 Computational Biology
"Computational Biology" is a descriptor in the National Library of Medicine's controlled vocabulary thesaurus,
MeSH (Medical Subject Headings). Descriptors are arranged in a hierarchical structure,
which enables searching at various levels of specificity.
A field of biology concerned with the development of techniques for the collection and manipulation of biological data, and the use of such data to make biological discoveries or predictions. This field encompasses all computational methods and theories applicable to MOLECULAR BIOLOGY and areas of computer-based techniques for solving biological problems including manipulation of models and datasets.
| Descriptor ID |
D019295
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| MeSH Number(s) |
H01.158.273.180
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| Concept/Terms |
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Below are MeSH descriptors whose meaning is more general than "Computational Biology".
Below are MeSH descriptors whose meaning is more specific than "Computational Biology".
This graph shows the total number of publications written about "Computational Biology" by people in UAMS Profiles by year, and whether "Computational Biology" was a major or minor topic of these publication.
To see the data from this visualization as text, click here.
| Year | Major Topic | Minor Topic | Total |
|---|
| 2017 | 1 | 1 | 2 | | 2016 | 0 | 3 | 3 | | 2015 | 1 | 7 | 8 | | 2014 | 3 | 4 | 7 | | 2013 | 4 | 5 | 9 | | 2012 | 3 | 4 | 7 | | 2011 | 3 | 4 | 7 | | 2010 | 3 | 2 | 5 | | 2009 | 5 | 1 | 6 | | 2008 | 3 | 4 | 7 | | 2007 | 1 | 5 | 6 | | 2006 | 5 | 2 | 7 | | 2005 | 4 | 2 | 6 | | 2004 | 2 | 2 | 4 | | 2003 | 2 | 1 | 3 | | 2002 | 0 | 2 | 2 | | 1996 | 1 | 0 | 1 |
To return to the timeline, click here.
Below are the most recent publications written about "Computational Biology" by people in Profiles over the past ten years.
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Li J, Zhao W, Akbani R, Liu W, Ju Z, Ling S, Vellano CP, Roebuck P, Yu Q, Eterovic AK, Byers LA, Davies MA, Deng W, Gopal YN, Chen G, von Euw EM, Slamon D, Conklin D, Heymach JV, Gazdar AF, Minna JD, Myers JN, Lu Y, Mills GB, Liang H. Characterization of Human Cancer Cell Lines by Reverse-phase Protein Arrays. Cancer Cell. 2017 Feb 13; 31(2):225-239.
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Rahmatallah Y, Zybailov B, Emmert-Streib F, Glazko G. GSAR: Bioconductor package for Gene Set analysis in R. BMC Bioinformatics. 2017 Jan 24; 18(1):61.
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Whitmore L, Miles AJ, Mavridis L, Janes RW, Wallace BA. PCDDB: new developments at the Protein Circular Dichroism Data Bank. Nucleic Acids Res. 2017 Jan 04; 45(D1):D303-D307.
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Fu Q, Qin T, Chen L, Liu CJ, Zhang X, Wang YZ, Hu MX, Chu HY, Zhang HW. miR-29a up-regulation in AR42J cells contributes to apoptosis via targeting TNFRSF1A gene. World J Gastroenterol. 2016 May 28; 22(20):4881-90.
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Bandrowski A, Brinkman R, Brochhausen M, Brush MH, Bug B, Chibucos MC, Clancy K, Courtot M, Derom D, Dumontier M, Fan L, Fostel J, Fragoso G, Gibson F, Gonzalez-Beltran A, Haendel MA, He Y, Heiskanen M, Hernandez-Boussard T, Jensen M, Lin Y, Lister AL, Lord P, Malone J, Manduchi E, McGee M, Morrison N, Overton JA, Parkinson H, Peters B, Rocca-Serra P, Ruttenberg A, Sansone SA, Scheuermann RH, Schober D, Smith B, Soldatova LN, Stoeckert CJ, Taylor CF, Torniai C, Turner JA, Vita R, Whetzel PL, Zheng J. The Ontology for Biomedical Investigations. PLoS One. 2016; 11(4):e0154556.
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Mak MP, Tong P, Diao L, Cardnell RJ, Gibbons DL, William WN, Skoulidis F, Parra ER, Rodriguez-Canales J, Wistuba II, Heymach JV, Weinstein JN, Coombes KR, Wang J, Byers LA. A Patient-Derived, Pan-Cancer EMT Signature Identifies Global Molecular Alterations and Immune Target Enrichment Following Epithelial-to-Mesenchymal Transition. Clin Cancer Res. 2016 Feb 01; 22(3):609-20.
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Flowers A, Lee JY, Acosta S, Hudson C, Small B, Sanberg CD, Bickford PC. NT-020 treatment reduces inflammation and augments Nrf-2 and Wnt signaling in aged rats. J Neuroinflammation. 2015 Sep 17; 12:174.
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Espinoza-Valles I, Vora GJ, Lin B, Leekitcharoenphon P, González-Castillo A, Ussery D, Høj L, Gomez-Gil B. Unique and conserved genome regions in Vibrio harveyi and related species in comparison with the shrimp pathogen Vibrio harveyi CAIM 1792. Microbiology. 2015 Sep; 161(9):1762-79.
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May M, Hwang KS, Miles J, Williams C, Niranjan T, Kahler SG, Chiurazzi P, Steindl K, Van Der Spek PJ, Swagemakers S, Mueller J, Stefl S, Alexov E, Ryu JI, Choi JH, Kim HT, Tarpey P, Neri G, Holloway L, Skinner C, Stevenson RE, Dorsky RI, Wang T, Schwartz CE, Kim CH. ZC4H2, an XLID gene, is required for the generation of a specific subset of CNS interneurons. Hum Mol Genet. 2015 Sep 01; 24(17):4848-61.
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Giannakakis A, Zhang J, Jenjaroenpun P, Nama S, Zainolabidin N, Aau MY, Yarmishyn AA, Vaz C, Ivshina AV, Grinchuk OV, Voorhoeve M, Vardy LA, Sampath P, Kuznetsov VA, Kurochkin IV, Guccione E. Contrasting expression patterns of coding and noncoding parts of the human genome upon oxidative stress. Sci Rep. 2015 May 29; 5:9737.
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Cao M, Chiriva-Internati M, Hermonat PL. AAV2 X increases AAV6 rep/cap-driven rAAV production. Virology. 2015 Aug; 482:84-8.
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Walworth N, Pfreundt U, Nelson WC, Mincer T, Heidelberg JF, Fu F, Waterbury JB, Glavina del Rio T, Goodwin L, Kyrpides NC, Land ML, Woyke T, Hutchins DA, Hess WR, Webb EA. Trichodesmium genome maintains abundant, widespread noncoding DNA in situ, despite oligotrophic lifestyle. Proc Natl Acad Sci U S A. 2015 Apr 07; 112(14):4251-6.
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Chang Z, Li G, Liu J, Zhang Y, Ashby C, Liu D, Cramer CL, Huang X. Bridger: a new framework for de novo transcriptome assembly using RNA-seq data. Genome Biol. 2015 Feb 11; 16:30.
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Peterson EA, Chavan SS, Bauer MA, Heuck CJ, Johann DJ. Revealing the inherent heterogeneity of human malignancies by variant consensus strategies coupled with cancer clonal analysis. BMC Bioinformatics. 2014; 15 Suppl 11:S9.
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Saddiki H, McAuliffe J, Flaherty P. GLAD: a mixed-membership model for heterogeneous tumor subtype classification. Bioinformatics. 2015 Jan 15; 31(2):225-32.
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Campa D, Martino A, Varkonyi J, Lesueur F, Jamroziak K, Landi S, Jurczyszyn A, Marques H, Andersen V, Jurado M, Brenner H, Petrini M, Vogel U, García-Sanz R, Buda G, Gemignani F, Ríos R, Vangsted AJ, Dumontet C, Martínez-López J, Moreno MJ, Stepien A, Watek M, Moreno V, Dieffenbach AK, Rossi AM, Butterbach K, Jacobsen SE, Goldschmidt H, Sainz J, Hillengass J, Orciuolo E, Dudzinski M, Weinhold N, Reis RM, Canzian F. Risk of multiple myeloma is associated with polymorphisms within telomerase genes and telomere length. Int J Cancer. 2015 Mar 01; 136(5):E351-8.
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Wanichthanarak K, Nookaew I, Petranovic D. yStreX: yeast stress expression database. Database (Oxford). 2014; 2014.
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Emmert-Streib F, de Matos Simoes R, Glazko G, McDade S, Haibe-Kains B, Holzinger A, Dehmer M, Campbell F. Functional and genetic analysis of the colon cancer network. BMC Bioinformatics. 2014; 15 Suppl 6:S6.
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Li G, Li M, Zhang Y, Wang D, Li R, Guimerà R, Gao JT, Zhang MQ. ModuleRole: a tool for modulization, role determination and visualization in protein-protein interaction networks. PLoS One. 2014; 9(5):e94608.
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Gatto F, Nookaew I, Nielsen J. Chromosome 3p loss of heterozygosity is associated with a unique metabolic network in clear cell renal carcinoma. Proc Natl Acad Sci U S A. 2014 Mar 04; 111(9):E866-75.
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Nagarajan R, Scutari M. Impact of noise on molecular network inference. PLoS One. 2013; 8(12):e80735.
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Griffith M, Griffith OL, Coffman AC, Weible JV, McMichael JF, Spies NC, Koval J, Das I, Callaway MB, Eldred JM, Miller CA, Subramanian J, Govindan R, Kumar RD, Bose R, Ding L, Walker JR, Larson DE, Dooling DJ, Smith SM, Ley TJ, Mardis ER, Wilson RK. DGIdb: mining the druggable genome. Nat Methods. 2013 Dec; 10(12):1209-10.
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Stahl JA, Chavan SS, Sifford JM, MacLeod V, Voth DE, Edmondson RD, Forrest JC. Phosphoproteomic analyses reveal signaling pathways that facilitate lytic gammaherpesvirus replication. PLoS Pathog. 2013 Sep; 9(9):e1003583.
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Jernås M, Malmeström C, Axelsson M, Nookaew I, Wadenvik H, Lycke J, Olsson B. MicroRNA regulate immune pathways in T-cells in multiple sclerosis (MS). BMC Immunol. 2013 Jul 29; 14:32.
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Smalling RL, Delker DA, Zhang Y, Nieto N, McGuiness MS, Liu S, Friedman SL, Hagedorn CH, Wang L. Genome-wide transcriptome analysis identifies novel gene signatures implicated in human chronic liver disease. Am J Physiol Gastrointest Liver Physiol. 2013 Sep 01; 305(5):G364-74.
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Chintapalli SV, Bhardwaj G, Babu J, Hadjiyianni L, Hong Y, Todd GK, Boosalis CA, Zhang Z, Zhou X, Ma H, Anishkin A, van Rossum DB, Patterson RL. Reevaluation of the evolutionary events within recA/RAD51 phylogeny. BMC Genomics. 2013 Apr 10; 14:240.
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Agren R, Liu L, Shoaie S, Vongsangnak W, Nookaew I, Nielsen J. The RAVEN toolbox and its use for generating a genome-scale metabolic model for Penicillium chrysogenum. PLoS Comput Biol. 2013; 9(3):e1002980.
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Ashby C, Johnson D, Walker K, Kanj IA, Xia G, Huang X. New enumeration algorithm for protein structure comparison and classification. BMC Genomics. 2013; 14 Suppl 2:S1.
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Prior FW, Clark K, Commean P, Freymann J, Jaffe C, Kirby J, Moore S, Smith K, Tarbox L, Vendt B, Marquez G. TCIA: An information resource to enable open science. Conf Proc IEEE Eng Med Biol Soc. 2013; 2013:1282-5.
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Smolock EM, Korshunov VA, Glazko G, Qiu X, Gerloff J, Berk BC. Ribosomal protein L17, RpL17, is an inhibitor of vascular smooth muscle growth and carotid intima formation. Circulation. 2012 Nov 13; 126(20):2418-27.
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Rahmatallah Y, Emmert-Streib F, Glazko G. Gene set analysis for self-contained tests: complex null and specific alternative hypotheses. Bioinformatics. 2012 Dec 01; 28(23):3073-80.
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Glazko GV, Zybailov BL, Rogozin IB. Computational prediction of polycomb-associated long non-coding RNAs. PLoS One. 2012; 7(9):e44878.
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Emmert-Streib F, de Matos Simoes R, Tripathi S, Glazko GV, Dehmer M. A Bayesian analysis of the chromosome architecture of human disorders by integrating reductionist data. Sci Rep. 2012; 2:513.
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Dees ND, Zhang Q, Kandoth C, Wendl MC, Schierding W, Koboldt DC, Mooney TB, Callaway MB, Dooling D, Mardis ER, Wilson RK, Ding L. MuSiC: identifying mutational significance in cancer genomes. Genome Res. 2012 Aug; 22(8):1589-98.
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Bhardwaj G, Ko KD, Hong Y, Zhang Z, Ho NL, Chintapalli SV, Kline LA, Gotlin M, Hartranft DN, Patterson ME, Dave F, Smith EJ, Holmes EC, Patterson RL, van Rossum DB. PHYRN: a robust method for phylogenetic analysis of highly divergent sequences. PLoS One. 2012; 7(4):e34261.
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Cheng BY, Zhi J, Santana A, Khan S, Salinas E, Forrest JC, Zheng Y, Jaggi S, Leatherwood J, Krug LT. Tiled microarray identification of novel viral transcript structures and distinct transcriptional profiles during two modes of productive murine gammaherpesvirus 68 infection. J Virol. 2012 Apr; 86(8):4340-57.
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Dale J, Price EP, Hornstra H, Busch JD, Mayo M, Godoy D, Wuthiekanun V, Baker A, Foster JT, Wagner DM, Tuanyok A, Warner J, Spratt BG, Peacock SJ, Currie BJ, Keim P, Pearson T. Epidemiological tracking and population assignment of the non-clonal bacterium, Burkholderia pseudomallei. PLoS Negl Trop Dis. 2011 Dec; 5(12):e1381.
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Frye RE. Special issue on techniques for measuring brain connectivity: advanced anatomic, function, effective and network neuroconnectivity techniques. Comput Biol Med. 2011 Dec; 41(12):1058-61.
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Chavan SS, Shaughnessy JD, Edmondson RD. Overview of biological database mapping services for interoperation between different 'omics' datasets. Hum Genomics. 2011 Oct; 5(6):703-8.
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Potnis N, Krasileva K, Chow V, Almeida NF, Patil PB, Ryan RP, Sharlach M, Behlau F, Dow JM, Momol M, White FF, Preston JF, Vinatzer BA, Koebnik R, Setubal JC, Norman DJ, Staskawicz BJ, Jones JB. Comparative genomics reveals diversity among xanthomonads infecting tomato and pepper. BMC Genomics. 2011 Mar 11; 12:146.
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Karlsson FH, Ussery DW, Nielsen J, Nookaew I. A closer look at bacteroides: phylogenetic relationship and genomic implications of a life in the human gut. Microb Ecol. 2011 Apr; 61(3):473-85.
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Martin L, Anguita A, Graf N, Tsiknakis M, Brochhausen M, Rüping S, Bucur A, Sfakianakis S, Sengstag T, Buffa F, Stenzhorn H. ACGT: advancing clinico-genomic trials on cancer - four years of experience. Stud Health Technol Inform. 2011; 169:734-8.
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Brochhausen M, Blobel B. Architectural approach for providing relations in biomedical terminologies and ontologies. Stud Health Technol Inform. 2011; 169:739-43.
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Liu K, Hogan WR, Crowley RS. Natural Language Processing methods and systems for biomedical ontology learning. J Biomed Inform. 2011 Feb; 44(1):163-79.
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Brochhausen M, Spear AD, Cocos C, Weiler G, Martín L, Anguita A, Stenzhorn H, Daskalaki E, Schera F, Schwarz U, Sfakianakis S, Kiefer S, Dörr M, Graf N, Tsiknakis M. The ACGT Master Ontology and its applications--towards an ontology-driven cancer research and management system. J Biomed Inform. 2011 Feb; 44(1):8-25.
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Hogan WR. Towards an ontological theory of substance intolerance and hypersensitivity. J Biomed Inform. 2011 Feb; 44(1):26-34.
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Smith B, Brochhausen M. Putting biomedical ontologies to work. Methods Inf Med. 2010; 49(2):135-40.
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Lavín JL, Ramírez L, Ussery DW, Pisabarro AG, Oguiza JA. Genomic analysis of two-component signal transduction proteins in basidiomycetes. J Mol Microbiol Biotechnol. 2010; 18(2):63-73.
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Hu R, Qiu X, Glazko G. A new gene selection procedure based on the covariance distance. Bioinformatics. 2010 Feb 01; 26(3):348-54.
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Chavan SS, Bauer MA, Scutari M, Nagarajan R. NATbox: a network analysis toolbox in R. BMC Bioinformatics. 2009 Oct 08; 10 Suppl 11:S14.
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Sims GE, Jun SR, Wu GA, Kim SH. Whole-genome phylogeny of mammals: evolutionary information in genic and nongenic regions. Proc Natl Acad Sci U S A. 2009 Oct 06; 106(40):17077-82.
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Lustgarten JL, Visweswaran S, Bowser RP, Hogan WR, Gopalakrishnan V. Knowledge-based variable selection for learning rules from proteomic data. BMC Bioinformatics. 2009 Sep 17; 10 Suppl 9:S16.
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Glazko GV, Emmert-Streib F. Unite and conquer: univariate and multivariate approaches for finding differentially expressed gene sets. Bioinformatics. 2009 Sep 15; 25(18):2348-54.
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Hu R, Qiu X, Glazko G, Klebanov L, Yakovlev A. Detecting intergene correlation changes in microarray analysis: a new approach to gene selection. BMC Bioinformatics. 2009 Jan 15; 10:20.
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Srikanta D, Sen SK, Huang CT, Conlin EM, Rhodes RM, Batzer MA. An alternative pathway for Alu retrotransposition suggests a role in DNA double-strand break repair. Genomics. 2009 Mar; 93(3):205-12.
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Wang K, Ussery DW, Brunak S. Analysis and prediction of gene splice sites in four Aspergillus genomes. Fungal Genet Biol. 2009 Mar; 46 Suppl 1:S14-8.
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Boyd EF, Cohen AL, Naughton LM, Ussery DW, Binnewies TT, Stine OC, Parent MA. Molecular analysis of the emergence of pandemic Vibrio parahaemolyticus. BMC Microbiol. 2008 Jun 30; 8:110.
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Nagarajan R, Clancy B. Phylogenetic proximity revealed by neurodevelopmental event timings. Neuroinformatics. 2008; 6(2):71-9.
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Sun J, Schnackenberg LK, Holland RD, Schmitt TC, Cantor GH, Dragan YP, Beger RD. Metabonomics evaluation of urine from rats given acute and chronic doses of acetaminophen using NMR and UPLC/MS. J Chromatogr B Analyt Technol Biomed Life Sci. 2008 Aug 15; 871(2):328-40.
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Hallin PF, Binnewies TT, Ussery DW. The genome BLASTatlas-a GeneWiz extension for visualization of whole-genome homology. Mol Biosyst. 2008 May; 4(5):363-71.
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Tsiknakis M, Brochhausen M, Nabrzyski J, Pucacki J, Sfakianakis SG, Potamias G, Desmedt C, Kafetzopoulos D. A semantic grid infrastructure enabling integrated access and analysis of multilevel biomedical data in support of postgenomic clinical trials on cancer. IEEE Trans Inf Technol Biomed. 2008 Mar; 12(2):205-17.
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Coenye T, Drevinek P, Mahenthiralingam E, Shah SA, Gill RT, Vandamme P, Ussery DW. Identification of putative noncoding RNA genes in the Burkholderia cenocepacia J2315 genome. FEMS Microbiol Lett. 2007 Nov; 276(1):83-92.
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Klebanov L, Glazko G, Salzman P, Yakovlev A, Xiao Y. A multivariate extension of the gene set enrichment analysis. J Bioinform Comput Biol. 2007 Oct; 5(5):1139-53.
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