research proposal for phd in bioinformatics

• Search This Site All UCSD Sites Faculty/Staff Search Term
• Diversity, Equity and Inclusion Statement
• Academic Employment
• Newsletters
• Past Events
• California Integrated Vital Records Registration System (Cal-IVRS)
• DECENTRALIZED
• Maryland Electronic Vital Records
• Protect Privacy
• RADx-rad DCC
• Rapid Response Data Discovery for COVID-19
• Strong Heart
• UCSD SureNet
• NLM Pre & Postdoctoral Training Grant Fellowship
• NIH Predoctoral Training Program
• How to Cite a Training Grant
• Computer Science and Engineering PhD
• Bioinformatics PhD
• Internships
• Visiting Students & Scholars
• Past Research
• Publications
• Breast Cancer Biomarkers
• Decision Support Systems
• Preserving Privacy
• Medical Device Safety

Education & Training

Phd in bioinformatics and systems biology with emphasis in biomedical informatics.

The PhD curriculum for our trainees consists of formal instruction to provide the intellectual framework for conducting research.

Biomedical Informatics Core

• Informatics in Clinical Environments (MED 265): 1 Students are introduced to the basics of healthcare systems and clinical information needs through direct observation and classroom discussion. Students are introduced to medical language, disease processes, and health care practices to provide context prior to direct patient observation at primary, specialty, emergency, and inpatient sites in conjunction with clinical faculty affiliated with the training program. Students examine how clinicians use history-taking, physical examination and diagnostic testing to establish diagnoses and prognoses. Medical decision-making is introduced in the context of available informatics tools and clinical documentation and communication processes. Post-observation classroom discussions encourage students to think critically of the processes they observed and formulate hypotheses about how informatics solutions can modify the processes.
• Modeling Clinical Data and Knowledge for Computation (MED 267): This course describes existing methods for representing and communicating biomedical knowledge. The course describes existing health care standards and modeling principles required for implementing data standards, including biomedical ontologies, standardized terminologies, and knowledge resources.

1  Students with a clinical background will replace MED 265 with an additional course: Bioinformatics Applications to Human Disease (MED 263).

Bioinformatics Core

The core courses provide foundations in the biological basis of human health and disease and the statistical discovery of medical knowledge from biological experimentation. These classes are taken during the first year.

• Bioinformatics II (BENG 202) :  Introduction to methods for sequence analysis, applications to genome and proteome sequences, and protein structure and sequence-structure analysis.
• Principles of Biomedical Informatics (MED 264) : students are introduced to the fundamental principles of BMI and to the problems that define modern healthcare. The extent to which BMI can address healthcare problems is explored. Topics covered include structuring of data, computing with phenotypes, integration of molecular, image and other non-traditional data types into electronic medical records, clinical decision support systems, biomedical ontologies, data and communication standards, data aggregation, and knowledge discovery.
• Bioinformatics IV (MATH 283):  Analysis of modern genomic data, sequence analysis, gene expression/functional genomics analysis, and gene mapping/applied population genetics. The course focuses on statistical modeling and inference.

For the fourth core class, choose one of the following. In the event that a student completes two or more of these with suitable grades, one will count as core and the other(s) as electives.

• Algorithms in Computational Biology (CSE 280A): (Formerly CSE 206B) The course focuses on algorithmic aspects of modern bioinformatics and covers the following topics: computational gene hunting, sequencing, DNA arrays, sequence comparison, pattern discovery in DNA, genome rearrangements, molecular evolution, computational proteomics, and others. Prerequisites: CSE202 preferred or consent of instructor. 
• Algorithms for Biological Data Analysis (ECE 208): This course introduces a series of general algorithmic techniques but uses computational evolutionary biology as the context. The course motivates each algorithmic concept using a specific biological application related to evolution and focuses the discussion on specific types of (big) data available in modern biological studies. Note: The instructor and the BISB program are in the process of getting approval from the Graduate Council to introduce this as a course and to allow it as a core option. While we await approval, the course is offered under a temporary course number, ECE 286, by Prof. Siavash Mirarab, with the title "Algorithms for Biological Data Analysis." The course code ECE 286 may be used by other special topics courses as well, so be sure to enroll in the correct one.
• Genomics, Proteomics, and Network Biology (Bioinformatics III, BENG 203/CSE283): This is core in the BISB track. In the BMI track, it may be taken as the 4th core class or as an elective. Anotating genomes, characterizing functional genes, profiling, reconstructioning pathways.  Prerequisites: Pharm 201, BENG 202/CSE282, or consent of instructor. 

All students in years 1 and 2 must take both seminars in fall, winter, and spring quarters.

• Current Trends in Biomedical Informatics (MED 262): Weekly talks by researchers introduce students to current research topics within BMI. Speakers are drawn from academia, health care organizations, industry, and government.
• Bioinformatics Student Research Talks (BNFO 283) : Weekly presentations by Bioinformatics and Systems Biology students about Research Projects that are proposed or completed. Faculty mentors are present to contribute critiques and suggestions.

All students must take one of the two ethics courses by the end of second year. However, funding sources may require that it be taken first year, so we recommend taking it the first year.

• Scientific Ethics (SOMI 226): see below description
• Ethics in Scientific Research (BIOM 219): Overview of ethical issues in scientific research, conflicts of interest; national, statewide and campus issues and requirement; ethical issues in publications; authorship; retention of research records; tracing of research records; attribution; plagiarism; copyright considerations; primary, archival and meeting summary publications; ethical procedures and policies; NIH, NSF, California and UC San Diego; case studies and precedents in ethics.

Research and Teaching

During the academic year, all students must be enrolled in the appropriate research course for their level. Students typically do three rotations in year 1 (BNFO 298) and then do research units (BNFO 299) with their thesis advisor in years 2 and later. BNFO 299 units may be varied to meet the full-time enrollment requirement of 12 units per quarter in fall, winter, and spring.

• Teaching Assistantship (TA) (BNFO 500) :  Students will be a TA for two quarters during second or third year. To prepare for this teaching, students will receive training through the Center for Teaching Development at UCSD.
• Research Rotation (BNFO 298) : Taken each quarter during first year to help determine the thesis adviser.
• Graduate Research (BNFO 299): Independent work by graduate students engaged in research and writing theses. S/U grades only. May be taken for credit fifteen times.

Students must take 16 units of elective courses, including 8 units from the BMI series and 4 units from the CS series. The final 4 units can be taken from any series. The two BMI core courses MED 265 (or MED 263 for students with a clinical background) and MED 267 count as electives. Please check this  BISB curriculum page  for the list of all approved electives and elective series. 

Formal Progress to Degree

There are three formal evaluations that students must complete prior to being awarded a PhD degree: 

• Qualifying Examination:  This examination must be passed prior to the end of the student’s second year of study. The written portion of the exam consists of the student preparing an NIH or NSF-style research proposal. This proposal is then defended in an oral examination. Once the student passes the oral portion of the exam, the student is deemed to be qualified for advancing into PhD thesis research.
• Advancement to PhD Candidacy:  Upon completion of formal course requirements, each student is required to take a written and oral qualifying examination that admits the student to the candidacy of the PhD Program. The exam is administered by the dissertation committee, which consists of five faculty members.
• Final Examination:  All students defend their thesis in a final oral examination.

How to Apply

Application for admission to graduate studies is made directly through the Bioinformatics and Systems Biology website.

To be considered for the NLM fellowship, in addition to submitting your application and documentation to the degree program of your choice, please send the following to dbmi fellowship at ucsd dot edu:

• Personal Statement- explaining why you are a good candidate for the fellowship and what you hope to accomplish as an NLM trainee, the specific kind of research and topics you are interested in studying and what your goals are after completing the fellowship.
• A current and up to date CV; and
• In the body of your email please indicate which degree program you are applying to.

• Director’s Welcome
• Participating Departments
• Frontiers in Computational Biosciences Seminar Series
• Current Ph.D. Students
• Current M.S. Students
• Bioinformatics Department Handbook
• B.I.G. Summer Institute
• The Collaboratory
• Diversity and Inclusiveness
• Helpful Information for Current Students
• Joint UCLA-USC Meeting
• Student Blog and Twitter Feed
• Social Gatherings
• Introduction to the Program
• Bioinformatics Admissions Information
• Admissions FAQs
• Student Funding
• Curriculum and Graduate Courses
• Research Rotations
• Qualifying Exams

Doctoral Dissertation

• Student Publications
• Admissions Information
• Capstone Project
• Undergraduate Courses
• Undergraduate and Masters Research
• Bioinformatics Minor Course Requirements
• Bioinformatics Minor FAQs
• Bioinformatics Minor End-of-Year Celebration
• For Engineering Students
• Graduate Program

The UCLA Bioinformatics Ph.D. Program

UCLA offers an integrated doctoral training for students interested in working at the interface of computer science, biology, and mathematics to address the fundamental challenges of contemporary genomic-scale research. The interdisciplinary Ph.D. program consists of an integrated one-year core curriculum, research rotations, over 50 elective courses, and faculty mentors spanning biology, mathematics, engineering, and medicine.

Doctoral Degree Requirements & Time-To-Degree

The program provides a comprehensive system of advising throughout a student’s graduate study.  During orientation, the advising committee and the program chair meet with new students to review first-year requirements.  Throughout their first term, students are expected to meet individually with the chair or other members of the advising committee to identify faculty is closest to the student’s own interests and whose laboratory rotations would be most appropriate to join.  At the end of the fall quarter, the entire advising committee meets with the first-year students to answer questions that have arisen.  In subsequent quarters, each student’s enrollment and performance in core courses and laboratory rotations are closely monitored, and students are counseled individually by the advising chair.  At the end of spring quarter of the first year, students submit a Faculty Mentor Approval form, co-signed by the proposed mentor, to the advising committee, which considers the choice of mentor and the ability of faculty to serve in this capacity.

The advising program continues after a student has chosen a faculty research mentor.  Each year, students receive a memorandum outlining current requirements (e.g., course electives, the written and oral qualifying examinations and midstream seminar).  The advising committee also meets annually to discuss student progress and identify potential problems.  Students then receive a letter assessing their current progress and making specific recommendations as needed.  An overall assessment of student progress is also made annually to the neuroscience committee.

In addition to the formal advising procedures outlined above, students are encouraged to seek advice on career development from faculty members in the Bioinformatics community at UCLA.  An annual retreat serves to allow informal and organized contacts between faculty and students, providing further opportunity for advising.

Major Fields or Subdisciplines

These fields include computer science, genomics, molecular evolution/comparative genomics, mathematics, neuroinformatics, proteomics and statistics.

Foreign Language Requirement

Course Requirements

Students must take the core courses, Chemistry and Biochemistry 202 (six units), M252 (six units), 260A-260B, Statistics M254, 12 units of laboratory rotation courses, and at least six units of seminar courses.

Students who have gaps in their previous training may take, with their adviser’s approval, appropriate undergraduate courses. However, these courses may not be applied toward the required courses for the doctoral degree.

Teaching Experience

One quarter of teaching experience is required.

Written and Oral Qualifying Examinations

Academic Senate regulations require all doctoral students to complete and pass University written and oral qualifying examinations prior to doctoral advancement to candidacy. Also, under Senate regulations the University oral qualifying examination is open only to the student and appointed members of the doctoral committee. In addition to University requirements, some graduate programs have other pre-candidacy examination requirements. What follows in this section is how students are required to fulfill all of these requirements for this doctoral program.

Doctoral students must complete the core curriculum before they are permitted to take the written and oral qualifying examinations. Students are required to pass a written qualifying examination that consists of a research proposal outside of their dissertation topic and the University Oral Qualifying Examination in which they defend their dissertation research proposal before their doctoral committee. Students are expected to complete the written examination by the beginning of the second year and the oral examination by the end of Spring Quarter of the third year.

During their first year, doctoral students perform laboratory rotations with program faculty whose research is of interest to them and select a dissertation adviser from the program faculty inside list by the end of their third quarter of enrollment. By the end of their second spring quarter, students must select a doctoral committee that consists of three program faculty and one outside member and is approved by the program chair and the Graduate Division. By the end of their second year, students must submit a written dissertation proposal.  All members of the doctoral committee must receive a copy of the proposal before the oral qualifying examination is scheduled.

Approximately one year after the successful completion of the qualifying examinations and advancement to doctoral candidacy, students must present, within an oral seminar format, a summary of their research to date and proposed future research.

Advancement to Candidacy

Students are advanced to candidacy upon successful completion of the written and oral qualifying examinations.

Every doctoral degree program requires the completion of an approved dissertation that demonstrates the student’s ability to perform original, independent research and constitutes a distinct contribution to knowledge in the principal field of study.

Final Oral Examination (Defense of the Dissertation)

Required for all students in the program.

Time-to-Degree

Students are expected to complete the written qualifying examination by the beginning of the second year of study and the University Oral Qualifying Examination by the end of Spring Quarter of the third year. The normative time-to-degree is 16 quarters.

Termination of Graduate Study and Appeal of Termination

University Policy

A student who fails to meet the above requirements may be recommended for termination of graduate study. A graduate student may be disqualified from continuing in the graduate program for a variety of reasons. The most common is failure to maintain the minimum cumulative grade point average (3.00) required by the Academic Senate to remain in good standing (some programs require a higher grade point average). Other examples include failure of examinations, lack of timely progress toward the degree and poor performance in core courses. Probationary students (those with cumulative grade point averages below 3.00) are subject to immediate dismissal upon the recommendation of their department. University guidelines governing termination of graduate students, including the appeal procedure, are outlined in Standards and Procedures for Graduate Study at UCLA .

Special Departmental or Program Policy

Students must receive at least a grade of B- in core courses or repeat the course. Students who received three grades of B- in core courses, who fail all or part of the written or oral qualifying examinations twice (the examination committee determines the form of re-examination for students who fail all or part of the written examination), or who fail to maintain minimum progress may be recommended for termination by vote of the entire interdepartmental program committee. Students may appeal a recommendation for termination in writing to the interdepartmental program committee and may personally present additional or mitigating information to the committee, in person or in writing.

Featured News

Researchers awarded $4.7 million to study genomic variation in stem cell production, dr. nandita garud recognized for her research on gut microbiome, ucla study reveals how immune cells can be trained to fight infections, ucla scientists decode the ‘language’ of immune cells, dr. eran halperin elected as fellow of international society for computational biology, upcoming events.

• There are no upcoming events.

Recent Student Publications

RECENT STUDENT PUBLICATIONS LINK-PLEASE CLICK!

Updates Coming Soon!

• Skip to Content
• Skip to Main Navigation
• Skip to Search

Indiana University Indianapolis Indiana University Indianapolis IU Indianapolis

• Undergraduate Majors
• Apply to the Accelerated Program
• Master's Degrees
• Doctoral Degrees & Minors
• Minors & Certificates
• Earn College Credits in High School
• General Education
• Artificial Intelligence
• Bioinformatics
• Computer Science
• Data Science
• Health Informatics
• Health Information Management
• Library & Information Science
• Informatics
• Media Arts and Science
• Online Technology Degrees
• Freshman Applicants
• Returning Students
• Master's Degree
• Doctoral Program
• Graduate Certificates
• Change or Declare your Major
• Admitted Students
• Student Ambassadors
• Incoming Undergraduate Scholarships
• Undergraduate Scholarships
• Graduate Scholarships
• Accelerated Program Cost & Aid
• Tuition Reduction
• Residential-Based Learning Community
• Honors Program
• Student Organizations
• Study Abroad
• Featured Employer Days
• Resume Reviews
• Portfolio Reviews
• Presentations and Workshops
• Employer Career Fair Registration
• Research Centers & Labs
• Undergraduate Research
• Research Events
• Luddy Strategic Plan
• Departments
• Meet Fred Luddy
• Faculty Openings
• Faculty & Staff Directory
• Media Requests
• Request Undergraduate Information
• Request Graduate Information
• Get involved
• Peer Advisors
• Find a Job or Internship
• F-1 Students & Internships
• Library & Information Science Internships
• Career Process & Resources
• Schedule an Appointment
• Request a Career Services Presentation
• Degree Requirements
• Forms & Policies
• Travel Funding
• Facilities & Technology Support
• Micro-Credentials

Luddy School of Informatics, Computing, and Engineering

• Alumni & Giving
• Student Portal

At the intersection of biology and technology

Research scientists in bioinformatics design computational tools and data science applications that make sense of staggering amounts of data, developing solutions that can improve health and save lives. Our Ph.D. degree program in Bioinformatics immerses you in course projects, independent research investigations, and lab rotations that integrate informatics, technology, statistics, machine learning, computational biology, genetics, genomics, proteomics, other life science fields—and many other disciplines—in new ways.

• Degrees & Courses

Bioinformatics Ph.D.

Expert faculty at indiana’s life science and it research campus.

Our bioinformatics degree programs put you in the heart of Indiana’s health care campus, where faculty inspire innovation and novel collaborations in high-through data analysis, big data mining, omics technologies, precision medicine, and many other translational research.

The Ph.D. in Bioinformatics is a 90-credit-hour program that includes core courses, research rotations, the choice of a minor, qualifying examinations, and a dissertation. Our curriculum provides a balance in wide-ranging fields, cutting-edge computing technology, state-of-the-art informatics skills, innovative research and scholarly activities, bioethics, effective teaching, and intellectual property, preparing graduates to succeed in post-doctoral careers. In addition to research and analytics, you’ll learn how to:

• Perform novel research projects
• Publish original articles
• Present inspiring findings at national conferences
• Create visual representations of complex data
• Design database systems
• Write effective grant proposals

Sarath Chandra Janga

Associate Professor, Bioinformatics, Data Science

Bohdan Khomtchouk

Assistant Professor, Bioinformatics, Data Science

Chia-Ying James Lin

Professor, Biomedical Engineering and Informatics

Juexin Wang

Assistant Professor, Bioinformatics

Jingwen Yan

Associate Professor, Bioinformatics

Get your questions answered

Request information.

Contact our graduate admissions team and get your questions answered.

Meet our student ambassadors

Get to know our student ambassadors and find out what life at Luddy is like.

Information Sessions

Register for a virtual information session.

Ready to get started?

• Register for an info session
• Learn how to apply

Luddy School of Informatics, Computing, and Engineering resources and social media channels

• Schedule a Visit

Additional links and resources

• Degrees & Majors
• Scholarships

Happening at Luddy

Information for.

• Current Students
• Faculty & Staff Intranet

Luddy Indianapolis

• MD | PhD Program
• Master's Programs
• PhD Programs
• Postdoctoral Fellows
• Residency & Fellowship
• Non-Degree Programs
• Visiting Students
• Campus Life at U-M
• Health & Wellness
• Building Your Community
• Accessibility & Disability
• Departments
• Centers & Institutes
• Interdisciplinary Programs
• Facts & Figures
• Medical School Leadership
• News & Stories
• Requirements
• Interview Day
• Admissions Chats
• AAMC Michigan's 35 Answers
• AAMC Michigan's 10 Financial Aid Answers
• Admitted Students
• Overview & Highlights
• Patient Interaction
• Chief Concern
• Years 3 & 4
• Learning Informatics
• Training Sites
• Leadership Program
• Global Health & Disparities
• Healthcare Innovation
• Health Policy
• Medical Humanities
• Patient Safety & Quality Improvement
• Scientific Discovery
• Doctoring Course
• Evidence-Based Medicine
• Interprofessional Education
• DEIAJ Curriculum
• Language Opportunities
• Curriculum Diagrams
• Grading & Assessments
• Guideline Budget
• Loans & Eligibility
• Scholarships & Grants
• Documents & Forms
• Tuition Refund Policies
• Consumer Information
• Extra Help for Current Students
• Contact the Office of Financial Aid
• Profiles & Demographics
• Culinary Connections
• Students with Disabilities
• Health & Wellbeing
• Arts & Humanities
• Diversity & Health Equity
• Dual Degrees
• More Possibilities
• Commencement
• Available PhD Programs
• Academic & Social Events
• MSTP Fellows
• Application Process
• Application Requirements
• MD | PhD Curriculum
• Undergrad Summer Program
• Contact the MD | PhD Program

Bioinformatics

• Biological Chemistry
• Cancer Biology
• Cell & Developmental Biology
• Cellular & Molecular Biology
• Genetics and Genomics
• Health Infrastructures & Learning Systems
• Microbiology & Immunology
• Molecular, Cellular & Developmental Biology
• Molecular & Cellular Pathology
• Molecular & Integrative Physiology
• Neuroscience
• Pharmacology
• Recruitment Events
• Interview Weekends
• Certificates & Dual Degrees
• Quantitative & Computational Biology Emphasis
• Training Grants
• Facilities & Resources
• Stipend & Benefits
• Professional Development
• Finding a Position
• Funding Your Postdoc
• Hiring Process
• Postdoc Preview
• International Postdocs
• ACGME Fellowships
• Non-Accredited Fellowships
• Postdoctoral Physician Scientist Training
• Salary & Benefits
• Prerequisites
• Visiting Residents & Fellows
• Application Overview & Requirements
• Tuition & Fees
• Timeline & Curriculum
• Information Sessions
• Program Details
• Undergrad Summer Research
• First Days Survival Guide
• Health Services
• Mental Health
• Health, Spirituality & Religion Program
• For Partners & Families
• Things to Do in Ann Arbor
• Getting Around
• Guiding Tools
• Graduate Medical Education
• Office of Continuing Medical Education
• Office of Faculty Affairs & Faculty Development
• Office of Graduate & Postdoctoral Studies
• Physician Scientist Education & Training
• Office of Medical Student Education
• Points of Blue

An all-encompassing, highly interdisciplinary field

Program Overview

The University of Michigan  Bioinformatics Graduate Program builds a strong foundation for Master’s and PhD students through comprehensive course offering, research training and mentoring.

Students in our program take courses in advanced math, modeling, statistics, computer programming, machine learning, informatics, comprehensive courses in introductory biology, genomics, proteomics, clinical informatics, environmental health, and much more. They are encouraged to take advantage of the enormous research and teaching resources across U-M.

Our students have an abundance of research opportunities in many subject areas under the mentorship of our 130 affiliated faculty members of the Center for Computational Medicine and Bioinformatics ( CCMB ). These faculty are from U-M Medical School, College of Engineering, College of Literature, Arts and Sciences, School of Public Health, School of Nursing, and School of Information. 

In 2023, the Bioinformatics Graduate Program maintains a student body of 87 PhD students, and over 120 Master's students. They are mentored by the 44 DCMB faculty and the 130 CCMB faculty. Faculty members with biological and more quantitative expertise are both well represented.

The Bioinformatics Graduate Program was created in 1999 and is housed in the Department of Computational Medicine and Bioinformatics ( DCMB ). 

Apply through our PIBS application

Bioinformatics offers an extensive range of research opportunities, from applications for clinical medical problems and specific diseases to computational work on synthetic biological systems. There are very active groups in:

• Artificial Intelligence (AI) and machine learning
• Genomics, regulatory genomics and epigenomics
• Protein structure, proteomics, and alternative splicing
• Multi-“omics” integrative bioinformatics
• Systems biology and networks analysis
• Biomedical data science, translational bioinformatics and pharmacogenomics
• Methodological development in computational biology
• Applications to complex genetic diseases
• 4D Nucleome
• Single Cell Analysis
• Signal/Image Processing and Machine Learning

Bioinformatics has had NIH supported training grants since 2005. Our students are eligible for a wide range of other training grant support related to more specific areas of research, such as genomics or cancer proteomics.

Students are required to take courses in each of the following areas:

• Introductory Bioinformatics
• Computing & Informatics
• Probability & Statistics
• Molecular Biology
• Bioinformatics 602 (Journal Club) taken once in the first year.
• Bioinformatics 603 (Journal Club) taken once; students present papers for discussion
• Research Responsibility and Ethics course (PIBS 503)
• One Advanced Bioinformatics course offered or cross-listed by the Bioinformatics Graduate Program
• One additional Advanced Bioinformatics course in any program

Details about courses available in each of these areas can be found on the department website . Courses may be offered by Bioinformatics or other units.

Attendance at weekly seminars is also expected. Offered seminars include a weekly series of invited guest speakers, “Tools & Tech” presentations that highlight a tool or technology, either under development or in current use, and BISTRO, a lively seminar where students present their ongoing research.

Preliminary Examination

Students take a preliminary exam in their second year, usually at the end of the 3rd or 4th term. The preliminary exam should show both creativity and skill, and should not be identical to the student’s thesis work. The aims of the examination are two-fold. The first aim is to demonstrate that students have developed the ability to analyze a scientific problem and develop appropriate strategies to carry out a research plan. The second aim is to demonstrate that students have enough Bioinformatics knowledge needed to carry out their thesis research. Students sometimes develop their prelim proposals into a paper and/or a thesis chapter later.

Teaching Requirement

Teaching, in Bioinformatics or in other departments, is encouraged and expected for at least one term from most Bioinformatics students. Individual circumstances such as English language ability, interest, and funding situation of the mentor are considered.

Expected Length of Program

The expected time to PhD graduation is 5 to 6 years.

Approximately 8-15 new students join the PhD program each year. Each term, contact between faculty and students is encouraged through research events & social gatherings. Given the interdisciplinary nature of the program, students are encouraged to develop and pursue their own research interests. In an effort to support students’ academic growth, the department and other units (such as Rackham Graduate School) offer funding to assist students with conference participation or workshop attendance.

Approximately 50% of program alumni choose academia, while others with go into industry with many working at biotechnology companies. Aware of this, current students are provided opportunities to meet with guest seminar speakers or visitors from industry. In addition, outside internships are encouraged if related to a student’s research as they have proven to be valuable experiences.

The program supports student-led initiatives that are focused on building community such as student organized social activities, a pre-Thanksgiving dinner, and group run in the local marathon. Separately, Bioinformatics coordinates an annual off-site weekend retreat and an annual picnic.

DCMB welcomes and supports several  student organizations :

• The Bioinformatics Graduate Student Association (BGSA)
• The Bioinformatics Black Student Union (BBSU)
• The Data Analysis Networking Group (DANG!)
• DCMB Girls Who Code Club

Alumni from the Bioinformatics Graduate Program pursue successful careers in academia, biotechnology and biomedical research in industry and government. Most of them are employed immediately after graduation.

Learn more about the Department of Computational Medicine and Bioinformatics.

We transform lives through bold discovery, compassionate care and innovative education.

• Diversity, Equity & Inclusion
• Find a Doctor
• Conditions & Treatments
• Patient & Visitor Guide
• Patient Portal
• Clinical Trials
• Research Labs
• Research Centers
• Cores and Resources
• Programs & Admissions
• Our Community
• Departments, Centers & Offices
• About the Medical School

Global Footer Secondary Navigation

PhD in Bioinformatics (Medical Informatics subfield)

The Medical Informatics Advising Committee, chaired by the Faculty Graduate Advisor, advises students during the first year and is available to students throughout the tenure of their study.

Upon entering their second year in the Medical Informatics Home Area, students will select a mentor who will serve as their dissertation chair, research advisor, and primary graduate advisor. Together the student and the mentor will convene a doctoral committee who will guide the student throughout their research, the University Oral Qualifying Exam, Doctoral Dissertation Defense, and will approve the final dissertation.

Individual Development Plan : Beginning with a mandatory training workshop in the first quarter of graduate study, students are required to generate an Individual Development Plan via myIDP Website:  http://myidp.sciencecareers.org/  in order to map out their academic and professional development goals throughout graduate school. The myIDP must be updated annually, and the resulting printed summary discussed with and signed by (Year 1) the student’s advising committee member, or (Years 2-5) thesis adviser, and then turned in to the Graduate Student Affairs Office to be placed in the student’s academic file each year by June 1.

Annual Committee Meetings : Beginning one year after advancement to doctoral candidacy, and in each year thereafter until completion of the degree program, students are required to meet annually with their doctoral committee. At each meeting, students give a brief, 30-minute oral presentation of their dissertation research progress to their committee. The purpose of the meeting is to monitor the student’s progress, identify difficulties that may occur as the student progresses toward successful completion of the dissertation and, if necessary, approve changes in the dissertation project. The presentation is not an examination.

Annual Progress Report : All students are required to submit a brief report (a one-page form is provided) of their time-to-degree progress and research activities indicating the principal research undertaken and any important results, research plans for the next year, conferences attended, seminars given, and publications appearing or manuscripts in preparation. Annual Progress report must be submitted to the Medical Informatics Home Area Students Affairs Office for review by the Program Director.

Course Requirements

Students must complete all of the following: (1) nine core courses (34 units) Bioengineering 220, 223A, 223B, 223C, 224A, 224B, M226, M227, and M228; (2) MIMG C234; (3) 8 units of Bioinformatics 596; (4) 4 units of 200-level seminar or journal club courses approved by the program; and (5) six electives, chosen from the following list: Bioinformatics M223, M226; Biomathematics 210, M230, M281, M282; Biostatistics 213, M232, M234, M235, 241, 276; Computer Science 240A, 240B, 241B, 245, 246, 247, 262A, M262C, 262Z, 263A, 265A, M268, M276A; Electrical and Computer Engineering 206, 210A, 210B, 211A, M217, 219; Information Studies 228, 246, 272, 277; Linguistics 218, 232; Neuroscience CM272; Physics in Biology and Medicine 210, 214. M248; Statistics 221, M231A, 231B, M232A, M232B, 238, M241, M243, M250, 256. Courses must be taken for a letter grade, unless offered on S/U grading basis only.

Teaching Experience

One quarter of teaching experience is required by the end of the third year.

Written and Oral Qualifying Examinations

Doctoral students must complete the core courses described above before they are permitted to take the written and oral qualifying examinations. Students are required to pass a written qualifying examination that consists of a research proposal outside of their dissertation topic and the University Oral Qualifying Examination in which they defend their dissertation research proposal before their doctoral committee. Students are expected to complete the written examination in the summer following the first year and the oral qualifying examination by the end of fall quarter of the third year. The written qualifying examination must be passed before the University Oral Qualifying Examination can be taken.

During their first year, doctoral students perform laboratory rotations with program faculty whose research is of interest to them and select a dissertation adviser from the program faculty inside list by the end of their third quarter of enrollment. By the end of their second spring quarter, students must select a doctoral committee that is approved by the program chair and the Graduate Division.

Written Qualifying Examination

The Written Qualifying Examination (WQE) must take place in the summer following the first year of doctoral study. In order to be eligible to take the WQE, students must have achieved at least two passing lab rotation evaluations, as well as at least a B average in all course work. Students are expected to formulate a testable research question and answer it, by carrying out a small, well-defined and focused project over a fixed one-month period. It must include the development of novel (bio)medical informatics methodology. The topic and methodologies are to be selected by the student. The topic requires advance approval by the faculty committee, and may not be a project from a previous course, a rotation project, a project related to the student’s prior research experience, an anticipated dissertation research topic, or an active or anticipated research project in the laboratory of the student’s mentor. The WQE must be the student’s own ideas and work exclusively. Students are expected to complete a WQE paper of publication quality (except for originality), with a maximum length of 10 pages, single-spaced, excluding figures and references. This paper is submitted to the Student Affairs Office and graded by a faculty committee on a pass or no-pass basis. Students who do not pass the examination are permitted one additional opportunity to pass, which must be submitted to and graded by the faculty committee no later than the end of the summer of the first year.

Oral Qualifying Examination

The University Oral Qualifying Examination must be completed and passed by the end of the fall quarter of the third year. Students prepare a written description of the scientific background of their proposed dissertation research project, the specific aims of the project, preliminary findings, and proposed (bio)medical informatics approaches for addressing the specific aims. This dissertation proposal must be written following an NIH research grant application format and be at least six pages, single spaced and excluding references, and is submitted to the students’ doctoral committee at least 10 days in advance of the examination. Exclusive of their doctoral committee members, students are free to consult with their dissertation adviser, or other individuals in formulating the proposed research. The examination consists of an oral presentation of the proposal by the student to the committee. The student’s oral presentation and examination are expected to demonstrate: (1) a scholarly understanding of the background of the research proposal; (2) well-designed and testable aims; (3) a critical understanding of the (bio)medical informatics, mathematical or statistical methodologies to be employed in the proposed research; and (4) an understanding of potential informatics outcomes and their interpretation. This examination is graded Pass, Conditional Pass, or Fail. If the doctoral committee decides that the examination reflects performance below the expected mastery of graduate-level content, the committee may vote to give the student a Conditional Pass. A student who receives a Conditional Pass will be required to modify or re-write their research proposal, so as to bring it up to required standard. In the case of a Conditional Pass, the student will be permitted to seek the advice of their committee in modifying or re-writing the proposal. Any required re-write or modification will be submitted to, and reviewed by the doctoral committee. A second oral presentation is not necessary unless the doctoral committee requires so. The signed Report on the Oral Qualifying Examination & Request for Advancement to Candidacy will be retained in the Graduate Student Affairs Office until the student has satisfied the doctoral committee’s request for revision or re-write. Students are allowed only one chance to revise or re-write their proposal.

Advancement to Candidacy

Students are advanced to candidacy upon successful completion of the written and oral qualifying examinations.

Doctoral Dissertation

Every doctoral degree program requires the completion of an approved dissertation that demonstrates the student’s ability to perform original, independent research and constitutes a distinct contribution to knowledge in the principal field of study.

Final Oral Examination (Defense of the Dissertation)

Required for all students in the program.

Time-to-Degree

Students are expected to complete the written qualifying examination in the summer following the first year of study and the University Oral Qualifying Examination by the end of fall quarter of the third year. Normative time-to-degree is five years (15 quarters).

Computational and Systems Biology PhD Program

Computational and systems biology.

The field of computational and systems biology represents a synthesis of ideas and approaches from the life sciences, physical sciences, computer science, and engineering. Recent advances in biology, including the human genome project and massively parallel approaches to probing biological samples, have created new opportunities to understand biological problems from a systems perspective. Systems modeling and design are well established in engineering disciplines but are newer in biology. Advances in computational and systems biology require multidisciplinary teams with skill in applying principles and tools from engineering and computer science to solve problems in biology and medicine. To provide education in this emerging field, the Computational and Systems Biology (CSB) program integrates MIT's world-renowned disciplines in biology, engineering, mathematics, and computer science. Graduates of the program are uniquely prepared to make novel discoveries, develop new methods, and establish new paradigms. They are also well-positioned to assume critical leadership roles in both academia and industry, where this field is becoming increasingly important.

Computational and systems biology, as practiced at MIT, is organized around "the 3 Ds" of description, distillation, and design. In many research programs, systematic data collection is used to create detailed molecular- or cellular-level descriptions of a system in one or more defined states. Given the complexity of biological systems and the number of interacting components and parameters, system modeling is often conducted with the aim of distilling the essential or most important subsystems, components, and parameters, and of obtaining simplified models that retain the ability to accurately predict system behavior under a wide range of conditions. Distillation of the system can increase the interpretability of the models in relation to evolutionary and engineering principles such as robustness, modularity, and evolvability. The resulting models may also serve to facilitate rational design of perturbations to test understanding of the system or to change system behavior (e.g., for therapeutic intervention), as well as efforts to design related systems or systems composed of similar biological components.

CSB Faculty and Research

More than 70 faculty members at the Institute participate in MIT's Computational and Systems Biology Initiative (CSBi). These investigators span nearly all departments in the School of Science and the School of Engineering, providing CSB students the opportunity to pursue thesis research in a wide variety of different laboratories. It is also possible for students to arrange collaborative thesis projects with joint supervision by faculty members with different areas of expertise. Areas of active research include computational biology and bioinformatics, gene and protein networks, regulatory genomics, molecular biophysics, instrumentation engineering, cell and tissue engineering, predictive toxicology and metabolic engineering, imaging and image informatics, nanobiology and microsystems, biological design and synthetic biology, neurosystems biology, and cancer biology.

The CSB PhD Program

The CSB PhD program is an Institute-wide program that has been jointly developed by the Departments of Biology, Biological Engineering, and Electrical Engineering and Computer Science. The program integrates biology, engineering, and computation to address complex problems in biological systems, and CSB PhD students have the opportunity to work with CSBi faculty from across the Institute. The curriculum has a strong emphasis on foundational material to encourage students to become creators of future tools and technologies, rather than merely practitioners of current approaches. Applicants must have an undergraduate degree in biology (or a related field), bioinformatics, chemistry, computer science, mathematics, statistics, physics, or an engineering discipline, with dual-emphasis degrees encouraged.

CSB Graduate Education

All students pursue a core curriculum that includes classes in biology and computational biology, along with a class in computational and systems biology based on the scientific literature. Advanced electives in science and engineering enhance both the breadth and depth of each student's education. During their first year, in addition to coursework, students carry out rotations in multiple research groups to gain a broader exposure to work at the frontier of this field, and to identify a suitable laboratory in which to conduct thesis research. CSB students also serve as teaching assistants during one semester in the second year to further develop their teaching and communication skills and facilitate their interactions across disciplines. Students also participate in training in the responsible conduct of research to prepare them for the complexities and demands of modern scientific research. The total length of the program, including classwork, qualifying examinations, thesis research, and preparation of the thesis is roughly five years.

The CSB curriculum has two components. The first is a core that provides foundational knowledge of both biology and computational biology. The second is a customized program of electives that is selected by each student in consultation with members of the CSB graduate committee. The goal is to allow students broad latitude in defining their individual area of interest, while at the same time providing oversight and guidance to ensure that training is rigorous and thorough.

Core Curriculum

The core curriculum consists of three classroom subjects plus a set of three research rotations in different research groups. The classroom subjects fall into three areas described below.

Modern Biology (One Subject): A term of modern biology at MIT strengthens the biology base of all students in the program. Subjects in biochemistry, genetics, cell biology, molecular biology, or neurobiology fulfill this requirement. The particular course taken by each student will depend on their background and will be determined in consultation with graduate committee members.

Computational Biology (One Subject): A term of computational biology provides students with a background in the application of computation to biology, including analysis and modeling of sequence, structural, and systems data. This requirement can be fulfilled by 7.91[J] / 20.490[J] Foundations of Computational and Systems Biology.

Topics in Computational and Systems Biology (One Subject): All first-year students in the program participate in / 7.89[J] Topics in Computational and Systems Biology, an exploration of problems and approaches in the field of computational and systems biology through in-depth discussion and critical analysis of selected primary research papers. This subject is restricted to first-year PhD students in CSB or related fields in order to build a strong community among the class. It is the only subject in the program with such a limitation.

Research Group Rotations (Three Rotations): To assist students with lab selection and provide a range of research activities in computational and systems biology, students participate in three research rotations of one to two months' duration during their first year. Students are encouraged to gain experience in experimental and computational approaches taken across different disciplines at MIT.

Advanced Electives

The requirement of four advanced electives is designed to develop both breadth and depth. The electives add to the base of the diversified core and contribute strength in areas related to student interest and research direction. To develop depth, two of the four advanced electives must be in the same research area or department. To develop breadth, at least one of the electives must be in engineering and at least one in science. Each student designs a program of advanced electives that satisfies the distribution and area requirements in close consultation with members of the graduate committee.

Additional Subjects: As is typical for students in other doctoral programs at MIT, CSB PhD students may take classes beyond the required diversified core and advanced electives described above. These additional subjects can be used to add breadth or depth to the proposed curriculum, and might be useful to explore advanced topics relevant to the student's thesis research in later years. The CSB Graduate Committee works with each graduate student to develop a path through the curriculum appropriate for his or her background and research interests.

Training in the Responsible Conduct of Research: Throughout the program, students will be expected to attend workshops and other activities that provide training in the ethical conduct of research. This is particularly important in interdisciplinary fields such as computational and systems biology, where different disciplines often have very different philosophies and conventions. By the end of the fourth year, students will have had about 16 hours of training in the responsible conduct of research.

Qualifying Exams: In addition to coursework and a research thesis, each student must pass a written and an oral qualifying examination at the end of the second year or the beginning of the third year. The written examination involves preparing a research proposal based on the student's thesis research, and presenting the proposal to the examination committee. This process provides a strong foundation for the thesis research, incorporating new research ideas and refinement of the scope of the research project. The oral examination is based on the coursework taken and on related published literature. The qualifying exams are designed to develop and demonstrate depth in a selected area (the area of the thesis research) as well as breadth of knowledge across the field of computational and systems biology.

Thesis Research: Research will be performed under the supervision of a CSBi faculty member, culminating in the submission of a written thesis and its oral defense before the community and thesis defense committee. By the second year, a student will have formed a thesis advisory committee that they will meet with on an annual basis.

Alternatively, use our A–Z index

Tackle the biggest challenges in biology, medicine and health in a world leading research environment, and prepare for your future career.

Attend an open day

PhD/MPhil Bioinformatics / Overview

Year of entry: 2025

• View full page

We require applicants to hold, or be about to obtain, an Upper Second class Honours degree, or the equivalent qualification gained outside the UK, in a related subject area for entry to a PhD programme. A Lower Second class Honours degree may be considered if applicants also hold a Master's degree with a Merit classification.

Full entry requirements

Apply online

Before applying you must:

• Choose a programme or find a project you want to apply for and check you’re eligible.
• Speak to the listed supervisor about your suitability for their project or programme.
• Understand how your project is funded and, if it is self-funded, consider how you plan on funding it.
• Read our ‘How to apply’ page to find out more and ensure you include all required supporting documents at the time of submission.

Visit our Faculty of Biology, Medicine and Health Postgraduate Research page to find out more.

Programme options

Programme overview.

• Undertake research in a field you’re passionate about and join a project addressing leading challenges in the area while working with some of Europe's leading researchers and academics.
• Choose to research at a university ranked and 6th in the UK (QS World University Rankings, 2025) and 2nd in the world for social and environmental impact (THE Impact Rankings, 2024), where 93% of research activity is ‘world leading’ or ‘internationally excellent’ (Research Impact Framework, 2021)
• Access some of the best research facilities in the world at the University, through our industry partners, and at hospitals around Greater Manchester.
• Benefit from dedicated support throughout your PhD journey, from pre-application to graduation and everything in between, through our Doctoral Academy
• Undergo training in transferable skills critical to developing early-stage researchers and professionals through the Doctoral Academy's training programme and progress into a career in research, academia or industry.

Visit our Faculty of Biology, Medicine and Health Postgraduate Research page to find out about upcoming open days and events.

For entry in the academic year beginning September 2025, the tuition fees are as follows:

• PhD (full-time) UK students (per annum): Standard £TBC, Low £11,500, Medium £17,500, High £23,500 International, including EU, students (per annum): Standard £27,000, Low £29,500, Medium £35,000, High £41,500
• PhD (part-time) UK students (per annum): Standard £TBC, Low £5,750, Medium £8,625, High £11,750 International, including EU, students (per annum): Standard £13,500, Low £14,750, Medium £17,500, High £20,755

Further information for EU students can be found on our dedicated EU page.

Contact details

Programmes in related subject areas.

Use the links below to view lists of programmes in related subject areas.

• Biosciences
• Informatics

Regulated by the Office for Students

The University of Manchester is regulated by the Office for Students (OfS). The OfS aims to help students succeed in Higher Education by ensuring they receive excellent information and guidance, get high quality education that prepares them for the future and by protecting their interests. More information can be found at the OfS website .

You can find regulations and policies relating to student life at The University of Manchester, including our Degree Regulations and Complaints Procedure, on our regulations website .

PhD Research Proposal Writing Adviser

We are seeking a PhD Research Proposal Writing Adviser to join our team of PNG-based academic experts. This role involves providing professional, short-term support to Australia Awards research awardees, including those pursuing master's by research, Master of Philosophy, and PhD degrees.

Contribute to a world where people, communities and the planet thrive.

Tetra Tech International Development is a leading development consulting firm working with government, businesses, and NGOs to solve complex development challenges in the Indo-Pacific region. For more information  please visit our website  .

The opportunity

Short Term Adviser position

Remote work inputs, with some travel to PNG

Up to 18 input days

Australia Awards PNG (AAPNG) 

Program Goal: To support Papua New Guinea to achieve its development goals through education, knowledge transfer, and institutional capacity building, and to build enduring relationships with Australia.

Australia Awards PNG (AAPNG) supports Papua New Guinea to achieve its development goals through education, knowledge transfer, and institutional capacity building, through enduring relationships with Australia. This is achieved through institution-to-institution partnerships and inclusive collaborations that produces high quality education and strengthens accredited training institutions in PNG.

Key responsibilities

• Develop, facilitate and manage a four-day research proposal writing workshop for up to 20 academic and research staff from tertiary and research institutions in Papua New Guinea. 
• Read, review and provide constructive criticism and expert advice on content and structure of research proposal outputs of participants in reasonable time. 
• Provide general academic advice and guidance in response to specific requests to inform the Australia Awards Scholarships team and DFAT (as requested).

Selection criteria

• Postgraduate qualifications in their area of specialisation.
• A demonstrated understanding of the political, economic, social, and historical context of PNG.
• At least five years of experience in teaching, supervising students, or conducting research in higher education, preferably in Australia or PNG.
• Experience in delivering training for higher degree research students.
• A strong academic publication history.
• Strong leadership, supervisory, advisory, and management skills.
• High-level interpersonal skills for building and maintaining relationships, delivering messages, andidentifying and managing issues.
• Fluency in spoken and written English

For a complete position description please click here.

How to apply

Click the "Apply for job" button. 

Applications will only be accepted via the Tetra Tech International Development Website. Emailed applications will be disregarded.

Please submit:

Resume (not to exceed four pages)

Statement of suitability (not to exceed two pages), demonstrating how your qualifications, experience, knowledge, skills and personal attributes align with the selection criteria

Please do not attach any other documentation

Apply before Friday, 1 November 2024 11:59 PM AEDT

Due to a high volume of applications, only shortlisted candidates will be contacted.