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5,053 research outcomes, page 1 of 506
  • publication . Article . 2009
    Open Access English
    Authors:
    Eunjung Lee; Hyunchul Jung; Predrag Radivojac; Jong-Won Kim; Doheon Lee;
    Publisher: American Medical Informatics Association
    Project: NSF | CAREER: Bioinformatics of... (0644017)

    Abstract Background Identifying disease causing genes and understanding their molecular mechanisms are essential to developing effective therapeutics. Thus, several computational methods have been proposed to prioritize candidate disease genes by integrating different d...

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  • publication . Other literature type . Article . Preprint . 2019
    Open Access
    Authors:
    Samir Rachid Zaim; Colleen Kenost; Joanne Berghout; Wesley Chiu; Liam Wilson; Hao Helen Zhang; Yves A. Lussier;
    Publisher: Cold Spring Harbor Laboratory
    Project: NIH | CANCER CENTER CORE SUPPOR... (2P30CA023074-12), NIH | University of Arizona - B... (3UG3OD023171-01S1), NIH | Immuno-Genetic Basis for ... (5U01AI122275-02)

    AbstractBackgroundIn this era of data science-driven bioinformatics, machine learning research has focused on feature selection as users want more interpretation and post-hoc analyses for biomarker detection. However, when there are more features (i.e., transcript) than...

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  • publication . Article . 2010
    Open Access
    Authors:
    Denise R. Koessler; Debra J. Knisley; Jeff Knisley; Teresa W. Haynes;
    Persistent Identifiers
    Project: NSF | Science First! (0742364)

    Abstract Background Determining the secondary structure of RNA from the primary structure is a challenging computational problem. A number of algorithms have been developed to predict the secondary structure from the primary structure. It is agreed that there is still r...

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  • publication . Article . 2005
    Open Access
    Authors:
    Lorraine K. Tanabe; Natalie Xie; Lynne H. Thom; Wayne Matten; W. John Wilbur;
    Persistent Identifiers
    Publisher: Springer Science and Business Media LLC

    Named entity recognition (NER) is an important first step for text mining the biomedical literature. Evaluating the performance of biomedical NER systems is impossible without a standardized test corpus. The annotation of such a corpus for gene/protein name NER is a dif...

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  • publication . Article . 2009
    Open Access English
    Authors:
    Andrew J. Bordner;
    Persistent Identifiers
    Publisher: BioMed Central

    Abstract Background Many integral membrane proteins, like their non-membrane counterparts, form either transient or permanent multi-subunit complexes in order to carry out their biochemical function. Computational methods that provide structural details of these interac...

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  • publication . Article . 2012
    Open Access
    Authors:
    Xiaogang Wu; Hui Huang; Madhankumar Sonachalam; Sina Reinhard; Jeffrey D. Shen; Ragini Pandey; Jake Y. Chen;
    Persistent Identifiers
    Publisher: Springer Nature

    Background: Current network-based microarray analysis uses the information of interactions among concerned genes/gene products, but still considers each gene expression individually. We propose an organized knowledgesupervised approach - Integrative eXpression Profiling...

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  • publication . Article . 2011
    Open Access
    Authors:
    Igor Chikalov; Peggy Yao; Mikhail Moshkov; Jean-Claude Latombe;
    Publisher: Springer Science and Business Media LLC

    Abstract Background Hydrogen bonds (H-bonds) play a key role in both the formation and stabilization of protein structures. They form and break while a protein deforms, for instance during the transition from a non-functional to a functional state. The intrinsic strengt...

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  • publication . Article . 2009
    Open Access English
    Authors:
    Wei Zhao; Kirk E. Hevener; Stephen W. White; Richard E. Lee; James M. Boyett;
    Persistent Identifiers
    Publisher: BioMed Central

    Abstract Background Receiver operating characteristic (ROC) curve is widely used to evaluate virtual screening (VS) studies. However, the method fails to address the "early recognition" problem specific to VS. Although many other metrics, such as RIE, BEDROC, and pROC t...

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  • publication . Article . 2005
    Open Access English
    Authors:
    Brown, C Titus; Xie, Yuan; Davidson, Eric H; Cameron, R Andrew;
    Persistent Identifiers
    Publisher: BioMed Central
    Project: NIH | Gene Library Resource for... (2P40RR015044-06), NIH | Computational Model of Ge... (5R01GM061005-08)

    Abstract Background Comparative sequence analysis is an effective and increasingly common way to identify cis-regulatory regions in animal genomes. Results We describe three tools for comparative analysis of pairs of BAC-sized genomic regions. Paircomp is a tool that do...

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  • publication . Article . 2015
    Open Access English
    Authors:
    Juan P. Steibel; Heng Wang; Ping-Shou Zhong;
    Persistent Identifiers
    Publisher: BioMed Central
    Project: NSF | Statistical inference for... (1209112), NSF | Collaborative Research: H... (1309156)

    Background Allelic specific expression (ASE) increases our understanding of the genetic control of gene expression and its links to phenotypic variation. ASE testing is implemented through binomial or beta-binomial tests of sequence read counts of alternative alleles at...

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5,053 research outcomes, page 1 of 506