 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 |
|---|
| 2021 | 1 | 0 | 1 | | 2020 | 4 | 2 | 6 | | 2019 | 2 | 4 | 6 | | 2018 | 6 | 6 | 12 | | 2017 | 4 | 5 | 9 | | 2016 | 4 | 5 | 9 | | 2015 | 2 | 6 | 8 | | 2014 | 3 | 3 | 6 | | 2013 | 4 | 5 | 9 | | 2012 | 3 | 4 | 7 | | 2011 | 3 | 3 | 6 | | 2010 | 3 | 2 | 5 | | 2009 | 5 | 1 | 6 | | 2008 | 3 | 4 | 7 | | 2007 | 1 | 5 | 6 | | 2006 | 5 | 3 | 8 | | 2005 | 4 | 2 | 6 | | 2004 | 2 | 2 | 4 | | 2003 | 3 | 2 | 5 | | 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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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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Springer A, Chachere D, Alsarkhi A, Zozus M. The Impact of Information Quality on Retracted Bioinformatics Literature. Stud Health Technol Inform. 2020 Jun 16; 270:1203-1204.
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Smith AK, Ropella GEP, McGill MR, Krishnan P, Dutta L, Kennedy RC, Jaeschke H, Hunt CA. Contrasting model mechanisms of alanine aminotransferase (ALT) release from damaged and necrotic hepatocytes as an example of general biomarker mechanisms. PLoS Comput Biol. 2020 06; 16(6):e1007622.
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Lieven C, Beber ME, Olivier BG, Bergmann FT, Ataman M, Babaei P, Bartell JA, Blank LM, Chauhan S, Correia K, Diener C, Dräger A, Ebert BE, Edirisinghe JN, Faria JP, Feist AM, Fengos G, Fleming RMT, García-Jiménez B, Hatzimanikatis V, van Helvoirt W, Henry CS, Hermjakob H, Herrgård MJ, Kaafarani A, Kim HU, King Z, Klamt S, Klipp E, Koehorst JJ, König M, Lakshmanan M, Lee DY, Lee SY, Lee S, Lewis NE, Liu F, Ma H, Machado D, Mahadevan R, Maia P, Mardinoglu A, Medlock GL, Monk JM, Nielsen J, Nielsen LK, Nogales J, Nookaew I, Palsson BO, Papin JA, Patil KR, Poolman M, Price ND, Resendis-Antonio O, Richelle A, Rocha I, Sánchez BJ, Schaap PJ, Malik Sheriff RS, Shoaie S, Sonnenschein N, Teusink B, Vilaça P, Vik JO, Wodke JAH, Xavier JC, Yuan Q, Zakhartsev M, Zhang C. MEMOTE for standardized genome-scale metabolic model testing. Nat Biotechnol. 2020 03; 38(3):272-276.
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Xu F, Ge C, Luo H, Li S, Wiedmann M, Deng X, Zhang G, Stevenson A, Baker RC, Tang S. Evaluation of real-time nanopore sequencing for Salmonella serotype prediction. Food Microbiol. 2020 Aug; 89:103452.
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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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Ling L, Ren X, Cao X, Hassan ABM, Mah S, Sathiyanathan P, Smith RAA, Tan CLL, Eio M, Samsonraj RM, van Wijnen AJ, Raghunath M, Nurcombe V, Hui JH, Cool SM. Enhancing the Efficacy of Stem Cell Therapy with Glycosaminoglycans. Stem Cell Reports. 2020 01 14; 14(1):105-121.
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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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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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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-Rodríguez 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, Vázquez-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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Langevin SM, Kuhnell D, Niu L, Biesiada J, Leung YK, Deka R, Chen A, Medvedovic M, Kelsey KT, Kasper S, Zhang X. Comprehensive mapping of the methylation landscape of 16 CpG-dense regions in oral and pharyngeal squamous cell carcinoma. Epigenomics. 2019 07; 11(9):987-1002.
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Der E, Suryawanshi H, Morozov P, Kustagi M, Goilav B, Ranabothu S, Izmirly P, Clancy R, Belmont HM, Koenigsberg M, Mokrzycki M, Rominieki H, Graham JA, Rocca JP, Bornkamp N, Jordan N, Schulte E, Wu M, Pullman J, Slowikowski K, Raychaudhuri S, Guthridge J, James J, Buyon J, Tuschl T, Putterman C. Tubular cell and keratinocyte single-cell transcriptomics applied to lupus nephritis reveal type I IFN and fibrosis relevant pathways. Nat Immunol. 2019 07; 20(7):915-927.
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Dix SR, Owen HJ, Sun R, Ahmad A, Shastri S, Spiewak HL, Mosby DJ, Harris MJ, Batters SL, Brooker TA, Tzokov SB, Sedelnikova SE, Baker PJ, Bullough PA, Rice DW, Thomas MS. Structural insights into the function of type VI secretion system TssA subunits. Nat Commun. 2018 11 12; 9(1):4765.
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Elias KM, Tsantoulis P, Tille JC, Vitonis A, Doyle LA, Hornick JL, Kaya G, Barnes L, Cramer DW, Puppa G, Stuckelberger S, Hooda J, Dietrich PY, Goggins M, Kerr CL, Birrer M, Hirsch MS, Drapkin R, Labidi-Galy SI. Primordial germ cells as a potential shared cell of origin for mucinous cystic neoplasms of the pancreas and mucinous ovarian tumors. J Pathol. 2018 12; 246(4):459-469.
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Kuznetsov VA, Bondarenko V, Wongsurawat T, Yenamandra SP, Jenjaroenpun P. Toward predictive R-loop computational biology: genome-scale prediction of R-loops reveals their association with complex promoter structures, G-quadruplexes and transcriptionally active enhancers. Nucleic Acids Res. 2018 09 06; 46(15):7566-7585.
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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, Brüschweiler 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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Causey JL, Ashby C, Walker K, Wang ZP, Yang M, Guan Y, Moore JH, Huang X. DNAp: A Pipeline for DNA-seq Data Analysis. Sci Rep. 2018 05 01; 8(1):6793.
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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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Wu B, Huang J, Zhang L, Kasukurthi MV, Huang F, Bian J, Fukuo K, Kazumi T. An integrative approach to investigate the association among high-sensitive C-reactive protein, body fat mass distribution, and other cardiometabolic risk factors in young healthy women. Methods. 2018 08 01; 145:60-66.
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Roberts BS, Hardigan AA, Moore DE, Ramaker RC, Jones AL, Fitz-Gerald MB, Cooper GM, Wilcox CM, Kimberly RP, Myers RM. Discovery and Validation of Circulating Biomarkers of Colorectal Adenoma by High-Depth Small RNA Sequencing. Clin Cancer Res. 2018 05 01; 24(9):2092-2099.
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Fok JHL, Hedayat S, Zhang L, Aronson LI, Mirabella F, Pawlyn C, Bright MD, Wardell CP, Keats JJ, De Billy E, Rye CS, Chessum NEA, Jones K, Morgan GJ, Eccles SA, Workman P, Davies FE. HSF1 Is Essential for Myeloma Cell Survival and A Promising Therapeutic Target. Clin Cancer Res. 2018 05 15; 24(10):2395-2407.
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Butt AT, Thomas MS. Iron Acquisition Mechanisms and Their Role in the Virulence of Burkholderia Species. Front Cell Infect Microbiol. 2017; 7:460.
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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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Shakir A, Ripperger M, Jiang Z, Wierenga KJ. Inferred inheritance of MorbidMap genes without OMIM clinical synopsis. Genet Med. 2018 04; 20(4):470-473.
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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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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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Zhang Q, Jun SR, Leuze M, Ussery D, Nookaew I. Viral Phylogenomics Using an Alignment-Free Method: A Three-Step Approach to Determine Optimal Length of k-mer. Sci Rep. 2017 01 19; 7:40712.
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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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Makhoul I. Cancer heterogeneity, patient diversity and next-generation cognitive computing. J Ark Med Soc. 2016 Dec; 113(6):126.
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Natale DA, Arighi CN, Blake JA, Bona J, Chen C, Chen SC, Christie KR, Cowart J, D'Eustachio P, Diehl AD, Drabkin HJ, Duncan WD, Huang H, Ren J, Ross K, Ruttenberg A, Shamovsky V, Smith B, Wang Q, Zhang J, El-Sayed A, Wu CH. Protein Ontology (PRO): enhancing and scaling up the representation of protein entities. Nucleic Acids Res. 2017 01 04; 45(D1):D339-D346.
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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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Cao S, Wendl MC, Wyczalkowski MA, Wylie K, Ye K, Jayasinghe R, Xie M, Wu S, Niu B, Grubb R, Johnson KJ, Gay H, Chen K, Rader JS, Dipersio JF, Chen F, Ding L. Divergent viral presentation among human tumors and adjacent normal tissues. Sci Rep. 2016 06 24; 6:28294.
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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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Shrestha RP, Horowitz J, Hollot CV, Germain MJ, Widness JA, Mock DM, Veng-Pedersen P, Chait Y. Models for the red blood cell lifespan. J Pharmacokinet Pharmacodyn. 2016 06; 43(3):259-74.
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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, Düsterhus 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, Kötter P, Krug D, Masschelein J, Melnik AV, Mantovani SM, Monroe EA, Moore M, Moss N, Nützmann 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-Gómez 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, Höfte 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, Méndez C, Metsä-Ketelä M, Micklefield J, Mitchell DA, Moore BS, Moreira LM, Müller 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, Süssmuth 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, Glöckner FO. Minimum Information about a Biosynthetic Gene cluster. Nat Chem Biol. 2015 Sep; 11(9):625-31.
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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 (Reading). 2015 Sep; 161(9):1762-1779.
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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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Vathipadiekal V, Wang V, Wei W, Waldron L, Drapkin R, Gillette M, Skates S, Birrer M. Creation of a Human Secretome: A Novel Composite Library of Human Secreted Proteins: Validation Using Ovarian Cancer Gene Expression Data and a Virtual Secretome Array. Clin Cancer Res. 2015 Nov 01; 21(21):4960-9.
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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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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. Annu Int Conf 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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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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