Ph.D. in Informatics - Bioinformatics Track

Turn data into breakthroughs in biology and medicine

If you're interested in solving real-world questions in biology and medicine using data, the Bioinformatics track might be the right fit for you. You’ll combine training in computer science, informatics, life sciences, chemistry, and statistics to explore areas like:

Sequence pattern recognition
Comparative and structural genomics
DNA sequencing and fragment assembly
Systems biology and models of evolution
Molecular modeling and drug design

You’ll build the skills to succeed in top research labs or industry roles, working alongside scientists at IU and through partnerships with other universities, research centers, and biotech companies.

What you'll learn

The Bioinformatics track prepares students to tackle biological and medical research questions through a blend of informatics, computer science, life sciences, chemistry, and statistics. You'll explore areas like genomics, systems biology, and drug design while gaining hands-on research experience through collaborations with scientists at IU and beyond.

Track faculty

Track Director

Volker Brendel

Computational genomics; plant genomics; social insect genomics.

Mehmet Dalkilic

Data Mining

Matthew Hahn

Genome-scale studies of organismal function and evolution.

Roni Khardon

Professor of Computer Science

Paul Macklin

Associate Professor

Haixu Tang

Computational mass spectrometry; mobile genetic elements; genome privacy; bacterial genomics and metagenomics.

Yuzhen Ye

Computational metagenomics; protein bioinformatics; biological pathway reconstruction/analysis.

Track guide

A student must successfully complete ninety (90) credit hours of graduate-level course work. The specific track requirements are listed below.

Required courses

In addition to the Informatics-wide requirements for INFO-I 501 and INFO-I 502 as well as two research rotation INFO-I 609 and/or INFO-I 709s, students in the Bioinformatics Track need to take the two bioinformatics core classes INFO-I 519 and INFO-I 529 and the seminar classes INFO-I 609 and INFO-I 708. All required courses provided by faculty in the Bioinformatics Track, including I609 and I709, are open to students from other tracks and programs.

I501: Introduction to Informatics
I502: Human-Centered Research Methods in Informatics (3 cr.)

INFO I519 Introduction to Bioinformatics (3 cr.)
INFO I529 Machine Learning in Bioinformatics (3 cr.)

INFO I609 Seminar I in Informatics (3 cr.)
INFO I709 Seminar II in Informatics (3 cr.)

NOTE: A student must take I609 and/or I709.

INFO I790 Informatics Research Rotation (3 cr.)

NOTE: A student must complete two rotations of I790. A third rotation will not count for course credit.

NOTE: These courses must be appropriate for a Ph.D. in Informatics.

NOTE: A student must complete an internal or external minor approved by the University Graduate School and the School. If a student selects an individualized minor, prior to taking courses, the University Graduate School must approve the proposed minor course list. There is no typical minor; however, students in the Bioinformatics track often pursue a minor in Biology, Computer Science, or Statistics.

NOTE: A student must have all electives approved by the student's advisor and the Director of Informatics Graduate Studies prior to enrolling in the course.

INFO I890 Thesis Readings and Research

In addition to required courses, faculty in the track offer courses that provide more targeted training in specific areas.

INFO I590 Topics in Informatics: SNP Discovery and Population Genetics
CSCI B555 Machine Learning
CSCI B565 Data Mining

Typical minors

Biology, Computer Science, or Statistics.

Qualifying exam

Written and oral examination topics are selected by the program committee based on subjects covered in the student’s earlier coursework. Generally, students choose one computational area (from machine learning, data mining, or algorithms) and one biological area (from molecular, structural, or evolutionary biology) to narrow the scope of examination, and then textbooks and literature used in the appropriate courses and specific research areas of the candidate are assigned for study. The typical written examination takes half a day each for the computational and biological components. In addition, the required breadth examination will similarly cover a student-chosen other area of Informatics, as covered in the candidate’s course work, and evaluated by the candidate’s outside member of their program committee.

Dissertation proposal and these

The Ph.D. candidate submits a thesis proposal to their thesis committee a couple of weeks before their Dissertation Proposal meeting. The candidate will give an open presentation about his/her thesis research topic at the meeting, followed by a closed meeting with their committee in which the candidate will answer questions and receive feedback from committee members. A draft of the dissertation thesis should be submitted to the thesis committee one month before the Dissertation Defense. If the candidate passed the defense, their thesis will need to be revised to incorporate the comments from the committee members.

Sample coursework:

Students typically take the INFO-I 501/I502 and BIO Track I519/I529 classes as well as the research rotations in their first two semesters. The required seminar courses and additional credit requirements are covered in years two and three, augmenting the student’s own research (mentored by their advisor).

Sample dissertation titles

Clark, Wyatt	Understanding protein function through statistical inference and evolutionary analysis
Pejaver, Vikas	Computational methods for understanding the impact of amino acid substitutions on protein function
Wang, Mingjie	Development and Application of Novel Methods for Comparative Metagenomics and Metatranscriptomics
Xin, Fuxiao	Methods for predicting functional residues in protein structures and understanding molecular mechanisms of disease
Yu, Chuan-Yih	Algorithms for automated identification and quantification of glycans and glycopeptides
Zhang, Quan	Functional Annotation of Metagenomes with a focus on Bacterial Immune Systems
Zhang, Simo	Computational methods for Improving genome assembly, annotation, and analysis
Zhang, Xinjun	ChacacterizingLsequence fe􀀺atures of human pathogenic variations and impact on post-transcriptional regulation
Zhao, Yongan	Privacy-preserving sharing and analysis on human genomic data

One School. Two Campuses. Infinite Possibilities.

More pathways at Luddy Indianapolis

Explore the Bioinformatics program available at IU's urban research campus in the heart of downtown Indianapolis.

Luddy School of
Informatics, Computing, and Engineering

Ph.D. in Informatics - Bioinformatics Track

Turn data into breakthroughs in biology and medicine

What you'll learn

Track faculty

Volker Brendel

Mehmet Dalkilic

Matthew Hahn

Roni Khardon

Paul Macklin

Haixu Tang

Yuzhen Ye

Track guide

Required courses

Typical minors

Qualifying exam

Dissertation proposal and these

Sample coursework:

Sample dissertation titles

More pathways at Luddy Indianapolis

Ready to start your journey at Luddy? Take the next step!

Ph.D. in Informatics - Bioinformatics Track

Turn data into breakthroughs in biology and medicine

What you'll learn

Track faculty

Track guide

Required courses

Informatics Core Requirements (6 cr.)

Bioinformatics Core Requirements (6 cr.)

Seminar Requirements (6 cr.)

Research Rotation Requirement (6 cr.)

Theory and Methodology Requirement (12 cr.)

Minor (6-15 cr.)

Electives (12-30 cr.)

Thesis Reading and Research (minimum of 21 cr. and a maximum of 30 cr.)

Optional courses

Typical minors

Qualifying exam

Dissertation proposal and these

Sample coursework:

Sample dissertation titles

Ready to start your journey at Luddy? Take the next step!

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