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Biology and Biochemistry

D-Index
66
Citations
88903
World Ranking
8418
National Ranking
3790

Overview

Paul D. Thomas is affiliated with the University of Southern California in the United States. Their research primarily focuses on the field of Computer Science with contributions across several subfields, including Artificial Intelligence, Information Systems, Molecular Biology, Management Science and Operations Research, and Genetics.

The main topics covered in their work span various areas such as Data Quality and Management, Topic Modeling, Natural Language Processing Techniques, Information Retrieval and Search Behavior, Speech and Dialogue Systems, Semantic Web and Ontologies, and aspects related to Obesity, Physical Activity, and Diet.

Their recent scholarly output includes papers published in prominent venues, reflecting diverse research interests within information retrieval and conversational systems. Notable publications include:

  • "A Flexible Framework for Offline Effectiveness Metrics," 2022, Proceedings of the 45th International ACM SIGIR Conference on Research and Development in Information Retrieval
  • "Differences in Language and Style Between Two Social Media Communities," 2021, Proceedings of the International AAAI Conference on Web and Social Media
  • "Report on the future conversations workshop at CHIIR 2021," 2021, ACM SIGIR Forum
  • "Theories of Conversation for Conversational IR," 2021, ACM Transactions on Information Systems
  • "Non-nutritive sweetened beverages versus water after a 52-week weight management programme: a randomised controlled trial," 2023, International Journal of Obesity

Their work has appeared in frequent publication venues such as:

  • ACM SIGIR Forum
  • arXiv (Cornell University)
  • Business Economics Sustainability Leadership and Innovation
  • Neuro-Oncology
  • Proceedings of the 45th International ACM SIGIR Conference on Research and Development in Information Retrieval

In addition to journal and conference papers, Paul D. Thomas has contributed to book publications, including the title "Simulating Information Retrieval Test Collections," released by Morgan & Claypool Publishers in 2020.

The collaborative nature of their research is evident through frequent co-authorship with several researchers, notably:

  • Nick Craswell (17 publications)
  • David Hawking (14 publications)
  • Bodo Billerbeck (14 publications)
  • Josh Ellingson (3 publications)
  • Johanne R. Trippas (2 publications)

Best Publications

  • The Sequence of the Human Genome

    J. Craig Venter;Mark D. Adams;Eugene W. Myers;Peter W. Li

  • The Gene Ontology Resource: 20 years and still GOing strong

    S. Carbon;E. Douglass;N. Dunn;B. Good

  • The Gene Ontology resource: enriching a GOld mine

    Seth Carbon;Eric Douglass;Benjamin M Good

  • PANTHER: a library of protein families and subfamilies indexed by function.

    Paul D. Thomas;Michael J. Campbell;Anish Kejariwal;Huaiyu Mi

  • PANTHER version 14: more genomes, a new PANTHER GO-slim and improvements in enrichment analysis tools

    Huaiyu Mi;Anushya Muruganujan;Dustin Ebert;Xiaosong Huang;Xiaosong Huang

  • Large-scale gene function analysis with the PANTHER classification system

    Huaiyu Mi;Anushya Muruganujan;John T Casagrande;Paul D Thomas

  • InterPro: the integrative protein signature database

    Sarah Hunter;Rolf Apweiler;Teresa K. Attwood;Amos Bairoch

  • The InterPro protein families and domains database: 20 years on.

    Matthias Blum;Hsin Yu Chang;Sara Chuguransky;Tiago Grego

  • PANTHER version 11: expanded annotation data from Gene Ontology and Reactome pathways, and data analysis tool enhancements.

    Huaiyu Mi;Xiaosong Huang;Anushya Muruganujan;Haiming Tang

  • Principles of protein folding--a perspective from simple exact models.

    Ken A. Dill;Sarina Bromberg;Kaizhi Yue;Klaus M. Fiebig

  • PANTHER in 2013: modeling the evolution of gene function, and other gene attributes, in the context of phylogenetic trees

    Huaiyu Mi;Anushya Muruganujan;Paul D. Thomas

  • InterPro in 2017-beyond protein family and domain annotations

    Robert D. Finn;Teresa K. Attwood;Patricia C. Babbitt;Alex Bateman

  • InterPro in 2019: improving coverage, classification and access to protein sequence annotations.

    Alex L. Mitchell;Teresa K. Attwood;Patricia C. Babbitt;Matthias Blum

  • The InterPro protein families database: the classification resource after 15 years

    Alex L. Mitchell;Hsin-Yu Chang;Louise C. Daugherty;Matthew Fraser

  • The MEROPS database of proteolytic enzymes, their substrates and inhibitors in 2017 and a comparison with peptidases in the PANTHER database

    Neil D Rawlings;Alan J Barrett;Paul D Thomas;Xiaosong Huang

  • InterPro in 2011: new developments in the family and domain prediction database

    Sarah Hunter;Philip Jones;Alex Mitchell;Rolf Apweiler

  • Protocol Update for large-scale genome and gene function analysis with the PANTHER classification system (v.14.0)

    Huaiyu Mi;Anushya Muruganujan;Xiaosong Huang;Xiaosong Huang;Dustin Ebert

  • PANTHER version 16: a revised family classification, tree-based classification tool, enhancer regions and extensive API.

    Huaiyu Mi;Dustin Ebert;Anushya Muruganujan;Caitlin Mills

  • The PANTHER database of protein families, subfamilies, functions and pathways.

    Huaiyu Mi;Betty Lazareva-Ulitsky;Rozina Loo;Anish Kejariwal

  • PANTHER version 10: expanded protein families and functions, and analysis tools

    Huaiyu Mi;Sagar Poudel;Anushya Muruganujan;John T. Casagrande

Frequent Co-Authors

Christopher J. Mungall
Christopher J. Mungall Lawrence Berkeley National Laboratory
Michael J. Abramson
Michael J. Abramson Monash University
Adrian J. Lowe
Adrian J. Lowe University of Melbourne
Suzanna E. Lewis
Suzanna E. Lewis Lawrence Berkeley National Laboratory
Pascale Gaudet
Pascale Gaudet Swiss Institute of Bioinformatics
Judith A. Blake
Judith A. Blake Edith Cowan University
Christophe Dessimoz
Christophe Dessimoz University College London
Alex Bateman
Alex Bateman European Bioinformatics Institute
Melanie C. Matheson
Melanie C. Matheson University of Melbourne
Peer Bork
Peer Bork European Molecular Biology Laboratory

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