|
Computational Biology Branch
Phone: 301-496-6041 National Library of Medicine
Email: sbalaji@ncbi.nlm.nih.gov National
Institutes of Health Web:http://ncbi.nlm.nih.gov/CBBresearch/Fellows/Balaji
8600 Rockville Pike Building 38A, Room 8N811L |
Education and Research experience
2004-present Post-doctoral
Fellow at NCBI, NLM, National Institutes
of
Dr. L. Aravind Group, Computational Biology Branch
2003-2004
Research
associate, Indian Institute of Science,
Sponsored under a grant from The Wellcome
Trust,
1998-2004 Ph. D.
(Computational Biology), Indian
Dr. N. Srinivasan’s
group, Molecular Biophysics Unit
1996-1998 M. Sc. in Physics, SSSIHL, Prashanti Nilayam,
Specialization in experimental Non-linear Optics
1993-1996 B. Sc. (Honours)
in Physics, SSSIHL, Prashanti
Nilayam,
Publications
Book
Chapters
1. General trends in the evolution of
prokaryotic transcriptional regulatory networks - M. Madan Babu, S. Balaji
and L. Aravind in Genome Dynamics (Ed: Volff Jean-Nicolas), Karger
Publishers.
Journals
1 indicates joint first author & *
indicates corresponding author
2007
2. S. Balaji*, Iyer, L.M., Madan Babu, M*, and Aravind, L. Comparison of transcriptional networks
from genetic and in vivo binding data: What do they reveal? Trends in Genetics (in press).
3.
4. S. Balaji and
Aravind, L. The RAGNYA fold: a novel fold with multiple topological variants found in
functionally diverse nucleic acid, nucleotide and peptide-binding proteins,
Nucleic Acids Res. 35: 5658-71.
5. Burroughs,
M., S. Balaji, Iyer, L.M. and Aravind, L. Small but versatile: the extraordinary
functional and structural diversity of the b-grasp fold,
Biology Direct 2(1):18.
6. S. Balaji* and
Aravind, L. The two faces of short-range evolutionary dynamics of regulatory
modes in bacterial transcriptional regulatory networks, Bioessays 29(7):625-9.
7. Anantharaman, V, Iyer, L.M., S. Balaji and Aravind, L. Comparative analysis of the extracellular proteins of apicomplexa. International Review of Cytology 262:1-74.
8.
Burroughs, M., S. Balaji, Iyer, L.M.
and Aravind, L. A novel superfamily with
the b-grasp fold
involved in binding diverse soluble ligands, Biology
Direct 2(4)
2006
9.
Madan Babu, M., Iyer, L.M., S. Balaji
and Aravind, L. The natural history of
the WRKY-GCM1 zinc fingers and the relationship between transcription factors
and transposons, Nucleic Acids Res.
34(22):6505-20.
10.
Madan Babu M, S. Balaji, Iyer, L.M. and Aravind,
L. Estimating the Prevalence and
Regulatory Potential the Telomere Looping Effect in Yeast, Cell Cycle 20(5).
11. S. Balaji1*, Madan Babu, M.1*,
Iyer, L.M.,
12. S. Balaji, Iyer, L.M., Aravind, L. and Madan Babu, M. Uncovering distributed robustness in protein regulatory networks, J Mol Biol. 360(1):204-12.
13.
Anantharaman V, S. Balaji and Aravind
L. The signaling helix: a common
functional theme in diverse signaling proteins. Biology
Direct. 1(1):25.
14.
S. Balaji and N. Srinivasan Comparison of sequence-based and
structure-based phylogenetic trees of homologous proteins: Inferences on
protein evolution, Journal of Biosciences
32:83-96.
15.
Iyer, L.M., S. Balaji, Koonin E.V. and
Aravind, L. Evolutionary genomics of
nucleo-cytoplasmic large DNA viruses, Virus Res
117(1):156-84.
2005
16.
S. Balaji, Madan Babu, M., Iyer, L.M., Aravind,
L. Discovery of the principal specific
transcription factors of Apicomplexa and their implication for the evolution of
the AP2-integrase DNA binding domains, Nucleic Acids
Res., 33(13):3994-4006.
17.
Aravind, L., Anantharaman, V.,
2004
18.
Pandit
SB, S. Balaji, Srinivasan N. Structural and functional characterization
of gene products encoded in the human genome by homology detection. IUBMB Life.
56(6):317-31.
19.
Pandit SB, Bhadra R, Gowri VS, S. Balaji,
Anand B and Srinivasan N. SUPFAM: a database of sequence superfamilies of
protein domains. BMC Bioinformatics. 15(5):28.
2003
20.
S. Balaji, Aruna and N. Srinivasan Tolerance to
the substitution of buried non-polar residues by charged residues in the
homologous protein structures. Proteins: Structure,
Function and Genetics. 53, 783-791.
21.
S.
Sopory, S. Balaji, N. Srinivasan and S. S. Visweswariah Modeling and
mutational analysis of the GAF domain of the cGMP-binding, cGMP-specific
phosphodiesterase, PDE5. FEBS
Letters. 539, 161-166.
22. V. S. Gowri, S. B. Pandit, P. S. Karthik, N. Srinivasan and S. Balaji Integration of related sequences with protein three-dimensional structural families in an updated version of PALI database. Nucleic Acids Res. 31, 486-488.
2001
23.
S. Balaji and N. Srinivasan Use of a database
of structural alignments and phylogenetic trees in investigating the
relationship between sequence and structural variability among homologous
proteins. PEDS. 14, 219-226.
24.
S. Sujatha, S. Balaji and N.
Srinivasan PALI - Web-interfaced access to a database of alignments and
phylogeny of homologous protein structures. Bioinformatics,
17, 375-376.
25.
S. Balaji, Sujatha, S. Sai Chetan Kumar and N.
Srinivasan PALI - A database of Phylogeny and ALIgnment of
homologous protein structures. Nucleic Acids Res.
29, 61-65.
Online Publications
1.
V.S. Gowri, S. Balaji, O. Krishnadev, S.B. Pandit and N. Srinivasan (release 2.3) PALI Nucleic
Acids Res. http://www3.oup.co.uk/nar/database/summary/274.
2.
O. Krishnadev, V.S. Gowri, S. Balaji, N. Srinivasan and S.B.
Pandit (release 1.5) SUPFAM Nucleic Acids Res.
http://www3.oup.co.uk/nar/database/summary/219.
3.
V.S. Gowri, S.B. Pandit, B. Anand, N.
Srinivasan and S. Balaji (2004) PALI
(release 2.2) Nucleic Acids Res. http://www3.oup.co.uk/nar/database/summary/274.
4.
S.B. Pandit, R. Bhadra, V.S. Gowri, S. Balaji, B. Anand and N. Srinivasan
(2004) SUPFAM (release 1.4) Nucleic Acids Res.
http://www3.oup.co.uk/nar/database/summary/219.
5.
S. Balaji, Sujatha,
S. Aruna, N.S. Mhatre and N. Srinivasan (2002) PALI (Release 1.3) Nucleic Acids Res.
http://www3.oup.co.uk/nar/database/summary/274.
Presentations / Posters
1.
(Invited
presentation) An integrated approach to understanding transcription regulation in
biological systems: from protein sequences to molecular interaction networks,
Sanger Institute, Cambridge, UK, Feb 2008.
2. (Seminar series) Differences in transcriptional networks reconstructed from genetic and ChIP-chip data: What do they mean? NCBI, NLM, NIH, Oct 2007.
3.
(Invited presentation) Discovery of the principal specific transcription
factors of Apicomplexa, Lambda Lunch, National Institutes of Health,
4.
(Seminar series) Principles of transcription factor co-regulation in
yeast transcriptional regulatory network, NCBI, NLM, NIH, Oct 2005.
5.
Comparison of sequence-based
and structure-based phylogenetic trees of homologous proteins: Inferences on
protein evolution, Joint retreat of Computational groups of the Indian Institute of
Science and National center for Biological Sciences,
6.
(Invited Presentation) A survey of Structural Classification of
Proteins, Protein folding society, Indian Institute of Science, Bangalore,
India, 21 Oct 2001.
7.
(Invited Presentation)
Application of J0 technique for optical interference based
characterization of materials, Department of Physics, Indian
8.
(Poster Presentation) PALI – a
database of phylogeny and alignment of homologous protein structures, International Symposium on Crystallography and Bioinformatics in
Structural Biology, Nov 22 - 25, 2001, Indian Institute of Science,
Professional Activities
Editorial board of Biology
Direct (discovery notes section), Reviewer for Nucleic Acids Res., Trends in
Genetics, BMC Systems Biology, BMC Evolutionary Biology, BMC genomics, BMC
Bioinformatics, Briefings in Bioinformatics, Bioinformatics, Proteins: Structure,
function and Bioinformatics and International Journal of Biological
Macromolecules.
Achievements
and Fellowships
·
NIH post-doctoral Fellowship
·
Nominated for best thesis award in the
Biological sciences division by the Molecular Biophysics Unit of India
Institute of Science,
·
Senior and Junior research fellowship for
graduate studies in computational biology from the Council for Scientific and
Industrial Research,
·
Selected for graduate studies in physics (in
the year 1998) by the Tata Institute of fundamental research,
·
Selected within top 8% of the candidates in
Graduate Aptitude Test in Engineering (in Physics) at the National level in
·
University 2nd rank holder in M.Sc
(Physics)
Technical
Skills
·
Operating Systems: UNIX (Solaris, LINUX),
Windows, DOS, Macintosh, X-Windows
·
Programming Languages: Perl, C, C++, FORTRAN,
Pascal, BASIC, MATLAB, HTML
·
Co-developer of a software package, TASS, in Perl for large
scale analysis of sequences and structures
Referees
Senior Investigator, National Center
for Biotechnology Information
National Library of Medicine (NLM)
National Institutes of Health (NIH)
BLDG 38A, Room 5N505, 8600 Rockville
Pike
Phone:
1-301-594-2445, Fax: 1-301-435-7794 or 1-301-480-9241
Email: aravind@ncbi.nlm.nih.gov
Associate Professor, Molecular
Biophysics Unit
Indian Institute of Science
Phone:
91-80-2932837, Fax: 91-80-360 0535 or 91-80-360 0683
Email: ns@mbu.iisc.ernet.in
Prinicpal Investigator, OBRR / DH / LH
Center for Biologics Evaluation and
Research
Food and
Phone: 1-301-827-0039, Fax: 1-301-402-2780
E-mail: Chava.kimchi-sarfaty@fda.hhs.gov
Investigator,
NLM,
NIH, Bldg 38A room 812 S
8600
Rockville Pike,
Phone: 1-301-402-1723, Fax:
1-301-480-4637
E-mail: przytyck@mail.nih.gov
5. Dr. M. Madan
Babu
Group Leader / Investigator
MRC-Laboratory
of Molecular Biology,
Hills
Road,
Phone: 44-1223-402
208, Fax: 44-1223-213556
Email: madanm@mrc-lmb.cam.ac.uk