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Tom Altman

TitleProfessor
InstitutionUniversity of Colorado Denver - Denver Campus
DepartmentCEDC-Computer SC & Engineering
Phone303/315-1401

    Collapse Bibliographic 
    Collapse selected publications
    Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications. Faculty can login to make corrections and additions.
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    1. Edgar RC, Taylor J, Lin V, Altman T, Barbera P, Meleshko D, Lohr D, Novakovsky G, Buchfink B, Al-Shayeb B, Banfield JF, de la Peña M, Korobeynikov A, Chikhi R, Babaian A. Petabase-scale sequence alignment catalyses viral discovery. Nature. 2022 02; 602(7895):142-147. PMID: 35082445.
      View in: PubMed
    2. Yin X, Altman T, Rutherford E, West KA, Wu Y, Choi J, Beck PL, Kaplan GG, Dabbagh K, DeSantis TZ, Iwai S. A Comparative Evaluation of Tools to Predict Metabolite Profiles From Microbiome Sequencing Data. Front Microbiol. 2020; 11:595910. PMID: 33343536.
      View in: PubMed
    3. Hahn AS, Altman T, Konwar KM, Hanson NW, Kim D, Relman DA, Dill DL, Hallam SJ. A geographically-diverse collection of 418 human gut microbiome pathway genome databases. Sci Data. 2017 04 11; 4:170035. PMID: 28398290.
      View in: PubMed
    4. Hanson NW, Konwar KM, Hawley AK, Altman T, Karp PD, Hallam SJ. Metabolic pathways for the whole community. BMC Genomics. 2014 Jul 22; 15:619. PMID: 25048541.
      View in: PubMed
    5. Shearer AG, Altman T, Rhee CD. Finding sequences for over 270 orphan enzymes. PLoS One. 2014; 9(5):e97250. PMID: 24826896.
      View in: PubMed
    6. Hu JC, Sherlock G, Siegele DA, Aleksander SA, Ball CA, Demeter J, Gouni S, Holland TA, Karp PD, Lewis JE, Liles NM, McIntosh BK, Mi H, Muruganujan A, Wymore F, Thomas PD, Altman T. PortEco: a resource for exploring bacterial biology through high-throughput data and analysis tools. Nucleic Acids Res. 2014 Jan; 42(Database issue):D677-84. PMID: 24285306.
      View in: PubMed
    7. Caspi R, Altman T, Billington R, Dreher K, Foerster H, Fulcher CA, Holland TA, Keseler IM, Kothari A, Kubo A, Krummenacker M, Latendresse M, Mueller LA, Ong Q, Paley S, Subhraveti P, Weaver DS, Weerasinghe D, Zhang P, Karp PD. The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of Pathway/Genome Databases. Nucleic Acids Res. 2014 Jan; 42(Database issue):D459-71. PMID: 24225315.
      View in: PubMed
    8. Altman T, Travers M, Kothari A, Caspi R, Karp PD. A systematic comparison of the MetaCyc and KEGG pathway databases. BMC Bioinformatics. 2013 Mar 27; 14:112. PMID: 23530693.
      View in: PubMed
    9. Karp PD, Paley S, Altman T. Data mining in the MetaCyc family of pathway databases. Methods Mol Biol. 2013; 939:183-200. PMID: 23192547.
      View in: PubMed
    10. Caspi R, Altman T, Dreher K, Fulcher CA, Subhraveti P, Keseler IM, Kothari A, Krummenacker M, Latendresse M, Mueller LA, Ong Q, Paley S, Pujar A, Shearer AG, Travers M, Weerasinghe D, Zhang P, Karp PD. The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of pathway/genome databases. Nucleic Acids Res. 2012 Jan; 40(Database issue):D742-53. PMID: 22102576.
      View in: PubMed
    11. Keseler IM, Collado-Vides J, Santos-Zavaleta A, Peralta-Gil M, Gama-Castro S, Muñiz-Rascado L, Bonavides-Martinez C, Paley S, Krummenacker M, Altman T, Kaipa P, Spaulding A, Pacheco J, Latendresse M, Fulcher C, Sarker M, Shearer AG, Mackie A, Paulsen I, Gunsalus RP, Karp PD. EcoCyc: a comprehensive database of Escherichia coli biology. Nucleic Acids Res. 2011 Jan; 39(Database issue):D583-90. PMID: 21097882.
      View in: PubMed
    12. Le T, Altman T, Gardiner K. HIGEDA: a hierarchical gene-set genetics based algorithm for finding subtle motifs in biological sequences. Bioinformatics. 2010 Feb 01; 26(3):302-9. PMID: 19996163.
      View in: PubMed
    13. Karp PD, Paley SM, Krummenacker M, Latendresse M, Dale JM, Lee TJ, Kaipa P, Gilham F, Spaulding A, Popescu L, Altman T, Paulsen I, Keseler IM, Caspi R. Pathway Tools version 13.0: integrated software for pathway/genome informatics and systems biology. Brief Bioinform. 2010 Jan; 11(1):40-79. PMID: 19955237.
      View in: PubMed
    14. Caspi R, Altman T, Dale JM, Dreher K, Fulcher CA, Gilham F, Kaipa P, Karthikeyan AS, Kothari A, Krummenacker M, Latendresse M, Mueller LA, Paley S, Popescu L, Pujar A, Shearer AG, Zhang P, Karp PD. The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of pathway/genome databases. Nucleic Acids Res. 2010 Jan; 38(Database issue):D473-9. PMID: 19850718.
      View in: PubMed
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