Paul D. Thomas

73.5k citations

74 papers · 21.0k indexed · 14 hit papers · h-index 39

Impact in

Molecular Biology top 0.2%
- Protein Structure and Dynamics
- RNA and protein synthesis mechanisms
- Bioinformatics and Genomic Networks
- Genomics and Phylogenetic Studies
- RNA modifications and cancer
- RNA Research and Splicing
- Epigenetics and DNA Methylation
Aging top 0.5%

Papers in

Molecular Biology 64
- Bioinformatics and Genomic Networks 36
- Genomics and Phylogenetic Studies 31
- Biomedical Text Mining and Ontologies 15
- Machine Learning in Bioinformatics 13
- Protein Structure and Dynamics 7
- Gene expression and cancer classification 7
- Gene Regulatory Network Analysis 7
Genetics 19
- Genomics and Rare Diseases 6

Co-authors: Huaiyu Mi Anushya Muruganujan Xiaosong Huang Dustin Ebert John T. Casagrande Anish Kejariwal Ken A. Dill Haiming Tang
Journals: Nucleic Acids Research (15 papers)Bioinformatics (5 papers)Proceedings of the National Academy of Sciences (4 papers)Protein Science (3 papers)Genome Research (3 papers)
Partner nations: United States United Kingdom Switzerland

In The Last Decade

Paul D. Thomas

72 papers receiving 20.8k citations

Hit Papers

14 papers align trajectories log scale

PANTHER: Making genome‐scale phylogenetics accessible to all 2021 · 896 citations

What are hit papers?

Hit papers significantly outperform the citation benchmark for their cohort. A paper qualifies if any of the following hold:

it has ≥500 total citations;
it reaches ≥1.5× the top-1% citation threshold for papers in the same subfield and year (the threshold is the minimum needed to enter the top 1%, not the average within it);
it reaches the top citation threshold in at least one of its specific research topics.

2021 Protein Science
2020 Nucleic Acids Research
2019 Nature Protocols
2018 Nucleic Acids Research
2017 Nucleic Acids Research
2016 Nucleic Acids Research
2015 Nucleic Acids Research
2013 Nature Protocols
2012 Nucleic Acids Research
2011 Briefings in Bioinformatics
2009 Methods in molecular biology
2003 Genome Research
2003 Nucleic Acids Research
1995 Protein Science

Peers

Countries citing papers authored by Paul D. Thomas

Since Specialization

Citations

This map shows the geographic impact of Paul D. Thomas'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 Paul D. Thomas with the expected number of citations based on a country's size and research output (numbers larger than one mean the country cites Paul D. Thomas more than expected).

Fields of papers citing papers by Paul D. Thomas

Since Specialization

Physical SciencesHealth SciencesLife SciencesSocial Sciences

This network shows the impact of papers produced by Paul D. Thomas. 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 Paul D. Thomas. The network helps show where Paul D. Thomas may publish in the future.

Co-authorship network

The 25 scholars most cited alongside Paul D. Thomas, linked wherever they have co-authored with each other. Click a name or a connecting line to browse the papers they share.

Border = papers with Paul D. Thomas Line = papers co-authored together Paul D. Thomas links everyone, so they are left out of the graph.

All Works

Sort: Min cites: Since: Top N: Style:

20 of 20 papers shown

#	Work
1	OrthoGrafter: Rapid Identification of Orthologs from Precomputed Placement in Phylogenetic Trees Journal of Molecular Evolution ·Christopher M. Williams, Paul D. Thomas	2025	0
2	Quest for Orthologs in the Era of Biodiversity Genomics Genome Biology and Evolution ·弘美上澤, Nicola Bordin, Salvatore Cosentino, Kawabe Kenichi, Natasha Glover, Michael Hiller, Yanhui Hu, Jaime Huerta‐Cepas, Luís Pedro Coelho, Wataru Iwasaki, Sina Majidian, Lamya-Charlotte Kanouni, Emma Persson, Thomas A. Richards, Toni Gabaldón, Erik L. L. Sonnhammer, Paul D. Thomas, Christophe Dessimoz, Ingo Ebersberger	2024	8
3	AI and the democratization of knowledge Scientific Data ·Christophe Dessimoz, Paul D. Thomas	2024	10
4	Annotation Query (AnnoQ): an integrated and interactive platform for large-scale genetic variant annotation Nucleic Acids Research ·Zhu Liu, Tremayne Mushayahama, 橘彩路, Dustin Ebert, Anushya Muruganujan, Shinichi Takata, Paul D. Thomas, Huaiyu Mi	2022	2
5	Bayesian parameter estimation for automatic annotation of gene functions using observational data and phylogenetic trees PLoS Computational Biology ·Monsalve Chavez, Duncan C. Thomas, John L. Morrison, Huaiyu Mi, Paul D. Thomas, Paul Marjoram	2021	1
6	PANTHER: Making genome‐scale phylogenetics accessible to all Protein Science ·Paul D. Thomas, Dustin Ebert, Anushya Muruganujan, Tremayne Mushayahama, Laurent‐Philippe Albou, Huaiyu Mi Hit paper breakdown →	2021	896
7	Setting the basis of best practices and standards for curation and annotation of logical models in biology—highlights of the [BC]2 2019 CoLoMoTo/SysMod Workshop Briefings in Bioinformatics ·Anna Niarakis, Martin Kuiper, Marek Ostaszewski, Rahuman S. Malik‐Sheriff, Cristina Casals‐Casas, Denis Thieffry, Tom C. Freeman, Paul D. Thomas, Vasundra Touré, Vincent Noël, Gautier Stoll, Julio Sáez-Rodríguez, Aurélien Naldi, Рада Борбаковна Шанмак, Ioannis Xénarios, Sylvain Soliman, Claudine Chaouiya, Tomáš Helikar, Laurence Calzone	2020	13
8	PEREGRINE: A genome-wide prediction of enhancer to gene relationships supported by experimental evidence PLoS ONE ·Shinichi Takata, Anushya Muruganujan, Dustin Ebert, Crystal N. Marconett, Juan Pablo Lewinger, Paul D. Thomas, Huaiyu Mi	2020	13
9	CausalTAB: the PSI-MITAB 2.8 updated format for signalling data representation and dissemination Bioinformatics ·Livia Perfetto, Márcio Luís Acencio, Glyn Bradley, Gianni Cesareni, (unknown), Dávid Fazekas, Henning Hermjakob, Tamás Korcsmáros, Martin Kuiper, Astrid Lægreid, Prisca Lo Surdo, Ruth C. Lovering, Sandra Orchard, Pablo Porras, Paul D. Thomas, Vasundra Touré, Celi Cristina Calamita Quiroga, Luana Licata	2019	20
10	Gene Ontology Causal Activity Modeling (GO-CAM) moves beyond GO annotations to structured descriptions of biological functions and systems Nature Genetics ·Paul D. Thomas, David P. Hill, Huaiyu Mi, David Osumi-Sutherland, Kimberly Van Auken, Seth Carbon, James P. Balhoff, Laurent‐Philippe Albou, Benjamin M. Good, Pascale Gaudet, Suzanna Lewis, Chris Mungall	2019	67
11	Protocol Update for large-scale genome and gene function analysis with the PANTHER classification system (v.14.0) Nature Protocols ·Huaiyu Mi, Anushya Muruganujan, Xiaosong Huang, Dustin Ebert, Shinichi Takata, Xinyu Guo, Paul D. Thomas Hit paper breakdown →	2019	967
12	Large-scale inference of gene function through phylogenetic annotation of Gene Ontology terms: case study of the apoptosis and autophagy cellular processes Database ·Marc Feuermann, Pascale Gaudet, Huaiyu Mi, Suzanna Lewis, Paul D. Thomas	2016	12
13	Large-scale gene function analysis with the PANTHER classification system Nature Protocols ·Huaiyu Mi, Anushya Muruganujan, John T. Casagrande, Paul D. Thomas Hit paper breakdown →	2013	1837
14	DRD1 associations with smoking abstinence across slow and normal nicotine metabolizers Pharmacogenetics and Genomics ·Won‐Ho Lee, Riju Ray, Andrew W. Bergen, Gary E. Swan, Paul D. Thomas, Rachel F. Tyndale, Neal L. Benowitz, Caryn Lerman, David V. Conti	2012	8
15	PANTHER in 2013: modeling the evolution of gene function, and other gene attributes, in the context of phylogenetic trees Nucleic Acids Research ·Huaiyu Mi, Anushya Muruganujan, Paul D. Thomas Hit paper breakdown →	2012	1339
16	PharmGKB summary Pharmacogenetics and Genomics ·Huaiyu Mi, Paul D. Thomas, Huijun Z. Ring, Ruhong Jiang, Katrin Sangkuhl, Teri E. Klein, Russ B. Altman	2010	10
17	PANTHER version 7: improved phylogenetic trees, orthologs and collaboration with the Gene Ontology Consortium Nucleic Acids Research ·Huaiyu Mi, Qing Dong, Anushya Muruganujan, Pascale Gaudet, Suzanna Lewis, Paul D. Thomas	2009	461
18	PANTHER version 6: protein sequence and function evolution data with expanded representation of biological pathways Nucleic Acids Research ·Huaiyu Mi, Nan Guo, Anish Kejariwal, Paul D. Thomas	2006	303
19	On the quality of tree-based protein classification Computer applications in the biosciences ·胡翔, Muhammet Emin Erdemli, Paul D. Thomas	2005	11
20	Altered Expression of the Lymphocyte Activation Markers CD30 and CD27 in Patients with Pouchitis Scandinavian Journal of Gastroenterology ·Paul D. Thomas, Alastair Forbes, R J Nicholls, Paul J. Ciclitira	2001	16

About Paul D. Thomas

Paul D. Thomas is a scholar working on Molecular Biology, Genetics, Spectroscopy, Computational Theory and Mathematics and Biophysics, having authored 74 papers that have together received 21.0k indexed citations. Recurring topics across this work include Bioinformatics and Genomic Networks (36 papers), Genomics and Phylogenetic Studies (31 papers), Biomedical Text Mining and Ontologies (15 papers), Machine Learning in Bioinformatics (13 papers), Protein Structure and Dynamics (7 papers), Gene expression and cancer classification (7 papers), Gene Regulatory Network Analysis (7 papers) and Genomics and Rare Diseases (6 papers). The work is most often cited by research in Molecular Biology (13.7k citations), Aging (281 citations), Cancer Research (2.1k citations), Genetics (3.4k citations) and Immunology (1.7k citations). Paul D. Thomas has collaborated with scholars based in United States, United Kingdom and Switzerland. Frequent co-authors include Huaiyu Mi, Anushya Muruganujan, Xiaosong Huang, Dustin Ebert, John T. Casagrande, Anish Kejariwal, Ken A. Dill, Haiming Tang, Michael J. Campbell and Suzanna Lewis. Their work appears in journals such as Nucleic Acids Research, Bioinformatics, Proceedings of the National Academy of Sciences, Protein Science and Genome Research.

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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