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Orientation . Biomedical Informatics Graduate Program. Presented by: Bill Hersh, Joanne Valerius Shannon McWeeney. Date: September 26, 2014. Overview of Today ’ s Activities. Welcome and Introductions Overview of Program and Tracks Student Pictures Staff Introductions

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Biomedical Informatics Graduate Program

Presented by: Bill Hersh, Joanne Valerius Shannon McWeeney

Date: September 26, 2014

overview of today s activities
Overview of Today’s Activities
  • Welcome and Introductions
  • Overview of Program and Tracks
  • Student Pictures
  • Staff Introductions
  • Professional Conduct
  • Lunch
  • Campus Tours
department of medical informatics clinical epidemiology dmice
Department of Medical Informatics &Clinical Epidemiology (DMICE)
  • One of 26 departments in OHSU School of Medicine
  • Mission is to provide leadership, discovery, and dissemination of knowledge in the areas of biomedical informatics and clinical epidemiology
    • Fulfilled through programs of research, education, and service
  • Department leadership
    • William Hersh, MD - Chair
    • Cynthia Morris, PhD - Vice Chair for Education and Training
    • Joan Ash, PhD - Vice Chair for Faculty Development
    • Shannon McWeeney, PhD, Head, Division of Bioinformatics & Computational Biology
    • David Dorr, MD, MS - Vice Chair for Clinical Informatics
    • Heidi Nelson, MD, MPH - Vice Chair for Clinical Epidemiology
dmice is a national leader
DMICE is a national leader
  • No official rankings, but OHSU informatics program is
    • 1 of 14 programs to have a National Library of Medicine NIH Training Grant for PhD and postdoctoral students
    • 1 of 9 programs funded under the Office of the National Coordinator Health IT Workforce Development Program
    • 1 of 8 programs funded by the NIH Fogarty Center Informatics Training for Global Health Program in collaboration with Hospital Italiano de Buenos Aires
    • Consistent recipient of research funding, appointment to national leadership positions, publication in high-profile journals, etc.
    • Highly accomplished alumni being productive in many different settings
  • Clinical epidemiology program also highly successful, especially in areas of evidence-based medicine and comparative effectiveness research
and innovator
And innovator
  • Early adopter of educational technologies and distance learning
  • Advancing with the cutting edge of the field
  • Informatics Discovery Lab – real-world solutions to real-world problems
    • http://www.ohsu.edu/idl
ohsu biomedical informatics graduate program
OHSU Biomedical Informatics GraduateProgram
  • http://www.ohsu.edu/informatics/
  • Overall goal of program is to train future professionals, researchers, and leaders in area of biomedical and health informatics
    • Tracks focus on different areas of larger field
    • All programs at graduate level, i.e., require a baccalaureate degree
  • Diverse students who typically fall into one of two categories
    • “First-career” students more likely to be full-time, on-campus, and from variety of backgrounds
    • “Career-changing” students likely to be part-time, distance, mostly (though not exclusively) from healthcare professions
program faculty and leadership
Program faculty and leadership
  • Overall program director – William Hersh, MD
  • Track leaders
    • William Hersh, MD – Clinical Informatics
    • Shannon McWeeney, PhD – Bioinformatics & Computational Biology
    • Joanne Valerius, PhD, RHIA – Health Information Management
  • Over 30 other faculty who teach, advise, mentor projects, etc.
program tracks
Program tracks
  • Clinical Informatics
    • Original track, focused on informatics in health, healthcare, public health, and clinical research settings
  • Bioinformatics and Computational Biology (BCB)
    • Focused on informatics in genomics. molecular biology, and their translational research aspects
  • Health Information Management (HIM)
    • Intersecting with clinical informatics, focused on HIM profession and leading to Registered Health Information Administrator (RHIA) certification
degrees and certificates
Degrees and certificates
  • Doctor of Philosophy (PhD)
    • For those who wish to pursue research, academia, or leadership careers
  • Master of Science (MS)
    • Research master’s, including for those with doctoral degrees in other fields who wish to pursue research careers
  • Master of Biomedical Informatics (MBI)
    • Professional master’s degree for practitioners and leaders
  • Graduate Certificate
    • Subset of master’s degree as an introduction or career specialization
  • Curriculum in each track for degree programs (master’s and PhD) organized into domains, each of which may have courses that are
    • Required
    • Individual competency (“k of n”)
    • Elective
  • Core curriculum of degree programs is knowledge base plus additional courses
    • MS = knowledge base + thesis
    • MBI = knowledge base + capstone (can be internship)
    • PhD = knowledge base + additional advanced work, including dissertation
building block approach
Building block approach


- Courses in domains:

- Clinical Informatics

- Bioinformatics

- Knowledge Base

- Advanced Research


- Biostatistics

- Cognate

- Doctoral Symposium

- Mentored Teaching

- Dissertation


- Courses in domains:

- Clinical Informatics

- Bioinformatics

- Health Information Management

- Thesis or Capstone

Graduate Certificate

- Courses in domains:

- Clinical Informatics

- Health Information Management


- Or introductory course

other programs
Other programs
  • Fellowships
    • Predoctoral and postdoctoral funding from National Library of Medicine, National Institutes of Health, Kaiser Permanente, and others
    • Clinical informatics fellowship for physicians starting in 2015
  • 10x10 (“ten by ten”)
    • Continuing education course in clinical informatics
    • Adaptation of on-line introductory course (BMI 510), with option to pursue further study at OHSU
    • Over 1800 have completed course since 2005, with about 20-25% going on to additional graduate study
overview of all ohsu informatics education
Overview of all OHSU informatics education

Graduate Education Clinical Fellowship

Single courses (e.g., 10x10)

Graduate Certificate

Master’s Degree


  • For physicians only (for now): ACGME-accredited clinical informatics fellowship, leading to board certification:
  • Didactic coursework
  • Project work
  • Clinical practice

NLM and other

training grants

ohsu informatics program provides value
OHSU informatics program provides value
  • For tuition and fees comparable to other programs, get
    • Cutting-edge curriculum based on solid foundation
    • Faculty who are international leaders in research and practice
    • Internship/practicum experience
    • Career development and advising
    • Connections to industry and others
alumni 558 people have earned 605 degrees and certificates
Alumni – 558 people have earned 605 degreesand certificates

International students from: Argentina, Singapore, Egypt, Israel, Thailand,

Zimbabwe, Saudi Arabia, China, etc.

some job titles and employers
Some job titles and employers
  • Product manager
  • Clinical informatics analyst
  • Informatics researcher
  • Librarian
  • Consultant
  • Project manager
  • Terminology engineer
  • Software engineer
  • Chief medical informatics officer
  • Information systems manager
  • Bioinformatician
  • Data manager
  • Database administrator/architect
  • Faculty
  • OHSU
  • Providence Health System
  • Kaiser-Permanente
  • Impact Advisors
  • Health Share of Oregon CCO
  • Epic
  • Cerner
  • NextGen
  • Sutter Health
  • National Library of Medicine
  • Harvard Medical School
  • University of Virginia
clinical informatics track
Clinical Informatics Track
  • Primary goal of clinical informatics track is to educate the future developers and managers of health care information systems
  • Individuals with a variety of backgrounds are provided a strong technical grounding in clinical informatics, health and medicine, computer science, and research methods so that they may assume positions that require a thorough understanding of both information technology and the health care environment
domains of clinical informatics
Domains of clinical informatics
  • Basic principles of biomedical informatics to problems in different domains of health and biomedicine
  • Operational knowledge of the human body in health and disease as well as the organization of the health care system
  • Principles of organizational behavior and management skills to biomedical informatics problems
  • Basic statistics and quantitative or qualitative research methods to evaluative research projects
  • Basic computer science principles to problems in health and biomedicine
  • Students will be adept in the tools of advanced scholarship , including the ability to address ethical issues in the field, communicate effectively in oral and written form, and complete a thesis (MS degree), capstone (MBI degree), or dissertation (PhD degree)
emerging aspects of clinical informatics
Emerging aspects of clinical informatics
  • Focus shifting from implementing to optimizing clinical informatics systems
    • Latest buzzword: analytics
      • In reality, program already offers course content in statistics, healthcare quality, clinical data standards, etc.
      • New courses and grant projects
  • For physicians, new subspecialty of clinical informatics
    • Subspecialty of any primary specialty
    • Additional certification options likely forthcoming for non-physicians
clinical informatics career pathways have diverse inputs and outputs
Clinical informatics career pathways havediverse inputs and outputs

Health care professions, e.g., medicine, nursing, etc.

Biomedical and health informatics education

(graduate level)

There is no single career

pathway, ladder, etc.

Natural and life sciences, e.g., biology, genetics, etc.

  • Jobs in:
  • Healthcare systems
    • Clinical leadership
    • IT leadership
  • Biomedical research
  • Industry
  • Academia

Computer science (CS), IT, and undergrad informatics

Health information management (HIM)

Others, e.g., business, library and info. science


Health Information Management Program


Director: Joanne Valerius, PhD, MPH, RHIA


one professional s viewpoint
One Professional’s Viewpoint

“Contributing to Health Care Without the Blood and Guts”

Lisa Kampa, M.A, RHIA

focus of program content
Focus of Program Content
  • Implementation of EHR.
  • Data Quality and Information Governance : Available, Accurate, Protected
  • Privacy and Security
  • Operational Management and Human Resource Development:
format of coursework
Format of Coursework
  • All coursework is delivered online except for the practical work experience or practicum
  • The practicum is a minimum of 40 hour in person experience in a healthcare setting to gain practical knowledge in field
from certificate to phd
From Certificate to PhD
  • The HIM curriculum has met accreditation standards of the Commission for Health Informatics and Health Information education.
  • Within our programs a student can take the curriculum through the following options:
    • Certificate
    • Masters
    • PhD cognate We need PhD’s in our field– and there are several professorships available
benefit of him track completion
Benefit of HIM track completion
  • At the completion of the program you can sit for the national certification exam.
  • When you pass the exam, you will have the credential RHIA, Registered Health Information Administrator which is known throughout the U.S. healthcare system.
  • Continued growth in field due to HIT.
him professional roles today
HIM Professional Roles Today
  • HIM professionals serve in various roles, including:
    • Director/Manager/Supervisor -Health Data Analyst
    • Researchers and Data Managers -Patient Portal Manager
    • EHR Trainer/Educator -Data Integrity Specialist
    • Chief Knowledge Officer -Clinical Vocabulary Manager
    • Clinical Documentation Specialist -Revenue Management
    • Educator in Higher Ed -Consultant
    • Compliance Officer -Privacy/Security Officer
    • Executive Suite in healthcare and vendor agencies
  • AHIMA Advocacy and Public Policy


  • Centers for Medicare and Medicaid Services EHR Incentive Programs


  • Health IT Buzz Blog


  • Office of the National Coordinator


  • Health Information Career Pathfinder


  • Health Information Management Concepts, Principles, and Practice, 4th Edition
  • Bureau of Labor Statistics


definition of biomedical informatics
Definition of Biomedical Informatics

Broad field: focused on the use of information and technology in health and biomedicine.

Clinical Informatics Focus on clinical medicine & health care.


Focus on issues in genomics, molecular and computational biology Emphasis on @OHSU on Translational Bioinformatics

clinical genomics individualized therapy in leukemia
Clinical Genomics: Individualized Therapy in Leukemia
  • AML: Acute myeloid leukemia
  • Need for novel therapies: current treatments very toxic and relapse is frequent outcome
  • Utilizing Next Generation Sequencing, siRNA and small molecule screens to identify drug targets
  • A template for personalized medicine in cancer

Dr. Brian Druker

Director, OHSU Knight Cancer Institute

Developed Gleevec one of first targeted cancer therapies

clinical genomics rationale for multi omics
Clinical Genomics: Rationale for Multi-OMICS

RNA-seq: Actionable overexpression


Genomic variation in DNA: Nothing actionable

Source: NY Times

bcb focus translational bioinformatics
BCB Focus: Translational Bioinformatics
  • Transform exponentially growing genetic, genomic, and biological data into diagnostics and therapeutics
  • Developcomputational approaches for
    • Data representation, annotation, and management
    • Analysis and Integration
    • Modeling, interpretation, and prediction
  • Active areas of study in the BCB track:
    • data analysis and integration for functional genomics
    • systems modeling for in silico hypothesis generation/prediction
    • text mining and information retrieval
    • imaging and computational neuroscience.
personalized medicine
Personalized Medicine

Source: Clinical Pharmacology & Therapeutics

curriculum objectives
Curriculum – Objectives
  • Train students to become sophisticated, interdisciplinary researchers and/or practitioners applying state-of-the-art computational methods to advance biological discovery
  • Enable them to apply their skills to a variety of jobs in academic, hospital, and industry settings.
bcb core sequence year 1
BCB Core Sequence (Year 1)
  • Bioinformatics and Computational Biology I: Algorithms
    • Algorithm development and application to biological problems
    • Class projects with data “hot off the presses”
  • Bioinformatics and Computational Biology II: Statistical Methods
    • Problem driven examination of quantitative issues in computational biology
    • Hands-on to allow integration and synthesis of concepts
bcb core sequence year 1 2
BCB Core Sequence (Year 1 & 2)
  • Computational Genetics (Year 2)
    • Bioinformatics and statistical concepts relating to genetic and genomic research questions
    • Examine data types used in high-throughput experiments
    • Discuss the lab experiments in the context of how the procedures impact the data generated
    • Experience with current databases used to store data types
  • Current topics in Computational Biology (Year 1)
    • Cutting-edge topics in the field (changes every year)
    • Some past topics: Systems Biology, Pharmacogenomics, Noncoding Genome
research experience for bcb year 1
Research Experience for BCB (Year 1)
  • BMI 552 Research in BCB
    • 10 week project co-mentored by basic scientist or clinician and DMICE faculty
    • Provides “hands-on”, on-site experience during your training
  • Internship opportunities: OCTRI, Knight Cancer Institute, PARC (internal) and Institute for Systems Biology, Pacific Biosciences etc (external)
analysis vs synthesis
Analysis vs. Synthesis
  • Graduate student mindset
  • Independent thinking: synthesis


career advice
Career Advice
  • Erase mental “barriers”
  • View your coursework as valuable – skills you can use and master
  • Don’t be afraid to ask questions
  • Feed your mind – this is a life long process
  • Don’t be afraid of change
  • Seek out research and volunteer opportunities – it will help you clarify what you are drawn to for possible career areas
  • Best path is one that you are good out, that you are passionate about and that is sustainable

Slide: S McWeeney

blog tweet share like and other good stuff
Blog, tweet, share, like and other good stuff

Chirpstory: Cold Spring Harbor Meeting

  • Emerging BCB culture
    • social interaction
    • open source
    • PLoS
    • SeqAnswers
    • ENCODE project



student progress
Student progress
  • Faculty are very busy BUT students are a top priority
  • They will state best way to contact them at beginning of course or advising, which is usually email
  • Program staff provide additional help and tools (e.g., forecasting sheets)
  • Faulty should respond to simple matters via email within two business days
  • More detailed responses may require meeting and/or involvement of program staff
key program personnel
Key Program Personnel
  • Diane Doctor, Student Support and Internship Coordinator
    • Email: doctord@ohsu.edu
    • Office: BICC 504, Office phone: 503-494-4794
  • Sarah Melton, Sakai Support
    • Email: sakai@ohsu.edu Office SON 476
    • Office: 503-494-7074 Toll Free: 877-972-5249
    • Office: BICC 404, Office phone: 503-494-2494
  • Virginia Lankes, Career Development Coordinator
    • Email: lankes@ohsu.edu
    • Office: BICC 404, Office phone: 503-494-2331
key program personnel1
Key Program Personnel
  • Lynne Schwabe, Administrative Assistant
    • Email: schwabel@ohsu.edu
    • Office: BICC 504, Office phone: 503-418-1566
  • Lauren Ludwig, Recruiting/Admissions
    • Email: ludwigl@ohsu.edu
    • Office: BICC 404, Office phone: 503-494-2252
  • Andrea Ilg, Educational Program Administrator
    • Email: ilgan@ohsu.edun@ohsu.edu
    • Office: BICC 504, Office phone: 503-494-2547
weekly informatics conference
Weekly Informatics Conference
  • Place to learn about new developments in field and project/employment opportunities.
  • Forum for students to present dissertation/thesis proposals, /dissertation/thesis defenses and research in progress.
  • Thursdays in BICC 124 (Theater) at 11:30 am (may change due to availability of speakers).
  • Attendance is taken – you are strongly encouraged to attend.
  • Pizza will be served, remember to RSVP to Lynne.
  • Presentations are recorded and posted to our You Tube channel https://www.youtube.com/channel/UCCekPERb6i3xXEDQxwlCeIA
registration course planning
Registration/Course Planning
  • Complete registration online. Instructions available on the “Student Resources” page
  • Course schedules are provided on the flash drive as well as on the online registration web page.
  • Forecasting worksheets are included on the flash drive and can be used as guidelines for planning your schedule.
  • 9.0+ credits = full-time student status.
  • 5.0 credits = part-time student status.
online course evaluations
Online Course Evaluations
  • The Sakai Course Evaluation Tool has been created to allow increased access to the course evaluations that are a required part of the School of Medicine curriculum. The tool is built into Sakai online courses.
    • Course evaluations are completed on a term-by-term basis and are a required part of the curriculum.
    • The feedback is instrumental in faculty planning.
student id badge
Student ID Badge
  • Work with Diane Doctor to ensure proper paperwork is complete to procure ID Badge
  • Day pass parking is $13 and needs to be purchased online at:


  • Pay station available at the Dotter Lot. Rate of $13 per day.
  • Tri-Met Bus Service
    • OHSU offers highly subsidized for annualTri-Met bus passes available in the Parking Office.
    • Students need to provide proof of full-time status to receive the bus pass at the discounted rate.
  • Tram and Streetcar
    • Your OHSU ID badge is good on the Tram and Streetcar.
  • Most students prefer to purchase textbooks online at: Amazon, Barnes and Noble, Powells, etc.
    • Make sure you have the correct ISBN number when ordering your book online.


  • Notices are sent via email.
  • ALL notifications will be sent to your OHSU email address!
student jobs
Student Jobs
  • A number of you are interested in part-time jobs.
  • We have the following available:
    • Teaching assistants – in classes you have previously completed.
    • Other projects in the department.
    • Pay starts at $15 per hour for 5-10 hours per week of work.
  • If interested, please email a resume to Diane at doctord@ohsu.edu.
remainder of today
Remainder of Today
  • Pictures/Short Break
  • Staff Introduction
  • Professional Conduct
  • Lunch
  • Campus Tours

These guidelines have been developed to enhance the students' training, maximizing the benefits to their profession and society, and to minimize actions that do not benefit the greater good and only selfishly serve the individual.


Academic achievement

  • Pursuit of knowledge
  • Advancement of the University mission
  • Respect
  • Responsible conduct in science
  • Favorable presentation of the University


  • Building teaching and communication skills
  • Involvement in professional societies
  • Community outreach for the sciences
unacceptable conduct by graduate students
Unacceptable conduct by graduate students
  • Providing or receiving unauthorized assistance in course work
    • Ask the instructor for each course what is authorized vs unauthorized assistance
  • Engaging in plagiarism – representing the work of another as one's own.
    • "work" can mean either the words or ideas
    • TurnItIn
    • "How to Recognize Plagiarism"
what happens if you are suspected of a violation
What happens if you are suspected of a violation
  • Most complaints are handled by the Professional Conduct Committee in DMICE
  • If unacceptable conduct has occurred, sanctions may be recommended, including
    • A change in grade for the course. (Note: the instructor may, in addition, change a grade on any assignment involved)
    • Letter of reprimand
    • Probation
    • Recommendation to the Dean for suspension or dismissal


Thank you!

end of orientation