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University Bulletin
Graduate Degree Programs

Bioinformatics and Genomics

Program Home Page

Contact Information:

Cooduvalli Shashikant
Program Co-chair
Css13@psu.edu
814-863-0658

James Broach
Program Co-chair
Jrb62@psu.edu
717-531-5470

Jean Pierce
Records Specialist
101 Life Science Building
The Pennsylvania State University
University Park PA 16802
Jep32@psu.edu
814-867-0371

Degrees conferred:

Ph.D., M.D./Ph.D., M.S.

THE GRADUATE FACULTY

The Program

The IGDP in BG is an interdepartmental program that engages faculty members from six colleges on two campuses. This broad-reaching Program provides students a wide range of understanding of multiple disciplines with specific expertise in a chosen area, and encourages interdisciplinary research that is truly changing biological research as well as health and lifestyles.

Admission Requirements

Admission requirements listed here are in addition to requirements stated in the GENERAL INFORMATION section of the Graduate Bulletin.

  • Fully completed, official online Penn State Graduate Application.
  • Paid, nonrefundable application fee (see Requirements for Graduate Admission for current fee).
  • Official transcripts from all post-secondary institutions attended.
  • Completed BG-specific questions on the Graduate Application.
  • Application for a U.S. visa (international applicants only).
  • Officially submitted Graduate Record Examination (GRE) General Test scores. Successful applicants generally have scores above the 75th percentile for each of the verbal, quantitative, and analytical writing section.
  • Names and contact information, including business email addresses, for three references.
  • Statement of goals that pertain to the life sciences including motivation for pursuing a research degree; research experience and interests; and professional experience. The statement should include problems that are of interest to the applicant and how the applicant’s past experiences have prepared him or her to pursue this research.
  • International applicants are required to submit English proficiency test scores, unless they are from one of the countries listed as exempt in the Graduate Bulletin. English proficiency test scores must meet or exceed the minimum acceptable scores listed in the Bulletin. Applicants to the BG program must have a minimum TOEFL score of 575 for the paper-based test, or a total score of 90 with a 19 on the speaking section for the Internet-based test (iBT). Successful applicants generally have a minimum score of 100 (including 23 on the speaking component) on the Internet-based test.  
  • Successful applicants generally will have a minimum 3.5 on a 4.0 scale junior/senior undergraduate grade point average, and will have completed course work in both quantitative and life science subjects.

DEGREE REQUIREMENTS

M.S. Degree

Requirements listed here are in addition to requirements stated in the DEGREE REQUIREMENTS section of the Graduate Bulletin.

For master’s degree, a minimum of 30 graduate credits and a 3.0 overall GPA are required. At least 18 credits in the 500 and 600 series combined must be included in the program. Required courses for master’s degree are: MCIBS 551 Genomics (3), MCIBS 554 Foundations in Data Driven Life Sciences (3), STAT 555, Statistical Analysis of Genomics Data (3), BMMB 852 Applied Bioinformatics (2), BIOL 405 Molecular Evolution (3), MCIBS 541 Critical Analysis of Bioinformatics and Genomics Research Topics (1 credit per semester, maximum of 2 credits), MCIBS 589 Colloquium in Bioinformatics and Genomics (3), MCIBS 591 Ethics in Life Sciences (1), MCIBS 596 Individual Studies (2), and MCIBS 600 Thesis Research (6). No more than 6 credits of Thesis Research may be counted toward 30 credit minimum. MCIBS 595 Internship and electives also count towards the minimum 30 credit requirement. Options are not offered for the M.S. degree.

Students must complete original laboratory research and internship that culminates in a thesis. The thesis must be accepted by the advisers and/or committee members, the head of the graduate program, and the Graduate School, and the student must pass a thesis defense.

Ph.D. Degree

Requirements listed here are in addition to requirements stated in the DEGREE REQUIREMENTS section of the Graduate Bulletin.

For the Ph.D., a minimum of 35 credits is required. During the first year of study, Ph.D. candidates are required to take 17 credits of core required courses: MCIBS 551 Genomics (3), MCIBS 554 Foundations in Data Driven Life Sciences (3), STAT 555, Statistical Analysis of Genomics Data (3), MCIBS 541 Critical Analysis of Bioinformatics and Genomics Research Topics (1 credit per semester, maximum of 2 credits), MCIBS 589 Colloquium in Bioinformatics and Genomics (3 credits total) MCIBS 591 Ethics in Life Sciences (1), and MCIBS 596, Individual Studies (2 credits total), representing three Research Rotations. Each candidate for the Ph.D. degree must fulfill written and spoken English communication requirements that are satisfied by preparing written and oral reports describing the laboratory rotations during the first year.

At the end of the first year, admission to Ph.D. candidacy is determined by performance in course work, laboratory rotations, and the BG Graduate Program Candidacy Examination. Students join their research laboratory by the end of the second semester of the first year.

The doctoral committee of a Ph.D. student is formed upon entry into the dissertation laboratory, and must comply with all Graduate Council requirements.  Students are strongly encouraged to consider joint co-advisers, each representing a different area of expertise within the field of bioinformatics and genomics.

During the second year, students may take additional courses in consultation with the doctoral committee. Students may select an option area in which they conduct research and take additional courses specified by the Option (see below). Students are not required to choose an Option. Additionally, students will complete one semester of Teaching Assistantship in a graduate or undergraduate course and complete required training to perform duties of Teaching Assistantship.

Ph.D. candidates must pass a comprehensive examination prior to the end of the fifth semester of enrollment, the written portion of which is in the format of a grant application. As part of this examination, the candidate also gives an oral presentation of this proposal to their doctoral committee.

A dissertation must be prepared and defended by each Ph.D. candidate. Students must present their dissertation in accordance with Graduate Council and Graduate School guidelines as described in the THESIS GUIDE: Requirements for the Preparation of Master's Theses and Doctoral Dissertations. To earn the Ph.D. degree, the dissertation must be accepted by the doctoral committee, the head of the graduate program, and the Graduate School and the student must pass a final oral examination (the dissertation defense).

The final examination of the doctoral candidate is an oral examination administered and evaluated by the entire doctoral committee. It consists of an oral presentation of the dissertation by the candidate and a period of questions and responses. These will relate in large part to the dissertation, but may cover the candidate's entire program of study, because a major purpose of the examination is also to assess the general scholarly attainments of the candidate. The portion of the examination in which the dissertation is presented is open to the University community and the public; therefore, it is expected that the examination will take place at University Park or the Hershey campus. It is expected that the Ph.D. candidate will have at least one paper submitted for publication in a major peer-reviewed scientific journal prior to the final oral examination.

Ph.D. students in Bioinformatics and Genomics may enroll in one of two options, but are not required to do so.

Option in Algorithms and Computation

Students are admitted to the Option in Algorithms and Computation after successfully completing: (1) the first year of the IGDP in BG; (2) three research rotations, of which at least two must be with faculty affiliated with the Algorithms and Computation Option; and (3) the candidacy examination. During the second year, Ph.D. candidates choosing this option will be required to take (1) CSE/BMMB 566 Algorithms and Data Structures in Bioinformatics (3); (2) one of the two courses CMPSC 465 Data Structures and Algorithms (3) or CSE 565 Algorithm Design and Analysis (4); and (3) two courses from a list of prescribed electives which includes, but is not limited to the following: CMPSC 431W Database Management Systems (3), CMPSC 450 Concurrent Scientific Programming (3), CSE 557 Concurrent Matrix Computations (3), CMPSC 464 Introduction to the Theory of Computation (3), CSE 583 Pattern Recognition – Principles and Applications (3), CSE 562 Probabilistic Algorithms (3), CMPEN 455 Digital Image Processing (3), and CMPEN 454 Fundamentals of Computer Vision (3) and CHE 512 Optimization in Biological Networks (3).

Option in Statistical Genomics

Students are admitted to the Option in Statistical Genomics, after successfully completing: (1) the first year of the IGDP in BG; (2) three research rotations, of which at least two must be with faculty affiliated with the Statistical Genomics Option; and (3) the candidacy examination. During the second year, Ph.D. candidates choosing this option will be required to take: (1) one of the two courses STAT 501 Regression Methods (3) or STAT 511 Regression Analysis and Modeling (3); (2) STAT 557 Data Mining I (3); and (3) two courses from a list of prescribed electives which includes, but is not limited to the following: STAT 414 Introduction to Probability Theory (3), STAT 415 Introduction to Mathematical Statistics (3), STAT 416 Stochastic Modeling (3), STAT 502 Analysis of Variance (3), STAT 504 Analysis of Discrete Data (3), STAT 505 Applied Multivariate Analysis (3), and STAT 540 Statistical Computing (3).

M.D./Ph.D. JOINT DEGREE PROGRAM

M.D./Ph.D. Admissions Requirements

Students interested in simultaneously pursuing an M.D. and Ph.D. degree must apply to the College of Medicine M.D. program using the national American Medical College Application Service (AMCAS) application system and indicate their intent to pursue the joint degree program. The College of Medicine M.D./Ph.D. Admissions Committee reviews applications and evaluates candidates for acceptance into both the M.D. and Ph.D. program. Students not accepted into the joint degree program can be referred to either the M.D. or Ph.D. program, depending on their qualifications.

The general admission requirements for the Ph.D. degree are listed above. Additional requirements for the joint degree are listed below.  Admissions requirements and applications for admission for Penn State College of Medicine are available at the M.D. Program section of the Penn State College of Medicine website. After the review committee has accepted an applicant to the joint degree program, s/he must apply to the Graduate School for admission to the graduate program. Students must be admitted to the joint degree program prior to taking the first course they intend to count towards the graduate degree.

In addition to the basic college level premedical school requirements for the Penn State College of Medicine (one each year of biology, chemistry, physics, math, and organic chemistry), the M.D./Ph.D. program has the following requirements:

  • Academic Achievement Applicants to our program generally have very strong grades and MCAT scores. In recent years, successful applicants have an average GPA of 3.75 and MCAT scores of 33-34. Applicants are not required to take the GREs.
  • Research Experience We are especially interested in students with a strong and sustained background in research. Students who have spent 1-2 years after graduation conducting research are strongly encouraged to apply. Alternatively in-depth research experience as an undergraduate can suffice.
  • Recommendations We are especially interested in receiving letters of recommendation from faculty with whom you conducted research and who can comment on your passion and potential for research.
  • Goals Applicants must be able to clearly articulate the reasons for pursuing the joint degree.
  • International Students All qualified students are eligible to apply regardless of citizenship.

 

M.D./Ph.D. Degree Requirements

Students must fulfill all requirements for each degree in order to be awarded that degree, subject to the double-counting of credits as outlined below. Degree requirements for the M.D. program are listed on the Penn State College of Medicine website. Degree requirements for the Ph.D. degree are listed in the Ph.D. Degree Requirements section above.

During the first two years of medical school, the student conducts at least three research rotations. After successful completion of the first two years of medical school the candidate enters the MCIBS Graduate Program.

During the summer after the second year of medical school M.D./Ph.D. students take Step 1 of the United States Medical Licensing Examination (USMLE), which serves in lieu of the knowledge based part of the candidacy examination for the BG program. Successful completion of BMS 506 A and B, which is taken in the second year of medical school, with a grade of B or higher meets the critical thinking and paper analysis requirement of the candidacy exam.

BG Program Requirements

The doctoral committee of an M.D./Ph.D. student in the BG program is formed upon entry into the dissertation laboratory, and must comply with all Graduate Council requirements. The committee must include at least two members of the BG program graduate faculty and one M.D./Ph.D. steering committee member.

The required courses: MCIBS 589, Colloquium, MCIBS 591, Ethics in the Life Sciences, MCIBS 551 Genomics, MCIBS 554 Foundations in Data Driven Life Sciences, MCIBS 541, Critical Analysis in BG Research Topics, STAT 555, Statistical Analysis of Genomics Data. In addition, based on the background and needs of the student the following elective courses will also be taken: BIOL 405, Molecular Evolution, STAT 500, Applied Statistics, BMMB 852, Applied Bioinformatics (2).

The BG program will accept SPM 711 Scientific Principles of Medicine (8 credits) in lieu of 6 credits of elective courses and 2 credits of MCBIS 596. If students accepted into the joint degree program are unable to complete the M.D. degree, they are still eligible to receive the Ph.D. degree if all Ph.D. degree requirements have been satisfied.

The M.D./Ph.D. candidate prepares a written comprehensive examination in the format of a grant application and gives an oral presentation of this proposal to their doctoral committee.

M.D./Ph.D. candidates are required to have at least one paper submitted for publication in a major peer-reviewed scientific journal prior to the final doctoral examination, and this must be accepted before they return to the third year of medical school. A dissertation must be prepared and defended by each M.D./Ph.D. candidate.

STUDENT AID

Graduate assistantships available to students in this program and other forms of student aid are described in the Student Aid section of the Graduate Bulletin. Students on graduate assistantships must adhere to the course load limits set forth in the Graduate Bulletin.

COURSES

Graduate courses carry numbers from 500 to 699 and 800 to 899. Advanced undergraduate courses numbered between 400 and 499 may be used to meet some graduate degree requirements when taken by graduate students. Courses below the 400 level may not. A graduate student may register for or audit these courses in order to make up deficiencies or to fill in gaps in previous education but not to meet requirements for an advanced degree.

Last Revised by the Department: Summer Semester 2017

Blue Sheet Item #: 46-01-000

Review Date: 8/22/2017

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