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Summary

Summary: Software application for retrieving, presenting and traversing information resources on the World Wide Web.

Top Publications

  1. Diaz A, Nellore A, Song J. CHANCE: comprehensive software for quality control and validation of ChIP-seq data. Genome Biol. 2012;13:R98 pubmed publisher
    ..CHANCE is available at https://github.com/songlab/chance. ..
  2. Halachev K, Bast H, Albrecht F, Lengauer T, Bock C. EpiExplorer: live exploration and global analysis of large epigenomic datasets. Genome Biol. 2012;13:R96 pubmed publisher
    ..All EpiExplorer analyses are performed dynamically within seconds, using an efficient and versatile text indexing scheme that we introduce to bioinformatics. EpiExplorer is available at http://epiexplorer.mpi-inf.mpg.de. ..
  3. Hou M, Tian F, Jiang S, Kong L, Yang D, Gao G. LocExpress: a web server for efficiently estimating expression of novel transcripts. BMC Genomics. 2016;17:1023 pubmed publisher
    ..The server is publicly available at http://loc-express.cbi.pku.edu.cn . ..
  4. Summers K, Hume D. Identification of the macrophage-specific promoter signature in FANTOM5 mouse embryo developmental time course data. J Leukoc Biol. 2017;102:1081-1092 pubmed publisher
    ..The FANTOM5 data are available on a comprehensive browser (http://fantom.gsc.riken.jp/zenbu/), which provides a resource for the study of macrophage transcriptional regulation and roles in mouse development. ..
  5. Yan J, Chuai G, Qi T, Shao F, Zhou C, Zhu C, et al. MetaTopics: an integration tool to analyze microbial community profile by topic model. BMC Genomics. 2017;18:962 pubmed publisher
    ..MetaTopics is the first interactive R package to integrate the state-of-arts topic model derived from statistical learning community to analyze and visualize the metagenomics taxonomy data. ..
  6. Zhou X, Li D, Zhang B, Lowdon R, Rockweiler N, Sears R, et al. Epigenomic annotation of genetic variants using the Roadmap Epigenome Browser. Nat Biotechnol. 2015;33:345-6 pubmed
  7. Blizniuk A, Furukawa S, Ueno M, Kawaguchi Y. Evaluation of English Websites on Dental Caries by Using Consumer Evaluation Tools. Oral Health Prev Dent. 2016;14:363-9 pubmed publisher
    ..The LIDA instrument was found to be more convenient than DISCERN and can be recommended to lay people for quick quality assessment. ..
  8. Pundir S, Martin M, O Donovan C. UniProt Protein Knowledgebase. Methods Mol Biol. 2017;1558:41-55 pubmed publisher
    ..This chapter introduces the functionality and data provided by UniProt. It describes example use cases for which you might come to UniProt and the methods to help you achieve your goals. ..
  9. Haussen D, Doppelheuer S, Schindler K, Grossberg J, Bouslama M, Schultz M, et al. Utilization of a Smartphone Platform for Electronic Informed Consent in Acute Stroke Trials. Stroke. 2017;48:3156-3160 pubmed publisher
    ..002). e-Consenting streamlined the consenting process in a randomized trial of patients with emergent large vessel occlusion strokes. ..

More Information

Publications26

  1. Ciemny M, Kurcinski M, Kozak K, Kolinski A, Kmiecik S. Highly Flexible Protein-Peptide Docking Using CABS-Dock. Methods Mol Biol. 2017;1561:69-94 pubmed publisher
    ..Finally, a tutorial for running CABS-dock from the command line or command line scripts is provided. The CABS-dock web server is available from http://biocomp.chem.uw.edu.pl/CABSdock/ . ..
  2. Ponyared P, Ponsawat J, Tongsima S, Seresangtakul P, Akkasaeng C, Tantisuwichwong N. ESAP plus: a web-based server for EST-SSR marker development. BMC Genomics. 2016;17:1035 pubmed publisher
    ..ESAP Plus can handle considerably large EST datasets. This EST-SSR discovery tool can be accessed directly from: http://gbp.kku.ac.th/esap_plus/ . ..
  3. . Expansion of the Gene Ontology knowledgebase and resources. Nucleic Acids Res. 2017;45:D331-D338 pubmed publisher
    ..To learn more, visit http://geneontology.org/. ..
  4. Tang Z, Bunn P, Tao R, Liu Z, Lin D. PreMeta: a tool to facilitate meta-analysis of rare-variant associations. BMC Genomics. 2017;18:160 pubmed publisher
    ..PreMeta processes summary statistics from the four packages to make them compatible and avoids the need to redo study-level analyses. PreMeta documentation and executable are available at: http://dlin.web.unc.edu/software/premeta . ..
  5. Russo F, Di Bella S, Bonnici V, Laganà A, Rainaldi G, Pellegrini M, et al. A knowledge base for the discovery of function, diagnostic potential and drug effects on cellular and extracellular miRNAs. BMC Genomics. 2014;15 Suppl 3:S4 pubmed publisher
    ..This allows users to improve the knowledge about the function, diagnostic potential, and the drug effects on cellular and circulating miRNAs. ..
  6. Van Bel M, Proost S, Van Neste C, Deforce D, Van de Peer Y, Vandepoele K. TRAPID: an efficient online tool for the functional and comparative analysis of de novo RNA-Seq transcriptomes. Genome Biol. 2013;14:R134 pubmed publisher
    ..Benchmarking and comparison against state-of-the-art transcript analysis tools reveals the efficiency and unique features of the TRAPID system. TRAPID is freely available at http://bioinformatics.psb.ugent.be/webtools/trapid/. ..
  7. Tun S, Lubell Y, Dondorp A, Fieldman T, Tun K, Celhay O, et al. Identifying artemisinin resistance from parasite clearance half-life data with a simple Shiny web application. PLoS ONE. 2017;12:e0177840 pubmed publisher
    ..falciparum infected patients after treatment with artemisinin derivatives, so that resistance to artemisinin can be identified. The tool can be accessed at bit.ly/id_artemisinin_resistance. ..
  8. Ferdman S, Minkov E, Bekkerman R, Gefen D. Quantifying the web browser ecosystem. PLoS ONE. 2017;12:e0179281 pubmed publisher
    ..Results may herald insight on how other evolving internet ecosystems may behave, and suggest a methodology for measuring this behavior. Specifically, applying such a methodology could transform the addon market. ..
  9. Coletta A, Molter C, Duque R, Steenhoff D, Taminau J, de Schaetzen V, et al. InSilico DB genomic datasets hub: an efficient starting point for analyzing genome-wide studies in GenePattern, Integrative Genomics Viewer, and R/Bioconductor. Genome Biol. 2012;13:R104 pubmed publisher
    ..The InSilico DB platform is a powerful collaborative environment, with advanced capabilities for biocuration, dataset sharing, and dataset subsetting and combination. InSilico DB is available from https://insilicodb.org. ..
  10. . UniProt: the universal protein knowledgebase. Nucleic Acids Res. 2017;45:D158-D169 pubmed publisher
    ..We provide a SPARQL endpoint that allows complex queries of the more than 22 billion triples of data in UniProt (http://sparql.uniprot.org/). UniProt resources can be accessed via the website at http://www.uniprot.org/. ..
  11. Mutarelli M, Marwah V, Rispoli R, Carrella D, Dharmalingam G, Oliva G, et al. A community-based resource for automatic exome variant-calling and annotation in Mendelian disorders. BMC Genomics. 2014;15 Suppl 3:S5 pubmed publisher
    ..This resource may become a valuable tool to help dissecting the genotype underlying the disease phenotype through an improved selection of putative patient-specific causative or phenotype-associated variations. ..
  12. Lee B, Tiong K, Chang J, Liew C, Abdul Rahman Z, Tan A, et al. DeSigN: connecting gene expression with therapeutics for drug repurposing and development. BMC Genomics. 2017;18:934 pubmed publisher
    ..This user-friendly platform could be used to identify drugs with unanticipated efficacy against cancer cell lines of interest, and therefore could be used for the repurposing of drugs, thus improving the efficiency of drug development. ..
  13. Mallona I, Peinado M. Truke, a web tool to check for and handle excel misidentified gene symbols. BMC Genomics. 2017;18:242 pubmed publisher
    ..following user's preferences. Truke is a data format conversion tool with a unique corrupted gene symbol detection utility. Truke is freely available without registration at http://maplab.cat/truke . ..
  14. Cheng X, Xiao X, Chou K. pLoc-mVirus: Predict subcellular localization of multi-location virus proteins via incorporating the optimal GO information into general PseAAC. Gene. 2017;628:315-321 pubmed publisher
    ..jci-bioinfo.cn/pLoc-mVirus/, by which users can easily get their desired results without the need to go through the complicated mathematics involved. ..
  15. Qiao Y, Quinlan A, Jazaeri A, Verhaak R, Wheeler D, Marth G. SubcloneSeeker: a computational framework for reconstructing tumor clone structure for cancer variant interpretation and prioritization. Genome Biol. 2014;15:443 pubmed publisher
    ..SubcloneSeeker is available at: https://github.com/yiq/SubcloneSeeker. ..
  16. Xu Z, Liu J, Ni W, Peng Z, Guo Y, Ye W, et al. GrTEdb: the first web-based database of transposable elements in cotton (Gossypium raimondii). Database (Oxford). 2017;2017: pubmed publisher
    ..http://www.grtedb.org/. ..
  17. Madden S, Clarke C, Gaule P, Aherne S, O Donovan N, Clynes M, et al. BreastMark: an integrated approach to mining publicly available transcriptomic datasets relating to breast cancer outcome. Breast Cancer Res. 2013;15:R52 pubmed
    ..The value of this tool will be in the preliminary assessment of putative biomarkers in breast cancer. It will be of particular use to research groups with limited bioinformatics facilities. ..