Gregg Thomas - Publications

July 2, 2024

The past year has been busy! From teaching and developing more workshops here in the Informatics Group (and helping to update the website!), to seeing friends and showing a poster about PhyloAcc at this year's TAGC in Washington D.C, and to finishing up several projects.

On top of that, I just welcomed my son, Wesley, into the world on June 20! With that being said, I'll be on leave for the next few months to get to know him.

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Archive

A fast, reproducible, high-throughput variant calling workflow for population genomics
Mirchandani C, Shultz AJ, Thomas GWC, Smith SJ, Baylis M, Arnold B, Corbett-Detig R, Enbody E, Sackton TB. Molecular Biology & Evolution.
doi: 10.1093/molbev/msad270

Genomics and conservation: Guidance from training to analyses and applications
Schiebelhut LM, Guillaume AS, Kuhn A, Schweizer RM, Armstrong EE, Beaumont MA, Byrne M, Cosart T, Hand BK, Howard L, Mussmann SM, Narum SR, Rasteiro R, Rivera-Colón, AG, Saarman N, Sethuraman A, Taylor HR, Thomas GWC, Wellenreuther M, Luikart G. 2023. Molecular Ecology Resources.
doi: 10.1111/1755-0998.13893

PhyloAcc-GT: A Bayesian method for inferring patterns of substitution rate shifts on targeted lineages accounting for gene tree discordance
  Yan H*, Hu Z*, Thomas GWC*, Edwards SV, Sackton TB, Liu JS. 2023. Molecular Biology & Evolution. 40(9).
  doi: 10.1093/molbev/msad195
  Website: https://phyloacc.github.io/

Origins and long-term patterns of copy-number variation in rhesus macaques
  Thomas GWC, Wang RJ, Nguyen J, Harris RA, Raveendran M, Rogers J, Hahn MW. 2021. Molecular Biology & Evolution. 38(4):1460-1471.
  doi: 10.1093/molbev/msaa303
  Resources: Figures

Genus-wide characterization of bumblebee genomes reveals variation associated with key ecological and behavioral traits of pollinators
Sun C, Huang J, ... Thomas GWC, ..., Hahn MW, ..., Mueller RL. 2021. Molecular Biology & Evolution. 38(2):486-501.
doi: 10.1093/molbev/msaa240

Paternal age in rhesus macaques is positively associated with germline mutation accumulation but not with measures of offspring sociability
Wang RJ, Thomas GWC, Raveendran M, Harris RA, Doddapaneni H, Muzny DM, Capitanio JP, Radivojac P, Rogers J, Hahn MW. 2020. Genome Research. 30:826-834.
doi: 10.1101/gr.255174.119

Gene content evolution in the arthropods
  Thomas GWC, Dohmen E, Hughes DST, Murali SC, Poelchau M, Glastad K, The i5K Phylogenomics Consortium,
  Chipman AD, Waterhouse RM, Bornberg-Bauer E, Hahn MW, Richards S. 2020. Genome Biology. 21(15).
  doi: 10.1186/s13059-019-1925-7
  Resources: ArthroFam website

Tissue-specific expression profiles and positive selection analysis in the tree swallow (Tachycineta bicolor) using a de novo transcriptome assembly
Bentz AB, Thomas GWC, Rusch DB, Rosvall KA. 2019. Scientific Reports. 9:15849.
doi: 10.1038/s41598-019-52312-4

Referee: reference genome quality scores
  Thomas GWC and Hahn MW. 2019. Genome Biology and Evolution. 11(5):1483-1486.
  doi: 10.1093/gbe/evz088
  Software: Referee

The comparative genomics and complex population history of Papio baboons
Rogers J, The Baboon Genome Analysis Consortium. 2019. Science Advances. 5(1).
doi: 10.1126/sciadv.aau6947

Evolution of salivary glue genes in Drosophila species
  Da Lage JL, Thomas GWC, Bonneau M, Courtier-Orgogozo V. 2019. BMC Evolutionary Biology. 19(36).
  doi: 10.1186/s12862-019-1364-9
  Resources: FigShare Drosophila 25 species phylogeny

Comparative analyses identify genomic features potentially involved in the evolution of birds-of-paradise
  Prost S, Armstrong EE, Nylander J, Thomas GWC, Suh A, Petersen B, Dalen L, Benz BW, Blom MPK,
  Palkopoulou E, Ericson PGP, Irestedt M. 2019. GigaScience. 8(5).
  doi: 10.1093/gigascience/giz003
  Resources: Website

Reproductive longevity predicts mutation rates in primates
  Thomas GWC, Wang RJ, Puri A, Harris RA, Raveendran M, Hughes DST, Murali SC, Williams LE,
  Doddapaneni H, Muzny DM, Gibbs RA, Abee CR, Galinski MR, Worley KC, Rogers J, Radivojac P, Hahn MW. 2018. Current Biology. 28(19):3193-3197.
  doi: 10.1016/j.cub.2018.08.050
  Resources: Website / Github repo

Clonal polymorphism and high heterozygosity in the celibate genome of the Amazon molly
Warren WC, García-Pérez R, ..., Thomas GWC, ..., Hahn MW, ..., Schartl M. 2018. Nature Ecology and Evolution. 2:669–679.
doi: 10.1038/s41559-018-0473-y

A model species for agricultural pest genomics: the genome of the Colorado potato beetle, Leptinotarsa decemlineata (Coleoptera: Chrysomelidae)
Schoville SD, Chen YH, ..., Thomas GWC, ..., Richards S. 2018. Scientific Reports. 8(1931).
doi: 10.1038/s41598-018-20154-1

Sooty mangabey genome sequence provides insight into AIDS resistance in a natural SIV host
Palesch D, Bosinger SE, ..., Thomas GWC, Hahn MW, ..., Silvestri G. 2018. Nature. 553:77-81.
doi: 10.1038/nature25140

The genome of the vervet (Chlorocebus aethiops sabaeus)
Warren WC, The Vervet Genome Consortium, Freimer NB. 2015. Genome Research. 25(12):1921-1933.
doi: 10.1101/gr.192922.115

Determining the null model for detecting adaptive convergence from genomic data: a case study using echolocating mammals
Thomas GWC and Hahn MW. 2015. Molecular Biology and Evolution. 32(5):1232-1236.
doi: 10.1093/molbev/msv013

Convergent evolution of the genomes of marine mammals
Foote AD*, Liu Y*, Thomas GWC*, Vinař T*, et al. 2015. Nature Genetics. 47(3):272-275.
doi: doi:10.1038/ng.3198

Highly evolvable malaria vectors: the genomes of 16 Anopheles mosquitoes
Neafsey DE, Waterhouse RM, The Anopheles Genome Consortium, Besansky NJ. 2015. Science. 347(6217):1258522
doi: 10.1126/science.1258522

Quantifying and mitigating reference bias in comparative genomics
Evolution Converence - 2023.06.25 - Contributed Talk - Slides

Prioritizing loci for ILS-aware rate analyses using phylogenetic concordance factors
Society of Molecular Biology and Evolution Global Symposium 2 (Sustainability, Equity, and Efficiency in Computational Biology) - 2022.07.12 - Virtual - Contributed Talk - Slides

Prioritizing loci for ILS-aware rate analyses using phylogenetic concordance factors
Evolution Conference - 2022.06.27 - Cleveland, OH - Contributed Talk - Slides

Speciation and introgression across the most species-rich radiation in mammals
Population, Evolutionary, and Quantitative Genetics Conference - 2022.06.09 - Pacific Grove, CA - Platform Talk - Slides

Patterns of genomic variation across the tree of life
UMass Lowell Departmental Seminar - 2022.03.25 - Lowell, MA - Invited Talk - Slides

Patterns of genomic variation across the tree of life
Harvard Museum of Comparative Zoology Lunchtime Seminar - 2022.03.21 - Cambridge, MA - Invited Talk - Slides

Pedigree sequencing and mutation rate variation in primates
American Association of Biological Anthropologists - 2021.04.15 - Virtual - Invited Talk - Slides

Patterns of molecular evolution in Arthropods (with Elias Dohmen)
Arthropod Genomics Symposium - 2020.07.21 - Virtual - Invited Talk - Slides

Reproductive longevity predicts mutation rates in primates
Population, Evolutionary, and Quantitative Genetics Conference - 2018.05.15 Madison, WI - Platform Talk - Slides

The evolution of the genes and genomes of 76 arthropod species
Evolution Conference - 2017.06.26 Portland, OR - Regular Talk - Slides (14 minute version)

The evolution of the genes and genomes of 76 arthropod species
Arthropod Genomics Symposium - 2017.06.09 - South Bend, IN - Invited Talk - Slides (20 minute version)

Gene tree reconciliation with MUL-trees for polyploid analysis
Evolution Conference - 2016.06.19 - Austin, TX - Regular Talk - Slides

Accounting for sequencing error in phylogenetics
Society of Systematic Biologists - 2015.05.21 - Ann Arbor, MI - Lightning Talk - Slides

Inferring molecular convergence from genomic data
Midwest Ecology and Evolution Conference - 2015.03.28 - Bloomington, IN - Contributed Talk - Slides

Convergent evolution of the genomes of marine mammals
Society of Molecular Biology and Evolution - 2014.06.12 - San Juan, PR - Contributed Talk - Slides

Inferring substitution rate shifts in a phylogeny with PhyloAcc
The Allied Genetics Conference (Population, Evolutionary, and Quantitative Genetics section) - 2024.03.09 - Washington D.C. - Poster

Molecular and morphological evolution across the most species-rich radiation in mammals
Evolution Conference - 2022.06.27 - Cleveland, OH - Poster

Causes and consequences of structural variation in the Macaca mulatta genome (first author Jelena Nguyen)
Center of Excellence for Women & Technology Research Experience for Undergraduates Symposium - 2019.04.12 - Bloomington, IN - Poster

Convergent evolution of the genomes of marine mammals
Genetics, Cellular, and Molecular Sciences Symposium - 2014.06.05 - Bloomington, IN - Poster

Healthy Habits for Data Science
Harvard FAS Informatics Group - Harvard University, Cambridge, MA -
Spring 2024

Bioinformatics Tips & Tricks
Harvard FAS Informatics Group - Harvard University, Cambridge, MA -
2023 Spring - 2023 Fall - 2024 Spring

Introduction to R
Harvard FAS Informatics Group - Harvard University, Cambridge, MA -
2023 Spring - 2023 Fall

Bayesian estimation of substitution rates with PhyloAcc
OEB275R Fall 2022 - Comparative Genomics: Phylogenetic Approaches to Linking Genomes and Phenotypes - Harvard University, Cambridge, MA - Workshop website

Introduction to Bioinformatics (with Rena Schweizer)
ConGen 2021: Population Genomic Data Analysis Course/Workshop - Virtual -
2021 - 2022 - 2023

Genome Assembly (with Ellie Armstrong)
ConGen: Population Genomic Data Analysis Course/Workshop - Virtual -
2020 - 2021 - 2022 - 2023