hamidreza Basseri Aaron Berlin Bruce W Birren Stephanie A Blandin Andrew I Brockman Thomas R Burkot Austin Burt Clara S Chan Cedric Chauve Joanna C Chiu Mikkel Christensen Carlo Costantini Victoria L M Davidson Elena Deligianni Tania Dottorini Vicky Dritsou Stacey B Gabriel Wamdaogo M Guelbeogo Andrew B Hall Mira V Han Thaung Hlaing Daniel S T Hughes Adam M Jenkins Xiaofang Jiang Irwin Jungreis Evdoxia G Kakani Maryam Kamali Petri Kemppainen Ryan C Kennedy Ioannis K Kirmitzoglou Lizette L Koekemoer Njoroge Laban Nicholas Langridge Mara K N Lawniczak Manolis Lirakis Neil F Lobo Ernesto Lowy Robert M MacCallum Chunhong Mao Gareth Maslen Charles Mbogo Jenny McCarthy Kristin Michel Sara N Mitchell Wendy Moore Katherine A Murphy Anastasia N Naumenko Tony Nolan Eva M Novoa Samantha O'Loughlin Chioma Oringanje Mohammad A Oshaghi Nazzy Pakpour Philippos A Papathanos Ashley N Peery Michael Povelones Anil Prakash David P Price Ashok Rajaraman Lisa J Reimer David C Rinker Antonis Rokas Tanya L Russell N'Fale Sagnon Maria V Sharakhova Terrance Shea Felipe A Simão Frederic Simard Michel A Slotman Pradya Somboon Vladimir Stegniy Claudio J Struchiner Gregg W C Thomas Marta Tojo Pantelis Topalis José M C Tubio Maria F Unger John Vontas Catherine Walton Craig S Wilding Judith H Willis Yi-Chieh Wu Guiyun Yan Evgeny M Zdobnov Xiaofan Zhou Flaminia Catteruccia George K Christophides Frank H Collins Robert S Cornman Andrea Crisanti Martin J Donnelly Scott J Emrich Michael C Fontaine William Gelbart Matthew W Hahn Immo A Hansen Paul I Howell Fotis C Kafatos Manolis Kellis Daniel Lawson Christos Louis Shirley Luckhart Marc A T Muskavitch José M Ribeiro Michael A Riehle Igor V Sharakhov Zhijian Tu Laurence J Zwiebel Nora J Besansky

Science 2015 Jan 27;347(6217):1258522. Epub 2014 Nov 27.

Eck Institute for Global Health and Department of Biological Sciences, University of Notre Dame, 317 Galvin Life Sciences Building, Notre Dame, IN 46556, USA.

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http://dx.doi.org/10.1126/science.1258522DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4380271PMC
January 2015

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

Am Nat 2015 Jan 26;185(1):70-86. Epub 2014 Nov 26.

Department of Biology, Indiana University, Bloomington, Indiana.

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http://dx.doi.org/10.1086/679108DOI Listing
January 2015

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

PLoS Comput Biol 2014 Dec 4;10(12):e1003998. Epub 2014 Dec 4.

School of Informatics and Computing, Indiana University, Bloomington, Indiana; Department of Biology, Indiana University, Bloomington, Indiana.

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http://dx.doi.org/10.1371/journal.pcbi.1003998DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4256071PMC
December 2014

Gibbon genome and the fast karyotype evolution of small apes.

Nature 2014 Sep;513(7517):195-201

Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, Texas 77030, USA.

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http://dx.doi.org/10.1038/nature13679DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4249732PMC
September 2014

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

Mol Ecol 2014 07 17;23(13):3133-57. Epub 2014 Jun 17.

Department of Biology, Indiana University, Bloomington, IN, 47405, USA.

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http://doi.wiley.com/10.1111/mec.12796
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http://dx.doi.org/10.1111/mec.12796DOI Listing
July 2014

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

Mol Ecol 2014 May 11;23(9):2242-59. Epub 2014 Apr 11.

Eck Institute for Global Health & Department of Biological Sciences, University of Notre Dame, Notre Dame, IN, 46556-0369, USA.

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http://dx.doi.org/10.1111/mec.12733DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4034741PMC
May 2014

Sequencing, assembling, and correcting draft genomes using recombinant populations.

G3 (Bethesda) 2014 Apr 16;4(4):669-79. Epub 2014 Apr 16.

Department of Biology, Indiana University, Bloomington, Indiana 47405.

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http://dx.doi.org/10.1534/g3.114.010264DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4059239PMC
April 2014

The human mutation rate is increasing, even as it slows.

Mol Biol Evol 2014 Feb 6;31(2):253-7. Epub 2013 Nov 6.

School of Informatics and Computing, Indiana University.

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http://dx.doi.org/10.1093/molbev/mst218DOI Listing
February 2014

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

Pac Symp Biocomput 2013 :344-55

Department of Biology and School of Informatics and Computing, Indiana University, 1001 E Third St., Bloomington, IN 47405, USA.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3587772PMC
December 2013

Estimating gene gain and loss rates in the presence of error in genome assembly and annotation using CAFE 3.

Mol Biol Evol 2013 Aug 24;30(8):1987-97. Epub 2013 May 24.

National Evolutionary Synthesis Center, Durham, North Carolina, USA.

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http://dx.doi.org/10.1093/molbev/mst100DOI Listing
August 2013

Rates and genomic consequences of spontaneous mutational events in Drosophila melanogaster.

Genetics 2013 Aug 3;194(4):937-54. Epub 2013 Jun 3.

Department of Biology, Indiana University, Bloomington, IN 47405, USA.

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http://dx.doi.org/10.1534/genetics.113.151670DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3730921PMC
August 2013

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

Evolution 2013 Aug 19;67(8):2376-84. Epub 2013 Apr 19.

Department of Biology, Indiana University, Bloomington, Indiana 47405, USA.

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http://dx.doi.org/10.1111/evo.12118DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3929462PMC
August 2013

Very low rate of gene conversion in the yeast genome.

Mol Biol Evol 2012 Dec 27;29(12):3817-26. Epub 2012 Jul 27.

Department of Biology, Indiana University, USA.

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http://dx.doi.org/10.1093/molbev/mss192DOI Listing
December 2012

Sex chromosomes evolved from independent ancestral linkage groups in winged insects.

Mol Biol Evol 2012 Jun 16;29(6):1645-53. Epub 2012 Jan 16.

Department of Biology, Indiana University, USA.

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http://dx.doi.org/10.1093/molbev/mss010DOI Listing
June 2012

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

Genetics 2012 Apr 29;190(4):1417-32. Epub 2011 Dec 29.

Eck Institute for Global Health, Department of Biological Sciences, University of Notre Dame, Notre Dame, Indiana 46556, USA.

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http://dx.doi.org/10.1534/genetics.111.137794DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3316653PMC
April 2012

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

Genome Biol Evol 2011 24;3:1381-90. Epub 2011 Oct 24.

Department of Biology, Indiana University, IN, USA.

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http://dx.doi.org/10.1093/gbe/evr109DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3242482PMC
March 2012

Inferring the history of interchromosomal gene transposition in Drosophila using n-dimensional parsimony.

Genetics 2012 Feb 17;190(2):813-25. Epub 2011 Nov 17.

Department of Biology and School of Informatics and Computing, Indiana University, Bloomington, Indiana 47405, USA.

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http://dx.doi.org/10.1534/genetics.111.135947DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3276645PMC
February 2012

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

Philos Trans R Soc Lond B Biol Sci 2012 Feb;367(1587):374-84

Department of Biology, Indiana University, Bloomington, IN 47405, USA.

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http://dx.doi.org/10.1098/rstb.2011.0188DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3233708PMC
February 2012

Genome-wide analysis of retrogene polymorphisms in Drosophila melanogaster.

Genome Res 2011 Dec;21(12):2087-95

Department of Biology, Indiana University, Bloomington, Indiana 47405, USA.

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http://dx.doi.org/10.1101/gr.116434.110DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3227099PMC
December 2011

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

Mol Ecol 2011 Jun 3;20(12):2567-80. Epub 2011 May 3.

Department of Biological Sciences, Eck Institute for Global Health, University of Notre Dame, Notre Dame, IN 46556, USA.

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http://dx.doi.org/10.1111/j.1365-294X.2011.05114.xDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3686099PMC
June 2011

Pervasive multinucleotide mutational events in eukaryotes.

Curr Biol 2011 Jun;21(12):1051-4

Department of Biology, Indiana University Bloomington, Bloomington, IN 47405, USA.

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http://dx.doi.org/10.1016/j.cub.2011.05.013DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4744473PMC
June 2011

Testing the ortholog conjecture with comparative functional genomic data from mammals.

PLoS Comput Biol 2011 Jun 9;7(6):e1002073. Epub 2011 Jun 9.

School of Informatics and Computing, Indiana University, Bloomington, Indiana, USA.

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http://dx.doi.org/10.1371/journal.pcbi.1002073DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3111532PMC
June 2011

Comparative and demographic analysis of orang-utan genomes.

Authors:
Devin P Locke LaDeana W Hillier Wesley C Warren Kim C Worley Lynne V Nazareth Donna M Muzny Shiaw-Pyng Yang Zhengyuan Wang Asif T Chinwalla Pat Minx Makedonka Mitreva Lisa Cook Kim D Delehaunty Catrina Fronick Heather Schmidt Lucinda A Fulton Robert S Fulton Joanne O Nelson Vincent Magrini Craig Pohl Tina A Graves Chris Markovic Andy Cree Huyen H Dinh Jennifer Hume Christie L Kovar Gerald R Fowler Gerton Lunter Stephen Meader Andreas Heger Chris P Ponting Tomas Marques-Bonet Can Alkan Lin Chen Ze Cheng Jeffrey M Kidd Evan E Eichler Simon White Stephen Searle Albert J Vilella Yuan Chen Paul Flicek Jian Ma Brian Raney Bernard Suh Richard Burhans Javier Herrero David Haussler Rui Faria Olga Fernando Fleur Darré Domènec Farré Elodie Gazave Meritxell Oliva Arcadi Navarro Roberta Roberto Oronzo Capozzi Nicoletta Archidiacono Giuliano Della Valle Stefania Purgato Mariano Rocchi Miriam K Konkel Jerilyn A Walker Brygg Ullmer Mark A Batzer Arian F A Smit Robert Hubley Claudio Casola Daniel R Schrider Matthew W Hahn Victor Quesada Xose S Puente Gonzalo R Ordoñez Carlos López-Otín Tomas Vinar Brona Brejova Aakrosh Ratan Robert S Harris Webb Miller Carolin Kosiol Heather A Lawson Vikas Taliwal André L Martins Adam Siepel Arindam Roychoudhury Xin Ma Jeremiah Degenhardt Carlos D Bustamante Ryan N Gutenkunst Thomas Mailund Julien Y Dutheil Asger Hobolth Mikkel H Schierup Oliver A Ryder Yuko Yoshinaga Pieter J de Jong George M Weinstock Jeffrey Rogers Elaine R Mardis Richard A Gibbs Richard K Wilson

Nature 2011 Jan;469(7331):529-33

The Genome Center at Washington University, Washington University School of Medicine, 4444 Forest Park Avenue, Saint Louis, Missouri 63108, USA.

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http://dx.doi.org/10.1038/nature09687DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3060778PMC
January 2011

Noncoding sequences near duplicated genes evolve rapidly.

Genome Biol Evol 2010 29;2:518-33. Epub 2010 Jun 29.

Gladstone Institute for Cardiovascular Disease, Gladstone Institutes, University of California-San Francisco, San Francisco, CA, USA.

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http://dx.doi.org/10.1093/gbe/evq037DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2942038PMC
December 2010

Gene copy-number polymorphism in nature.

Proc Biol Sci 2010 Nov 30;277(1698):3213-21. Epub 2010 Jun 30.

Department of Biology and School of Informatics and Computing, Indiana University, Bloomington, IN 47405, USA.

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http://dx.doi.org/10.1098/rspb.2010.1180DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2981937PMC
November 2010

Retrogenes reveal the direction of sex-chromosome evolution in mosquitoes.

Genetics 2010 Oct 26;186(2):763-6. Epub 2010 Jul 26.

School of Informatics and Computing, Indiana University, Bloomington, IN 47405, USA.

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http://dx.doi.org/10.1534/genetics.110.118794DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2954464PMC
October 2010

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

Evolution 2010 Jun 8;64(6):1541-57. Epub 2010 Mar 8.

Department of Biology, Indiana University, 1001 East Third Street, Bloomington, Indiana 47405, USA.

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http://dx.doi.org/10.1111/j.1558-5646.2010.00990.xDOI Listing
June 2010

Nonallelic gene conversion in the genus Drosophila.

Genetics 2010 May 9;185(1):95-103. Epub 2010 Mar 9.

Department of Biology, Indiana University, Bloomington, IN 47405, USA.

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http://dx.doi.org/10.1534/genetics.110.115444DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2870979PMC
May 2010

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

Trends Genet 2010 Feb 18;26(2):51-3. Epub 2010 Jan 18.

University of Southern California, Program in Molecular and Computational Biology, Los Angeles, CA 90089, USA.

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http://dx.doi.org/10.1016/j.tig.2009.12.005DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2826431PMC
February 2010

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

Mol Biol Evol 2010 Jan;27(1):103-11

Department of Biology, Indiana University, Bloomington, IN, USA.

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http://dx.doi.org/10.1093/molbev/msp210DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2877554PMC
January 2010

Distinguishing among evolutionary models for the maintenance of gene duplicates.

Authors:
Matthew W Hahn

J Hered 2009 Sep-Oct;100(5):605-17. Epub 2009 Jul 13.

Department of Biology and School of Informatics, Indiana University, Bloomington, IN 47405, USA.

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http://dx.doi.org/10.1093/jhered/esp047DOI Listing
October 2009

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

J Comput Biol 2009 Oct;16(10):1419-27

Department of Biology and School of Informatics and Computing, Indiana University, Bloomington, IN 47405, USA.

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http://dx.doi.org/10.1089/cmb.2009.0085DOI Listing
October 2009

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

Genome Biol Evol 2009 Jul 7;1:176-88. Epub 2009 Jul 7.

Department of Biology and Graduate Program in Genetics, The Pennsylvania State University, USA.

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http://dx.doi.org/10.1093/gbe/evp018DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2817413PMC
July 2009

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

Genetics 2009 Jun 23;182(2):615-22. Epub 2009 Mar 23.

School of Informatics, Indiana University, Bloomington, IN 47405, USA.

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http://dx.doi.org/10.1534/genetics.109.101428DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2691768PMC
June 2009

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

J Mol Evol 2009 Jun 27;68(6):679-87. Epub 2009 May 27.

Department of Biology and School of Informatics, Indiana University, 1001 E. 3rd Street, Bloomington, IN 47405, USA.

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http://dx.doi.org/10.1007/s00239-009-9241-6DOI Listing
June 2009

Adaptive evolution of young gene duplicates in mammals.

Genome Res 2009 May;19(5):859-67

School of Informatics, Indiana University, Bloomington, IN 47405, USA.

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http://dx.doi.org/10.1101/gr.085951.108DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2675974PMC
May 2009

Identifying parent-daughter relationships among duplicated genes.

Pac Symp Biocomput 2009 :114-25

Department of Biology and School of Informatics, Indiana University, Bloomington, IN 47405, USA.

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March 2009

Abundant genetic variation in transcript level during early Drosophila development.

Evol Dev 2008 Nov-Dec;10(6):683-9

Department of Evolution and Ecology, University of California, Davis, CA 95616, USA.

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http://dx.doi.org/10.1111/j.1525-142X.2008.00281.xDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4417501PMC
January 2009

The life and death of gene families.

Bioessays 2009 Jan;31(1):29-39

Department of Biology, University of Texas, Arlington, TX, USA.

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http://doi.wiley.com/10.1002/bies.080085
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January 2009

"Reverse ecology" and the power of population genomics.

Evolution 2008 Dec 26;62(12):2984-94. Epub 2008 Aug 26.

School of Informatics, Indiana University, Bloomington, IN, USA.

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http://dx.doi.org/10.1111/j.1558-5646.2008.00486.xDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2626434PMC
December 2008

Gain and loss of phosphorylation sites in human cancer.

Bioinformatics 2008 Aug;24(16):i241-7

School of Informatics, Indiana University, 901 East Tenth Street, Bloomington, IN 47408, USA.

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http://dx.doi.org/10.1093/bioinformatics/btn267DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2732209PMC
August 2008

Differential gene expression in incipient species of Anopheles gambiae.

Mol Ecol 2008 May 21;17(10):2491-504. Epub 2008 Apr 21.

Center for Global Health and Infectious Diseases, Department of Biological Sciences, University of Notre Dame, Notre Dame, IN 46556, USA.

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http://dx.doi.org/10.1111/j.1365-294X.2008.03774.xDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3670799PMC
May 2008

Toward a selection theory of molecular evolution.

Authors:
Matthew W Hahn

Evolution 2008 Feb;62(2):255-65

Department of Biology and School of Informatics, 1001 E. 3rd Street, Indiana University, Bloomington, IN 47405, USA.

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http://dx.doi.org/10.1111/j.1558-5646.2007.00308.xDOI Listing
February 2008