Bioinformatics

The UAB Undergraduate Program in Bioinformatics (BIOI) is an interdisciplinary major between the Institute of Informatics and Department of Genetics in the School of Medicine and the Department of Computer Science in the College of Arts and Sciences. Our society's accelerated scientific growth is generating an unprecedented quantity of information, while computer science is learning how to handle this information through developments in data science. In particular, data from the sequencing of the human genome is helping us better understand living systems and is guiding treatment of human disease through precision medicine. That information must be stored, managed, and analyzed to reveal its biological meaning to help shape the future of research and healthcare.

Bioinformatics is the discipline that connects the biological sciences, genetics, chemistry, computer science, data science, IT, engineering, applied mathematics, biostatistics, computing, and biomedical engineering. This new major is designed to build on these disciplines and provide students with a marketable degree — with an extensive background in an array of subjects — that will provide cutting-edge employment opportunities, as well as a platform for success in graduate school, medical school, and other clinical-professional schools.

As the first B.S. in Bioinformatics in the state of Alabama, this program will train students in basic concepts and skills to perform computational analysis of biological data — including the human genome. This will also create a well-trained workforce who can take on future healthcare challenges in the state of Alabama.

As members of an interdisciplinary program at UAB, Bioinformatics students will be able to participate in research with faculty from departments across the university, including:

  • School of Medicine Basic Science Departments
  • School of Medicine Clinical Science Departments
  • Computer Science
  • Biology
  • Biostatistics

Admissions

High school students with an ACT score of 28 or higher and a GPA of 3.5 or higher (the UAB Honors College admissions criteria) are eligible for immediate acceptance into the Bioinformatics major.  Current UAB students, or transfer students, with a 3.0 GPA are eligible for Bioinformatics.   Incoming freshman or transfer and current UAB students may be admitted into Pre-Bioinformatics with a 2.8 GPA.  Remaining in Pre-Bioinformatics requires the maintenance of a 2.8 overall UAB GPA.

Advising and Information

John Johnstone

Bioinformatics Co-Director
Associate Professor, Department of Computer Science
email
(205) 975-5633

Elliot Lefkowitz

Bioinformatics Co-Director
Professor, Department of Microbiology; Informatics Institute
email
(205) 934-1946

Courtney Blair White

Academic Advisor
email
(205) 934-7019

Major in Bioinformatics

RequirementsHours
Core Curriculum Requirements 141
CAS 112Success in College1
PSDO 200Introduction to Research1
Mathematics Courses 2
MA 125Calculus I4
or MA 225 Calculus I - Honors
MA 126Calculus II4
or MA 226 Calculus II - Honors
Biology Courses 2
BY 123Introductory Biology I4
BY 124Introductory Biology II4
BY 210Genetics3
Chemistry Courses 2
CH 115
CH 116
General Chemistry I
and General Chemistry I Laboratory
4
CH 117
CH 118
General Chemistry II
and General Chemistry II Laboratory
4
CH 235
CH 236
Organic Chemistry I
and Organic Chemistry I Laboratory
4
Computer Science Courses
CS 103Introduction to Computer Science in Python4
CS 203Object-Oriented Programming4
CS 250Discrete Structures3
CS 303Algorithms and Data Structures3
Informatics Courses
INFO 101Introductory Bioinformatics Seminar 31
PUH 250Biostatistics3
GGSC 310Genome Structure and Organization3
INFO 302Bioinformatics-I3
INFO 403Bioinformatics-II3
INFO 404Biological Data Management3
INFO 499Bioinformatics Capstone 3
Major Electives15
Organic Chemistry II
Fundamentals of Biochemistry
Fundamentals of Scientific Investigation
Molecular Genetics
Cell Biology
Advanced Molecular Genetics
Functional Genomics and Systems Biology
Genetic Basis of Human Disease
Research in Bioinformatics
Honors Bioinformatics Research
Systems Programming
Automata and Formal Languages
Probability and Statistics in Computer Science
Big Data Programming
Computer Security
Computer Vision and Convolutional Neural Networks
Data Visualization
Machine Learning
Introduction to Linear Algebra
Algebra I: Linear
General Physics I
General Physics II
Introduction to Biophysics I
Engineering in Biology
Bioinstrumentation
Medical Image Processing
General Physics I Laboratory
General Physics II Laboratory
Total Hours122

Please note the hours to degree may vary due to prerequisite requirements. For undergraduate programs, at minimum of 120 hours of undergraduate credit is required for degree.  General electives may be taken to meet the hour requirement if necessary. 

Honors in Bioinformatics

Purpose

The Bioinformatics Honors Program offers outstanding, highly motivated students the opportunity to develop research skills in preparation for graduate work or a professional career. 

Eligiblity

In order to be accepted into the Bioinformatics Honors program, you must:

  • Have completed at least 45 credit hours.
  • Have a 3.5 GPA in Bioinformatics (INFO) and Biology courses.
  • Have a 3.2 GPA overall.
  • Have already completed CS 203 Object-Oriented Programming and GGSC 310 Genome Structure and Organization
  • Have arranged with a faculty sponsor to do a research project, approved by a Bioinformatics program director. 
  • Honors Research in Bioinformatics may also be taken as part of the University Honors Programs.  BIOI majors generally enter their research labs in the fall semester of their junior year; however, they may begin research in the spring semester of their sophomore year, or earlier, with permission of the Program Directors. 

Requirements

To successfully complete the Bioninformatics Honors Program you will need to:

  • Complete 6 semester hours of INFO 498 Honors Bioinformatics Research.  Students may substitute 3 of the 6 required INFO 498 credit hours with an equivalent research course (with prior approval of a program director).
  • Submit a formal research report by the end of each semester of Honors Research.  The proposal should include a summary of the student's research findings incorporating an introduction, methods, and relevant literature review. 
  • Complete a formal written report in the form of a scientific paper.
  • Submit an oral or poster presentation at UAB Expo during their junior or senior year.  Under special circumstances, the poster may be presented at other times of the year pending approval of the Program Directors. 
First Year
First TermHoursSecond TermHours
BY 123
123L
4BY 124
124L
4
CAS 1121CH 115
CH 116
4
CS 1034INFO 1011
EH 1013MA 125 or 2254
PHL 1163EH 1023
 15 16
Second Year
First TermHoursSecond TermHours
BY 2103CS 2503
CH 117
CH 118
4GGSC 3103
CS 2034INFO 1011
MA 126 or 2264PUH 2503
 Core Area II or IV 3
 PSDO 2001
 15 14
Third Year
First TermHoursSecond TermHours
CH 235
CH 236
4INFO 4033
CS 3033Major Elective Course 3
INFO 3023Major Elective Course 3
Core Area II or IV3Major Elective Course 3
Core Area II or IV3Core Area II or IV3
 16 15
Fourth Year
First TermHoursSecond TermHours
INFO 4043INFO 4993
Major Elective Course3Major Elective Course3
Major Elective Course3Major Elective Course3
Core Area II or IV3Major Elective Course3
Core Area II or IV3Core Area II or IV3
 15 15
Total credit hours: 121

Courses

INFO 101. Introductory Bioinformatics Seminar. 1 Hour.

Faculty-led seminar course that exposes students to cutting edge research topics and career opportunities in the field of bioinformatics. Students will read assigned articles and be prepared for discussion. Subject matter varies by term and students will take this course during multiple semesters for a maximum of two credits.

INFO 302. Bioinformatics-I. 3 Hours.

Introduction to bioinformatics and methodologies, with emphasis on concepts and application of informatics tools to molecular biology. Focus on experimental models to collect data from genomics, transcriptomics and proteomics, applied statistics when it relates to experimental design, construction of bioinformatics tools into pipelines, representing biological data, biological sequence analysis, gene annotation, basic R programming, basic web/data analysis programming using Perl/python, sharing of biological information, social/legal aspects of open science.
Prerequisites: BY 210 [Min Grade: C] and CS 203 [Min Grade: C] and PUH 250 [Min Grade: C] and INFO 101 [Min Grade: C]

INFO 403. Bioinformatics-II. 3 Hours.

Development of computational algorithms to solve biological questions with a significant problem-solving component. This includes computational techniques such as dynamic programming, optimization, hidden Markov models, graph algorithms, and other mathematical and statistical approaches. In addition, data mining and machine learning methods in computational biology will be covered.
Prerequisites: INFO 302 [Min Grade: C] and CS 303 [Min Grade: C]

INFO 404. Biological Data Management. 3 Hours.

Introduction of biological data management concepts, theories, and applications. Basic concepts such as data representation, database modeling, ontology representation, and relational database queries will be introduced. Various database systems, particularly relational databases and emerging big data techniques, will be introduced. Application of biological data management in biology will be covered using case studies of high-impact widely used biological databases.
Prerequisites: INFO 302 [Min Grade: C]

INFO 412. Visual Analytics for Bioinformatics. 3 Hours.

In this course, we will explore the use of visualization techniques as a concise and effective way to help analyze, understand, interpret and communicate complex biological data. Principles of design, visual rhetoric/communication, and appropriate usage will be introduced. We will cover representation of different data types, concentrating on those generated by data-rich platforms such as next-generation sequencing applications, flow/mass cytometry, and proteomics, and will discuss the use of visualization techniques applied to assessing data quality and troubleshooting. Various topics including dimension reduction, hierarchical visualizations, unsupervised learning, graph theory, networks/layouts and interactivity will be discussed. We will review the algorithmic underpinnings of various methods that lead to their appropriate and effective use. Finally, we will review a variety of genomics/bioinformatics-related visualization tools that are available. We will use Matlab throughout the course to create beautiful and effective visualizations.

INFO 497. Research in Bioinformatics. 1-3 Hour.

Research in Bioinformatics for non-honors students under the supervision of a faculty sponsor.
Prerequisites: PSDO 200 [Min Grade: C]

INFO 498. Honors Bioinformatics Research. 3 Hours.

Honors Research is an innovative course that will provide undergraduate students with an opportunity to engage in rigorous scholarly practice of the core bioinformatics skills necessary for performing independent research. Program faculty will closely work with students to identify a project that explores an area of interest for the student based on the integration of prior learning. Students will be performing bioinformatics analyses on laboratory data or publicly available large-scale data, incorporate quality control and develop software pipelines.
Prerequisites: PSDO 200 [Min Grade: C]

INFO 499. Bioinformatics Capstone. 3 Hours.

Students will be allowed to rotate to different program faculty or continue with their mentor from BY/CS 498 Bioinformatics Capstone Research I. With close mentoring and guidance from program faculty, the student will identify a capstone project or continue their existing bioinformatics project. The capstone project is expected to culminate in a formal scholarly work reflecting integration of the scientific knowledge gained through the project. The scholarly work may take the form or a written manuscript or semester report.
Prerequisites: INFO 403 [Min Grade: C] and INFO 404 [Min Grade: C] and PSDO 200 [Min Grade: C]