Jimmy Lin

Summary

Affiliation: University of Maryland
Country: USA

Publications

  1. pmc Searching for SNPs with cloud computing
    Ben Langmead
    Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, 615 North Wolfe Street, Baltimore, Maryland 21205, USA
    Genome Biol 10:R134. 2009
  2. pmc PubMed related articles: a probabilistic topic-based model for content similarity
    Jimmy Lin
    College of Information Studies, University of Maryland, College Park, Maryland, USA
    BMC Bioinformatics 8:423. 2007
  3. pmc PageRank without hyperlinks: reranking with PubMed related article networks for biomedical text retrieval
    Jimmy Lin
    National Center for Biotechnology Information, National Library of Medicine, Bethesda, Maryland, USA
    BMC Bioinformatics 9:270. 2008
  4. pmc Is searching full text more effective than searching abstracts?
    Jimmy Lin
    National Center for Biotechnology Information, National Library of Medicine, Bethesda, Maryland, USA
    BMC Bioinformatics 10:46. 2009
  5. ncbi request reprint Prediction of regulatory networks: genome-wide identification of transcription factor targets from gene expression data
    Jiang Qian
    Department of Ophthalmology, Johns Hopkins Medical School, Baltimore, MD 21287, USA
    Bioinformatics 19:1917-26. 2003
  6. pmc Genome-wide prediction and characterization of interactions between transcription factors in Saccharomyces cerevisiae
    Xueping Yu
    Wilmer Institute, Johns Hopkins University School of Medicine, Baltimore, MD 21287 USA
    Nucleic Acids Res 34:917-27. 2006
  7. pmc Identification of tissue-specific cis-regulatory modules based on interactions between transcription factors
    Xueping Yu
    Wilmer Institute, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
    BMC Bioinformatics 8:437. 2007
  8. ncbi request reprint Transcriptional regulatory network prediction
    Jimmy Lin
    Wilmer Eye Institute, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
    Biotechnol Genet Eng Rev 22:45-62. 2006

Collaborators

  • W John Wilbur
  • Eric Z Yu
  • Xueping Yu
  • Jiang Qian
  • Ben Langmead
  • Donald J Zack
  • Steven L Salzberg
  • Michael C Schatz
  • Mihai Pop
  • Tomohiro Masuda
  • Noriko Esumi
  • Haiyuan Yu
  • Nicholas M Luscombe
  • Mark Gerstein

Detail Information

Publications8

  1. pmc Searching for SNPs with cloud computing
    Ben Langmead
    Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, 615 North Wolfe Street, Baltimore, Maryland 21205, USA
    Genome Biol 10:R134. 2009
    ..Crossbow is available from http://bowtie-bio.sourceforge.net/crossbow/...
  2. pmc PubMed related articles: a probabilistic topic-based model for content similarity
    Jimmy Lin
    College of Information Studies, University of Maryland, College Park, Maryland, USA
    BMC Bioinformatics 8:423. 2007
    ..We also describe a novel technique for estimating parameters that does not require human relevance judgments; instead, the process is based on the existence of MeSH in MEDLINE...
  3. pmc PageRank without hyperlinks: reranking with PubMed related article networks for biomedical text retrieval
    Jimmy Lin
    National Center for Biotechnology Information, National Library of Medicine, Bethesda, Maryland, USA
    BMC Bioinformatics 9:270. 2008
    ..Thus, a MEDLINE record represents a node in a vast content-similarity network. This article explores the hypothesis that these networks can be exploited for text retrieval, in the same manner as hyperlink graphs on the Web...
  4. pmc Is searching full text more effective than searching abstracts?
    Jimmy Lin
    National Center for Biotechnology Information, National Library of Medicine, Bethesda, Maryland, USA
    BMC Bioinformatics 10:46. 2009
    ..Two retrieval models are examined: bm25 and the ranking algorithm implemented in the open-source Lucene search engine...
  5. ncbi request reprint Prediction of regulatory networks: genome-wide identification of transcription factor targets from gene expression data
    Jiang Qian
    Department of Ophthalmology, Johns Hopkins Medical School, Baltimore, MD 21287, USA
    Bioinformatics 19:1917-26. 2003
    ..g. simple correlation over the timecourse), and current analysis methods, such as hierarchical clustering, have not been very successful in deciphering them...
  6. pmc Genome-wide prediction and characterization of interactions between transcription factors in Saccharomyces cerevisiae
    Xueping Yu
    Wilmer Institute, Johns Hopkins University School of Medicine, Baltimore, MD 21287 USA
    Nucleic Acids Res 34:917-27. 2006
    ..Our prediction and characterization of TF interactions may help to understand the transcriptional regulatory networks in eukaryotic systems...
  7. pmc Identification of tissue-specific cis-regulatory modules based on interactions between transcription factors
    Xueping Yu
    Wilmer Institute, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
    BMC Bioinformatics 8:437. 2007
    ..Motivated by increasing evidence that some DNA regulatory regions are not evolutionary conserved, we have developed an approach for cis-regulatory region identification that does not rely upon evolutionary sequence conservation...
  8. ncbi request reprint Transcriptional regulatory network prediction
    Jimmy Lin
    Wilmer Eye Institute, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
    Biotechnol Genet Eng Rev 22:45-62. 2006