1. Center for Informatics
  2. Research Informatics
  3. Meet the team
  4. Samir Courdy

Samir Courdy

SVP, Informatics

Bio

I have a very diverse background in computer science and software engineering. My breadth of expertise, training, and knowledge will serve me well in ensuring the successful implementation of this multi-institution research collaboration. I am responsible for all aspects of software development, and implementation of real-world solutions focused on the delivery of precision medicine. To that end, developing integrated solutions for clinical, translational, basic, and population science research has been part of what I have delivered on for the last 20 years serving as Chief Research Informatics Officer at Huntsman Cancer Institute (HCI). This

experience will serve me well in doing much of the same at the City of Hope Comprehensive Cancer Center, The Beckman Institute and the Medical Center. I serve as the Vice President in the Center for Informatics and Director of Research Informatics. I work very closely with the Chief Informatics Officer and members of the Senior Leadership to develop strategic plans to meet the growing needs of the organization. I aim to meet the needs and requirements of the CTSA grant, provide guidance and plan effort for each project, run coordination meetings, manage staff, and provide strategic direction for architecture, projects, and technology. I oversee clinical, basic, translational, and population science research applications and

database development; as well as developing bioinformatics tools and algorithms to support principal investigators in their research. My role includes research informatics strategic planning, budgeting, project management, analysis, systems design, architecture, staff management, resource assignment, and establishing collaborative relationships with other HCI and Health Sciences departments. I am an active member of CI4CC, ACM, AMIA, ASCO, AACR/AACI.

While at Huntsman Cancer Institute, I was responsible for the design and implementation of several systems, including an enhanced Research Subject Registry, a Biospecimen Tracking and management System (itBioPath), a translational research software system for the Biorepository and Molecular Pathology Core (BMP), and a Comprehensive Clinical Cancer Research System (CCR) with a robust and extensible meta model enabling all cancer groups to co-exist in the same database, managed by a very complex security model which is compliant with IRB and HIPAA regulations. My team released GNomEx, a High Throughput Next-Gen Sequencing LIMS system, for use by HCI and the University of Utah community. The team

completed work on an analysis suite built upon the Integrated Genome Browser (IGB) and the Distributed Annotation System (DAS/2), along with an internally developed publishing suite GenoPub. GNomEx and GenoPub were both released as open source projects and are available for download on GitHub. GNomEx was also integrated with the Biospecimen System (itBioPath) to provide linkages between genomic and clinical data.

I devised a solution to capture genomic data from Next-Gen Sequencing labs and incorporating the results into a model that is query-able and associated with clinical phenotypic data in CCR. The design and implementation of these systems enabled HCI to participate in ORIEN (Oncology Research Information Exchange Network) seamlessly and without any need for adopting or implementing new technology solutions. The development of a Chemical Screens Annotation and Management System (CSAM) was also completed. I have also developed a natural language processing workflow for identifying and extracting clinical and diagnostic information from surgical pathology reports, physicians’ notes and radiology documents. This project is utilizing a third-party software package from Linguamatics. In my current role at City of Hope I will be developing and implementing many solutions that are based on my prior experience to enhance access to high quality data for research, clinical care, and precision medicine initiatives

Education

INSTITUTION AND LOCATION                      DEGREE          MM/YY             FIELD OF STUDY

University of Utah, Salt Lake City, UT              BS                    06/17               Computer Science

University of Utah, Salt Lake City, UT              MBA                 05/14               Business Administration

Positions and Honors

Positions and Employment

1987-1994       Software Engineer II, Evans & Sutherland Computer Corp., Salt Lake City, UT

1994-1997       Senior Software Engineer, Fidelity Investments Systems Company, Salt Lake City, UT

1997                Principal Software Engineer, Prosolvia Research, Salt Lake City, UT

1997-1999       Technical Advisor, McKessonHBOC, Salt Lake City, UT

1999-2000       Senior Technical Advisor, Huntsman Cancer Institute, Salt Lake City, UT

2000-2006       Software Development Manager, Huntsman Cancer Institute, Salt Lake City, UT

2006-               Director, Research Informatics Shared Resource, Huntsman Cancer Institute, University of Utah, Salt Lake City, UT

2014-               Chief Research Information Officer, Huntsman Cancer Institute, University of Utah

 

Other Experience and Professional Memberships

2002-               Biomedical Research Institutes Information Technology Exchange (BRIITE)

2006-               American Medical Informatics Association (AMIA)

2010-2014       Association for Computing Machinery (ACM)

2010- 2018      Cardiovascular Disease Consortium Informatics Subcommittee (CvDC)

2010-               Bench to Bassinet Informatics Committee (B2B)

2012-               Cancer Centers Administrators Forum (CCAF)

2012-2013       Association of Medical Directors of Information Systems (AMDIS)

2013-               Cancer Informatics for Cancer Centers (CI4CC)

2014-2018       High Risk Cancer Research Advisory Committee (HRCRAC)

2014-2017       CTSA Biorepository Executive Committee

2014-2018       Flatiron Executive and Research Committees

 

Honors

1985                Phi Eta Sigma (National Honor Society) member

1988                Recipient of Stock Options Award Program. Awarded two Keystone awards and two ‘On the Spot’ awards at HBOC for technical excellence and effort

1990-1993       Three Extra Step Awards, for exceptional effort on the F14D/A6E weapons training systems and the S70 helicopter trainer, at Evans & Sutherland

1995-1996       Awarded 100 Chairman Shares for two consecutive years at Fidelity Investments. Two

Presidents Awards, one for achieving CMM level 2 certification on the API development team. A second for technical merit on the Fidelity Investments Institutional Services DST data conversion. One ‘You’ve Earned It’ award for extra effort at Fidelity Investments

Research Support

Ongoing Research Support

 

5P30CA042014-25                                          Beckerle (PI)                            05/09/97-11/30/18

 

NIH/NCI                                  

Cancer Center Support Grant

This grant supports the research infrastructure of the Cancer Center. It promotes scientific excellence

through coordinated, broad-based, interdisciplinary programs and support of state-of-the-art shared research resources. Cancer Center research programs include Cancer Control and Population Sciences, Cell Response and Regulation, Experimental Therapeutics, and Nuclear Control of Cell Growth and Differentiation.

Role: Chief Research Informatics Officer and Director, Research Informatics Shared Resource

Joe Yost (PI)

NIH

Cardiovascular Disease Consortium CvDC

Bench 2 Bassinet B2B

Neli Ulrich (PI)                          5/2017 – 12/2018

NIH/NCI

U01 Colocare Grant

 

Completed Research Support

PPG                                                                             Randy Burt

 

Bibliography

  1. Nix DA, Courdy SJ, Boucher KM (2008) Empirical methods for controlling false positives and estimating confidence in ChIP-Seq peaks. BMC Bioinformatics 9:523. PMCID: PMC2628906
  2. Nix DA, Di Sera TL, Dalley BK, Milash BA, Cundick RM, Quinn KS, Courdy SJ (2010) Next generation tools for genomic data generation, distribution, and visualization. BMC Bioinformatics 11:455. PMCID: PMC2944281
  3. Courdy SJ, Haroldsen C, Hammer A, Spigle C, Schaefer C, Pimentel R, Fraser A, Barlow J, Hurdle JF (2010) Finding subjects for clinical research using state-wide, multi-source data: The Utah Population Database limited cohort tool 2010 AMIA clinical research informatics summit (Distinguished Award Winner)
  4. Hurdle JF, Haroldsen SC, Hammer A, Spigle C, Fraser AM, Mineau GP, Courdy SJ (2013) Identifying clinical/translational research cohorts: Ascertainment via querying an integrated multi-source database. J Am Med Inform Assoc 20:164-71. PMCID: PMC3555332
  5. DeRose YS, Gligorich KM, Wang G, Georgelas A, Bowman P, Courdy SJ, Welm AL, Welm BE (2013) Patient-derived models of human breast cancer: Protocols for in vitro and in vivo applications in tumor biology and translational medicine. Curr Protoc Pharmacol Chapter 14: Unit 14.23. PMCID: MC3630511
  6. DeRose YS, Gligorich KM, Wang G, Georgelas A, Bowman P, Courdy SJ, Welm AL, Welm BE (2013) Patient-derived models of human breast cancer: Protocols for in vitro and in vivo applications in tumor biology and translational medicine. Curr Protoc Pharmacol Chapter 14: Unit 14.23. PMCID:PMC3630511
  7. Samir Courdy, Tonya Disera, Cindy Spigle, Carolyn Ross, Isaac Kunz, Philip Bernard, Rohit Kelkar, Srikanth Adiga, Shantanu Deshpande, Satishchandra Pal, Atul Kaushal, Anoop Kunchukuttan (2009) Biospecimen Data Collaboration Through caBIG™ and caTissue, Breast Cancer Biospecimen Data Elements Export-Import Tools Using caTissue. 2009 caBIG National Meeting, Washington DC.
  8. Samir Courdy, Tonya Disera, Cindy Spigle, Carolyn Ross, Isaac Kunz, Philip Bernard, Srikanth Adiga, Rohit Kelkar, Richa Batra, Sumit Gurav, Sameer Thakur, Anoop Kunchukuttan (2009) Pathology Report Extraction Tool at HCI, Natural Language Surgical Path Report Extraction. 2009 caBIG™ National Meeting, Washington DC.
  9. Geraldine P. Mineau, Samir J. Courdy, Cody Haroldsen,1 Andrew Hammer, Cindy Spigle, Carole Schaefer, Richard Pimentel, Alison Fraser, Jahn Barlow, John F. Hurdle (2010), Finding Subjects for Clinical Research Using State-wide, Multi-source Data: the Utah Population Database Limited Cohort Tool, winner “Distinguished Poster Award” presented at the AMIA Clinical Research Informatics, San Francisco.
  10. Isaac Kunz, Samir J. Courdy, Automated Pathology Data Extraction of Surgical Pathology Reports, presented at AMIA Now 2010
  11. Joyce Niland PhD1, Rebecca Ottesen MS1, Isaac Kunz MS2, Janet Nikowitz1, Weizhong Zhu PhD1, Leanne Goldstein DrPH1, Tarik Courdy2, Mike Chang PhD1, Ajay Shah PhD1, Samir Courdy2 MBA; 1Iterative Interactive Enrichment (IIE) of Natural Language Processing (NLP) of Patient Electronic Medical Records (EMR) Shared Across Institutions