Refereed Publications

  • James C. Costello, Daniel Schrider, Jeff R. Gehlhausen, and Mehmet M. Dalkilic. "Data-Driven Ontologies." The Pacific Symposium on Biocomputing (Submitted).
  • James C. Costello, Mehmet M. Dalkilic, Scott M. Beason, Jeff R. Gehlhausen, Rupali Patwardhan, Sumit Middha, Brian D. Eads, and Justen Andrews. "Gene Networks in Drosophila melanogaster: Integrating Experimental Data to Predict Gene Function." PLoS Genetics (In Review).
  • Teyia Kijimoto, Debra Rose, James C. Costello, Zouijan Tang, Armin Moczek, and Justen Andrews. "Expressed sequence tag resources and their application in horned beetles, an emerging model system in evolutionary developmental biology." BMC Genomics (In Review).
  • James C. Costello, Mira V. Han, and Matthew W. Hahn. "Limitations of pseudogenes in identifying gene lossses." Recomb-CG 2008 (Accepted).
  • Yong Li, James C. Costello, Alisah Holloway, and Matthew Hahn. "'Reverse Ecology' and the power of population genomics." Evolution (In Press).
  • James C. Costello, Amy Cash, Mehmet Dalkilic, and Justen Andrews. "Data Pushing: a Fly-centric guide to Bioinformatics tools" Fly 2(1):1-18. 2008.

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  • Drosophila Comparative Genome Sequencing and Analysis Consortium. "Evolution of genes and genomes on the Drosophila phylogeny" Nature 450(7167):203-218. 2007.

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  • James C. Costello, Jade Buchannan-Carter, Mehmet Dalkilic, and Justen Andrews. "Integrating Drosophila Data to Discover Disease-Rleated Protein Interactions in Human" IEEE Symposium on Computational Intelligence in Bioinformatics and Computational Biology. Honolulu, HI. 2007.
  • James C. Costello, Mehmet Dalkilic, Rupali Patwardhan, Sumit Middha, Brian Eads, John Colbourne, Junguk Hur, Keval Mehta, and Justen Andrews. "Network Properties of a Gene Network Built from Drosophila melanogaster Data" NetSci. Bloomington, IN. 2006.
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  • Mehmet Dalkilic, Wyatt Clark, James C. Costello, and Predrag Radivojac. "Using Compression to Identify Classes of Inauthentic Texts" In Proceedings SIAM Conference on Data Mining pages 603-607, 2006.
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  • Mehmet Dalkilic and James C. Costello. "BioKnOT: Biological Knowledge through Ontologies and TFIDF" SIGIR Workshop: Search and Discovery in Bioinformatics. 2004.
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  • Mehmet Dalkilic, James C. Costello, and Arjjit Sengupta. "Semantic Thumbnails: A Novel Method for Summarizing Document Collections" Proceedings of SIGDOC. 2004.
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  • Kazuhiro Seki, James C. Costello, Vasanth Singan, and Javed Mostafa. "TREC 2004 Genomic Track Experiments." In Proceedings of TREC 2004; Genomics Track. 2004.
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Invited Publications

  • Mehmet Dalkilic, James C. Costello, Wyatt Clark, and Predrag Radivojac. "From protein-disease associations to disease informatics" Frontiers in Bioscience. 13:3391-3407. 2008.
  • Brian Eads, Amy Cash, Kevin Bogart, James C. Costello, and Justen Andrews. "Troubleshooting Microarray Hybridizations" Methods in Enzymology. 411:34-49, 2006.

Posters Presentations

  • James C. Costello, Jeff R. Gehlhausen, Daniel R. Schrider, and Mehmet M. Dalkilic. "Data-Driven Ontologies: A Tool to Discover Relationships Between Biological Processes from Genomic Data." ISMB/ISCB Student Conference 2008.
  • James C. Costello, Meng Li, and Martin Stone. "Automated Identification of Protein Scaffold Structures" 3rd Annual Indiana Bioinformatics Conference. 2006.
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  • James C. Costello, Mehmet Dalkilic, Rupali Patwardhan, Sumit Middha, Junguk Hur, Keval Mehta, Amit Saple, John Colbourne, Brian Eads, and Justen Andrews. "InGeNE: Integrated Gene Network Explorer." i-Conference. Penn State University. 2005.
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Technical Reports

  • Kevin Bogart, James C. Costello, Brian Eads, Elizabeth Bohuski, and Justen Andrews. "Amino Allyl Labeling and Hybridization Protocol" CGB Technical Report 2006-06. The Center for Genomics and Bioinformatics, Indiana University, Bloomington, Indiana.
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  • James C. Costello and Justen Andrews. "Re-Annotation of DGRC-1 Amplicon Microarrays from Drosophila melanogaster Annotation version 3.1 to version 4.1." CGB Technical Report 2006-07 The Center for Genomics and Bioinformatics, Indiana University, Bloomington, Indiana.
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  • James C. Costello and Monica Sentmanat, and Kevin Bogart. "DGRC Hybridization Troubleshooting Guide" CGB Technical Report 2006-12 The Center for Genomics and Bioinformatics, Indiana University, Bloomington, Indiana.
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