ECOD: integrating classifications of protein domains from experimental and predicted structures.

Autor: Schaeffer RD; Department of Biophysics, University of Texas Southwestern Medical Center, 5323 Harry Hines Blvd. Dallas, TX, 75390-8816 USA., Medvedev KE; Department of Biophysics, University of Texas Southwestern Medical Center, 5323 Harry Hines Blvd. Dallas, TX, 75390-8816 USA., Andreeva A; European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK., Chuguransky SR; European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK., Pinto BL; European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK., Zhang J; Eugene McDermott Center for Human Growth and Development, University of Texas Southwestern Medical Center, 5323 Harry Hines Blvd. Dallas, TX, 75390-8591, USA.; Harold C. Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, 5323 Harry Hines Blvd. Dallas, TX, 75390- USA., Cong Q; Department of Biophysics, University of Texas Southwestern Medical Center, 5323 Harry Hines Blvd. Dallas, TX, 75390-8816 USA.; Eugene McDermott Center for Human Growth and Development, University of Texas Southwestern Medical Center, 5323 Harry Hines Blvd. Dallas, TX, 75390-8591, USA.; Harold C. Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, 5323 Harry Hines Blvd. Dallas, TX, 75390- USA., Bateman A; European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK., Grishin NV; Department of Biophysics, University of Texas Southwestern Medical Center, 5323 Harry Hines Blvd. Dallas, TX, 75390-8816 USA.; Department of Biochemistry, University of Texas Southwestern Medical Center, 5323 Harry Hines Blvd. Dallas, TX, 75390-9038, USA.

Publikováno v: Nucleic acids research [Nucleic Acids Res] 2024 Nov 20. Date of Electronic Publication: 2024 Nov 20.

Structure classification of the proteins from Salmonella enterica pangenome revealed novel potential pathogenicity islands.

Autor: Medvedev KE; Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA. Kirill.Medvedev@UTSouthwestern.edu., Zhang J; Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA.; Eugene McDermott Center for Human Growth and Development, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA., Schaeffer RD; Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA., Kinch LN; Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA.; Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA., Cong Q; Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA.; Eugene McDermott Center for Human Growth and Development, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA., Grishin NV; Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA.; Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA.

Publikováno v: Scientific reports [Sci Rep] 2024 May 28; Vol. 14 (1), pp. 12260. Date of Electronic Publication: 2024 May 28.

Deep Learning for Subtypes Identification of Pure Seminoma of the Testis.

Autor: Medvedev KE; Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, TX, USA., Acosta PH; Lyda Hill Department of Bioinformatics, University of Texas Southwestern Medical Center, Dallas, TX, USA., Jia L; Department of Pathology, University of Texas Southwestern Medical Center, Dallas, TX, USA., Grishin NV; Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, TX, USA.; Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, TX, USA.

Publikováno v: Clinical pathology (Thousand Oaks, Ventura County, Calif.) [Clin Pathol] 2024 Feb 18; Vol. 17, pp. 2632010X241232302. Date of Electronic Publication: 2024 Feb 18 (Print Publication: 2024).

Pan-cancer structurome reveals overrepresentation of beta sandwiches and underrepresentation of alpha helical domains.

Autor: Medvedev KE; Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA. Kirill.Medvedev@UTSouthwestern.edu., Schaeffer RD; Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA., Chen KS; Department of Pediatrics, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA.; Children's Medical Center Research Institute, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA., Grishin NV; Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA.; Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA.

Publikováno v: Scientific reports [Sci Rep] 2023 Jul 25; Vol. 13 (1), pp. 11988. Date of Electronic Publication: 2023 Jul 25.

Integrated Molecular Analysis Reveals 2 Distinct Subtypes of Pure Seminoma of the Testis.

Autor: Medvedev KE; Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, TX, USA., Savelyeva AV; Department of Urology, University of Texas Southwestern Medical Center, Dallas, TX, USA., Chen KS; Department of Pediatrics, University of Texas Southwestern Medical Center, Dallas, TX, USA.; Children's Medical Center Research Institute, University of Texas Southwestern Medical Center, Dallas, TX, USA., Bagrodia A; Department of Urology, University of Texas Southwestern Medical Center, Dallas, TX, USA.; Department of Urology, University of California San Diego Health, La Jolla, CA, USA., Jia L; Department of Pathology, University of Texas Southwestern Medical Center, Dallas, TX, USA., Grishin NV; Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, TX, USA.; Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, TX, USA.

Publikováno v: Cancer informatics [Cancer Inform] 2022 Oct 31; Vol. 21, pp. 11769351221132634. Date of Electronic Publication: 2022 Oct 31 (Print Publication: 2022).