Computer Science and Informatics

 

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  • Yu, P.; Wild, D.J. (Chemistry Central Ltd., 2012)
    Relating chemical features to bioactivities is critical in molecular design and is used extensively in the lead discovery and optimization process. A variety of techniques from statistics, data mining and machine learning ...
  • Fodor, A.A; DeSantis, T.Z; Wylie, K.M; Badger, J.H; Ye, Y.; Hepburn, T.; Hu, P.; Sodergren, E.; Liolios, K.; Huot-Creasy, H.; Birren, B.W.; Earl, A.M. (Public Library of Science, 2012)
    The goal of the Human Microbiome Project (HMP) is to generate a comprehensive catalog of human-associated microorganisms including reference genomes representing the most common species. Toward this goal, the HMP has ...
  • Wu, Y.-W.; Rho, M.; Doak, T.G.; Ye, Y. (American Society for Microbiology, 2012)
    The NIH Human Microbiome Project (HMP) has produced several hundred metagenomic data sets, allowing studies of the many functional elements in human-associated microbial communities. Here, we survey the distribution of ...
  • Rho, M.; Wu, Y.-W.; Tang, H.; Doak, T.G.; Ye, Y. (Public Library of Science, 2012)
    CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) loci, together with cas (CRISPR-associated) genes, form the CRISPR/Cas adaptive immune system, a primary defense strategy that eubacteria and archaea ...
  • Yu, P.; Wild, D.J. (Chemistry Central, 2012)
    Relating chemical features to bioactivities is critical in molecular design and is used extensively in the lead discovery and optimization process. A variety of techniques from statistics, data mining and machine learning ...
  • Shuai, X.; Pepe, A.; Bollen, J. (Public Library of Science, 2012)
    We analyze the online response to the preprint publication of a cohort of 4,606 scientific articles submitted to the preprint database arXiv.org between October 2010 and May 2011. We study three forms of responses to these ...
  • Seal, A.; Passi, A.; Jaleel, U.C.A.; Consortium, O.S.D.D.; Wild, D.J. (Chemistry Central, 2012)
    Experimental screening of chemical compounds for biological activity is a time consuming and expensive practice. In silico predictive models permit inexpensive, rapid "virtual screening" to prioritize selection of compounds ...
  • Huse, S.M.; Ye, Y.; Zhou, Y.; Fodor, A.A. (Public Library of Science, 2012)
    We explore the microbiota of 18 body sites in over 200 individuals using sequences amplified V1-V3 and the V3-V5 small subunit ribosomal RNA (16S) hypervariable regions as part of the NIH Common Fund Human Microbiome ...
  • Kaur, J.; Hoang, D.T.; Sun, X.; Patil, S.; Menczer, F. (Public Library of Science, 2012)
    The use of quantitative metrics to gauge the impact of scholarly publications, authors, and disciplines is predicated on the availability of reliable usage and annotation data. Citation and download counts are widely ...
  • Wang, M.; Ye, Y.; Tang, H. (Mary Ann Liebert, Inc. publishers, 2012)
    The wide applications of next-generation sequencing (NGS) technologies in metagenomics have raised many computational challenges. One of the essential problems in metagenomics is to estimate the taxonomic composition of a ...
  • Weng, L.; Flammini, A.; Vespignani, A.; Menczer, F. (Nature Publishing Group, 2012)
    The wide adoption of social media has increased the competition among ideas for our finite attention. We employ a parsimonious agent-based model to study whether such a competition may affect the popularity of different ...
  • Chen, Bin; Ding, Ying; Wild, David J. (PLoS Computational Biology, 2012-07)
    The rapidly increasing amount of public data in chemistry and biology provides new opportunities for large-scale data mining for drug discovery. Systematic integration of these heterogeneous sets and provision of algorithms ...
  • Beckwith, Lee (Indiana University School of Informatics and Computing, 2012)
    Qualitative research methodologies were used in order to better understand how well currently available mobile phone interfaces are designed to match the way Japanese is thought of by native speakers. A conceptual design ...
  • Stolterman, Erik; Wiltse, Heather; Chen, Siyu; Lewandowski, Vincent; Pak, Leo (Indiana University School of Informatics and Computing, 2012)
    The underlying motivation for our research is the need for a deeper understanding of human-computer interaction that can speak to the increasingly varied and intricate forms of interactivity and interfaces that are present ...
  • Stolterman, Erik; Beckwith, Lee; Chang, Wanling; Jiang, Hongyuan; Sulgrove, Alexander; White, Jeremy (Indiana University School of Informatics and Computing, 2012)
    To communicate a design can be seen as consisting of at least two aspects: presentation and argumentation. In our research we have taken on the task of studying how practicing interaction designers approach the challenge ...
  • Wild, David J.; Desai, Pankaj; Qiu, Judy; Moorthy, Ganesh; Chen, Bin; Shin, Jae Hong; Sun, Yuyin; Wang, Huijun; Ding, Ying; Tang, Jie; He, Bing (Public Library of Science, 2011-12-06)
    Much life science and biology research requires an understanding of complex relationships between biological entities (genes, compounds, pathways, diseases, and so on). There is a wealth of data on such relationships in ...
  • Wild, David J.; Qiu, Judy; He, Bing; Dong, Xiao; Tang, Jie; Ding, Ying; Wang, Huijun (PLoS, 2011-03-23)
    The overwhelming amount of available scholarly literature in the life sciences poses significant challenges to scientists wishing to keep up with important developments related to their research, but also provides a useful ...
  • Wild, David J.; Ding, Ying; Chen, Bin (Chemistry Central Ltd., 2012-03-08)
    Background: Systems chemical biology and chemogenomics are considered critical, integrative disciplines in modern biomedical research, but require data mining of large, integrated, heterogeneous datasets from chemistry and ...
  • Wild, David J.; Lajiness, Michael S.; Ding, Ying; Challa, Sashikiran; Sun, Yuyin; Zhu, Qian (BioMed Central Ltd., 2011-06-23)
    Background: Semantic Web Technology (SWT) makes it possible to integrate and search the large volume of life science datasets in the public domain, as demonstrated by well-known linked data projects such as LODD, Bio2RDF, ...
  • Jeong, Jaesung; Lee, Junho; Ahn, Yong-Yeol; Choi, Myung-Kyu; Sohn, Yunkyu (PLoS, 2011-05)
    The modular organization of networks of individual neurons interwoven through synapses has not been fully explored due to the incredible complexity of the connectivity architecture. Here we use the modularity-based community ...

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