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    Archived pages: 169 . Archive date: 2014-10.

  • Title: i2b2: Informatics for Integrating Biology & the Bedside
    Descriptive info: .. About Us.. Driving Biology Projects.. Software.. Resources.. Events.. Training.. News.. Collaborations.. Publications.. MISSION.. i2b2 (Informatics for Integrating Biology and the Bedside) is an NIH-funded National Center for Biomedical Computing based at Partners HealthCare System.. The i2b2 Center is developing a scalable informatics framework that will enable clinical researchers to use existing clinical data for discovery research and, when combined with IRB-approved genomic data, facilitate the design of targeted therapies for individual patients with diseases having genetic origins.. This platform currently enjoys wide international adoption by the CTSA network, academic health centers, and industry.. i2b2 is funded as a cooperative agreement with the National Institutes of Health.. DRIVING BIOLOGY PROJECTS.. RESOURCES.. Overview.. Current DBPs.. Autoimmune/CV Diseases.. Diabetes/CV Diseases.. Past DBPs.. Airways Diseases.. Hypertension.. Type 2 Diabetes Mellitus.. Huntington's Disease.. Major Depressive Disorder.. Rheumatoid Arthritis.. Obesity.. Computational Tools.. De-Identification Demo.. NLP Research Data Sets.. NLP Shared Tasks.. Academic Users' Group.. Publication Data.. SOFTWARE.. HIGHLIGHTS.. ***.. i2b2 Installations Worldwide.. ***i2b2 AUG AND SHRINE ANNUAL CONFERENCE***.. July 10-11, 2014.. SLIDES.. *** i2b2 NLP DATA SET #5 (from 2011 Challenge) ***.. A complete set of annotated and unannotated, deidentified patient discharge summaries from the First, Second (Obesity),Third (Medication) and Fourth Shared Tasks for Challenges in NLP for Clincial Data are now available to the community for research purposes.. Check it out at our.. NLP Data Sets page.. Please note you must register.. AND submit a DUA for access.. *** Publications In the News ***.. Ananthakrishnan AN, Cagan A, Gainer VS, Cheng SC, Cai T, Szolovits P, Shaw SY, Churchill S, Karlson EW, Murhpy SN, Kohane IS, Liao KP.. HIgher plasma vitamin D is associated with reduced risk of Clostridium difficile infection in patients with inflammatory bowel diseases.. Aliment Pharmacol Ther.. 2014 May;39(10):1136-42.. doi: 10.. 1111/apt.. 12706.. Epub 2014 Mar 18.. PMID: 24541590.. Ananthakrishnan AN, Cagan A, Gainer VS, Cai T, Cheng SC, Scoville E, Konijeti GG, Szolovits P, Shaw SY, Churchill  ...   2014;73:1170-5.. PMC3815491.. McMurry AJ, Murphy SN, MacFadden D, Weber G, Simons WW, Orechia J, Bickel J, Wattanasin N, Gilbert C, Trevvett P, Churchill S, Kohane IS.. SHRINE: enabling nationally scalable multi-site disease studies.. 2013;8(3):55811.. PMC3591385.. *** i2b2 ROADMAP for 2013 ***.. Release 1.. 7 = Temporal Query enabled i2b2.. Now available at our.. Software Page.. Version 1.. 7 of the i2b2 software features two important innovations.. The first is the introduction of temporal queries, an implementation of the temporal theory development from Core 1.. This will allow the definition of events from collections of observations, and then the ordering of those events to occur in specific sequences with a specified number of intervening hours or days.. The second innovation is support for the identity management cell which will enable the maintenance of protected health information in a separate area of the i2b2 Hive.. The workflows that begin with unencrypted, fully identified notes or other kinds of identified data will be able to produce de-identified data at various levels.. Depending on the transformation chosen, de-identified data may also be linked back to its original identified data.. Release i2b2-CT = Clinical-Trial enabled i2b2.. In the summer of 2014 we are planning on the release of a version of i2b2 which represents a bundle of Community Supported i2b2 Plug-ins and Tools.. This version will specifically support the end to end use case for the discovery of a set of patients for a clinical trial.. Current plug-ins and features will be enhanced and new features added from the i2b2 community to provide increasingly focused selection capabilities to narrow down to a final, well qualified patient set.. The process of advancing the levels of approval by data use agreements and institutional review boards will be supported to allow the recruitment process to proceed with the maximal respect for patient privacy and confidentiality.. Contact.. |.. Sitemap.. Search.. 2014 Partners Healthcare.. design by Digizyme..

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  • Title: i2b2: Informatics for Integrating Biology & the Bedside
    Descriptive info: Introduction.. Mission Statement.. Structure.. Contact Info.. Sponsors.. Links.. Informatics for Integrating Biology and the Bedside (i2b2) is an NIH-funded National Center for Biomedical Computing (NCBC) based at Partners HealthCare System in Boston, Mass.. Established in 2004 in response to an NIH Roadmap Initiative RFA, this NCBC is one of four national centers awarded in this first competition (.. http://www.. bisti.. nih.. gov/ncbc/.. ); currently there are seven NCBCs.. One of 12 specific initiatives in the New Pathways to Discovery Cluster, the NCBCs will initiate the development of a national computational infrastructure for biomedical computing.. The NCBCs and related R01s constitute the National Program of Excellence in Biomedical Computing.. The i2b2 Center, led by Director Isaac Kohane, M.. D.. , Ph.. , Professor of Pediatrics at Harvard Medical School at Children's Hospital Boston, is comprised of six cores involving investigators from the Harvard-affiliated hospitals, MIT, Harvard School of Public Health, Harvard Medical School and the Harvard/MIT Division of  ...   3) are being developed and tested in several diseases (airways disease, hypertension, type 2 diabetes mellitus, Huntington s Disease, rheumatoid arthritis, major depressive disorder, inflammatory bowel disease, multiple sclerosis) (Core 2 Driving Biological Projects).. The i2b2 Center (Core 4) offers a Summer Institute in Bioinformatics and Integrative Genomics for qualified undergraduate students, supports an Academic Users' Group of over 250 members, sponsors annual Shared Tasks for Challenges in Natural Language Processing for Clinical Data, distributes an NLP DataSet for research purpose, and sponsors regular Symposia and Workshops for the community.. Dissemination (Core 5) of i2b2 tools to the national science community occurs through a public portal based at Harvard Medical School and will be further facilitated by an anticipated partnership with Morehouse School of Medicine to facilitate transfer of new technologies to institutions working with underserved populations.. The i2b2 components, membership and dynamics among them are depicted in the following figure.. [.. back to top.. ].. Home..

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  • Title: i2b2: Informatics for Integrating Biology & the Bedside
    Descriptive info: The disease-based driving biology projects (DBP's) serve as the testbed of i2b2.. It is where we field, test and debug the methodologies and tools developed in Cores 1 and 3.. For this reason we recognize that it is incumbent on us to use the DBP's to maximize interactions, oversight and corrections in the directions of Core 1 and 3.. Consequently for each DBP, we have ensured the following:.. On each DBP there is an assigned computational/bioinformatics co-investigator to ensure that there is a very close collaboration between the clinical-genomic investigator and the methodologies and tools developed in Cores 1 and 3.. Also this computational co-investigator provides a tighter loop for feedback and advice than would be ordinarily available.. Frequent meetings between the clinical investigators of each DBP and the methodologists from Core 1 and 3 (see.. Zak Kohane's  ...   following criteria:.. The diseases in question are of clinical significance.. The PIs have particularly strong research track records.. The proposed research plans are good models for future clinical research using genomic technologies in combination with traditional clinical data types.. The PIs evinced strong and enthusiastic willingness to work together with computational researchers and engineers to help improve/further their own research agenda.. The degree to which the methods developed will be models for clinical research of complex diseases in which a component of their phenotype show familial aggregation, but no clear Mendelian segregation.. This is not to say that there will not be many productive clinical investigations of largely monogenic disease for a long time to come and indeed one of our DBP s is placed foursquare on the transition from monogenic to complex diseases.. View.. current.. and.. past.. DBPs..

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  • Title: i2b2: Informatics for Integrating Biology & the Bedside
    Descriptive info: i2b2 Software.. i2b2 Community Wiki.. i2b2 JIRA Bug Tracker.. Archived Source Code.. Contributed.. Tutorial.. Guestbook *.. Statistics *.. Current Version.. 1.. 7.. 03a.. Release Notes.. Use the links below to access the software repository where you will find the project source code, executable files, XSD files, PDF files and more.. Launch the AJAX web client in your web browser.. View By:.. Cells.. List.. Enter a keyword below to filter the list of available documents:.. Project.. Management.. Ontology.. High.. Performance.. Computing.. Plug-in.. Text.. Analyzer.. File.. Repository.. Data.. (CRC).. Export.. Natural.. Language.. Processing.. Identity.. Correlation.. Analysis.. Import.. PFT.. Workflow.. Framework.. Table View.. Patient.. Counts.. i2b2.. Web Client.. Application.. Workbench.. Annotator.. i2b2 Hive.. Project Management.. Core Server Side i2b2 Cell.. This cell is used to provide user authentication and manage group and role information.. It also keeps track of what cells are part of the hive.. Installation Guide.. Messaging Guide.. Design Document.. Go to Download.. Ontology Management.. This cell manages the terminology and knowledge information typically used in the hive.. It is contacted for, or distributes knowledge to, cells during most of the hives transactions.. Architecture Document.. High Performance Computing.. i2b2 Workbench Plug-in.. The High Performance Computing plug-in allows users to take advantage of resources available on a remote location, generally a compute cluster.. Plug-in is downloaded through workbench.. Text Analyzer.. The Text Analyzer plug-in allows for the decrypting and view of the notes data in the CRC.. Help Guide.. File Repository.. This cell holds large files of data including radiological images and genetic sequences.. The files are generally referenced from the Data Repository Cell.. Data Repository (CRC).. This cell holds the phenotypic and genotypic data of the hive in a structured format.. Data queries and visualizations are available through this cell.. Plugin Analysis Document.. Export Tool.. The export data view will enable users to export data from the dimension and mapping tables.. Natural Language Processing.. Optional Server Side i2b2 Cell.. This cell manipulates text reports to extract specific terms and knowledge from them.. These concepts are then used to achieve various representations of the data.. Identity Management.. This cell is used to manage a patient's protected health information in a manner consistent with the HIPAA privacy rule.. Patient data is available only as a HIPAA defined "Limited Data Set" to most of the hive.. Correlation Analysis.. This specialized analysis cell uses mutual information theory to calculate observed correlations within the data of the hive.. This type of cell represents an important achievement of the hive.. Import Tool.. The import data view will enable users to import data into the dimension and mapping tables.. PFT Processing.. This specialized processing cell expects a pulmonary function report in a specific format and yields the embedded test values thru parsing the report.. It works as part of the hive only for this specific, localized purpose.. Workflow Framework.. This cell is used to process information in steps through various parts of the hive.. Most processed information will come to reside in the Data Repository Cell or as a display to the user.. Table View Plug-in.. The i2b2 plug-in for viewing data in various tables and other graphical forrmats.. Patient Counts Plug-in.. Optional Server Side CRC Plug-in.. This server-side CRC plug-in calculates patient count breakdown for the children  ...   NLP Installation Guide.. NLP Messaging Guide.. NLP Architecture Guide.. Correlation Analysis Plug-in Installation Guide.. Correlation Analysis Plug-in Messaging Guide.. Correlation Analysis Plug-in Design Document.. Import Data Plug-in Help Guide.. PFT Processing Installation Guide.. PFT Processing Messaging Guide.. PFT Processing Architecture Document.. IM Framework Installation Guide.. IM Framework Messaging Guide.. IM Framework Design Document.. IM Framework Architecture Document.. Workflow Framework Installation Guide.. Workflow Framework Messaging Guide.. Workflow Framework Design Document.. Workflow Framework Architecture Document.. Table View Plug-in Help Guide.. Patient Counts Plug-in Functional Specification.. i2b2 Web Client Application Install Guide.. i2b2 Web Client Application Project Request Guide.. i2b2 Workbench Application Installation Guide.. i2b2 Workbench Application Tutorial Document.. i2b2 Workbench Application Developer's Guide.. First.. Prev.. of.. Next.. Last.. Loading.. Download the Windows or Macintosh executable.. Download the VMWare image to run both the client and server.. Download the source code and build the client and server from scratch.. Version:.. Release Date:.. July 1, 2014.. License:.. i2b2 Open Source License.. The i2b2 Workbench is a collection of client-side components that communicate with i2b2 Cells and help aggregate their functionality in the Hive.. Each component is designed as an Eclipse-based plug-in that interacts with a hive cell; collectively these plug-ins provide a cohesive entity to tie all the i2b2 cells together.. After you have downloaded and installed the software, please use the following demo login to authenticate:.. Demo Account.. User:.. demo.. Password:.. demouser.. Select the appropriate file below for download:.. Download.. File Size.. Type.. i2b2Workbench-win-1702.. zip.. 105 MB.. Windows v1.. (Core Cells Only) with features.. i2b2Workbench-mac-1702.. 75 MB.. Macintosh v1.. (Core Cells Only) with featuress.. i2b2Workbench_Documentation_1702.. 2.. 4 MB.. i2b2 Workbench Documentation v1.. August 28, 2014.. Below is the complete VMware i2b2 server installed on CentOS.. Only tested on VMware fusion and Player.. After you have downloaded and installed the VMware image, please use the following login for CentOS:.. CentOS Account.. (or root).. i2b2vmware-1703a.. 6 GB.. VMware Core Image v1.. 03a.. vmware_Install_Guide_17.. pdf.. 866 kB.. VMware Installation Guide v1.. The i2b2 Source is a collection of both client and server source code and can be used to build the i2b2 Server and Workbench from scratch.. The source code files for the i2b2 Core Hive Cells, i2b2 Workbench and Web Client are listed below.. Demo data and the current documentation can also be downloaded.. i2b2core-src-1703.. 56 MB.. Core Source Code Server v1.. 03.. i2b2Workbench-src-1702.. 98 MB.. Core Source Code Client v1.. i2b2webclient-1703a.. 5.. 0 MB.. Web Client Source v1.. i2b2createdb-1702.. 27 MB.. i2b2 Data for Oracle, PostgreSQL and Sql Server.. i2b2core-doc-1702.. 12 MB.. i2b2 Documentation v1.. Optional components are available below for download:.. i2b2PFT-src-13.. 35 MB.. PFT Client/Server Source v1.. 3.. i2b2NLP-src-10.. 13 MB.. NLP Client/Server Source v1.. 0.. CorrelationAnalysis-client-src-10.. 3.. 5 MB.. Correlation Analysis Client Source v1.. HPC-src-10.. 6.. 7 MB.. HPC Client/Server source v1.. i2b2crcplugin-patientcount-17.. 38 MB.. CRC Patient Count Plug-in v1.. 7.. i2b2tableview-14.. 26 MB.. Table View Plug-in v1.. 4.. i2b2DerivedDataMarts-src-14.. 97 kB.. Derived Data Marts v1.. i2b2exportdata-15.. 8.. 6 MB.. Export Data Plug-in v1.. 5.. i2b2annotator-15.. Annotator Plug-in v1.. i2b2textanalyzer-15.. 638 kB.. Text Analyzer Plug-in v1.. i2b2importdata-15.. 16 MB.. Import Data Plug-in v1.. Older Versions:.. Previous releases can be found on the.. Archived Source Code web page.. Please submit any bugs that you may encounter using our.. bug tracking web page..

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  • Title: i2b2: Informatics for Integrating Biology & the Bedside
    Descriptive info: The most important challenge of i2b2 is to disseminate the computational tools, methodologies, biomedical data sets and educational materials widely within the biomedical and computational research communities.. To do so we have committed to make all the resources freely available to all interested parties.. In this section you will find access to all of  ...   to use these resources.. The preferred method of citation or reference is provided in each subsection.. Please note that for some resources (e.. g.. software) the use of the resource requires accepting a specific (e.. OpenSource) license.. Please read the particulars of each license to see how it might impact your current and future use..

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  • Title: i2b2: Informatics for Integrating Biology & the Bedside
    Descriptive info: Grand Rounds.. Symposium 2009.. Symposium 2008.. AUG Activities.. The following is an index of the various activities undertaken by i2b2 to enhance awareness of the broad issues facing the scientific community as regards biomedical computing and how i2b2 is addressing this challenge by using the byproducts of routine clinical care for discovery research.. Please use the links for more details.. 2011:.. First Dedicated i2b2 Academic Users' Group Meeting.. NLP Workshop.. June 28-June 29, 2011.. Boston, MA.. Please see.. AUG Webpage.. for slides and video.. All Hands Presentation:.. "Translational Informatics at J&J: Changing the game inside, changing the game outside?".. Eric D.. Perakslis, PhD, VP Research R D, J J.. March 18, 2011.. Academic Users' Group Meeting.. AMIA Summit on Translational Bioinformatics.. March 7, 2011.. Parc 55 Hotel.. San Francisco, CA.. i2b2 Software v.. 1.. 6 Tutorial Video.. 2009-2010:.. Tutorial: i2b2 How to : Installation, Startup and Extending its Functionality.. AMIA Now!.. May 25, 2010 1:30-3:45.. Arizona Grant Resort, Phoenix, AR.. Seminar:.. "What Did I Work on in Washington?".. John Glaser, PhD, co-PI i2b2, Partners CIO, Advisor to ONC.. April 16, 2010.. Tutorial:.. "How to i2b2".. March 10, 2010 8:30-12.. San Francisco, CA.. March 10, 2010 6-8 pm.. Symposium: Widening the Use if EMR for Research.. October 13, 2009.. Natcher Auditorium.. National Library of Medicine.. Bethesda, MD.. Academic Users' Group Meeting.. (AUG Page.. ).. October 11, 2009.. 2008-2009:.. Academic Users' Group Meeting (.. AUG Page.. May 5, 2009.. University of Washington (in conjunction with CICTR Meeting).. Seattle, WA.. October 15, 2008.. NIH.. Bethesda, MD (in conjunction with annual CTSA IT meeting).. 2007-2008:.. Academic Users' Group Workshop (.. AUG Page).. April 10, 2008.. Bray Room, New Research Building.. 77 Avenue Louis Pasteur..  ...   4-5:30 PM:.. Harry Ostrer, M.. , Professor of Pediatrics, Pathology and Medicine, NYU.. Who Are the Jews? A 4,000 Year Genetic Retrospective.. NRB Amphitheater, 77 Avenue Louis Pasteur, Boston, MA.. Grand Rounds: October 5, 2006, 4-5:30 PM:.. Edward Rubin, M.. , Director, U.. S.. Department of Energy Joint Genome Institute and Director, Genomics Division, Lawrence Berkeley National Laboratory.. Extreme Comparative Genomics.. NRB Rotunda, 77 Avenue Louis Pasteur, Boston, MA.. 2005-2006:.. (Streaming Videos).. Grand Rounds: May 4, 2006, 4-5:30 PM:.. Donald Lindberg, M.. , Director, National Library of Medicine, NIH.. Open Access Literature, Open Access Databases and More.. Walter Amphitheater, Medical Education Center, Harvard Medical School.. 260 Longwood Avenue, Boston, MA.. Streaming video is available.. Grand Rounds: April 6, 2006, 4-5:30 PM:.. Julie Gerbeding, M.. , Director, Center for Disease Control.. Epidemiology, Pandemics and the Role of IT in Public Health.. Bornstein Amphitheater.. Brigham and Women's Hospital, 75 Francis Street, Boston, MA.. Streaming video is available by clicking.. Grand Rounds: January 11, 2006, 4-5:30 PM:.. David Botstein, Ph.. , Director, Lewis-Sigler Institute, Princeton University.. HIM Lecture Room, #0138.. HMS New Research Building, 77 Avenue Louis Pasteur, Boston, MA.. Training the Next Generation of Biologists in Quantitative Biology.. Grand Rounds: November 3, 2005, 4-5:30 PM:.. David Brailer, M.. , National Coordinator for Health Information Technology, U.. Department of Health and Human Services.. ,.. Washington, D.. C.. HIM Lecture Room, NRB 0100, 77 Avenue Louis Pasteur, Boston.. The Decade of Health IT.. Grand Rounds: September 29, 2005, 4-5:30 PM :.. Jan-Eric Litton, Ph.. , Professor of Medical Epidemiology and Biostatistics, Karolinska Institute, Stockholm Sweden.. Karolinska Institute Biobank: Enabling Infrastructure Including High Throughput Phenotyping Technologies.. (requires real player to view).. Last edited July 19, 2011..

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  • Title: i2b2: Informatics for Integrating Biology & the Bedside
    Descriptive info: Predoctoral.. Postdoctoral.. i2b2 participates in two programs designed to train students in bioinformatics and integrative genomics:.. Summer Scholars in Bioinformatics and Integrative Genomics (Summer BIG).. (http://web.. mit.. edu//hstsummer).. Organizationally located within the MIT Summer Research Program and administered collaboratively with the Harvard-MIT Division of Health Sciences and Technology (HST), this program is designed to facilitate the involvement of talented students in research aspects of the fields of engineering and science, in particular those from disadvantaged background such as underrepresented minorities, or first-generation college students.. This summer program seeks to identify talented sophomores and juniors from around the country who could benefit from spending a summer on the Harvard Medical School-Harvard teaching hospitals-MIT campuses working in a research laboratory under the tutelage and guidance of experienced scientists participating in the various i2b2 interdisciplinary projects focused on the application of informatics to enhance clinical research in the genomic era.. The program also includes lectures by i2b2 faculty, planned readings and discussions of research and results, and exercises in data analysis.. Participants learn skills fundamental to the task of extracting information from the huge amount of data produced by the international Human Genome Project and the many applications thereof.. See.. 2009 Summer Scholars Program.. for this year's lecture program.. Undergraduate schools represented to date include: Morehouse College, Howard University,  ...   in 2005 we have graduated 57 students, including 29 women and 25 underrepresented minority students.. Of the 40 who have graduated from college, we continue to be in touch with 32 of our grads, 28 of whom are currently in biomedical graduate programs, including three in our HST Bioionformatics and Integrative Genomics Program.. Funding for this program derives from multiple sources including the i2b2 U54, NHGRI, NLM and HST.. Bioinformatics and Integrative Genomics (BIG) Ph.. Program (.. http://big.. chip.. org.. ).. To address the acute shortage of researchers in functional genomics with the necessary quantitative knowledge base to manage the vast amounts of data generated by the Human Genome Project, the Harvard-MIT Division of Health Sciences and Technology (HST) has created a new doctoral training track in bioinformatics and integrative genomics.. It is administered through HST s Medical Engineering and Medical Physics (MEMP) program, a highly successful graduate program that trains students in engineering and physical sciences to solve problems in science, biology and medicine.. In BIG, bioinformatics is viewed in a broader sense to comprise the overall activity of extracting the functional dependencies of biological systems from the data generated by sequence, mircroproteomics and metabolism-probing technologies.. This program is co-directed by Isaac Kohane ( i2b2 Center Director) and Leonid Mirny, HST and Physics at MIT..

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  • Title: i2b2: Informatics for Integrating Biology & the Bedside
    Descriptive info: From I2B2.. General interest.. Read how Eric Persaklis, VP of R D Informatics at Centocor R D (J J) has partnered with Recombinant Data Corp.. to build transMART - a translational informatics enterprise data warehouse that uses the i2b2 platform to pull in and integrate information from all the company's trials together with numerous existing public repositories and annotated relevant literature.. Bio-IT World, January  ...   that is, through volunteers who agree to provide their personal health information (phenotype and genotype).. See article in.. NEJM 2005, 353:2074-2077.. by Zak Kohane and Russ Altman (Symbios NCBC) and followup in.. The Personal Genome blog.. Mining Clinical Data with i2b2.. By Maureen McDonough, Bio-ITWorld Staff/August 8, 2005.. Harvard project to scan millions of medical files.. By Gareth Cook, Globe Staff | July 3, 2005..

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  • Title: i2b2: Informatics for Integrating Biology & the Bedside
    Descriptive info: Scientific Collaborations.. i2b2 Installations.. Data Sharing Network (SHRINE).. Use of our Software.. Data Sharing Policy.. Opportunities for Industry.. Underrepresented Minorities.. During the years while i2b2 is finalizing both its prototype Clinical Research Chart (CRC; see.. Hive Page.. ) and associated stand-alone analytical tools for dissemination to the national community, we are engaged in several ad hoc collaborations that inform our development activities through valuable insights and active input from the wider community.. To give you a flavor of what we're up to with these various intersections which go beyond our original scope, we offer the following catalog of activities in which we endeavor to:.. Collaborate within the NCBC Network.. A project within one of our original DBPs (Brain Structure and Long Term Treatment with SSRIs in Major Depressive Disorder, Dan Iosifescu, MD, MSc, PI; see.. their i2b2 page.. ) collaborated directly with NAMIC investigator Martha Shenton, PhD, to apply state-of-the-art algorithms developed by her Psychiatry Neuroimagine Laboratory to raw images captured from routine clinical records by i2b2 phenotypic extraction methodologies.. i2b2 continues to actively participate in the NCBC-wide forum for the purpose of enabling the widest possible user access to the collective network's toolkits.. These activities include posting of Biositemaps at each Center's website, a dedicated volume of JAMIA showcasing the network's contributions, and presentations at relevant professional meetings regarding network resources.. Support widespread adoption of the i2b2 software platforms.. The advent of the CTSA (Centers for Translation Science Awards) program has provided a unique opportunity to share our model for using existing clinical repositories with academic health centers interested in new approaches to translational research.. i2b2 has worked closely with the main hospitals within the Harvard Catalyst CTSA (Mass General, Brigham and Women's Hospital, Beth Israel Deaconness Medical Center, Children's Hospital Boston, Dana Farber Cancer Center) to facilitate their adoption of i2b2 instances as a vehicle for conducting clinical research at these heterogeneous biomedical research institutions and as a prelude to sharing aggregate data by means of a web-based, federated query system (SHRINE).. i2b2 has actively participated in the design and implementation of the SHRINE (Shared Health Research Informatics Network) system, the software for which is currently available open source (.. https://open.. med.. harvard.. edu/display/SHRINE/Software.. ) at:.. Harvard Catalyst CTSA for the sharing of aggregate data counts for demographics, diagnoses, meds and labs.. In a collaboration with the West Coast consortium CICTR (U Wash, UCSF, UCDavis) to enable their federation for the sharing of aggregate data totals.. A pan European public-private consortium which is currently evaluating the SHRINE platform to support their drug discovery efforts.. A supplemental CTSA award to Harvard Catalyst is supporting the deployment of a SHRINE alliance across the i2b2 instances at UTH, UW, UCSF, UMichigan, and Wake Forest Baptist Medical Study for a study on the co-morbities of autism.. As an extension of our broad partnership with Morehouse School of Medicine, we were very pleased to support their interest in incorporating the CRC prototype into the clinical infrastructure proposed in their CTSA application.. This effort was facilitated by support from Recombinant Data Corp.. Our.. (clinical champions and informatics implementers at the academic health centers which are installing the i2b2 software) continues to collaborate and synergize on improvements to existing software, to identify new Hive cells of mutual interest, and to make these freely availabe to the user community.. Membership currently includes over 275 individual members from 50+ institutions, including over half of the CTSAs and six international sites.. AUG.. for details.. Expand our mandate as a NCBC through new docking funding.. Second round DBP PIs Roy Perlis and Jordan Smoller have built on their i2b2 work in Major Depressive Disorder to win two independent RO1s:.. R01 MH086026, Building a Risk Stratification Model for Treatment Resistance in Major Depressive Disorder, PI Roy Perlis.. See also:.. International Antidepressant Response Consortium (ARC).. www.. i2b2.. org/work/arc.. htm.. R01 MH08542, Internaltional Cohort Collection for Bipolar Disorder, PI Jordan Smoller.. Susanne Churchill, Ph.. D, Anthony Amato, MD.. : The i2b2 team has been awarded an industry sponsored DBP to use our data mining methodology to search for unique gene signatures in a characterized disease subphenotype.. Shawn Muphy, M.. : 3UL1RR025758-02S Subcontract, Sharing Clinical Images using i2b2 and SHRINE, supports the development and dissemination  ...   multiple markers and epistatic and gene by environment interactions) through the i2b2 portal as Hive cells.. , was awarded an NHGRI RO1 (HG003354) Decoding Gene Expression Control Using Conditional Clustering by Dynamics to develop computational methods to identify cellular control mechanisms from genome-wide experiments and disseminate these through the i2b2 portal.. Core 1 colleague Shamil Sunyaev, Ph.. , is PI of a NIGMS award (GM078598).. New Methods and Enhanced Software for Predicting Functional SNPs.. Sunyaev is working with Dr.. Inna Dubchak (photo, left) at VISTA to develop improved SNP targeting methods which will be made available via the i2b2 portal as both a stand alone program and as a Hive cell.. We were able to work directly with Dr.. Dubchak to expand the list of target genes in our Hypertension DBP and, as a further result, were pleased to collaborate in the submission of a newly funded second RO1, Comparative Genomics of Non-coding Regions to Facilitate Translational Research (RO1HL091495).. Diabetes DBP leader Mary Elizabeth Patti, M.. , participated on an subcontract with James Lyons-Weiler, Ph.. , at the University of Pittsburgh to develop robust proteomic profiles that are predictive of various insulin resistant states leading up to diabetes mellitus.. Explore innovative ways to acquire tissue samples for linking genomic analyses to clinical records w/o direct consent.. i2b2 continues to actively work with a novel system under development at Brigham and Women's Hospital, Boston, to use discarded clinical blood samples for genetic evaluation and linkage to anonymized clinical records.. Because both records and samples are anonymized (but linked through the anonymized id's), patient privacy is strictly maintained.. This concept, which has been instrumental to all of our DBPs, has led to an award from the NLM Crimson-i2b2 integration for high-throughput, scalable sample collection (R01 LM010100) by Lynn Bry, M.. D, Ph.. D, at BWH to develop a workflow Hive Cell for the CRC.. i2b2 Team Member Brian Wilson is actively supporting this project.. Develop Relevance Network Software.. that will enable healthcare systems to identify highly significant and novel associations across the entire spectrum of healthcare data.. Zak Kohane has been collaborating with Vlad Valtchinov, Ph.. (right, with daughter Yvana) to develop a new Hive Cell that will test the hundreds of millions of potential associations across clinical diagnoses and laboratory findings (including clinical genetics) for statistical significance at a level which merits additional follow-up.. Preliminary studies have suggested several novel correlations between clinical findings and metabolic pathways that may suggest new disease classifications and therapeutic targets.. This work was initially supported by funding from Partners HealthCare IT.. Expand our Education and Outreach Program.. In order to stabilize funding for and grow - our collegiate Summer Institute in Bioinformatics and Integrative Genomics, we have combined forces with a Ph.. program under the direction of Zak Kohane which is administered by the Harvard-MIT Division of Health Sciences and Technology and funded by NHGRI.. In the recent competing renewal to the NHGRI, we received six slots for URM summer students.. Coupled with i2b2 funding this gives us a total of 12-16 slots in our undergrad program.. Formation of the Boston Area Diversity Action Plan (DAP) Working Group as a spinoff of NHGRI's focus on the importance of DAPs for entities working at the genomics interface, several of the local programs which sponsor undergraduate, post baccalaureate, and postdoctoral training that emphasize inclusion of URMs and first generation college students have come together to share approaches, planned lectures and seminars, social activities and, where appropriate, applicants.. Current membership includes i2b2, the Harvard-MIT Health Sciences and Technology Bioinformatics and Integrative Genomics Ph.. T32, the Diversity Initiative for Scientific Research at the Broad Institute, Model Organism Databases (Harvard University, Jackson Lab, Stanford University, Cal Tech, and University of Oregon Consortium), the CEGS at Harvard Medical School, and the CEGS at the Dana Farber Cancer Institute.. We have collaborated with NHGRI to sponsor our i2b2 Minority Postdoctoral Fellowship Program, which has supported two fellows.. One of these, Dr.. Adam Davis, subsequently was awarded a K99 from the NHLBI and is now completing the R00 portion of the K99 as an Assistant Professor of Medicine at Morehouse School of Medicine.. He also continues to serve as the Teaching Assistant for our Summer Institute..

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  • Title: i2b2: Informatics for Integrating Biology & the Bedside
    Descriptive info: i2b2 Publications.. Noteworthy Selection.. Chronologically.. Facilitated by i2b2.. By Interest Area.. i2b2 PUBLICATIONS 2005-2012.. A.. Butte AJ, Kohane IS.. Creation and implications of a phenome-genome network.. Nature Biotechnology.. 2006;24(1):55-62.. PMID: 16404398.. Demonstrated how NLP on experimental labels could be combined with systematic gene expression measurements across public databases to provide useful retaxonomization of disease.. In many ways presaged the IOM report on Precision Medicine.. Citations: 90 Impact Factor 23.. 26.. Kohane IS, Masys DR, Altman RA.. The incidentalome: a threat to genomic medicine.. J Am Med Assoc.. 2006 Jul 12;296(2):212-5.. PMID: 16835427.. Opened up the dialog of the clinical consequences of high throughput measurements in the absence of the kind of high-throughput population studies that i2b2 made possible.. Widely cited in the lay press (e.. g WSJ, NPR) as well as citations in the scholarly publications.. Citations: 73 Impact Factor 30.. Murphy SN, Churchill SE, Bry L, Chueh H, Cai T, Weiss S, et al.. Instrumenting the health care enterprise for discovery research in the genomic era.. Genome Res.. 2009;360(13)1278-81.. PMID:19602638.. Summarized the design features of i2b2 that allowed phenotyping and sample collection to occur two orders magnitude more rapidly and at a tenth of the cost.. In addition to scholarly citations, it helped lead to the adoption of i2b2 at over 72 major academic health centers internationally.. Citations: 23 Impact Factor 13.. 6.. Weber GM, Murphy SN, McMurry AJ, Macfadden D, Nigrin DJ, Churchill S, Kohane IS.. The Shared Health Research Information Network (SHRINE): a prototype federated query tool for clinical data repositories.. J Am Med Inform Assoc.. 2009 Sep-Oct;16(5):624-30.. PMID: 19567788.. Described how a distributed query system across multiple i2b2 instances allowed the sharing of patient study data across institutions nationwide in near-real-time while allowing each healthcare institution to maintain autonomous control of their own data.. In doing so, this publication provided the template for multiple SHRINE installations covering 8 to 60 institutions for a variety of large studies.. Citations: 20, Impact Factor 3.. Cai C, Tian L, Lloyd-Jones D, Wei LJ.. Evaluating subject-level incremental values of new markers for risk classification rule.. Biometrics.. 2009;.. In the original i2b2 publication we set ourselves the goal of reframing the evaluation of biomarkers which often, especially early in the genomic era, just described the performance characteristics of the biomarker itself and not with comparison to the best use of existing conventional clinical data.. This manuscript is one of several our team published that developed a framework for understanding the incremental contribution to diagnostics (and progrnostics) of novel biomarkers.. Citations: 6 Impact Factor 1.. 87.. Brownstein J, Murphy S, Goldfine A, Grant R, Sordo M, Gainer V, Colecchi J, Dubey A, Nathan, D, Glaser J, Kohane I.. Rapid identification of myocardial infarction risk associated with diabetic medications using electronic medical records.. Diabetes Care 2010 Mar;33(3):526-31.. PMID: 2009093.. After an earlier proof of concept publication showing the retrospective identification of Vioxx-associated increased cardiovascular disease burden, this publication demonstrated that i2b2 could be used in the midst of national controversies requiring a big data approach to pubic health.. We identified and quantified the increased myocardial infarction risk of rosiglitazone (Avandia) relative to other drugs in the same class used for the treatment of diabetes mellitus.. This publication was one of a handful cited by the FDA in the black box ing of the drug and its subsequent near-disappearance from the market.. Citations 17 Impact Factor 8.. 07.. Tatonetti NP, Denny, JC, Murphy SN, Fernald GH, Krishnan G, Castro V, Yue P, Tsau PS, Kohane IS, Roden DM, Altman RB.. Detecting drug interactions from adverse-event reports: Interaction between paroxetine and pravastatin increases blood glucose leels.. Clin Pharm Therapeutics.. 2011 Jun;90:133-42.. PMID: 21613990.. A demonstration of how EHR-based methods could go from a signal in an FDA database to validation in three academic health centers in less than 3 months.. Citations: 13 Impact Factor 6.. 04.. Kohane, IS.. Using electronic health records to drive discovery in disease genomics.. Nat Rev Genet.. 2011 Jun;12(6):417-428.. 1038/nrg2999.. PMID: 21587298.. A summary of EHR-driven genomic disease research demonstrating the broad impact that i2b2 has had.. Citations 14 Impact Factor 38.. Mirny LA, Lander ES, Dekker J.. Comprehensive mapping of long-range interactions reveals folding principles of the human genome.. Science.. 2009;326(5950):289-93.. An example from one of many of our core 1 computational biology resarchers (Mirny) that developed novel biological insights using computational methods.. Citations 357, Impact Factor 31.. 2.. Kurreeman F, Liao K, Chibnik L, Hickey B, Stahl E, Gainer V, Li G, Bry L, Mahan S, Ardlie K, Thomson B, Szolovits P, Churchill S, Murphy SN, Cai T, Raychaudhuri S, Kohane I, Karlson E, Plenge R.. Genetic basis of autoantibody positive and negative Rheumatoid Arthritis risk in a multi-ethnic cohort derived from Electronic Health Records.. Am J Human Gen.. 2011 Jan 7;88:57-69.. Demonstration that not only can i2b2 be used to perform cost-effective genetic studies but they a) reproduce prior studies and b) go beyond prior studies by including under-represented minorities (which are even more underrepresented in traditional cohort studies) and studying the genetics of both antibody positive and negative rheumatoid arthritis.. Citations: 12 Impact factor 10.. B.. Kohane IS.. , Altman RA.. Health-information altruists a potentially critical resource.. New Engl J Med.. 2005;353:2074-7.. Sordo M, Zeng Q.. On sample size and classification accuracy: A performance comparison.. Lecture Notes in Computer Science.. 2005;3745:193-201.. Fraser HSF, Biodich P, Moodley D, Choi S, Mamlin B,.. Szolovits P.. Implementing electronic records systems in developing countries.. Informatics in Primary Care.. 2005;13:83-95.. Wolfe CJ,.. , Butte AJ.. Systematic survey reveals general applicability of guilt-by-association within gene coexpression networks.. BMC Bioinformatics.. 2005;6:227.. Tian L, Greenberg SA, Kong SW, Altschuler J,.. Kohane I, Park P.. Discovering statistically significant pathways in expression profiling studies.. Proc Natl Acad Sci USA.. 2005;102(38)13544-9.. Lee S,.. Kohane I, Kasif S.. Genes involved in complex adaptive processes tend to have highly conserved upstream regions in mammalian genomes.. BMC Genomics.. 2005;6:168.. PMID: 16309559.. Wu CH, Kasif S.. GEMS: A web server for biclustering analysis of expression data.. Nucleic Acids Res.. 2005;33:W596-9.. Kryukov GV, Schmidt S, Sunyaev S.. Small fitness effect of mutations in highly conserved non-coding regions.. Human Mol Gen.. 2005;4:2221-2229.. Butte AJ,.. , Masys DR, Altman RA.. 2006;296(2):212-5.. Murphy SN, Mendis ME, Berkowitz DA, Kohane I, Chueh H.. Integration of clinical and genetic data in the i2b2 architecture.. AMIA Annu Symp Proc.. 2006:1040.. PMID:17238659.. Carter SL, Eklund AC,.. , Haris LN, Szallasi Z.. A signature of chromosomal instability inferred from gene expression profiles predicts clinical outcome in multiple human cancers.. Nat Gen.. 2006;38(9):1043-48.. Brownstein JS.. , Cassa CC,.. , Mandl KD.. An unsupervised classification method for inferring original case locations from low-resolution disease maps.. Internatl J Health Geographics.. 2006;5:56.. Rachlin J, Cohen DD, Cantor C,.. Kasif S.. Biological context networks: a mosaic view of the interactome.. Nature/Embo Molecular Systems Biology.. 2006;2:1.. Kong SW, Pu WT,.. Park PJ.. A multivariate approach for integrating genome-wide expression data and biological knowledge.. Bioinformatics.. 2006;22:2373-80.. Zeng QT, Goryachev S, Weiss S, Sordo M, Murphy SN, Lazarus R.. Extracting principal diagnosis, co-morbidity and smoking status for asthma research: Evaluation of a natural language processing system.. BMC Med Inform Med Decision Making.. 2006;6:30.. Goryachev S, Sordo M, Zeng QT.. A suite of natural language processing tools developed for the i2b2 project.. 2006:931.. Bramsen P, Deshpande P, Lee YK,.. Barzilay R.. Finding temporal order in discharge summaries.. 2006:81-85.. PMID:17238307.. Sibanda T, He T, Szolovits P, Uzuner Ö.. Syntactically-informed semantic category recognizer for discharge summaries.. 2006:714 718.. Uzuner Ö, Szolovits P, Kohane I.. i2b2 Workshop on Natural Language Processing challenges for clinical records.. 2006:81-5.. 2006:714-718.. Sibanda T, Uzuner Ö.. Role of local context in de-identification of ungrammatical, fragmented text.. Proceedings of the North American Chapter of Association for Computational Linguistics/Human Language Technology (NAACL-HLT 2006), New York, NY, June 5-7, 2006.. pp.. 65-73.. Gusella JF, Macdonald ME.. Huntington's Disease: Seeing the pathogenic process through a genetic lens.. Trends Biochem Sci.. 2006 Sept;31(9):533-40.. PMID: 16829072.. McMurry AJ, Gilbert CA, Reis BY,.. Chueh HC, Kohane IS.. A self scaling, distributed architecture for public health, research, and clinical care.. 2007;14(4):527-33.. Loscalzo J,.. , Barabasi AL.. Human disease classification in the postgenomic era: a complex systems approach to human pathobiology.. Mol Syst Biol.. 2007;3:124.. Murphy SN, Mendis M, Hackett K, Kuttan R, Pan W, Phillips L,.. et al.. Architecture of the open-source clinical research chart from Informatics for Integrating Biology and the Bedside.. 2007 Oct 11;548-52.. PMID:18693896.. Dubey A, Herrick C, Murphy SN.. Mining for associations between categorical data items in a clinical data repository.. 2007 Oct 11:945.. PMID:18694045.. Gainer V, Hackett K, Mendis M, Kuttan R, Pan W, Phillips L, Chueh H, Murphy SN.. Using the i2b2 Hive for clinical discovery: An example.. 2007 Oct 11:959.. PMID:18694059.. Mendis M, Wattanasin N, Kuttan R, Pan W, Hackett K, Gainer V, Chueh H, Murphy SN.. Integration of Hive and Cell software in the i2b2 architecture.. 2007 Oct 11:1048.. PMID:18694146.. Evans SR, Li L,.. Wei LJ.. Data monitoring in clinical trials using predictions.. Drug Information J.. 2007;41:733-742.. Tian T.. Cai T.. , Goetghebeur E,.. Model evaluation based on the distribution of estimated absolute prediction error.. Biometrika.. 2007;94:297-311.. Uno H, Cai T, Tian L, and Wei LJ.. Evaluating prediction rules for t-year survivors with censored regression models.. 2007;102:527-37.. Brownstein JS, Sordo M, Kohane IS.. , Mandl Kl.. Telltale heart: population based surveillance model reveals association with rofecoxib and celecoxib with myocardial infarction.. PlosOne.. 2007;9(9):e840.. Reis BY,.. An epidemiological network model for disease outbreak detection.. PLoS Med.. 2007;4(6):e210.. Goldstein I.. , Arzrumtsyan A,.. Uzuner Ö.. Three approaches to automatic assignment of ICD-9-CM codes to radiology reports.. 2007 Oct 11:279-83.. Uzuner Ö, Luo Y, Szolovits P.. Evaluating the state-of-the-art in automatic de-identification.. 2007;14(5):550-563.. Turchin A, Kolatkar NS, Pendergrass ML,.. Computational analysis of non-adherence and non-attendance using the text of narrative physician notes in the electronic medical record.. Med Inform Internet Med.. 2007;32(2):93-102.. Inaoka H, Fukuoka Y,.. Kohane I.. Evidence of spatially bound gene regulation in Mus musculus: Decreased gene expression proximal to microRNA genomic location.. Proc Natl Acad Sci.. 2007;104(12)5020-5.. Kryukov GV.. , Pennacchio LA,.. Sunyaev SR.. Most rare missense alleles are deleterious in humans: implications for complex disease and association studies.. 2007 Apr;80(4):727-39.. Asthana S, Noble WS,.. Kryukov G.. , Grant CE,.. Sunyaev S.. , Stamatoyannopoulos JA.. Widely distributed non-coding purifying selection in the human genome.. 2007;104(30):12410-5.. Asthana S, Roytberg M, Stamatoyannopoulos J,.. Analysis of sequence conservation at nucleotide resolution.. PLoS Comput Biol.. 2007;Dec;3(12):e254.. Spirin V,.. Schmidt S.. , Pertsemlidis A, Cooper RS, Cohen JC,.. Common single-nucleotide polymorphisms act in concert to affect plasma levels of high-density lipoprotein cholesterol.. Am J Hum Genet.. 2007 Oct 19;81(6).. Widely distributed noncoding purifying selection in the human genome.. ENCODE Consortium (.. Sunyaev.. Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project.. Nature.. 2007 Jun 14;447(7146):799-816.. Ahituv N, Kavaslar N, Schackwitz W, Ustaszewska A, Martin J, Hebert S, Doelle H, Ersoy B,.. Schmidt S,.. Yosef N, Ruppin E, Sharan R, Vaisse C,.. , Dent R, Cohen J, McPherson R, Pennacchio LA.. Medical sequencing at the extremes of human body mass.. 2007;80(4):779-91.. Allocco DJ, Song Q, Gibbons GH,.. Ramoni MF, Kohane IS.. Geography and genography: Prediction of continental origin using randomly selected single nucleotide polymorphisms.. 2007;8:68.. Dotan-Cohen D, Melkman AA,.. Hierarchical tree snipping: clustering guided by prior knowledge.. 2007;23(24):3335-42.. Carey VJ.. , Morgan M, Falcon S,.. Lazarus R.. , Gentleman R.. GGtools: analysis of genetics of gene expression in Bioconductor.. 2007;23(4):522-523.. Kolesov G.. , Virnau P, Kardar M,.. Mirny LA.. Protein knot server: Detection of knots in protein structures.. Nucleic Acids Research 2007;35(10):W425-8.. Galan-Caridad JM, Harel S, Arenzana TL, Hou ZE, Doetsch FK,.. , Reizis B.. Zfx controls the self-renewal of embryonic and hematopoietic stem cells.. Cell.. 2007; 129(2):345-57.. Kolesov G, Wunderlich Z.. , Laikova O.. , Gelfand MS,.. How gene order is influenced by the biophysics of transcription regulation.. 2007;104(35):13948-53.. Gomez-Uribe C, Verghese GC,.. Operating regimes of signaling cycles: statics, dynamics, and noise filtering.. 2007;3(12):e246.. Lee JM.. , Ivanova EV, Seong IS, Cashorali T,.. Kohane I, Gusella JF, MacDonald ME.. Unbiased gene expression analysis implicates the huntingtin polyglutamine tract in extra-mitochondrial energy metabolism.. PLoS Genet.. 2007;3(8):e135.. PMID: 17708681.. Gusella JF, Macdonald M.. Genetic criteria for Huntington's Disease pathogenesis.. Brain Res Bull.. 2007 Apr 30;72(2-3):78-82.. PMID: 17352930.. Liu M, Liberzon A, Kong SW, Weil RL,.. Park PJ, Kohane IS, Kasif.. S.. Network-based analysis of affected biological processes in Type 2 diabetes models.. PLoS Genetics.. 2007;3:0001-0015.. 1371/journal.. pgen.. 0030096.. Dubey AK, Gainer V, Murphy SN.. Simulated yields of prospective specimen collection from specific patient cohorts using retrospective data from a research patient data repository.. 2008 Nov 6:935.. PMID:18999309.. Mendis M, Phillips L, Kuttan R, Pan W, Gainer V, Kohane I, Murphy SN.. Integrating outside modules into the i2b2 architecture.. 2008 Nov 6:1054.. PMID:18999021.. Scheufele EL,.. Dubey AK, Murphy SN.. A study of the age attribute in a query tool for a clinical data warehouse.. 2008 Nov 6:1123.. PMID:18999019.. Sordo M, Colecchi J, Dubey AK,.. Gainer V, Murphy SN.. STROBE-Based Methodology for Detection of Adverse Events across Multiple Communities.. 2008 Nov 6:1144.. PMID:18998965.. Dinov ID, Rubin D, Lorensen W, Dugan J, Ma J,.. Murphy S.. , Kirschner B, Bug W, Sherman M, Floratos A, Kennedy D, Jagadish HV, Schmidt J, Athey B, Califano A, Musen M, Altman R, Kikinis R,.. , Delp S, Parker DS, Toga AW.. iTools: A framework for classification, categorization and integration of computational biology resources.. PLoS ONE.. 2008;3(5): e2265.. PMID:18509477.. Wang T, Plaisant C, Quinn A, Stanchak R,.. Murphy SN.. , Shneiderman B.. Aligning temporal data by sentinel events: Discovering patterns in electronic health records, Proc ACM.. 2008 April 5;10:457-466.. Cai T, Tian L,.. Solomon S,.. Predicting future responses based on possibly misspecified working models.. 2008;95(1):75-92.. Second i2b2 workshop on natural language processing challenges for clinical records.. 2008 Nov 6:1252-3.. PMID:18998924.. Uzuner Ö, Goldstein I, Kohane I.. Identifying patient smoking status from medical discharge records.. J Am Med Inform.. 2008;15(1):14-24.. PMID:17947624.. Zhang Y, Szolovits P.. Patient-specific learning in real time for adaptive monitoring in critical care.. J Biomed Inform.. 2008;41(3):452-460.. PMID:18463000.. Uzuner Ö, Sibanda T, Luo Y, Szolovits P.. A de-identifier for medical discharge summaries.. Artificial Intelligence Med.. 2008;42(1):13-35.. Uzuner Ö, Zhang X, Sibanda T.. Two approaches to assertion classification.. 2008 Nov 6:752.. PMID:18990049.. Goryachev S.. , Kim H,.. Zeng-Treitler Q.. Identification and extraction of family history information from clinical records.. 2008 Nov 6:247-51.. PMID:18999129.. Lohmueller KE, Indap AR,.. Boyko AR, Hernandez RD, Hubisz MJ, Sninsky JJ, White TJ,.. , Nielsen R, Clark AG, Bustamante CD.. Proportionally more deleterious genetic variation in European than in African populations.. 2008 Feb 21;451(7181):994-7.. PMID:18288194.. Gorlov IP, Gorlova OY,.. , Spitz MR, Amos CI.. Shifting paradigm of association studies: Value of rare single-nucleotide polymorphisms.. 2008;82(1):100-12.. PMID:18179889.. Naxerova K.. , Bult CJ, Peaston A, Fancher K, Knowles BB,.. Kasif S, Kohane IS.. Analysis of gene expression in a developmental context emphasizes distinct biological leitmotifs in human cancers.. Genome Biol.. 2008;9(7):R108.. PMID: 18611264.. Beckstead WA.. , Bjork BC, Stottmann RW,.. ,.. Beier DR.. SNP2RFLP: A computational tool to facilitate genetic mapping using benchtop analysis of SNPs.. Mammalian Genome.. 2008 Oct-Dec;19(10-12):687-90.. Boyko A, Hernandez R,.. Schmidt S, Sunyaev S.. , Nielsen R, Clark A, Bustamante C.. Assessing the evolutionary impact of amino acid mutations in the human genome.. 2008;4(5)e1000083.. PMID:18516229.. Gerasimova A, Kondrashov FA, Adzhubei IA, Kondrashov AS,.. Hypermutable non-synonymous sites are under stronger negative selection.. 2008;Nov;4(11):e1000281.. PMID:19043566.. Jiang X, Nariai N, Steffen M,.. , Kolaczyk ED.. Integration of relational and hierarchical network information for protein function prediction.. 2008;9:350.. PMID:18721473.. Kolesov G, Mirny LA.. Using evolutionary information to find specificity determining and co-evolving residues, In Computational Systems Biology, edited by Jason Mcdermott, Springer-Verlag New York Inc, 2008.. Tafvizi A.. , Huang F, Leith JS, Fersht AR,.. , van Oijen AM.. Tumor suppressor p53 slides on DNA with low friction and high stability.. Biophys J.. 2008;95(1):L01-2.. 2008; 9:350.. Wunderlich Z, Mirny LA.. Spatial effects on the speed and reliability of protein-DNA search.. 2008;36(11):3570-8.. PMID:18453629.. Rahi SJ, Virnau P,.. , Kardar M.. Predicting transcription factor specificity with all-atom models.. 2008;36(19):6209-17.. PMID:18829719.. Himes BE, Kohane IS, Ramoni MF, Weiss ST.. Characterization of patients who suffer asthma exacerbations using data extracted from electronic medical records.. 2008 Nov 6:308-12.. PMID:18999057.. Doria A,.. Patti ME.. , Kahn CR.. The emerging genetic architecture of type 2 diabetes.. Cell Metabolism.. 2008;8(3):186-200.. PMID:18762020.. The twin questions of personalized medicine: Who are you and whom do you most resemble? Genome Med.. 2009;1(1):4.. Mandl KD,.. No small change for the health information economy.. N Engl J Med.. 2009;360(13):1278-81.. Weber GM, Murphy SN.. , McMurry AJ, Macfadden D,  ...   Gainer VS,.. , Cai T, Goryachev S, Zeng Q,.. Gallagher PJ, Fava M, Weilburg JB,.. Churchill SE, Kohane IS, Smoller JW.. Using electronic medical records to enable large-scale studies in psychiatry: Treatment Resistant Depression as a model.. Psychol Med.. 2012 Jan;42(1):41-50.. PMID: 21682950.. Castro V,.. Gallagher PJ, Clements CC,.. Murphy SN, Gainer VS.. , Weilburg JB, Fava M,.. Churchill SE, Kohane IS, Smoller JW, Iosifescu DV, Perlis RH.. Incident user cohort study of risk for gastrointestinal bleed and stroke in individuals with Major Depressive Disorder treated with antidepressants.. Brit Med J Open.. 2012 Mar 30;2(2):e000544.. PMID:22466034.. Kohane IS, Churchill SE, Murphy SN.. A translational engine at the national scale: informatics for integrating biology and the bedside.. 2012;19(2)181-5.. Epub 2011 Nov 10.. PMID:22081225.. Mandl KD, Mandel JC,.. , Bernstam EV, Ramoni RL, Kreda DA, McCoy JM, Adida B,.. The SMART Platform: early experience enabling substitutable applications for electronic health records.. 2012 Mar 17.. (Epub ahead of print) PMID:22427539.. Wu ST, Liu H, Tao C, Musen MA, Chute GG, and.. Shah.. NH.. Unified Medical Language System term occurrences in clinical notes: a large-scale corpus analysis.. 2012 Jun 1;19(e1):e149-e156.. PMID:22493050.. Harpaz R, Dumouchel W,.. Shah NH.. , Madigan D, Ryan P, Friedman C.. Novel data-mining methodologies for adverse drug event discovery and analysis.. Clin Pharm Ther 2012 May 2.. PMID: 22549283.. Carroll RJ, Thompson WK, Eyler AE, Mandelin AM,.. , Zink RM, Pacheco JA, Boomershine CS, Lasko TA, Xu H,.. Karlson EW, Perez RG, Gainer VS, Murphy SN.. , Ruderman EM, Pope RM,.. Plenge RM.. , Kho AN,.. Liao KP.. , Denny JC.. Portability of an algorithm to identify rheumatoid arthritis in electronic health records.. 2012 Jun 1;19(e1):e162-e169.. Epub 2012 Feb 28.. PMID: 22374935.. Kurreeman FA.. , Stahl EA, Okada Y, Liao K, Diogo D, Raychaudhuri S, Freudenberg J, Kochi Y, Patsopoulos NA, Gupta N; CLEAR investigators, Sandor C, Bang SY, Lee HS, Padyukov L, Suzuki A, Siminovitch K, Worthington J, Gregersen PK, Hughes LB, Reynolds RJ, Bridges SL Jr, Bae SC, Yamamoto K,.. Use of a multiethnic approach to identify rheumatoid- arthritis-susceptibility loci, 1p36 and 17q12.. 2012 Mar 9;90(3):524-32.. PMID: 22365150.. Sittig DF, Hazlehurst BL, Brown J,.. , Rosenman M, Tarczy-Hornoch P, Wilcox AD.. A survey of informatics platforms that enable distributed comparative effectiveness research using multiinstitutional heterogenous clinical data.. Med Care.. 2012 July;50(P):S49-59.. 1097/MLR.. obo13e318259co2b.. PMID:22692259.. Gallagher PJ, Castro V, Fava M, Weilburg JB,.. Murphy SN, Gainer VS, Churchill SE, Kohane IS, Iosifescu DV, Smoller JW, Perlis RH.. Antidepressant response in individuals with major depressive disorder exposed to NSAIDs: a pharmacovigilance study.. Am J Psychiatry (in press).. Hoogenboom WS, Perlis RH, Smoller JW, Zeng-Treitler Q, Gainer VS, Murhph SN, Churchill SE, Kohane IS,.. Shenton ME.. , Iosifescu DV.. Feasibility of studying brain morphology in major depressive disorder with structural magnetic resonance imaging and clinical data from the electronic medical record: A pilot study.. Psych Res.. 2012: accepted.. ***********************************.. Publications facilitated by i2b2.. From the First NLP Challenge:.. Wellner B, Huyck M, Mardis S, Aberdeen J, Morgan M, Peshkin L, Yeh A, Hitzeman J, HirschmanL: Rapidly retargetable approaches to de-identification in medical records.. 2007;14:564-573.. Epub 2007 Jun 28.. Szarvas Gy.. , Farkas R, Busa-Fekete R.. State-of-the-art anonymisation of medical records using an iterative machine learning framework.. 2007;14:574-580.. Savova G, Ogren P, Duffy P, Buntrock J, Chute C.. Mayo Clinic NLP System for patient smoking status sdentification.. 2008;15(1):25-28.. Epub 2007 Oct 18.. Wicentowski R, Sydes MR.. Using implicit information to iIdentify smoking status in smoke-blind medical discharge summaries.. 2008; 15(1):29-31.. Cohen AM.. Five-way smoking status classification using text hot-spot identification and error-correcting output codes.. 2008; 15(1):32-35.. Clark C, Good K, Jezierny L, Macpherson M, Wilson B, Chajewska U.. Identifying smokers with a medical extraction system.. 2008;15(1):36-39.. Heinze DT, Morsch ML, Potter BC, Sheffer RE Jr.. A Life Medical i2b2 NLP Smoking Challenge system architecture methodology.. 2008;15(1):40-43.. Hara K.. Applying a SVM based chunker and a text classifier to the Deid Challenge.. Available as JAMIA on-line supplement to Uzuner et all at.. jamia.. org.. Pedersen T.. Determining smoker status using supervised and unsupervised learning with lexical features.. McMormick PJ, Elhadad N, Stetson PD.. Use of semantic features to classify patient smoking status.. AMIA Annu Symp Proc 2008;6:450-4.. From the Second NLP Challenge:.. Farkas R, Szarvas G, Hegedüs I, Almási A, Vincze V, Ormándi R, Busa-Fekete R.. Semi-automated construction of decision rules to predict morbidities from clinical texts.. July 2009;16(4):601-5.. Epub 2009 Apr 23.. Yang H, Spasic I, Keane JA, Nenadic G.. A text mining approach to the prediction of a disease status from clinical discharge summaries.. J Am Med Informs Assoc.. July 2009;16(4):596-600.. Kyle H.. Ambert, Aaron M.. Cohen.. A system for classifying disease comorbidity status from medical discharge summaries using automated hotspot and negated concept detection.. July 2009;16(4):590-5.. Ware H, Mullett CJ, Jagannathan J.. Natural Language Processing (NLP) Framework to assess clinical conditions.. July 2009;16(4):585-9.. Solt I, Tikk D, Gal V, Kardkovics ZT.. Semantic classification of diseases in discharge summaries using a context-aware rule based classifier.. July 2009;6(4):578-9.. Mishra NK, Cummo DM, Arnzen JJ, Bonander J.. A rule-based approach for identifying obesity and its co-morbidities in medical discharge summaries.. 2009;16(4): 576-9.. Childs LC, Taylor RJ, Simonsen L, Heintzelman NH, Kowalski KM, Enelow R.. Description of a rule-based system for the i2b2 Challenge in Natural Language Processing for Clinical Data.. 2009; 6(4):571-5.. From the Third NLP Challenge:.. Manabu Torii, Kavishwar Wagholikar, Hongfang Liu.. Using machine learning for concept extraction on clinical documents from multiple data sources.. JAMIA 2011;Published Online First: 27 June 2011 doi:10.. 1136/amiajnl-2011-000155.. Leonard W D'Avolio, Thien M Nguyen, Sergey Goryachev, Louis D Fiore.. Automated concept-level information extraction to reduce the need for custom software and rules development.. JAMIA 2011;Published Online First: 22 June 2011 doi:10.. 1136/amiajnl-2011-000183.. Anne-Lyse Minard, Anne-Laure Ligozat, Asma Ben Abacha, Delphine Bernhard, Bruno Cartoni,LouiseDeléger, Brigitte Grau, Sophie Rosset, Pierre Zweigenbaum, Cyril Grouin.. Hybrid methods for improving information access in clinical documents: concept, assertion, and relation identification.. JAMIA 2011;Published Online First: 19 May 2011 doi:10.. 1136/amiajnl-2011-000154.. Berry de Bruijn, Colin Cherry, Svetlana Kiritchenko, Joel Martin, Xiaodan Zhu.. Machine-learned solutions for three stages of clinical information extraction: the state of the art at i2b2 2010.. JAMIA 2011;Published Online First: 12 May 2011 doi:10.. 1136/amiajnl-2011-000150.. Cheryl Clark, John Aberdeen, Matt Coarr, David Tresner-Kirsch, Ben Wellner, Alexander Yeh,Lynette Hirschman.. MITRE system for clinical assertion status classification.. JAMIA 2011;Published Online First: 22 April 2011 doi:10.. 1136/amiajnl-2011-000164.. Kirk Roberts, Sanda Harabagiu.. A flexible framework for deriving assertions from electronic medical records.. JAMIA 2011;Published Online First:1 July 2011 doi:10.. 1136/amiahnl-2011-000152.. Min Jiang, Yukun Chen, Mei Liu, S Trent Rosenbloom, Subramani Mani, Joshua C Denny,HuaXu.. A study of machine-learning-based approaches to extract clinical entities and their assertions from discharge summaries.. JAMIA 2011;Published Online First: 20 April 2011 doi:10.. 1136/amiajnl-2011-000163.. From the Fourth NLP Challenge.. Özlem Uzuner, Andreea Bodnari, Shuying Shen, Tyler Forbush, John Pestian, Brett R South.. J Am Med Inform Assoc 2012;19:786-791 Published Online First: 24 February 2012 doi:10.. Siddhartha Reddy Jonnalagadda, Dingcheng Li, Sunghwan Sohn, Stephen Tze-Inn Wu, Kavishwar Wagholikar, Manabu Torii, Hongfang Liu.. Coreference analysis in clinical notes: a multi-pass sieve with alternate anaphora resolution modules.. J Am Med Inform Assoc 2012;19:867-874 Published Online First: 16 June 2012 doi:10.. 1136/amiajnl-2011-000766.. Bryan Rink, Kirk Roberts, Sanda M Harabagiu.. A supervised framework for resolving coreference in clinical records.. J Am Med Inform Assoc 2012;19:875-882 Published Online First: 19 May 2012 doi:10.. 1136/amiajnl-2012-000810.. Henry Ware, Charles J Mullett, Vasudevan Jagannathan, Oussama El-Rawas.. Machine learning-based coreference resolution of concepts in clinical documents.. J Am Med Inform Assoc 2012;19:883-887 Published Online First: 12 May 2012 doi:10.. 1136/amiajnl-2011-000774.. Hong-Jie Dai, Chun-Yu Chen, Chi-Yang Wu, Po-Ting Lai, Richard Tzong-Han Tsai, Wen-Lian Hsu.. Coreference resolution of medical concepts in discharge summaries by exploiting contextual information.. J Am Med Inform Assoc 2012;19:888-896 Published Online First: 3 May 2012 doi:10.. 1136/amiajnl-2012-000808.. Yan Xu, Jiahua Liu, Jiajun Wu, Yue Wang, Zhuowen Tu, Jian-Tao Sun, Junichi Tsujii, Eric I-Chao Chang.. A classification approach to coreference in discharge summaries: 2011 i2b2 challenge.. J Am Med Inform Assoc 2012;19:897-905 Published Online First: 13 April 2012 doi:10.. 1136/amiajnl-2011-000734.. Prateek Jindal, Dan Roth.. Using domain knowledge and domain-inspired discourse model for coreference resolution for clinical narratives.. J Am Med Inform Assoc amiajnl-2011-000767Published Online First: 10 July 2012 doi:10.. 1136/amiajnl-2011-000767.. C.. Systems Medicine:.. Kohane.. IS, Altman RA.. Health-information atruists a potentially critical resource.. , Masys DR,.. Altman RA.. The twin questions of personalized medicine: who are you and whom do you most resemble? Genome Med.. Murphy SN, Churchill SE, Bry L, Chueh H, Cai T, Weiss S,.. Weber GM, Murphy SN, McMurry AJ,.. Macfadden D, Nigrin DJ,.. Valtchinov VI and Kohane IS.. Bioinfomatics, accepted 2011.. Informatics Tool Development and Application:.. 2006;p.. 1040.. Murphy SN, Mendis M, Hackett K, Kuttan R, Pan; W, Phillips L, et al.. 2007;p.. 548-52.. , Herrick C,.. 945.. Using the i2b2 Hive for clinical discovery: an example.. 2007; p.. 959.. 1048.. Aligning temporal data by sentinel events: Discovering patterns in electronic health records, Proceedings of ACM, April 5-10, 2008.. 457-466.. 2008;p.. 935.. 1054.. 1123.. Sordo M, Colecchi J,.. 1144.. Kohane I,.. Delp S, Parker DS, Toga AW.. Proc.. 2010 AMIA Fall Symposium: 807-811.. Predictive Medicine:.. Nat Gen 2006;38(9):1043-48.. Tian T,.. Uno H, Cai T,.. Tian L, and.. , Tian L, Solomon S,.. Tian L,.. , Piankov N, Cremieux P,.. Effectively combining independent 2 by 2 tables for valid inferences in meta analysis with all available data but no artificial continuity corrections for studies with zero events and its application to the analysis of Rosiglitazone's Cardiovascular disease related event data.. Biostatistics, 2009 in press.. Cai C.. , Tian L, Lloyd-Jones D,.. 2009;in revision.. Statistics in Medicine,2009; accepted.. , Tian L,.. Uno H.. , Solomon D,.. Biometrika, in press.. 2009.. Combining information for robust prediction of survival outcomes.. 2009;accepted.. Wang R, Tian L,.. Annals of Applied Statistics, 2009; in press.. , Hunter D, Hu F.. Tian L, Wang R,.. Biometrics, in revision.. , Tian L, Wong P,.. analysis of randomized comparative clinical trial data for personalized treatent selections.. 2011, in press.. , Solomon S,.. Population Based Studies (including Pharmacovigilance):.. Internatl J Health Geographics 2006;5:56.. , Sordo M,.. 2007;9 (9) e840.. An epidemiological network model for disease outbreak Detection.. , Grant R, Sordo M,.. Gainer V.. , Colecchi J, Dubey.. A, Nathan, D, Glaser J, Kohane I.. Diabetes Care 2010;33(3):526-31.. Pearson JF, Bachireddy C, Shyamprasad S, Goldfine AB,.. Tatonetti NP, Denny, JC,.. , Yue P, Tsau PS,.. 2011;90(3):133-40.. Natural Language Processing:.. Implementing electronic records systems in developing countries,.. 2005; 13:83-95.. Zeng QT, Goryachev S, Weiss S, Sordo M, Murphy SN, Lazarus, R.. BMC Med Inform and Med Decision Making.. Goryachev S, Sordo M, Ngo L, Zeng QT.. Implementation and evaluation of four different methods of negation detection.. Technical report, DSG.. AMIA Annu Symp Proc 2006:p.. 931.. 2006.. 2006: 714 718.. i2b2 Workshop on Natural Language Processing.. challenges for clinical records.. Uzuner Ö, Goldstein I, Kohane.. I.. Artificial intelligence Med.. 6:752.. Goryachev S, Kim H, Zeng-Treitler Q.. 2008; pp.. 247-51.. Specializing for predicting obesity and its o-morbidities.. Semantic Relations for Problem-Oriented Medical Records.. 2009; p.. 661.. Sibanda T, He T, Szolovits P, Uzuner Ö.. 2006;pp714-718.. 2010 i2b2/VA Challenge on Concepts, Assertions, and Relations in Clinical Text.. From the First NLP Challenge:.. From the Second NLP Challenge:.. JAMIA.. 2011;Published Online First: 27 June 2011 doi:10.. Automated concept-level information extraction to reduce the need for custom software and rules development.. 2011;Published Online First: 22 June 2011 doi:10.. 2011;Published Online First: 19 May 2011 doi:10.. 2011;Published Online First: 12 May 2011 doi:10.. 2011;Published Online First: 22 April 2011 doi:10.. 2011;Published Online First: 20 April 2011 doi:10.. 1136/amiajnl-2011-000784.. Genomics:.. 2006; 2:1.. Kohane, I.. Liu M, Liberzon A, Kong SW, Lai WR,.. Park PJ, Kohane.. IS et al.. Network-based analysis of affected biological processes in type 2 diabetes models.. 2007;3(6):e96.. Kryukov GV, Pennacchio LA,.. 2007;Apr;80(4):727-39.. Lohmueller KE, Indap AR, Schmidt S, Boyko AR, Hernandez RD, Hubisz MJ, Sninsky JJ, White TJ,.. 2008;Feb 21;451(7181):994-7.. ENCODE Consortium.. Kryukov G,.. Schmidt S, Yosef N, Ruppin E, Sharan R, Vaisse C,.. Geography and genography: prediction of continental origin using randomly selected single nucleotide polymorphisms.. Dotan-Cohen, Melkman AA,.. Liu M, Liberson A, Kong SW, Lai WR,.. Park PJ, Kohane IS, Kasif S.. Network based analysis of affected biological processes in type 2 diabetes models.. Shifting paradigm of association studies: value of rare single-nucleotide polymorphisms.. Naxerova K, Bult CJ, Peaston A, Fancher K, Knowles BB,.. , Bjork BC, Stottmann RW.. , Sunyaev S.. , Beier DR.. SNP2RFLP: Mammal.. Genome.. A computational tool to facilitate genetic mapping using benchtop analysis of SNPs.. 2008; Oct-Dec;19(10-12):687-90.. Schmidt S, Gerasimova A, Kondrashov FA, Adzhubei IA, Kondrashov AS,.. 2009;Apr;41(4):393-5.. 2009;Mar 10;106(10):3871-6.. Davis A,.. Tian Z, Palmer N, Schmid P, Yao H, Galdzicki M,.. Berger B.. , et al.. , Bianco AC, Goldfine AB,.. , Cantor C, Kasif S.. Genomics Tools:.. Ggtools: analysis of genetics of gene expression in Bioconductor.. Carey V, Davis A.. Protein and DNA Biophysics:.. Kolesov G,.. Using evolutionary information to find specificity determining and co-evolving residues.. In Computational Systems Biology, Humana Press, 2007.. Kolesov G, Virnau P, Kardar M,.. Protein knot server: detection of knots in protein structures.. Nucleic Acids Research 2007;35(10)W425-8.. Kolesov G, Wunderlich Z, Laikova O, Gelfand MS,.. 2008, in press.. Galan-Caridad JM, Harel S.. , Arenzana TL, Hou ZE, Doetsch FK,.. Kolesov G, Wunderlich Z, Laikova O.. Tafvizi A, Huang F, Leith JS, Fersht AR,.. Wunderlich Z,.. 2008;6(11):3570-8.. 2009; in press.. Mirny LA,.. ,.. , Slutsky M, Wunderlich Z, Tafvizi A, Leith J, Kosmrlj A.. How a protein searches for its site on DNA: the mechanism of facilitated diffusion J.. 42 No.. 43 (30 October 2009) 434013.. , Lander ES, Dekker J.. , Alexandrov LB, Gelev V, Dagon ,Block J,.. , Rasmussen K, Bishop AR, Usheva A.. 1371.. journal.. pone.. 0019800.. From the Asthma DBP:.. 2008;308-12.. , Raby B.. , Qiu W, Silverman E.. K.. ,Weiss S.. T.. , "Quantifying the effects of allele frequency differences and allelic phase on LD captured by tag SNPs derived from incompletely ascertained data: Theoretical basis, models and impact on LD mapping", Oral presentation and Proceedings of the American Society of Human Genetics Annual Meeting 2006, New Orleans.. Himes B.. E.. , Kohane I.. , Ramoni M.. F.. , Weiss S.. 2008 Nov 6; 308-12.. , Day Y.. Prediction of Chronic Obstructive Pulmonary Disease (COPD) in asthma patients using electronic medical records.. 2009;308-12.. , Klanderman B.. 2011 Apr;127(4):1067-9.. From the Huntington s Disease DBP:.. Huntington's disease: seeing the pathogenic process through a genetic lens.. 2006;Sep;31(9):533-40.. PMID: 16829072.. , Ivanova EV, Seong IS,.. Cashorali T, Kohane I, Gusella JF, MacDonald ME.. Genetic criteria for Huntington's disease pathogenesis.. 2007;Apr 30;72(2-3):78-82.. Kohane IS, Gusella JF.. 2011;20(14):2846-60.. Gusella JF, MacDonald ME.. Differential effects of the Huntington's Disease CAG mutation in striatum and cerebullum are quantitative not qualitative.. 2011;20(21):4258-67.. From the Diabetes DBP:.. Isganaitis E, Jimenez-Chillaron J, Woo M, Chow A, DeCoste J, Vokes M, Liu M,.. 2009;May;58(5):1192-200.. PMID: 19208909.. Pihlajamaki J.. , Boes T, Kim EY, Dearie F, Kim BW, Schroeder J, Mun E, Nasser I,.. Cell Metabolism 2008;8(3); 186-200.. , Itkonen P, Crunkhorn S, Vänttinen M, Dearie F, Boes T, Jimenez-Chillaron J, Lappalainen T, Miettinen P,.. Park P.. , Nasser I,.. Goldfine AB.. , Laakso M,.. Expression of splicing factor genes is reduced in human obesity: links to altered Lipin 1 splicing and enhanced lipogenesis.. Submitted and under revision, Cell Metabolism.. 2009;116 (2): 99-111.. , Corvera S.. Endocrine Reviews, in press.. From the Rheumatoid Arthritis DBP:.. Kurreeman F, Liao K,.. Chibnik L, Hickey B, Stahl E,.. , Li G,.. Bry L.. , Mahan S, Ardlie K, Thomson B,.. Szolovits P, Churchill S, Murphy SN, Cai T, Raychaudhuri S, Kohane I, Karlson E, Plenge R.. From the Major Depressive Disorder DBP:.. 2011; June 10:1-10.. Castro V, Gallagher PJ, Clements CC, Murphy SN, Gainer VS, Weilburg JB, Fava M, Churchill SE, Kohane IS, Smoller JW, Iosifescu DV, Perlis RH.. Hoogenboom WS, Perlis RH, Smoller JW, Zeng0-Treitler Q, Gainer VS, Murphy SN, Churchill SE, Kohane IS, Shenton ME, Iosifescu DV.. Limbic system white matter microstructure and long-term treatment outcome in Major Depressive Disorder: A diffusion tensor imaging study using legacy data.. PMID:22540406.. Gallagher PJ, Castro V, Fava M, Weilburg JB, Murphy SN, Gainer VS, Churchill SE, Kohane IS, Iosifescu DV, Smoller JW, Perlis RH.. Antidepressant response in individuals with Major Depressive Disorder exposed to NSAIDS: a pharmacovigilance study.. Hoogenboom WS, Perlis RH, smoller JW, Zeng0Treitler Q, Gainer VS, Murphy SN, Churchill SE, Kohane IS, Shenton ME, Iosifescu DV.. Feasibility of styding brain morphology in Major Depressive Disorder with structural magnetic resonance imagine and clinical data from the electronic medical record: A pilot study.. Psych..

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