Archived News


DBMI Student Naoki Orrii's paper appears in PLOS ONE.

Wiki-Pi: A Web-Server of Annotated Human Protein-Protein Interactions to Aid in Discovery of Protein FunctionNaoki Orii1,2, Madhavi K. Ganapathiraju11 Department of Biomedical Informatics, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America,2 Language Technologies Institute, Carnegie Mellon University, Pittsburgh, Pennsylvania, United States of AmericaAbstract:Protein-protein interactions (PPIs) are the basis of biological functions. Knowledge of the interactions of a protein can help understand its molecular function and its association with different biological processes and pathways. Several publicly available databases provide comprehensive information about individual proteins, such as their sequence, structure, and function. There also exist databases that are built exclusively to provide PPIs by curating them from published literature. The information provided in these web resources is protein-centric, and not PPI-centric. The PPIs are typically...

DBMI paper a 'hot pick' at AMIA

MS Student Chuck Borromeo and faculty members Titus Schleyer, Michael Becich, Harry Hochheiser were listed as the 'hotpick' under Interactive Systems for their paper entitled: "Finding Collaborators: Towards Interactive Tools for Research Network Systems"

DBMI DREAM Team Delivers Silver!

Under the mentorship of Associate Professor Xinghua Lu, DBMI Postdocs Chunhai Cai and Songjian Lu and PhD candidates Hatice Osmanbeyoglu and Lujia Chen placed *second* in the international DREAM Breast Challenge to develop computational models that accurately predict prognosis of individual patients from the METABRIC genome-wide molecular profiling data including gene expression and copy number profile. More than 200individuals organized into around 50 teams submitted over 1000 models. Our own DBMI team came in second, and is currently preparing an invited presentation at the DREAM conference and a future publication. DBMI continues to be at the intersection of informatics and personalized medicine. Congratulations to the team on this fine accomplishment.More information on the Sage Bionetworks DREAM Breast Challenge can be found at:

Marc Clayton paper has been accepted by Annals of Pharmacotherapy

Boyce RD, Collins C, Clayton M, Kloke J, Horn J. Inhibitory Metabolic Drug Interactions with Newer Psychotropic Drugs: Inclusion in Package Inserts and Influences of Concurrence in Drug Interaction Screening Software. Annals of Pharmacotherapy. Volume 46. Epub 2012 Oct 2. DOI 10.1345/aph.1R150.

Ruhsary Ruxit paper accepted at International Workshop on Collaborative Big Data.

R. Rexit, F. Tsui, J. Espino, S. Wesaratchakit, Y. Ye, P. Chrysanthis, Using a distributed search engine to identify optimal product sets for use in an outbreak detection system, International Workshop on Collaborative Big Data (C-Big 2012), October 14, 2012, Pittsburgh, Pennsylvania

Department of Biomedical Informatics at 2012 AMIA Fall Symposium

Papers/Podium Presentations:   Berty HL, Simon M, Chapman BE A Semi-Automated Automated Classification of Pulmonary Hypertension Based on Features of Computed Tomography Pulmonary Angiography Images (AMIA-0884-A2012.R1) Date: Monday, Nov 5       Time:  10:30 AM – 12:00 PM               Session: S20   Borromeo C, Schleyer T, Becich M, Hochheiser H Finding Collaborators: Towards Interactive Tools for Research Network Systems (AMIA-0857-A2012) Date: Monday, Nov 5       Time:  3:30 PM – 5:00 PM                  Session: S39   Bekhuis T, Demner-Fushman D, Crowley R Research Designs in Mesh and Emtree: A Comparative Study of Coverage (AMA-0188-A2012) Date: Tuesday, Nov 6       Time:  10:30 AM – 12:00 PM  ...

Himanshu Grover's paper has been accepted at the International Workshop on Collaborative Big Data (C-Big 2012)

Grover, H., Gopalakrishnan, V. Efficient Processing of Models for Large-scale Shotgun Proteomics Data. In Proceedings of the International Workshop on Collaborative Big Data (C-Big 2012), Pittsburgh, PA, October 14, 2012. View PDF

Tanja Bekhuis, PhD featured on NLM Grantee Spotlight

Recently recruited Assistant Professor Dr. Tanja Bekhuis was featured on the National Library of Medicine website for her recent paper appearing in Artificial Intelligence in Medicine. Tanja's work bridges informatics, machine learning and library science, and leads the way to innovations in how systematic reviews are performed.

DBMI Alumnus Jonathan Bickel, MD and team save money and improve patient safety at Boston Children's Hospital

Boston Children's Hospital is dramatically improving patient safety and methods to make treatment more effective using bioinformatics under the direction of Dr. Jonathan Bickel, a former DBMI alumnus.Read More

DBMI Alumnus William Hogan, MD and a team from UAMS developed software selected for use in the National Children's Study

Aug. 13, 2012 | Software developed by University of Arkansas for Medical Sciences (UAMS) researchers was selected recently for use in the National Children’s Study, the largest-ever investigation of child health.  Read More>>

The Department of Biomedical Informatics has moved to newly-renovated Offices at Baum

We've moved!!  The Department of Biomedical Informatics has moved to newly-renovated Offices at Baum which is located at 5607 Baum Boulevard, Pittsburgh, PA 15206 on the fourth and fifth floors (formerly the Dodge dealership).  This 27,000 square foot area currently houses 17 faculty, 10 managers, 35 graduate students, 6 research fellows, more than 30 software engineers/developers. The main entrance is located on the S. Fairmount Street side of the building. View Directions

Pitt Researchers Awarded $8.3 Million NIH Grant to Study Sarcoidosis, Alpha-1 Antitrypsin Deficiency

PITTSBURGH, June 27, 2012 – A multidisciplinary team at the University of Pittsburgh will be leading a national effort to explore the relationships between the bacteria that live in the lungs, gene activation patterns, and disease progression. The project aims to learn more about the causes and progression of two potentially deadly yet under-studied lung diseases, alpha-1 antitrypsin (A1AT) deficiency and sarcoidosis, as well as possibly to identify new treatments for them. Funded by a three-year, $8.3 million grant from the National Institutes of Health, the Genomic Research in A1AT and Sarcoidosis study (GRADS) Genomics and Informatics Center will obtain patient samples from seven clinical centers across the nation and use a combination of sophisticated genome and microbiome profiling techniques with advanced computational methods to identify  biomarkers that indicate the current status of the lung diseases and predict their progression and response to the therapy,...

Guest Speaker for Annual Biomedical Informatics Training Program Retreat

The Annual Biomedical Informatics Training Program Retreat will be held on August 23 and 24, 2012.  We are pleased to announce that alumnus Constantin Aliferis, MD, MS, PhD, Director of the Center for Health Informatics and Bioinformatics at New York University Langone Medical Center, will be our guest speaker.

Biomedical Informatics Online Certificate Program Approved

Great News! The University of Pittsburgh and the School of Medicine have approved the Biomedical Informatics Online Certificate program and will begin with the spring term in January, 2013.The Biomedical Informatics Online Certificate program is a 15 credit (minimum) experience. The Online Certificate program will serve students with a wide variety of goals and backgrounds, including those in the Health Science Libraries' Library/Informatics Traineeship, complementing our existing biomedical training programs (on-site Certificate program, Masters program, PhD program). The online program curriculum will be identical to that of the on-site Certificate program in regards to educational goals, skills and competencies; however, course offerings may be more limited than the on-site course selections.Stay tuned for continued updates on application availability and instructions.

2011 Training Program Graduate Robyn Reed accepts position at Penn State Hershey

Robyn Reed, B.S., M.A., M.L.I.S.  (2011, Biomedical Informatics Health Sciences Library Certificate, 2010, Library & Information Science, University of Pittsburgh) happily announces she has obtained an exciting new position as a Biomedical Informatics and Emerging Technologies Librarian at Penn State Hershey in the George T. Harrell Health Sciences Library, beginning in June 2012.  “It should be a very exciting job since it is an evolving position as well as a tenured faculty post.  The position involves supporting basic and clinical biomedical research initiatives, implementing online library services, working in areas such as molecular biology, clinical informatics and e-science, and providing library instruction as well as teaching credit classes.”  Robyn plans to extend her IT education as she develops into this position and looks forward to working collaboratively with IT departments in helping to redesign the library’s website and working with content...