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March 2012, Volume 19, Issue 2

[Author index]

Cover
  1. Highlights
  2. Editorial
  3. Perspectives
  4. Brief communications
  5. Research and applications
  6. Messages from AMIA
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Issue information

[Front cover][Table of contents PDF][Editorial board PDF]

Highlights

  • Informatics research to enable clinically relevant, personalized genomic medicine

    • Lucila Ohno-Machado
    J Am Med Inform Assoc 2012;19:149-150 doi:10.1136/amiajnl-2012-000844

Editorial

  • National centers for biomedical computing: from the BISTI report to the future

    • Jeremy M Berg
    J Am Med Inform Assoc 2012;19:151-152 Published Online First: 18 January 2012 doi:10.1136/amiajnl-2011-000800

Perspectives

  • Translational informatics: an industry perspective

    • Michael N Cantor
    J Am Med Inform Assoc 2012;19:153-155 Published Online First: 11 January 2012 doi:10.1136/amiajnl-2011-000588

  • Advantages of genomic complexity: bioinformatics opportunities in microRNA cancer signatures

    • Yves A Lussier,
    • Walter M Stadler,
    • James L Chen
    J Am Med Inform Assoc 2012;19:156-160 Published Online First: 18 November 2011 doi:10.1136/amiajnl-2011-000419
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  • Reconciliation of the cloud computing model with US federal electronic health record regulations

    • Eugene J Schweitzer
    J Am Med Inform Assoc 2012;19:161-165 Published Online First: 4 July 2011 doi:10.1136/amiajnl-2011-000162
    Editor's Choice

Brief communications

  • The NIH National Center for Integrative Biomedical Informatics (NCIBI)

    • Brian D Athey,
    • James D Cavalcoli,
    • H V Jagadish,
    • Gilbert S Omenn,
    • Barbara Mirel,
    • Matthias Kretzler,
    • Charles Burant,
    • Raphael D Isokpehi,
    • Charles DeLisi,
    • the NCIBI faculty, trainees, and staff
    J Am Med Inform Assoc 2012;19:166-170 Published Online First: 19 November 2011 doi:10.1136/amiajnl-2011-000552

  • Using systems and structure biology tools to dissect cellular phenotypes

    • Aris Floratos,
    • Barry Honig,
    • Dana Pe'er,
    • Andrea Califano
    J Am Med Inform Assoc 2012;19:171-175 Published Online First: 10 November 2011 doi:10.1136/amiajnl-2011-000490

  • The National Alliance for Medical Image Computing, a roadmap initiative to build a free and open source software infrastructure for translational research in medical image analysis

    • Tina Kapur,
    • Steve Pieper,
    • Ross Whitaker,
    • Stephen Aylward,
    • Marianna Jakab,
    • Will Schroeder,
    • Ron Kikinis
    J Am Med Inform Assoc 2012;19:176-180 Published Online First: 10 November 2011 doi:10.1136/amiajnl-2011-000493

  • A translational engine at the national scale: informatics for integrating biology and the bedside

    • Isaac S Kohane,
    • Susanne E Churchill,
    • Shawn N Murphy
    J Am Med Inform Assoc 2012;19:181-185 Published Online First: 10 November 2011 doi:10.1136/amiajnl-2011-000492

  • Simbios: an NIH national center for physics-based simulation of biological structures

    • Scott L Delp,
    • Joy P Ku,
    • Vijay S Pande,
    • Michael A Sherman,
    • Russ B Altman
    J Am Med Inform Assoc 2012;19:186-189 Published Online First: 10 November 2011 doi:10.1136/amiajnl-2011-000488

  • The National Center for Biomedical Ontology

    • Mark A Musen,
    • Natalya F Noy,
    • Nigam H Shah,
    • Patricia L Whetzel,
    • Christopher G Chute,
    • Margaret-Anne Story,
    • Barry Smith,
    • and the NCBO team
    J Am Med Inform Assoc 2012;19:190-195 Published Online First: 10 November 2011 doi:10.1136/amiajnl-2011-000523

  • iDASH: integrating data for analysis, anonymization, and sharing

    • Lucila Ohno-Machado,
    • Vineet Bafna,
    • Aziz A Boxwala,
    • Brian E Chapman,
    • Wendy W Chapman,
    • Kamalika Chaudhuri,
    • Michele E Day,
    • Claudiu Farcas,
    • Nathaniel D Heintzman,
    • Xiaoqian Jiang,
    • Hyeoneui Kim,
    • Jihoon Kim,
    • Michael E Matheny,
    • Frederic S Resnic,
    • Staal A Vinterbo,
    • and the iDASH team
    J Am Med Inform Assoc 2012;19:196-201 Published Online First: 10 November 2011 doi:10.1136/amiajnl-2011-000538

  • The Center for Computational Biology: resources, achievements, and challenges

    • Arthur W Toga,
    • Ivo D Dinov,
    • Paul M Thompson,
    • Roger P Woods,
    • John D Van Horn,
    • David W Shattuck,
    • D Stott Parker
    J Am Med Inform Assoc 2012;19:202-206 Published Online First: 10 November 2011 doi:10.1136/amiajnl-2011-000525

  • Utility of gene-specific algorithms for predicting pathogenicity of uncertain gene variants

    • David K Crockett,
    • Elaine Lyon,
    • Marc S Williams,
    • Scott P Narus,
    • Julio C Facelli,
    • Joyce A Mitchell
    J Am Med Inform Assoc 2012;19:207-211 Published Online First: 28 October 2011 doi:10.1136/amiajnl-2011-000309

Research and applications

  • Use of diverse electronic medical record systems to identify genetic risk for type 2 diabetes within a genome-wide association study

    • Abel N Kho,
    • M Geoffrey Hayes,
    • Laura Rasmussen-Torvik,
    • Jennifer A Pacheco,
    • William K Thompson,
    • Loren L Armstrong,
    • Joshua C Denny,
    • Peggy L Peissig,
    • Aaron W Miller,
    • Wei-Qi Wei,
    • Suzette J Bielinski,
    • Christopher G Chute,
    • Cynthia L Leibson,
    • Gail P Jarvik,
    • David R Crosslin,
    • Christopher S Carlson,
    • Katherine M Newton,
    • Wendy A Wolf,
    • Rex L Chisholm,
    • William L Lowe
    J Am Med Inform Assoc 2012;19:212-218 Published Online First: 19 November 2011 doi:10.1136/amiajnl-2011-000439

  • Impact of data fragmentation across healthcare centers on the accuracy of a high-throughput clinical phenotyping algorithm for specifying subjects with type 2 diabetes mellitus

    • Wei-Qi Wei,
    • Cynthia L Leibson,
    • Jeanine E Ransom,
    • Abel N Kho,
    • Pedro J Caraballo,
    • High Seng Chai,
    • Barbara P Yawn,
    • Jennifer A Pacheco,
    • Christopher G Chute
    J Am Med Inform Assoc 2012;19:219-224 Published Online First: 16 January 2012 doi:10.1136/amiajnl-2011-000597

  • Importance of multi-modal approaches to effectively identify cataract cases from electronic health records

    • Peggy L Peissig,
    • Luke V Rasmussen,
    • Richard L Berg,
    • James G Linneman,
    • Catherine A McCarty,
    • Carol Waudby,
    • Lin Chen,
    • Joshua C Denny,
    • Russell A Wilke,
    • Jyotishman Pathak,
    • David Carrell,
    • Abel N Kho,
    • Justin B Starren
    J Am Med Inform Assoc 2012;19:225-234 doi:10.1136/amiajnl-2011-000456

  • Exploiting domain information for Word Sense Disambiguation of medical documents

    • Mark Stevenson,
    • Eneko Agirre,
    • Aitor Soroa
    J Am Med Inform Assoc 2012;19:235-240 Published Online First: 7 September 2011 doi:10.1136/amiajnl-2011-000415
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  • Identifying disease genes and module biomarkers by differential interactions

    • Xiaoping Liu,
    • Zhi-Ping Liu,
    • Xing-Ming Zhao,
    • Luonan Chen
    J Am Med Inform Assoc 2012;19:241-248 Published Online First: 20 December 2011 doi:10.1136/amiajnl-2011-000658
    Editor's Choice

  • A vector space model approach to identify genetically related diseases

    • Indra Neil Sarkar
    J Am Med Inform Assoc 2012;19:249-254 Published Online First: 6 January 2012 doi:10.1136/amiajnl-2011-000480

  • Predicting the outcome of renal transplantation

    • Julia Lasserre,
    • Steffen Arnold,
    • Martin Vingron,
    • Petra Reinke,
    • Carl Hinrichs
    J Am Med Inform Assoc 2012;19:255-262 Published Online First: 28 August 2011 doi:10.1136/amiajnl-2010-000004

  • Calibrating predictive model estimates to support personalized medicine

    • Xiaoqian Jiang,
    • Melanie Osl,
    • Jihoon Kim,
    • Lucila Ohno-Machado
    J Am Med Inform Assoc 2012;19:263-274 Published Online First: 7 October 2011 doi:10.1136/amiajnl-2011-000291
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  • Incorporating molecular and functional context into the analysis and prioritization of human variants associated with cancer

    • Thomas A Peterson,
    • Nathan L Nehrt,
    • DoHwan Park,
    • Maricel G Kann
    J Am Med Inform Assoc 2012;19:275-283 doi:10.1136/amiajnl-2011-000655

  • Multiplex meta-analysis of RNA expression to identify genes with variants associated with immune dysfunction

    • Alexander A Morgan,
    • Vasilios J Pyrgos,
    • Kari C Nadeau,
    • Peter R Williamson,
    • Atul Janardhan Butte
    J Am Med Inform Assoc 2012;19:284-288 doi:10.1136/amiajnl-2011-000657
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  • A comparison of cataloged variation between International HapMap Consortium and 1000 Genomes Project data

    • Carrie C Buchanan,
    • Eric S Torstenson,
    • William S Bush,
    • Marylyn D Ritchie
    J Am Med Inform Assoc 2012;19:289-294 doi:10.1136/amiajnl-2011-000652
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  • Complex-disease networks of trait-associated single-nucleotide polymorphisms (SNPs) unveiled by information theory

    • Haiquan Li,
    • Younghee Lee,
    • James L Chen,
    • Ellen Rebman,
    • Jianrong Li,
    • Yves A Lussier
    J Am Med Inform Assoc 2012;19:295-305 Published Online First: 25 January 2012 doi:10.1136/amiajnl-2011-000482
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  • Translating Mendelian and complex inheritance of Alzheimer's disease genes for predicting unique personal genome variants

    • Kelly Regan,
    • Kanix Wang,
    • Emily Doughty,
    • Haiquan Li,
    • Jianrong Li,
    • Younghee Lee,
    • Maricel G Kann,
    • Yves A Lussier
    J Am Med Inform Assoc 2012;19:306-316 doi:10.1136/amiajnl-2011-000656
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  • Integrated morphologic analysis for the identification and characterization of disease subtypes

    • Lee A D Cooper,
    • Jun Kong,
    • David A Gutman,
    • Fusheng Wang,
    • Jingjing Gao,
    • Christina Appin,
    • Sharath Cholleti,
    • Tony Pan,
    • Ashish Sharma,
    • Lisa Scarpace,
    • Tom Mikkelsen,
    • Tahsin Kurc,
    • Carlos S Moreno,
    • Daniel J Brat,
    • Joel H Saltz
    J Am Med Inform Assoc 2012;19:317-323 Published Online First: 24 January 2012 doi:10.1136/amiajnl-2011-000700
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Messages from AMIA

  • President's column: reflections on AMIA's past 3 years

    • Edward H Shortliffe
    J Am Med Inform Assoc 2012;19:325-326 doi:10.1136/amiajnl-2012-000861

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