Informatics Publications

2011

  • Sarkar IN. A vector model based approach to identify genetically related diseases. AMIA Annu Symp Proc. 2011. (accepted)
  • Chen ES, Manaktala S, Sarkar IN, Melton GB. A multi-site content analysis of social history information in clinical notes. AMIA Annu Symp Proc. 2011. (accepted)
  • Ye H, Chen ES. Attribute utility motivated k-anonymization of datasets to support the heterogeneous needs of biomedical researchers. AMIA Annu Symp Proc. 2011. (accepted)
  • Kost R, Littenberg B, Chen ES. Assessing disease co-occurrences using association rule mining and public health data sets. AMIA Annu Symp Proc. 2011. (accepted abstract)
  • Sarkar IN, Butte AJ, Lussier YA, Tarczy-Hornoch P, Ohno-Machado L. Translational bioinformatics: linking knowledge across biological and clinical realms. J Am Med Inform Assoc. 2011 Jul 1;18(4):354-7. [ PubMed ]
  • Nabhan AR, Sarkar IN. The impact of taxon sampling on phylogenetic inference: a review of two decades of controversy. Brief Bioinform. 2011 Mar 23. [ PubMed ]
  • Scotch M, Sarkar IN, Mei C, Leaman R, Cheung KH, Ortiz P, Singraur A, Gonzalez G. Enhancing phylogeography by improving geographical information from GenBank. J Biomed Inform. 2011 Jun 24. [ PubMed ]
  • Chen ES, Sarkar IN. Towards structuring unstructured GenBank metadata for enhancing comparative biological studies. AMIA Summits Transl Sci Proc. 2011:6-10.
  • Fitzsimmons LF, Flemer S Jr, Wurthmann AS, Deker PB, Sarkar IN, Wargo MJ. Small-Molecule Inhibition of Choline Catabolism in Pseudomonas aeruginosa and Other Aerobic Choline-Catabolizing Bacteria. Appl Environ Microbiol. 2011 Jul;77(13):4383-9. [ PubMed ]

2010

  • Sarkar IN. Biomedical informatics and translational medicine. J Transl Med. 2010 Feb 26;8:22. [ PubMed ]
  • Chen ES, Sarkar IN. MeSHing molecular sequences and clinical trials: a feasibility study. J Biomed Inform. 2010 Jun;43(3):442-50. [ PubMed ]
  • Mercier CE, Dunn MS, Ferrelli KR, Howard DB, Soll RF; Vermont Oxford Network ELBW Infant Follow-Up Study Group. Neurodevelopmental outcome of extremely low birth weight infants from the Vermont Oxford network: 1998-2003. Neonatology. 2010 Jun;97(4):329-38. [ PubMed ]
  • Melton GB, Raman N, Chen ES, Sarkar IN, Pakhomov S, Madoff RD. Evaluation of family history information within clinical documents and adequacy of HL7 clinical statement and clinical genomics family history models for its representation: a case report. J Am Med Inform Assoc. 2010 May 1;17(3):337-40. [ PubMed ]
  • Sarkar IN. Leveraging biomedical ontologies and annotation services to organize microbiome data from Mammalian hosts. AMIA Annu Symp Proc. 2010 Nov 13;2010:717-21. [ PubMed ]
  • Chen ES, Melton GB, Engelstad ME, Sarkar IN. Standardizing clinical document names using the HL7/LOINC document ontology and LOINC codes. AMIA Annu Symp Proc. 2010 Nov 13;2010:101-5. [ PubMed ]
  • Kocherlakota R, Barrantes R, Bond J, Sarkar IN. UVM BioDesktop and DepotJunction: informatics infrastructure and core facility management application. AMIA Summits Transl Sci Proc. 2010.
  • Wright A, Chen ES, Maloney FL. An automated technique for identifying associations between medications, laboratory results and problems. J Biomed Inform. 2010 Dec;43(6):891-901. [ PubMed ]
  • Scotch M, Mei C, Brandt C, Sarkar IN, Cheung K. At the intersection of public-health informatics and bioinformatics: using advanced Web technologies for phylogeography. Epidemiology. 2010 Nov;21(6):764-8. [ PubMed ]
  • Min GS, Sarkar IN, Siddall ME. Salivary transcriptome of the North American medicinal leech, Macrobdella decora. J Parasitol. 2010 Dec;96(6):1211-21. [ PubMed ]
  • Kvist S, Sarkar IN, Erséus C. Genetic variation and phylogeny of the cosmopolitan marine genus Tubificoides (Annelida: Clitellata: Naididae: Tubificinae). Mol Phylogenet Evol. 2010 Nov;57(2):687-702. [ PubMed ]

2009

  • Lussier YA, Sarkar IN. Selected proceedings of the 2009 Summit on Translational Bioinformatics. BMC Bioinformatics. 2009 Sep 17;10 Suppl 9:I1. [ PubMed ]
  • Butte AJ, Sarkar IN, Ramoni M, Lussier Y, Troyanskaya O. Selected proceedings of the First Summit on Translational Bioinformatics 2008. BMC Bioinformatics. 2009 Feb 5;10 Suppl 2:I1. [ PubMed ]
  • Sarkar IN, Schenk R, Miller H, Norton CN. LigerCat: using "MeSH Clouds" from journal, article, or gene citations to facilitate the identification of relevant biomedical literature. AMIA Annu Symp Proc. 2009 Nov 14;2009:563-7. [ PubMed ]
  • Miller H, Norton CN, Sarkar IN. GenBank and PubMed: How connected are they? BMC Res Notes. 2009 Jun 9;2:101. [ PubMed ]
  • Chen ES, Maloney FL, Shilmayster E, Goldberg HS. Laying the groundwork for enterprise-wide medical language processing services: architecture and process. AMIA Annu Symp Proc. 2009 Nov 14;2009:97-101. [ PubMed ]
  • Kost R, Chen ES, Littenberg B, Pakhomov S, Bond J, Smith S. Automatically assessing evidence of foot exam for diabetic care by natural language processing of unstructured electronic clinical notes. AMIA Annu Symp Proc. 2009 Nov 14;2009:919.
  • Lee NJ, Chen ES, Currie LM, Donovan M, Hall EK, Jia H, John RM, Bakken S. The effect of a mobile clinical decision support system on the diagnosis of obesity and overweight in acute and primary care encounters. ANS Adv Nurs Sci. 2009 Jul-Sep;32(3):211-21. [ PubMed ]
  • Chen ES. Data, text, and web mining in healthcare. Encyclopedia of Database Systems. 2009:692-6.
  • Sarkar IN. Biodiversity informatics: the emergence of a field. BMC Bioinformatics. 2009 Nov 10;10 Suppl 14:S1. [ PubMed ]