Parallel Prefix on Fully Connected Direct Connection Machines. - Clyde P. Kruskal; Larry Rudolph; Tom Madej (ICPP, 1986)

An application of group testing to the file comparison problem. - Tom Madej (ICDCS, 1989)

Topics in combinatorics and combinatorial algorithms - Thomas Madej (1989)

The interval inclusion number of a partially ordered set. - Tom Madej; Douglas B. West (Discret. Math., 1991)

Bounds for the crossing number of the N-cube. - Tom Madej (J. Graph Theory, 1991)

Interval number of special posets and random posets. - Tom Madej; Douglas B. West (Discret. Math., 1995)

MMDB: Entrez's 3D structure database. - Aron Marchler-Bauer; Kenneth J. Addess; Colombe Chappey; Lewis Y. Geer; Thomas Madej; Yo Matsuo; Yanli Wang; Stephen H. Bryant (Nucleic Acids Res., 1999)

MMDB: 3D structure data in Entrez. - Yanli Wang; Kenneth J. Addess; Lewis Y. Geer; Thomas Madej; Aron Marchler-Bauer; Diane Zimmerman; Stephen H. Bryant (Nucleic Acids Res., 2000)

MMDB: Entrez's 3D-structure database. - Yanli Wang; John B. Anderson; Jie Chen 039; Lewis Y. Geer; Siqian He; David I. Hurwitz; Cynthia A. Liebert; Thomas Madej; Gabriele H. Marchler; Aron Marchler-Bauer; Anna R. Panchenko; Benjamin A. Shoemaker; et al. (Nucleic Acids Res., 2002)

MMDB: Entrez's 3D-structure database. - Jie Chen 039; John B. Anderson; Carol DeWeese-Scott; Natalie D. Fedorova; Lewis Y. Geer; Siqian He; David I. Hurwitz; John D. Jackson; Aviva R. Jacobs; Christopher J. Lanczycki; Cynthia A. Liebert; Chunlei Liu 002; et al. (Nucleic Acids Res., 2003)

CDD: a curated Entrez database of conserved domain alignments. - Aron Marchler-Bauer; John B. Anderson; Carol DeWeese-Scott; Natalie D. Fedorova; Lewis Y. Geer; Siqian He; David I. Hurwitz; John D. Jackson; Aviva R. Jacobs; Christopher J. Lanczycki; Cynthia A. Liebert; Chunlei Liu 002; et al. (Nucleic Acids Res., 2003)

MMDB: annotating protein sequences with Entrez's 3D-structure database. - Yanli Wang; Kenneth J. Addess; Jie Chen 039; Lewis Y. Geer; Jane He; Siqian He; Shennan Lu; Thomas Madej; Aron Marchler-Bauer; Paul A. Thiessen; Naigong Zhang; Stephen H. Bryant (Nucleic Acids Res., 2007)

Knowledge-based annotation of small molecule binding sites in proteins. - Ratna R. Thangudu; Manoj Tyagi; Benjamin A. Shoemaker; Stephen H. Bryant; Anna R. Panchenko; Thomas Madej (BMC Bioinform., 2010)

Database resources of the National Center for Biotechnology Information. - Eric W. Sayers; Tanya Barrett; Dennis A. Benson; Evan Bolton; Stephen H. Bryant; Kathi Canese; Vyacheslav Chetvernin; Deanna M. Church; Michael DiCuccio; Scott Federhen; Michael Feolo; Lewis Y. Geer; et al. (Nucleic Acids Res., 2010)

Inferred Biomolecular Interaction Server - a web server to analyze and predict protein interacting partners and binding sites. - Benjamin A. Shoemaker; Dachuan Zhang; Ratna R. Thangudu; Manoj Tyagi; Jessica H. Fong; Aron Marchler-Bauer; Stephen H. Bryant; Tom Madej; Anna R. Panchenko (Nucleic Acids Res., 2010)

Database resources of the National Center for Biotechnology Information. - Eric W. Sayers; Tanya Barrett; Dennis A. Benson; Evan Bolton; Stephen H. Bryant; Kathi Canese; Vyacheslav Chetvernin; Deanna M. Church; Michael DiCuccio; Scott Federhen; Michael Feolo; Ian M. Fingerman; et al. (Nucleic Acids Res., 2011)

MMDB: 3D structures and macromolecular interactions. - Thomas Madej; Kenneth J. Addess; Jessica H. Fong; Lewis Y. Geer; Renata C. Geer; Christopher J. Lanczycki; Chunlei Liu 002; Shennan Lu; Aron Marchler-Bauer; Anna R. Panchenko; Jie Chen 039; Paul A. Thiessen; et al. (Nucleic Acids Res., 2012)

Database resources of the National Center for Biotechnology Information. - Eric W. Sayers; Tanya Barrett; Dennis A. Benson; Evan Bolton; Stephen H. Bryant; Kathi Canese; Vyacheslav Chetvernin; Deanna M. Church; Michael DiCuccio; Scott Federhen; Michael Feolo; Ian M. Fingerman; et al. (Nucleic Acids Res., 2012)

IBIS (Inferred Biomolecular Interaction Server) reports, predicts and integrates multiple types of conserved interactions for proteins. - Benjamin A. Shoemaker; Dachuan Zhang; Manoj Tyagi; Ratna R. Thangudu; Jessica H. Fong; Aron Marchler-Bauer; Stephen H. Bryant; Thomas Madej; Anna R. Panchenko (Nucleic Acids Res., 2012)

MMDB and VAST+: tracking structural similarities between macromolecular complexes. - Thomas Madej; Christopher J. Lanczycki; Dachuan Zhang; Paul A. Thiessen; Renata C. Geer; Aron Marchler-Bauer; Stephen H. Bryant (Nucleic Acids Res., 2014)

iCn3D, a web-based 3D viewer for sharing 1D/2D/3D representations of biomolecular structures. - Jiyao Wang; Philippe Youkharibache; Dachuan Zhang; Christopher J. Lanczycki; Renata C. Geer; Thomas Madej; Lon Phan; Minghong Ward; Shennan Lu; Gabriele H. Marchler; Yanli Wang; Stephen H. Bryant; et al. (Bioinform., 2020)

Database resources of the national center for biotechnology information. - Eric W. Sayers; Evan E. Bolton; J. Rodney Brister; Kathi Canese; Jessica Chan; Donald C. Comeau; Ryan Connor; Kathryn Funk; Chris Kelly; Sunghwan Kim 002; Tom Madej; Aron Marchler-Bauer; et al. (Nucleic Acids Res., 2022)

IgStrand: A universal residue numbering scheme for the immunoglobulin-fold (Ig-fold) to study Ig-proteomes and Ig-interactomes. - Caesar Tawfeeq; Jiyao Wang; Umesh Khaniya; Thomas Madej; James Song; Ravinder Abrol; Philippe Youkharibache (PLoS Comput. Biol., 2025)