I am a PhD student in computer science.
My advisor is Dr.
Chiranjib
Bhattacharya. My research interests include :
Computational Biology and Algorithms
Proteins are one of the most important class of biological
macromolecules, showing an astonishing variety of functions. Such a
variety in functions of a protein is achieved through a hierarchy of
protein structures starting from primary till quaternary structures
showing increasing complexity. Tertiary structures of proteins are
described by the 3-dimensional coordinates of it's building blocks,
called amino acids.
Main area of my research has been to develop algorithms and learning
techiniques for analysing protein tertiary structures. I have developed
two algorithms for comparing protein tertiary structures, one of which
is fast, and is suitable of retrieval of proteins from a large
database. The other algorithm is more robust towards indels, and has
been shown to produce a better quality of alignment than state of the
art programs for comparing protein structures. I have also developed
kernels on protein structures which have been used for protein
structure classification.
Machine Learning
Analysis of biological data using machine learning techniques has
become an important area of research due to the complexity and inherent
noise in biological systems. A lot of techniques have been developed
for analysis of sequence data. However, relatively fewer number of
techniques exist for analysis of structural data, e.g. protein
structures.
I have used spectral projection techniques for deriving consistent
projections of the residues of a protein structure, which was used to
design a new algorithm for comparing protein structures. This new
algorithm also has connections with the spectral graph matching
techniques. I have also design various kernels for analysis of protein
structures using kernel methods. I am also interested in using
graphical models for protein structure analysis.
For more details, please see my publications
page.
Some Links and Resources
Bioinformatics
Here is a list of journals and
conferences in Computational Biology
that I have assembled.
Here is an annotated list of resources
that are in Structural Bioinformatics, most of which are freely
available on the web.
Some useful resources that I
collected.
A nice tutorial
on Protein Structures for beginners from Birkbeck college.
Machine
Learning
A list of journals, conferences
and web resources.
Programming
and Implementation Resources
JMAT : Matrix
programming library in Java.
HartMath : Computer Algebra Tool
in Java. The site also has references to other java based Math
libraries.
Latex and Tex
Here
are some explanations for the poor quality of PDF documents generated
by Latex and lot more about types of fonts, etc.
Copyleft 2007
Sourangshu Bhattacharya
Feel free to copy !! Why duplicate effort ?
Only give me some credit.
See GNU GPL.