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Center for Computational Molecular Biology

The prime intellectual mission of Brown University’s Center for Computational Molecular Biology (CCMB) is to promote the development, implementation and application of analytical and computational methods to foundational questions in the biological and medical sciences. The research programs of the Core Faculty in CCMB lie fundamentally at the intersection of computer science, evolutionary biology, mathematics, and molecular and cellular biology.

Biological questions that currently unite the CCMB Core and Associate Faculty are: How do genotypes and genes interact to produce phenotypes, and how does this happen from womb to tomb? What drives the formation, maintenance and evolutionary transformations of communities of organisms over time? Quantitative questions that currently unite the CCMB faculty are: how can we design powerful algorithms to make sense of the sea of data produced in the genomic era? What principles are required for a theoretical framework to completely model cellular systems?

The research challenges at the heart of CCMB are a rich source of mathematical problems motivated by the complex nature of genomes, disease processes and evolutionary relationships. These challenges are both multi-scale (with units of interest ranging from molecules to communities of organisms) and large-scale (data-intensive, due to advances in sequencing technologies). Thus, CCMB rounds out the broader landscape of research in methodological development at Brown University by partnering with and complementing the Data Science Initiative and the Brown Center for Biomedical Informatics.

In addition to these research interests, CCMB Faculty members are actively involved in the operation of Brown’s NIH-funded COBRE Center for the Computational Biology of Human Disease, and administer both an undergraduate concentration and an interdisciplinary doctoral program in Computational Biology. This is a short video about our Ph.D. program in Computational Biology.

Computational Biology

Computational biology involves the analysis and discovery of biological phenomena using computational tools, and the algorithmic design and analysis of such tools. The field is widely defined and includes foundations in computer science, applied mathematics, statistics, biochemistry, molecular biology, genetics, ecology, evolution, anatomy, neuroscience, and visualization. 

Students may pursue a Bachelor of Arts or a Bachelor of Science. Students pursuing the ScB have the option of electing a concentration in Computational Biology with one of three focus areas: Computer Sciences, Biological Sciences, or Applied Mathematics & Statistics. Both programs require a senior capstone experience that pairs students and faculty in creative research collaborations.

Standard program for the A.B. degree

Prerequisites:2
Introductory Calculus, Part II
Advanced Placement Calculus
The Foundation of Living Systems
General Core Requirements: Biology2
Genetics
Biochemistry
Cell and Molecular Biology
General Core Requirements: Chemistry1
Equilibrium, Rate, and Structure
Organic Chemistry
General Core Requirements: Computer Science2
Introduction to Object-Oriented Programming and Computer Science
and Introduction to Algorithms and Data Structures
OR
Computer Science: An Integrated Introduction
and Computer Science: An Integrated Introduction
OR
Accelerated Introduction to Computer Science
and Computer Science: An Integrated Introduction
and Introduction to Software Engineering
and Introduction to Computer Systems
and Theory of Computation
General Core Requirements: Probability & Statistics1
Statistical Inference I
OR
Probability for Computing and Data Analysis
OR
Probability
Comp Bio Core Course Requirements4
Computational Molecular Biology
Inference in Genomics and Molecular Biology
AND two of the following:
Algorithmic Foundations of Computational Biology
Population Genetics
Human Population Genomics
Machine Learning
Computational Probability and Statistics
Statistical Inference II
Additional course with Director approval
Total Credits12

University Writing Requirement:

As part of Brown’s writing requirement, all students must demonstrate that they have worked on their writing both in their general studies and their concentration. There are a number of ways for Computational Biology concentrators to fulfill these requirements:

  • Enrolling in an independent study: CSCI 1970, BIOL 1950, APMA 1970
  • Writing an Honors Thesis
  • Taking a “WRIT” course in the final two years

Capstone Experience

Students enrolled in the computational biology concentration will complete a research project in their senior year under faculty supervision.  The themes of such projects evolve with the field and the technology, but should represent a synthesis of the various specialties of the program. The requirements are either one semester of reading and research with a CCMB Faculty member or approved advisor, or a 2000-level Computational Biology course.

Standard program for the Sc.B. degree

Prerequisites
MATH 0100Introductory Calculus, Part II (or equivalent)1
or MATH 0170 Advanced Placement Calculus
BIOL 0200The Foundation of Living Systems (or equivalent)1
General Core Course Requirements: Biology
BIOL 0470Genetics (prerequisite BIOL 0200 or equivalent)1
BIOL 0280Biochemistry1
or BIOL 0500 Cell and Molecular Biology
General Core Requirements: Chemisty
CHEM 0330Equilibrium, Rate, and Structure1
or CHEM 0350 Organic Chemistry
General Core Requirements: Computer Science2-4
Introduction to Object-Oriented Programming and Computer Science
and Introduction to Algorithms and Data Structures
OR
Computer Science: An Integrated Introduction
and Computer Science: An Integrated Introduction
OR
Accelerated Introduction to Computer Science
and Computer Science: An Integrated Introduction
and Introduction to Software Engineering
and Introduction to Computer Systems
CSCI 0220Introduction to Discrete Structures and Probability1
General Core Requirements: Probability & Statistics
APMA 1650Statistical Inference I1
or CSCI 1450 Probability for Computing and Data Analysis
or MATH 1610 Probability
General Core Requirements: Computational Biology
CSCI 1810Computational Molecular Biology1
APMA 1080Inference in Genomics and Molecular Biology1
Capstone Experience1
Directed Research/Independent Study
Individual Independent Study
Six courses in one of the following three tracks:6
Computer Science Track:
Three of the following:
Introduction to Computer Graphics
Database Management Systems
Artificial Intelligence
Probabilistic Methods in Computer Science
Design and Analysis of Algorithms
or other Computer Science courses approved by the concentration advisor
Three of the following:
Introduction to Computer Systems
Introduction to Software Engineering
Algorithmic Foundations of Computational Biology
Statistical Methods in Bioinformatics, I
Statistical Inference II
Population Genetics
Human Population Genomics
Computational Probability and Statistics
Biological Sciences track
At least four courses comprising a coherent theme in one of the following areas: Biochemistry, Ecology, Evolution, or Neurobiology.
AND select two courses from the following:
Algorithmic Foundations of Computational Biology
Statistical Methods in Bioinformatics, I
Statistical Inference II
Population Genetics
Human Population Genomics
Computational Probability and Statistics
Applied Mathematics & Statistics Track:
At least three courses from the following:
Statistical Inference II
Computational Probability and Statistics
Artificial Intelligence
Methods of Applied Mathematics I, II
and Methods of Applied Mathematics I, II
OR
Applied Partial Differential Equations I
and Applied Ordinary Differential Equations
At least three of the following:
Population Genetics
Algorithmic Foundations of Computational Biology
Statistical Methods in Bioinformatics, I
Quantitative Models of Biological Systems
Human Population Genomics
Total Credits18-20

Honors:

 In order to be considered a candidate for honors, students will be expected to maintain an outstanding record, with no "C's" in concentration courses and with a minimum of an "A-" average in concentration courses. In addition, students should take at least one semester, and are strongly encouraged to take 2 semesters, of reading and research with a CCMB faculty member or approved advisor. Students must submit to a public defense of their theses to be open to the CCMB community.

  • Students seeking honors are advised to choose a Thesis Advisor prior to the end of their Junior year
  • Students must complete the Registration form for Comp Bio and submit it to CCMB@BROWN.EDU

Any deviation from these rules must be approved by the director of undergraduate studies, in consultation with the student's advisor.

Computational Biology

The Center for Computational Molecular Biology (CCMB) offers Ph.D. degrees in Computational Biology to train the next generation of scientists to perform cutting edge research in the multidisciplinary field of Computational Biology.  During the course of their Ph.D. studies students will develop and apply novel computational, mathematical , and statistical techniques to problems in the life sciences. Students in this program must achieve mastery in three areas - computational science, molecular biology, and probability and statistical inference - through a common core of studies that spans and integrates these areas.

The Ph.D. program in Computational Biology draws on course offerings from the disciplines of the Center’s Core faculty members. These areas are Applied Mathematics (APMA), Computer Science (CS), the Division of Biology and Medicine (BioMed), Brown Center for Biomedical Informatics (BCBI), and the School of Public Health/Biostats (SPH). Our faculty and Director of Graduate Studies (DGS) work with each student to develop the best plan of coursework and research rotations to meet the student’s goals in their research focus and satisfy the University’s requirements for graduation.

Applicants should state a preference for at least one of these areas in their personal statement or elsewhere in their application.  In addition, students interested in the intersection of Applied Mathematics and Computational Biology are encouraged to apply directly to the Applied Mathematics Ph.D. program, and also to contact relevant CCMB faculty members.

Our PhD program assumes the following prerequisites: mathematics through intermediate calculus, linear algebra and discrete mathematics, demonstrated programming skill, and at least one undergraduate course in chemistry and in molecular biology. Exceptional strengths in one area may compensate for limited background in other areas, but some proficiency across the disciplines must be evident for admission.

The application process to the CCMB graduate program is run through the Graduate School (http://www.brown.edu/academics/gradschool/)