World's Best Scientists 2026 revealed!

D-Index & Metrics

Genetics

D-Index
66
Citations
25451
World Ranking
2576
National Ranking
1144

Overview

Thomas Brettin is affiliated with Argonne National Laboratory in the United States. Their research spans several intertwined domains, primarily grounded in biochemistry, genetics, and molecular biology, along with substantial contributions in computer science.

The scientist's main fields of study include:

  • Biochemistry, Genetics and Molecular Biology
  • Computer Science

Within these broad disciplines, their work further focuses on specific subfields such as:

  • Molecular Biology
  • Computational Theory and Mathematics
  • Materials Chemistry
  • Artificial Intelligence
  • Infectious Diseases

The research topics covered reflect an emphasis on computational approaches and biomedical applications. Key areas include:

  • Computational Drug Discovery Methods
  • Machine Learning in Materials Science
  • Gene expression and cancer classification
  • Genetics, Bioinformatics, and Biomedical Research
  • Bioinformatics and Genomic Networks
  • Protein Structure and Dynamics
  • Genomics and Phylogenetic Studies

Frequent collaborators in their research efforts include Rick Stevens, Alexander Partin, Maulik Shukla, Fangfang Xia, and Yitan Zhu. This network points to interdisciplinary partnerships across computational biology and related fields.

Thomas Brettin has published extensively in several notable venues, with multiple publications appearing in the following outlets:

  • arXiv (Cornell University)
  • Scientific Reports
  • bioRxiv (Cold Spring Harbor Laboratory)
  • Briefings in Bioinformatics
  • Journal of Clinical Oncology

Selected recent papers by the scientist include:

  • "Introducing the Bacterial and Viral Bioinformatics Resource Center (BV-BRC): a resource combining PATRIC, IRD and ViPR," 2022, Nucleic Acids Research
  • "Converting tabular data into images for deep learning with convolutional neural networks," 2021, Scientific Reports
  • "Deep learning methods for drug response prediction in cancer: Predominant and emerging trends," 2023, Frontiers in Medicine
  • "High-Throughput Virtual Screening and Validation of a SARS-CoV-2 Main Protease Noncovalent Inhibitor," 2021, Journal of Chemical Information and Modeling
  • "Ensemble transfer learning for the prediction of anti-cancer drug response," 2020, Scientific Reports

Best Publications

  • RASTtk: A modular and extensible implementation of the RAST algorithm for building custom annotation pipelines and annotating batches of genomes

    Thomas Brettin;Thomas Brettin;James J. Davis;James J. Davis;Terry Disz;Robert A. Edwards;Robert A. Edwards

  • Improvements to PATRIC, the all-bacterial Bioinformatics Database and Analysis Resource Center

    Alice R. Wattam;James J. Davis;James J. Davis;Rida Assaf;Sébastien Boisvert

  • KBase: The United States Department of Energy Systems Biology Knowledgebase.

    Adam P. Arkin;Adam P. Arkin;Robert W. Cottingham;Christopher S. Henry;Nomi L. Harris

  • Genome sequencing and analysis of the biomass-degrading fungus Trichoderma reesei (syn. Hypocrea jecorina).

    Diego Martinez;Diego Martinez;Randy M Berka;Bernard Henrissat;Markku Saloheimo

  • Three Genomes from the Phylum Acidobacteria Provide Insight into the Lifestyles of These Microorganisms in Soils

    Naomi L. Ward;Jean F. Challacombe;Jean F. Challacombe;Peter H. Janssen;Peter H. Janssen;Bernard Henrissat

  • The PATRIC Bioinformatics Resource Center: expanding data and analysis capabilities.

    James J. Davis;James J. Davis;Alice R. Wattam;Alice R. Wattam;Ramy K. Aziz;Thomas S. Brettin;Thomas S. Brettin

  • Genome, transcriptome, and secretome analysis of wood decay fungus Postia placenta supports unique mechanisms of lignocellulose conversion

    Diego Martinez;Diego Martinez;Jean Challacombe;Ingo Morgenstern;David Hibbett

  • Genomewide search in Canadian families with inflammatory bowel disease reveals two novel susceptibility loci.

    John D. Rioux;Mark S. Silverberg;Mark J. Daly;A. Hillary Steinhart

  • Classification, nomenclature, and database development for hepatitis C virus (HCV) and related viruses: proposals for standardization

    B Robertson;G Myers;C Howard;T Brettin

  • Genomic and genetic analyses of diversity and plant interactions of Pseudomonas fluorescens

    Mark W. Silby;Ana M. Cerdeño-Tárraga;Georgios S. Vernikos;Stephen R. Giddens

  • Comparative genomics reveals mechanism for short-term and long-term clonal transitions in pandemic Vibrio cholerae.

    Jongsik Chun;Christopher J. Grim;Nur A. Hasan;Je Hee Lee

  • Mapping of a gene for type 2 diabetes associated with an insulin secretion defect by a genome scan in Finnish families.

    Melanie M. Mahtani;Elisabeth Widén;Elisabeth Widén;Markku Lehto;Jeffrey Thomas

  • The complete genome sequence of Moorella thermoacetica (f. Clostridium thermoaceticum).

    Elizabeth Pierce;Gary Xie;Gary Xie;Ravi D. Barabote;Ravi D. Barabote;Elizabeth Saunders;Elizabeth Saunders

  • Deinococcus geothermalis: The Pool of Extreme Radiation Resistance Genes Shrinks

    Kira S. Makarova;Marina V. Omelchenko;Elena K. Gaidamakova;Vera Y. Matrosova

  • Temperature regulation of virulence factors in the pathogen Vibrio coralliilyticus

    Nikole E Kimes;Christopher J Grim;Christopher J Grim;Wesley R Johnson;Nur A Hasan

  • Pathogenomic Sequence Analysis of Bacillus cereus and Bacillus thuringiensis Isolates Closely Related to Bacillus anthracis

    Cliff S. Han;Gary Xie;Jean F. Challacombe;Michael R. Altherr

  • Characterization of the MODY3 phenotype. Early-onset diabetes caused by an insulin secretion defect.

    M Lehto;T Tuomi;M M Mahtani;E Widén

  • Genome sequence of the cellulolytic gliding bacterium Cytophaga hutchinsonii.

    Gary Xie;Gary Xie;David C. Bruce;David C. Bruce;Jean F. Challacombe;Jean F. Challacombe;Olga Chertkov;Olga Chertkov

  • Antimicrobial Resistance Prediction in PATRIC and RAST.

    James J. Davis;Sébastien Boisvert;Thomas Brettin;Thomas Brettin;Ronald W. Kenyon

  • Corrigendum: Genome sequencing and analysis of the biomass-degrading fungus Trichoderma reesei (syn. Hypocrea jecorina)

    Diego Martinez;Randy M Berka;Bernard Henrissat;Markku Saloheimo

Frequent Co-Authors

Cliff Han
Cliff Han Los Alamos National Laboratory
David Bruce
David Bruce Pebble Labs
Lynne Goodwin
Lynne Goodwin Los Alamos National Laboratory
Miriam Land
Miriam Land Oak Ridge National Laboratory
John C. Detter
John C. Detter Los Alamos National Laboratory
Jonathan A. Eisen
Jonathan A. Eisen University of California, Davis
Loren Hauser
Loren Hauser Digital Infuzion (United States)
Patrick S. G. Chain
Patrick S. G. Chain Los Alamos National Laboratory
Alla Lapidus
Alla Lapidus Saint Petersburg State University
Nikos C. Kyrpides
Nikos C. Kyrpides Joint Genome Institute

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