 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 publications.
To see the data from this visualization as text, click here.
| Year | Major Topic | Minor Topic | Total |
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| 2025 | 1 | 2 | 3 | | 2024 | 1 | 2 | 3 | | 2023 | 1 | 1 | 2 | | 2022 | 1 | 2 | 3 | | 2021 | 2 | 3 | 5 | | 2020 | 2 | 1 | 3 | | 2019 | 4 | 4 | 8 | | 2018 | 5 | 1 | 6 | | 2017 | 2 | 2 | 4 | | 2016 | 2 | 4 | 6 | | 2015 | 1 | 2 | 3 | | 2014 | 1 | 3 | 4 | | 2013 | 3 | 4 | 7 | | 2012 | 3 | 2 | 5 | | 2011 | 3 | 1 | 4 | | 2010 | 2 | 1 | 3 | | 2009 | 9 | 2 | 11 | | 2008 | 9 | 4 | 13 | | 2007 | 0 | 4 | 4 | | 2006 | 4 | 2 | 6 | | 2005 | 2 | 1 | 3 | | 2004 | 0 | 2 | 2 | | 2003 | 2 | 2 | 4 | | 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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Lu D, Kalantar KL, Glascock AL, Chu VT, Guerrero ES, Bernick N, Butcher X, Ewing K, Fahsbender E, Holmes O, Hoops E, Jones AE, Lim R, McCanny S, Reynoso L, Rosario K, Tang J, Valenzuela O, Mourani PM, Pickering AJ, Raphenya AR, Alcock BP, McArthur AG, Langelier CR. Simultaneous detection of pathogens and antimicrobial resistance genes with the open source, cloud-based, CZ ID platform. Genome Med. 2025 May 06; 17(1):46.
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Rahmatallah Y, Glazko G. Improving data interpretability with new differential sample variance gene set tests. BMC Bioinformatics. 2025 Apr 14; 26(1):103.
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Saini N, Tiwari AK, Leahy R, Thorat N, Kulkarni A. Transforming brain cancer biomarker research with patinformatics and SWOT analysis. Drug Discov Today. 2025 Mar; 30(3):104314.
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Bokulich NA, Robeson MS. Bioinformatics challenges for profiling the microbiome in cancer: pitfalls and opportunities. Trends Microbiol. 2024 Dec; 32(12):1163-1166.
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Saad-Roy CM, Morris SE, Boots M, Baker RE, Lewis BL, Farrar J, Marathe MV, Graham AL, Levin SA, Wagner CE, Metcalf CJE, Grenfell BT. Impact of waning immunity against SARS-CoV-2 severity exacerbated by vaccine hesitancy. PLoS Comput Biol. 2024 Aug; 20(8):e1012211.
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Bar O, Vahey E, Mintz M, Frye RE, Boles RG. Reanalysis of Trio Whole-Genome Sequencing Data Doubles the Yield in Autism Spectrum Disorder: De Novo Variants Present in Half. Int J Mol Sci. 2024 Jan 18; 25(2).
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Chappell K, Byrum SD. Understanding PTM Cross Talk Through a Visualization Tool, PTMViz. Methods Mol Biol. 2024; 2836:57-65.
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Janes RW, Wallace BA. DichroPipeline: A suite of online and downloadable tools and resources for protein circular dichroism spectroscopic data analyses, interpretations, and their interoperability with other bioinformatics tools and resources. Protein Sci. 2023 Dec; 32(12):e4817.
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Zhang D, Hong L, Zhang RS, Zhang Q, Yao J, Wang J, Zhang N. Identification of the key mechanisms of action of Si-Ni-San in uveitis using bioinformatics and network pharmacology. Medicine (Baltimore). 2023 Aug 25; 102(34):e34615.
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Khalili P, Maddah R, Maleknia M, Shateri Amiri B, Forouzani F, Hasanvand A, Rezaeeyan H. Evaluation of Genes and Molecular Pathways Involved in the Progression of Monoclonal Gammopathy of Undetermined Significance (MGUS) to Multiple Myeloma: A Systems Biology Approach. Mol Biotechnol. 2023 Aug; 65(8):1275-1286.
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Gao Y, Lin KT, Jiang T, Yang Y, Rahman MA, Gong S, Bai J, Wang L, Sun J, Sheng L, Krainer AR, Hua Y. Systematic characterization of short intronic splicing-regulatory elements in SMN2 pre-mRNA. Nucleic Acids Res. 2022 01 25; 50(2):731-749.
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Ramalli SG, Miles AJ, Janes RW, Wallace BA. The PCDDB (Protein Circular Dichroism Data Bank): A Bioinformatics Resource for Protein Characterisations and Methods Development. J Mol Biol. 2022 06 15; 434(11):167441.
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Robeson MS, O'Rourke DR, Kaehler BD, Ziemski M, Dillon MR, Foster JT, Bokulich NA. RESCRIPt: Reproducible sequence taxonomy reference database management. PLoS Comput Biol. 2021 11; 17(11):e1009581.
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Udaondo Z. Big data and computational advancements for next generation of Microbial Biotechnology. Microb Biotechnol. 2022 01; 15(1):107-109.
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Sadr AS, Abdollahpour Z, Aliahmadi A, Eslahchi C, Nekouei M, Kiaei L, Kiaei M, Ghassempour A. Detection of structural and conformational changes in ALS-causing mutant profilin-1 with hydrogen/deuterium exchange mass spectrometry and bioinformatics techniques. Metab Brain Dis. 2022 01; 37(1):229-241.
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Datta A, Flynn NR, Barnette DA, Woeltje KF, Miller GP, Swamidass SJ. Machine learning liver-injuring drug interactions with non-steroidal anti-inflammatory drugs (NSAIDs) from a retrospective electronic health record (EHR) cohort. PLoS Comput Biol. 2021 07; 17(7):e1009053.
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Dillon MR, Bolyen E, Adamov A, Belk A, Borsom E, Burcham Z, Debelius JW, Deel H, Emmons A, Estaki M, Herman C, Keefe CR, Morton JT, Oliveira RRM, Sanchez A, Simard A, V?zquez-Baeza Y, Ziemski M, Miwa HE, Kerere TA, Coote C, Bonneau R, Knight R, Oliveira G, Gopalasingam P, Kaehler BD, Cope EK, Metcalf JL, Robeson Ii MS, Bokulich NA, Caporaso JG. Experiences and lessons learned from two virtual, hands-on microbiome bioinformatics workshops. PLoS Comput Biol. 2021 06; 17(6):e1009056.
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Rhone ET, Bardhi E, Bontha SV, Walker PD, Almenara JA, Dumur CI, Cathro H, Maluf D, Mas V. An Integrated Transcriptomic Approach to Identify Molecular Markers of Calcineurin Inhibitor Nephrotoxicity in Pediatric Kidney Transplant Recipients. Int J Mol Sci. 2021 May 21; 22(11).
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Jenjaroenpun P, Wongsurawat T, Wadley TD, Wassenaar TM, Liu J, Dai Q, Wanchai V, Akel NS, Jamshidi-Parsian A, Franco AT, Boysen G, Jennings ML, Ussery DW, He C, Nookaew I. Decoding the epitranscriptional landscape from native RNA sequences. Nucleic Acids Res. 2021 01 25; 49(2):e7.
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Jacobson DK, Honap TP, Ozga AT, Meda N, Kagon? TS, Carabin H, Spicer P, Tito RY, Obregon-Tito AJ, Reyes LM, Troncoso-Corzo L, Guija-Poma E, Sankaranarayanan K, Lewis CM. Analysis of global human gut metagenomes shows that metabolic resilience potential for short-chain fatty acid production is strongly influenced by lifestyle. Sci Rep. 2021 01 18; 11(1):1724.
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Patel L, Shukla T, Huang X, Ussery DW, Wang S. Machine Learning Methods in Drug Discovery. Molecules. 2020 Nov 12; 25(22).
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Deshpande S, Tytarenko RG, Wang Y, Boyle EM, Ashby C, Schinke CD, Thanendrarajan S, Zangari M, Zhan F, Davies FE, Morgan GJ, van Rhee F, Walker BA. Monitoring treatment response and disease progression in myeloma with circulating cell-free DNA. Eur J Haematol. 2021 Feb; 106(2):230-240.
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Zhang Q. Testing Differential Gene Networks under Nonparanormal Graphical Models with False Discovery Rate Control. Genes (Basel). 2020 02 05; 11(2).
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Smolander J, Stupnikov A, Glazko G, Dehmer M, Emmert-Streib F. Comparing biological information contained in mRNA and non-coding RNAs for classification of lung cancer patients. BMC Cancer. 2019 Dec 03; 19(1):1176.
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Deng P, Hoffman JB, Petriello MC, Wang CY, Li XS, Kraemer MP, Morris AJ, Hennig B. Dietary inulin decreases circulating ceramides by suppressing neutral sphingomyelinase expression and activity in mice. J Lipid Res. 2020 01; 61(1):45-53.
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Cochran AL, Cisler JM. A flexible and generalizable model of online latent-state learning. PLoS Comput Biol. 2019 09; 15(9):e1007331.
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Byrum SD, Washam CL, Patterson JD, Vyas KK, Gilbert KM, Blossom SJ. Continuous Developmental and Early Life Trichloroethylene Exposure Promoted DNA Methylation Alterations in Polycomb Protein Binding Sites in Effector/Memory CD4+ T Cells. Front Immunol. 2019; 10:2016.
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Quan J, Langelier C, Kuchta A, Batson J, Teyssier N, Lyden A, Caldera S, McGeever A, Dimitrov B, King R, Wilheim J, Murphy M, Ares LP, Travisano KA, Sit R, Amato R, Mumbengegwi DR, Smith JL, Bennett A, Gosling R, Mourani PM, Calfee CS, Neff NF, Chow ED, Kim PS, Greenhouse B, DeRisi JL, Crawford ED. FLASH: a next-generation CRISPR diagnostic for multiplexed detection of antimicrobial resistance sequences. Nucleic Acids Res. 2019 08 22; 47(14):e83.
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Bolyen E, Rideout JR, Dillon MR, Bokulich NA, Abnet CC, Al-Ghalith GA, Alexander H, Alm EJ, Arumugam M, Asnicar F, Bai Y, Bisanz JE, Bittinger K, Brejnrod A, Brislawn CJ, Brown CT, Callahan BJ, Caraballo-Rodr?guez AM, Chase J, Cope EK, Da Silva R, Diener C, Dorrestein PC, Douglas GM, Durall DM, Duvallet C, Edwardson CF, Ernst M, Estaki M, Fouquier J, Gauglitz JM, Gibbons SM, Gibson DL, Gonzalez A, Gorlick K, Guo J, Hillmann B, Holmes S, Holste H, Huttenhower C, Huttley GA, Janssen S, Jarmusch AK, Jiang L, Kaehler BD, Kang KB, Keefe CR, Keim P, Kelley ST, Knights D, Koester I, Kosciolek T, Kreps J, Langille MGI, Lee J, Ley R, Liu YX, Loftfield E, Lozupone C, Maher M, Marotz C, Martin BD, McDonald D, McIver LJ, Melnik AV, Metcalf JL, Morgan SC, Morton JT, Naimey AT, Navas-Molina JA, Nothias LF, Orchanian SB, Pearson T, Peoples SL, Petras D, Preuss ML, Pruesse E, Rasmussen LB, Rivers A, Robeson MS, Rosenthal P, Segata N, Shaffer M, Shiffer A, Sinha R, Song SJ, Spear JR, Swafford AD, Thompson LR, Torres PJ, Trinh P, Tripathi A, Turnbaugh PJ, Ul-Hasan S, van der Hooft JJJ, Vargas F, V?zquez-Baeza Y, Vogtmann E, von Hippel M, Walters W, Wan Y, Wang M, Warren J, Weber KC, Williamson CHD, Willis AD, Xu ZZ, Zaneveld JR, Zhang Y, Zhu Q, Knight R, Caporaso JG. Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2. Nat Biotechnol. 2019 08; 37(8):852-857.
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Ormseth MJ, Solus JF, Sheng Q, Ye F, Wu Q, Guo Y, Oeser AM, Allen RM, Vickers KC, Stein CM. Development and Validation of a MicroRNA Panel to Differentiate Between Patients with Rheumatoid Arthritis or Systemic Lupus Erythematosus and Controls. J Rheumatol. 2020 02; 47(2):188-196.
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Chen YZ, Kl?ditz K, Lee ES, Nguyen DP, Yuan Q, Johnson J, Lee-Yow Y, Hall A, Mitani S, Xia NS, Fadeel B, Xue D. Structure and function analysis of the C. elegans aminophospholipid translocase TAT-1. J Cell Sci. 2019 02 28; 132(5).
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He G, Liang Y, Chen Y, Yang W, Liu JS, Yang MQ, Guan R. A hotspots analysis-relation discovery representation model for revealing diabetes mellitus and obesity. BMC Syst Biol. 2018 12 14; 12(Suppl 7):116.
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Kiaei M, Balasubramaniam M, Govind Kumar V, Shmookler Reis RJ, Moradi M, Varughese KI. ALS-causing mutations in profilin-1 alter its conformational dynamics: A computational approach to explain propensity for aggregation. Sci Rep. 2018 08 30; 8(1):13102.
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Slavov SH, Stoyanova-Slavova I, Mattes W, Beger RD, Br?schweiler BJ. Computational identification of structural factors affecting the mutagenic potential of aromatic amines: study design and experimental validation. Arch Toxicol. 2018 07; 92(7):2369-2384.
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Gokulan K, Bekele AZ, Drake KL, Khare S. Responses of intestinal virome to silver nanoparticles: safety assessment by classical virology, whole-genome sequencing and bioinformatics approaches. Int J Nanomedicine. 2018; 13:2857-2867.
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Zhang Q. A powerful nonparametric method for detecting differentially co-expressed genes: distance correlation screening and edge-count test. BMC Syst Biol. 2018 05 16; 12(1):58.
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Musa A, Ghoraie LS, Zhang SD, Glazko G, Yli-Harja O, Dehmer M, Haibe-Kains B, Emmert-Streib F. A review of connectivity map and computational approaches in pharmacogenomics. Brief Bioinform. 2018 05 01; 19(3):506-523.
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Khanal T, Choi K, Leung YK, Wang J, Kim D, Janakiram V, Cho SG, Puga A, Ho SM, Kim K. Loss of NR2E3 represses AHR by LSD1 reprogramming, is associated with poor prognosis in liver cancer. Sci Rep. 2017 09 06; 7(1):10662.
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Nagarajan R, Upreti M. An ensemble predictive modeling framework for breast cancer classification. Methods. 2017 12 01; 131:128-134.
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Janes RW. PDB2CD visualises dynamics within protein structures. Eur Biophys J. 2017 Oct; 46(7):607-616.
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Chen L, Jenjaroenpun P, Pillai AM, Ivshina AV, Ow GS, Efthimios M, Zhiqun T, Tan TZ, Lee SC, Rogers K, Ward JM, Mori S, Adams DJ, Jenkins NA, Copeland NG, Ban KH, Kuznetsov VA, Thiery JP. Transposon insertional mutagenesis in mice identifies human breast cancer susceptibility genes and signatures for stratification. Proc Natl Acad Sci U S A. 2017 03 14; 114(11):E2215-E2224.
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Glazko G, Rahmatallah Y, Zybailov B, Emmert-Streib F. Extracting the Strongest Signals from Omics Data: Differentially Expressed Pathways and Beyond. Methods Mol Biol. 2017; 1613:125-159.
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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 01 04; 45(D1):D303-D307.
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Utturkar SM, Cude WN, Robeson MS, Yang ZK, Klingeman DM, Land ML, Allman SL, Lu TY, Brown SD, Schadt CW, Podar M, Doktycz MJ, Pelletier DA. Enrichment of Root Endophytic Bacteria from Populus deltoides and Single-Cell-Genomics Analysis. Appl Environ Microbiol. 2016 09 15; 82(18):5698-708.
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Xu Z, Taylor JA, Leung YK, Ho SM, Niu L. oxBS-MLE: an efficient method to estimate 5-methylcytosine and 5-hydroxymethylcytosine in paired bisulfite and oxidative bisulfite treated DNA. Bioinformatics. 2016 12 01; 32(23):3667-3669.
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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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Shibata A, Okuno T, Rahman MA, Azuma Y, Takeda J, Masuda A, Selcen D, Engel AG, Ohno K. IntSplice: prediction of the splicing consequences of intronic single-nucleotide variations in the human genome. J Hum Genet. 2016 Jul; 61(7):633-40.
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Paugh SW, Coss DR, Bao J, Laudermilk LT, Grace CR, Ferreira AM, Waddell MB, Ridout G, Naeve D, Leuze M, LoCascio PF, Panetta JC, Wilkinson MR, Pui CH, Naeve CW, Uberbacher EC, Bonten EJ, Evans WE. MicroRNAs Form Triplexes with Double Stranded DNA at Sequence-Specific Binding Sites; a Eukaryotic Mechanism via which microRNAs Could Directly Alter Gene Expression. PLoS Comput Biol. 2016 Feb; 12(2):e1004744.
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Medema MH, Kottmann R, Yilmaz P, Cummings M, Biggins JB, Blin K, de Bruijn I, Chooi YH, Claesen J, Coates RC, Cruz-Morales P, Duddela S, D?sterhus S, Edwards DJ, Fewer DP, Garg N, Geiger C, Gomez-Escribano JP, Greule A, Hadjithomas M, Haines AS, Helfrich EJ, Hillwig ML, Ishida K, Jones AC, Jones CS, Jungmann K, Kegler C, Kim HU, K?tter P, Krug D, Masschelein J, Melnik AV, Mantovani SM, Monroe EA, Moore M, Moss N, N?tzmann HW, Pan G, Pati A, Petras D, Reen FJ, Rosconi F, Rui Z, Tian Z, Tobias NJ, Tsunematsu Y, Wiemann P, Wyckoff E, Yan X, Yim G, Yu F, Xie Y, Aigle B, Apel AK, Balibar CJ, Balskus EP, Barona-G?mez F, Bechthold A, Bode HB, Borriss R, Brady SF, Brakhage AA, Caffrey P, Cheng YQ, Clardy J, Cox RJ, De Mot R, Donadio S, Donia MS, van der Donk WA, Dorrestein PC, Doyle S, Driessen AJ, Ehling-Schulz M, Entian KD, Fischbach MA, Gerwick L, Gerwick WH, Gross H, Gust B, Hertweck C, H?fte M, Jensen SE, Ju J, Katz L, Kaysser L, Klassen JL, Keller NP, Kormanec J, Kuipers OP, Kuzuyama T, Kyrpides NC, Kwon HJ, Lautru S, Lavigne R, Lee CY, Linquan B, Liu X, Liu W, Luzhetskyy A, Mahmud T, Mast Y, M?ndez C, Mets?-Ketel? M, Micklefield J, Mitchell DA, Moore BS, Moreira LM, M?ller R, Neilan BA, Nett M, Nielsen J, O'Gara F, Oikawa H, Osbourn A, Osburne MS, Ostash B, Payne SM, Pernodet JL, Petricek M, Piel J, Ploux O, Raaijmakers JM, Salas JA, Schmitt EK, Scott B, Seipke RF, Shen B, Sherman DH, Sivonen K, Smanski MJ, Sosio M, Stegmann E, S?ssmuth RD, Tahlan K, Thomas CM, Tang Y, Truman AW, Viaud M, Walton JD, Walsh CT, Weber T, van Wezel GP, Wilkinson B, Willey JM, Wohlleben W, Wright GD, Ziemert N, Zhang C, Zotchev SB, Breitling R, Takano E, Gl?ckner FO. Minimum Information about a Biosynthetic Gene cluster. Nat Chem Biol. 2015 Sep; 11(9):625-31.
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