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Computational Biology & Bioinformatics

biology department

Computational Biology is a multidisciplinary field that integrates mathematics and biology. One major area of computational biology involves the design, implementation, and application of algorithms to answer fundamentally important questions in biology, such as the following:

What is the energy landscape in the folding process of the molecular RNA? (RNA is involved in both transcription and translation, as well as post-transcriptional modification, such as expression-level silencing or knock-down of certain genes via small interfering RNA. Understanding the optimal and suboptimal secondary structures of RNA plays an important role in all these processes).

How can one computationally determine whether a newly sequenced protein appears to be a G-coupled protein receptor, and if so, how can one computationally determine its most likely ligand?

How can one ascribe (automatically) the function of newly found genes in high through-put experiments?

How can one determine an optimal alignment of two proteins or nucleotide sequences, which might yield the most likely common molecular ancestor, or alternatively, which might suggest why some variants of a protein are dysfunctional?

Are certain regions in this alignment more likely or reliable than others?

Does a protein fold to its unique three-dimensional shape, necessary to perform its functional role, through a specific folding pathway, or is thermodynamics sufficient to drive the folding process?

How does a virus assemble its shell (capsid) from a single or small number of proteins (without invoking any deux ex machina)?

Can one determine, using mathematics, computer science and biology experiments, when and where the most recent common ancestor of modern man lived?

If such questions pique your imagination, then consider graduate studies in Computational Biology & Bioinformatics at Boston College.


Faculty Research Topics in Computational Biology & Bioinformatics

Peter Clote, Ph.D.
Algorithm design and implementation in areas such as protein folding on lattice models, computing the energy spectrum of RNA, time warping application to functional genomics, Boltzmann probability in sequence alignments, motif detection using generalized weight matrices, neural nets, support vector machines, etc. In addition, this is the fourth year in which Prof. Clote is co-organizer of the weekly M.I.T. Bioinformatics Seminar.

Michelle Meyer, Ph.D.
Computational biology, non-coding RNA discovery and validation, molecular evolution, RNA and protein structure.

Babak Momeni, Ph.D.
Systems biology of microbial communities; mathematical modeling of biological systems; microbial ecology.

Tim van Opijnen, Ph.D.
Microbial Systems Biology; drug/gene interaction networks and the development of new antimicrobials, the development of genome-wide next generation sequencing strategies to link genotypes to phenotypes, and the engineering of bacteria with new traits and novel applicability.


Computational Biology & Bioinformatics Program at Boston College

Bioinformatics is a vibrant, rapidly changing multidisciplinary research field, driven by newly emergent technologies. What better way to prepare a career in bioinformatics/computational biology than studying at Boston College, a nationally reputed university situated in Boston, one of the strongest bioinformatics research and development centers of the United States.

With two current bioinformatics faculty members and a commitment by the university administration to continue faculty recruitment and buildup in bioinformatics and computational biology, bioinformatics is becoming one of the focal areas of the Biology Department. Higgins Hall, home of the Biology and Physics Departments, was renovated for over $80 million two years ago, and now houses state-of-the-art research laboratory facilities as well as a rack-mounted, multi-node BioCluster Unix platform named Clavius (after the 16th century German Jesuit mathematician, Christopher Clavius, a friend of Galileo), ideal for intensive bioinformatics computation.

The Biology Department of Boston College is now accepting graduate students in the Bioinformatics/Computational Biology track of graduate studies in Biology. Graduate study requirements are listed in the Graduate Studies section of the webpages for the Biology Department. In addition to the Biology Graduate core courses, additional bioinformatics courses will be required—details are under consideration by a committee and will be posted later in the year. Issues concerning possible remedial coursework in the following disciplines will be handled on a case-by-case basis:

  • Biology and chemistry, for entering graduate students with undergraduate degree in math, computer science, physics, statistics, or related field
  • Programming and math, for entering graduate students with undergraduate degree in biology having taken only calculus.

—Peter Clote