Thomas Brettin

22.5k total citations · 1 hit paper
97 papers, 6.5k citations indexed

About

Thomas Brettin is a scholar working on Molecular Biology, Genetics and Computational Theory and Mathematics. According to data from OpenAlex, Thomas Brettin has authored 97 papers receiving a total of 6.5k indexed citations (citations by other indexed papers that have themselves been cited), including 61 papers in Molecular Biology, 15 papers in Genetics and 12 papers in Computational Theory and Mathematics. Recurrent topics in Thomas Brettin's work include Genomics and Phylogenetic Studies (27 papers), Computational Drug Discovery Methods (12 papers) and Antibiotic Resistance in Bacteria (7 papers). Thomas Brettin is often cited by papers focused on Genomics and Phylogenetic Studies (27 papers), Computational Drug Discovery Methods (12 papers) and Antibiotic Resistance in Bacteria (7 papers). Thomas Brettin collaborates with scholars based in United States, France and South Korea. Thomas Brettin's co-authors include Rick Stevens, Fangfang Xia, James J. Davis, Maulik Shukla, Robert Olson, Alice R. Wattam, Ross Overbeek, Gordon D. Pusch, Veronika Vonstein and Svetlana Gerdes and has published in prestigious journals such as Proceedings of the National Academy of Sciences, Nucleic Acids Research and Journal of Clinical Investigation.

In The Last Decade

Thomas Brettin

93 papers receiving 6.3k citations

Hit Papers

align trajectories

What are hit papers?

Hit papers significantly outperform the citation benchmark for their cohort. A paper qualifies if it has ≥500 total citations, achieves ≥1.5× the top-1% citation threshold for papers in the same subfield and year (this is the minimum needed to enter the top 1%, not the average within it), or reaches the top citation threshold in at least one of its specific research topics.

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

2015 2.0k citations Thomas Brettin, James J. Davis et al. Scientific Reports profile →

Peers — A (Enhanced Table)

Peers by citation overlap · career bar shows stage (early→late) cites · hero ref

Name	h						Papers	Cites
Thomas Brettin United States	37	3.2k	1.5k	897	770	738	97	6.5k
Matthew R. Laird Canada	15	3.3k 1.0×	1.1k 0.7×	512 0.6×	499 0.6×	365 0.5×	17	5.2k
David Arndt Canada	12	4.3k 1.3×	1.4k 0.9×	442 0.5×	576 0.7×	439 0.6×	19	7.2k
Geoffrey L. Winsor Canada	20	3.3k 1.0×	913 0.6×	1.1k 1.2×	655 0.9×	998 1.4×	28	5.0k
Gordon D. Pusch United States	17	5.0k 1.5×	2.8k 1.8×	526 0.6×	814 1.1×	741 1.0×	22	7.7k
W. Florian Fricke United States	38	3.3k 1.0×	1.1k 0.7×	709 0.8×	847 1.1×	805 1.1×	63	6.2k
Maulik Shukla United States	20	4.2k 1.3×	2.3k 1.5×	365 0.4×	803 1.0×	862 1.2×	44	7.3k
Thomas Abeel United States	27	4.9k 1.5×	1.4k 0.9×	967 1.1×	535 0.7×	644 0.9×	78	8.3k
S. Brook Peterson United States	25	2.8k 0.9×	1.1k 0.7×	1.0k 1.1×	1.2k 1.6×	525 0.7×	37	5.4k
Todd J. Treangen United States	28	4.9k 1.5×	1.7k 1.1×	1.1k 1.2×	721 0.9×	865 1.2×	92	7.7k
Cristina De Castro Italy	39	2.4k 0.7×	755 0.5×	536 0.6×	542 0.7×	514 0.7×	202	5.5k

Countries citing papers authored by Thomas Brettin

Since Specialization

Citations

This map shows the geographic impact of Thomas Brettin's research. It shows the number of citations coming from papers published by authors working in each country. You can also color the map by specialization and compare the number of citations received by Thomas Brettin with the expected number of citations based on a country's size and research output (numbers larger than one mean the country cites Thomas Brettin more than expected).

Fields of papers citing papers by Thomas Brettin

Since Specialization

Physical SciencesHealth SciencesLife SciencesSocial Sciences

This network shows the impact of papers produced by Thomas Brettin. Nodes represent research fields, and links connect fields that are likely to share authors. Colored nodes show fields that tend to cite the papers produced by Thomas Brettin. The network helps show where Thomas Brettin may publish in the future.

Co-authorship network of co-authors of Thomas Brettin

This figure shows the co-authorship network connecting the top 25 collaborators of Thomas Brettin. A scholar is included among the top collaborators of Thomas Brettin based on the total number of citations received by their joint publications. Widths of edges represent the number of papers authors have co-authored together. Node borders signify the number of papers an author published with Thomas Brettin. Thomas Brettin is excluded from the visualization to improve readability, since they are connected to all nodes in the network.

All Works

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20 of 20 papers shown

Narykov, Oleksandr, Thomas Brettin, Yvonne A. Evrard, et al.. (2025). Data imbalance in drug response prediction: multi-objective optimization approach in deep learning setting. Briefings in Bioinformatics. 26(2).

Brettin, Thomas, et al.. (2025). BioR5: A Three-Layer Architecture for Biological Reasoning in Scientific AI. 594–601.

Brace, Alexander, et al.. (2024). High Performance Binding Affinity Prediction with a Transformer-Based Surrogate Model. 571–580. 1 indexed citations

Partin, Alexander, Thomas Brettin, Yitan Zhu, et al.. (2023). Deep learning methods for drug response prediction in cancer: Predominant and emerging trends. Frontiers in Medicine. 10. 1086097–1086097. 59 indexed citations

Narykov, Oleksandr, Thomas Brettin, Yvonne A. Evrard, et al.. (2023). Integration of Computational Docking into Anti-Cancer Drug Response Prediction Models. Cancers. 16(1). 50–50. 6 indexed citations

Bhattacharya, Tanmoy, Thomas Brettin, James H. Doroshow, et al.. (2019). AI Meets Exascale Computing: Advancing Cancer Research With Large-Scale High Performance Computing. Frontiers in Oncology. 9. 984–984. 22 indexed citations

Nguyen, Marcus, Thomas Brettin, S. Wesley Long, et al.. (2018). Developing an in silico minimum inhibitory concentration panel test for Klebsiella pneumoniae. Scientific Reports. 8(1). 421–421. 123 indexed citations

Long, S. Wesley, Matthew Ojeda Saavedra, Concepcion Cantu, et al.. (2017). Whole-Genome Sequencing of a Human Clinical Isolate of the Novel Species Klebsiella quasivariicola sp. nov. Genome Announcements. 5(42). 41 indexed citations

Brettin, Thomas, James J. Davis, Terry Disz, et al.. (2015). RASTtk: A modular and extensible implementation of the RAST algorithm for building custom annotation pipelines and annotating batches of genomes. Scientific Reports. 5(1). 8365–8365. 1988 indexed citations breakdown →

10.

Nakatsu, Cindy H., Ravi D. Barabote, David Bruce, et al.. (2013). Complete genome sequence of Arthrobacter sp. strain FB24. Standards in Genomic Sciences. 9(1). 106–116. 17 indexed citations

11.

Be, Nicholas A., James B. Thissen, Shea N. Gardner, et al.. (2013). Detection of Bacillus anthracis DNA in Complex Soil and Air Samples Using Next-Generation Sequencing. PLoS ONE. 8(9). e73455–e73455. 23 indexed citations

12.

Novichkov, Pavel S., Thomas Brettin, Paramvir Dehal, et al.. (2012). RegPrecise web services interface: programmatic access to the transcriptional regulatory interactions in bacteria reconstructed by comparative genomics. Nucleic Acids Research. 40(W1). W604–W608. 18 indexed citations

13.

Quest, Daniel, et al.. (2011). Scenario driven data modelling: a method for integrating diverse sources of data and data streams. BMC Bioinformatics. 12(S10). S17–S17. 3 indexed citations

14.

Haley, Bradd J., Christopher J. Grim, Nur A. Hasan, et al.. (2010). The pre‐seventh pandemic Vibrio cholerae BX 330286 El Tor genome: evidence for the environment as a genome reservoir. Environmental Microbiology Reports. 2(1). 208–216. 4 indexed citations

15.

Barabote, Ravi D., Gary Xie, Thomas Brettin, et al.. (2009). Complete Genome Sequence of Francisella tularensis Subspecies holarctica FTNF002-00. PLoS ONE. 4(9). e7041–e7041. 33 indexed citations

16.

Riley, Monica, James T. Staley, Antoine Danchin, et al.. (2008). Genomics of an extreme psychrophile, Psychromonas ingrahamii. BMC Genomics. 9(1). 210–210. 80 indexed citations

17.

Siddaramappa, Shivakumara, A. J. Duncan, Thomas Brettin, & Thomas J. Inzana. (2006). Comparative analyses of two cryptic plasmids from Haemophilus somnus (Histophilus somni). Plasmid. 55(3). 227–234. 7 indexed citations

18.

Pajukanta, Päivi, Michele Cargill, Laura Viitanen, et al.. (2000). Two Loci on Chromosomes 2 and X for Premature Coronary Heart Disease Identified in Early- and Late-Settlement Populations of Finland. The American Journal of Human Genetics. 67(6). 1481–1493. 130 indexed citations

19.

Rioux, John D., Mark S. Silverberg, Mark J. Daly, et al.. (2000). Genomewide Search in Canadian Families with Inflammatory Bowel Disease Reveals Two Novel Susceptibility Loci. The American Journal of Human Genetics. 66(6). 1863–1870. 383 indexed citations

20.

Lehto, Markku, Melanie M. Mahtani, Elisabeth Widén, et al.. (1997). Characterization of the MODY3 phenotype. Early-onset diabetes caused by an insulin secretion defect.. Journal of Clinical Investigation. 99(4). 582–591. 168 indexed citations

Rankless uses publication and citation data sourced from OpenAlex, an open and comprehensive bibliographic database. While OpenAlex provides broad and valuable coverage of the global research landscape, it—like all bibliographic datasets—has inherent limitations. These include incomplete records, variations in author disambiguation, differences in journal indexing, and delays in data updates. As a result, some metrics and network relationships displayed in Rankless may not fully capture the entirety of a scholar's output or impact.

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