RBHS Strategic Plan / Progress Report
Informatics Complementary Program
Lead - David J. Foran, Ph.D.
June 11, 2015

FY15 – The informatics team at Rutgers Cancer Institute of NJ worked closely with the Rutgers
Discovery Informatics Institute and the Office of Information Technology to acquire and establish
high-performance computing resources equipped with high-speed communication backplanes,
accelerators and a high-capacity (PB) parallel storage system. This infrastructure will speed
progress in cutting edge data science applications that span the biological and physical sciences
and medicine while facilitating investigative research across RBHS and the Rutgers community.
 Recent progress: This equipment and these technologies are being made available to facilitate
investigative research in cancer, environmental and occupational health, infection and
inflammation, neuroscience, and community health.
Recent, relevant activities:
 Working with key investigators throughout Rutgers School of Arts and Sciences and Rutgers
School of Engineering, a $10 million equipment grant has been secured from state of NJ. Dr.
Manish Parashar serves as the overall PI for the project. Dr. David Foran serves as the lead
investigator for the subproject focused on computational imaging applications in medicine.
 Working with key investigators throughout Rutgers Robert Wood Johnson Medical School and
Graduate School of Biomedical Sciences, a $1.7 million NIH has been funded. Dr. Les Michelson
serves as the overall PI for the project. Dr. David Foran serves as the lead investigator for the
subproject focused on high-throughput bioinformatics and biomarker discovery.
 February 25, 2015 – Organized and sponsored open house event hosted at the Fiber Optics
Auditorium at Rutgers, featuring an introduction to the Rutgers Discovery Informatics Institute,
review of new projects and initiatives and several interactive sessions and workshops.
 April 29, 2015 – Organized and sponsored Symposium on Big Data and the Transformation of
Society. Dr. Foran served as Chair & Invited Speaker for the Panel on Big Data & HealthCare
hosted at Rowan University, Glassboro, NJ.
Plans for FY16:
 The funds secured through the equipment grant from the State and the new NIH grant will
continue to be used in the next phase of infrastructure improvements aimed at supporting and
facilitating ongoing and new research initiatives in the physical and population sciences,
medicine, and large-scale projects across RBHS and the Rutgers community.
FY15 – The informatics team at CINJ has established strong, productive relationships with
RUDCR Infinite Biologics, RWJUH and Office of Information Technology leading to the successful
implementation of the workflow and standard operating procedures for exchanging tissue
samples and performing gene analysis and professional interpretation. This infrastructure and
technology has direct relevance to multiple units and research groups across RBHS and
investigators throughout the Rutgers community.
 Recent Progress: Our team worked closely with pathologists, systems biologists and data
scientists leading to certification from both Clinical Laboratory Improvement Amendments (CLIA)
and the College of American Pathologists (CAP).
Recent, relevant activities:
 Hai Su, Yong Shen, Fuyong Xing, Xin Qi, Kim M. Hirshfield, Ling Yang, David J. Foran. Robust
Automatic Breast Cancer Staging Using a Combination of Functional Genomics and Image-Omics.
Su H, Xing F, Shen Y, Qi X, Yang L. Proceeding of the IEEE International Conference on
Engineering in Medicine and Biology Society. Milan, Italy. In press.
 Kim Hirshfield, Shridar Ganesan, Lorna Rodriguez, David J. Foran. Clinical Utility of
Comprehensive Genomic Profiling for Management of Rare or Refractory Cancers. Clinical
Cancer Research. In review.
 Sharathkumar Bhagavathi, Lauri Goodell, Chang Chan, Jeffrey Rosenfeld, David J. Foran, Lorna
Rodriguez, Li Liang. Validation of a Droplet PCR-based Assay for the Detection of Somatic
Variants in Solid Tumors. Association for Molecular Pathology (AMP) 2015 Annual Meeting.
Austin, TX. In review.
This report summarizes progress to-date on informatics complementary program initiatives and identifies
plans for FY2016. As requested, this document is intentionally brief.

RBHS Strategic Plan / Progress Report
Informatics Complementary Program
Lead - David J. Foran, Ph.D.

Our informatics team at Rutgers Cancer Institute has partnered with, Extract Systems, to
integrate new software modules into the clinical and research workflow at CINJ to allow
automated natural language processing and extraction of unstructured data embedded in paperbased documents into discrete fields to reduce reliance on manual extraction methods. These
solutions will likely have applications throughout RBHS.
 At the same time, the informatics development team has undertaken a project with Informatica
Corporation to develop the methods and software to allow automated standardization of data
originating from disparate sources including Electronic Medical Records (EMR); Clinical Trial
Management Systems (CTMS), Tumor Registries, Biospecimen Repositories, Radiology and
Pathology archives and next generation sequencing devices so that the information can be
reliably mapped and transmitted to facilitate continued expansion of the newly developed clinical
data warehouse at CINJ. The capabilities provided by these resources will make it feasible to
conduct high-throughput screening, stratification of patient populations, mining of large data sets,
and generate and test new hypotheses in a range of RBHS related research areas including
investigative oncology and biomedical research.
Plans for FY16:
 Our team will continue to expand our expertise in gene panel analysis. We will offer parallel
services in support of basic science investigators in FY16.
 Dr. Foran will submit a new R01 titled “A Precision Medicine Platform for Integrated Analysis of
Imaging & Genomics Signatures” which is being prepared in response to the request for
applications, “Development of Technologies in Biomedical Computing, Informatics and Big Data
Science”.
FY15 – The Biomedical Informatics Programs and Shared Resources at Rutgers Cancer Institute of
New Jersey have been reorganized to include divisions for (1) Research Computing (Manish
Parshar); (2) Bioinformatics and Systems Biology (Chang Chan); (3) Computational Imaging
(Dimitris Metaxas and John Nosher); and (4) Chem Informatics (Bill Welsh). This structure has
already been shown to facilitate collaboration with investigators throughout the Graduate School of
Biomedical Sciences, Rutgers Medical Schools and the Ernest Mario School of Pharmacy.
 Recent Progress: The divisions provide direct informatics support to PI’s both within and outside of
the CINJ who are engaged in fundable and publishable translational research.
Recent, relevant activities:
The computational imaging division has forged productive collaborations with investigators from the
departments of pathology, surgery, medical oncology and the research computing division.
 Daihou Wang, David J. Foran, Jian Ren, Hua Zhong, Isaac Y. Kim and Xin Qi. Exploring
Automatic Prostate Histopathology Image Gleason Grading via Local Structure Modeling.
Proceeding of the IEEE International Conference on Engineering in Medicine and Biology
Society. Milan, Italy. In press.
 Tahsin Kurc, Xin Qi, Daihou Wang, Fusheng Wang, George Teodoro, Lee Cooper, Michael
Nalisnik, Lin Yang, Joel Saltz, David J. Foran. Scalable Analysis of Big Data Pathology Cohorts
using Efficient Methods and High-Performance Computing Strategies. BMC Bioinformatics. In
review.
The division of Cheminformatics develops and implements computational methods and tools to
accelerate CINJ’s mission in translational medicine to link bench and bedside.
 Collaboration with Dr. X. F. Steven Zheng, CINJ, to discover small-molecule inhibitors of
superoxide dismutase 1 (SOD1) that recently has been discovered to play a key role in the
development of liver and lung cancer.
 Collaboration with Dr. Joseph Bertino, CINJ, to discovery small-molecule modulators of the
tyrosine kinase Axl as therapeutics treatments for prostate cancer. Dr. Ray Birge (NJMS) is also
a collaborating lead on this project. This project was recently funded by a New Jersey Health
Foundation (NJHF) Signature grant.

This report summarizes progress to-date on informatics complementary program initiatives and identifies
plans for FY2016. As requested, this document is intentionally brief.
RBHS Strategic Plan / Progress Report
Informatics Complementary Program
Lead - David J. Foran, Ph.D.

Poster presentation entitled “Cheminformatics in Drug Discovery the Cancer Drug Discovery MiniSymposium held April 10, 2015, at the Center for Integrative Proteomics Research, Piscataway,
NJ.

FY15 - Establish multidisciplinary research structures and effective leadership that will encourage
synergistic cross-disciplinary collaborations; ensure curriculum development and provisioning of
learning opportunities while fostering centers of excellence.
 Recent progress: Our informatics team has reorganized assets and expanded upon several existing
programs to support a collaborative environment across disciplines while establishing and
international reputation and reaching out to the private sector.
Recent, relevant activities:
 Established seminar series in computational imaging with Dept. of Radiology, Rutgers – Robert
Wood Johnson Medical School, faculty from Rutgers Department of Biomedical Engineering and
RWJUH.
 Active rotation in Medical Informatics and Computational Imaging jointly supported by Rutgers –
Robert Wood Johnson Hospital and Rutgers Cancer Institute of NJ is open to third and fourth year
residents in Pathology and Radiology. This rotation has spawned multiple new cross-disciplinary
projects.
 Investigators from Rutgers Cancer Institute and RDI2 are working with investigators across
campuses to plan a Rutgers-wide Biology & Medical Data Science retreat and workshop. Our team
has established the organizing committee and has identified October 22, 2015 as the date for a Fall
retreat and workshop. Dr. Stephen K. Burley has agreed to serve as a speaker along with a list of
other national and internationally recognized experts.
 Wu Y, Moss, R, Nosher JL, Foran DJ. Predicting Radioembolization Response Using
Computational Image Analysis. 2015 International Conference of the Radiological Society of North
America, Chicago, IL. In review.
Plans for FY16:
 As the chair for the Program and Organizing Committee, Dr. Foran has worked with other team
members to establish an International Workshop on High-Performance Computing in Biomedical
Image Analysis at the 18th Conference on Medical Image Computing and Computer Assisted
Intervention to be held at the Munich, Germany. Oct., 2015.
 The informatics team will continue to reach out to collaborators at IBM, Bristol Meyers Squib, J &
J, and Siemens Corporate Research to establish private sector internships for graduate students
in Graduate School of Biomedical Sciences, Rutgers Cancer Institute of NJ and Rutgers
Discovery Informatics Institute.
 The team is working with a cross-disciplinary team of investigators in planning and preparing a
T32 Pre-doctoral training in Biomedical Big Data Science grant submission.

FY15: Recruit the talent and expertise to support computational and data-enabled science and
engineering, computer science and engineering including full time computational and data
researchers, educators, and programmers.
 Recent Progress: Our team has been working with faculty across RBHS, Rutgers School of Arts and
Sciences and Rutgers School of Engineering in the recruitment of additional Systems Biology Faculty
and Bioinformatics staff scientists and postdocs.
Recent, relevant activities:
 Recruitment of (1) Jeffrey Rosenfeld, Ph.D. (Senior Biomedical Informatics Scientist); (2) Youyi
Peng, Ph.D. (Biomedical Informatics Scientist); (3) Esma Yildirim, Ph.D. (Postdoc in
Bioinformatics and High-Performance Computing); (4) Hossein Khiabanian, Ph.D (Assistant
Professor) from the Center for Computational Biology and Bioinformatics at Columbia University
and (5) Ying Chen, Ph.D. (Senior Bioinformatics Scientist) from Oncology Division of Eli Lilly.
Planned activities for FY16:
 The informatics team working towards the recruitment of additional Systems Biology Faculty;
Bioinformatics staff scientists; and postdocs.
This report summarizes progress to-date on informatics complementary program initiatives and identifies
plans for FY2016. As requested, this document is intentionally brief.