|
S.
Balaji (aka Balaji Santhanam), Ph. D.
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
Thesis
Comparative analyses of homologous protein sequences
and structures: Inferences on protein evolution, Indian Institute of Science,
Bangalore, India. Awarded in Mar 2004
Book Chapters (2)
2007
1. General
trends in the evolution of prokaryotic transcriptional regulatory networks - M. Madan Babu, S. Balaji and L. Aravind in Genome Dynamics 3 66-80 (Ed: Volff Jean-Nicolas), Karger
Publishers.
2. 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. (Ed: Kwang W.
Jeon), Academic Press 7/11/2007
Journals (26) 1 indicates joint
first author & * indicates corresponding author
2008
3. S. Balaji*, Iyer L.M. and Aravind L*. HPC2 and Ubinuclein define a novel family of
histone chaperones conserved throughout eukaryotes. Molecular
Biosystems (minor revision requested).
4. Raja
Jothi1, S. Balaji1, Arthur Wuster, Joshua Grochow,
Jorg Gsopner, Teresa M. Przytycka, L. Aravind and Madan M. Babu Dissecting the dynamics of
yeast transcription factors Nature Molecular Systems
Biology (Major Revision from).
5. Thiago M. Venancio, S. Balaji, Lakshminarayan M. Iyer and
L. Aravind. Systems analysis of ubiquitin-like modification pathway reveals an
extensive impact on the proteome and strong cross-talk with other key
regulatory processes (Under Review in Genome Biology).
6. 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 24:319-23. 5/31/2008
2007
7. 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. 8/21/2007
8. 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. 7/29/2007
(Review)
9.
S. Balaji1*, M. Madan Babu1* and Aravind, L. Interplay between
network structures, regulatory modes and
sensing mechanisms of transcription factors in the transcriptional regulatory
network of E. coli, J Mol Biol 372:1108-22. 7/3/2007
10. 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. 7/2/2007
11.
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). 1/24/2007
2006
12.
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. 12/12/2006
13.
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. 11/27/2006
14.
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). 10/16/2006
15.
Anantharaman V, S.
Balaji and Aravind L. The signaling
helix: a common functional theme in diverse signaling proteins. Biology Direct. 1(1):25. 9/5/2006
16. S. Balaji1*, Madan Babu, M.1*,
Iyer, L.M.,
17. 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. 4/27/2006
18.
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. 2/21/2006
(Review)
2005
19.
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. 7/21/2005
20.
Aravind, L.,
Anantharaman, V.,
2004
21.
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. Jun 2004 (Review)
22.
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. 3/15/2004
2003
23.
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. 12/1/2003
24.
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. 3/27/2003
25. 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. 1/1/2003
2001
26.
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. Apr
2001
27.
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. Apr 2001
28.
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. 1/1/2001
Online Publications (5)
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.
1.
Madan
Babu M.1, S. Balaji1, Iyer, L.M. and Aravind, L.
Elucidation of evolutionary scenarios for the emergence of regulatory hubs in
transcriptional regulatory networks.
2.
S.
Geetha, Courtni E. Allen, Robert Fathke, Susan Garfield, Stephen Wincovitch,
Jordan Newell, Rachel Lieber, Elizabeth Plum, Jill Paterson, Kenji Soejima,
Scott Friedman, S. Balaji and
Chava Kimchi-Sarfaty ADAMTS13, THE Von Willebrand cleavage protease, reaches
the nucleus in its pathway.
3. Seshasayee, A., S. Balaji, L.
Aravind, N. Luscombe and M. Madan Babu. Elucidation of principles of core in
biological networks.
4. Anantharaman,
V, S. Balaji and Aravind, L. TASS: A package for large scale
sequence and structure analysis.
Presentations/
Posters/ Proceedings of Meetings
1.
Understanding eukaryotic transcription regulation
through an integrated approach, Center for Cancer Systems Biology, Dana-Farber
Cancer Institute, Harvard Medical School, Boston, 2008. (Invited presentation)
2. Understanding transcription regulation
at systems-level through an integrated approach. The Lewis-Sigler Institute for
Integrative Genomics, Princeton University, 2008. (Invited presentation)
3. Understanding
transcription regulation in eukaryotes through an integrated approach, Broad
Institute of MIT and Harvard, Boston, 2008. (Invited presentation)
4. Understanding transcription regulation
at systems-level through an integrated approach, Boston University, Boston,
2008. (Invited presentation)
5.
An integrated
approach to understanding transcription regulation in biological systems: from
protein sequences to molecular interaction networks, Sanger Institute,
Cambridge, UK, Feb 2008. (Invited presentation)
6. Differences in
transcriptional networks reconstructed from genetic and ChIP-chip data: What do
they mean? NCBI, NLM, NIH, Oct 2007. (Seminar series)
7.
Discovery of the principal
specific transcription factors of Apicomplexa, Lambda Lunch, National
Institutes of Health, USA, Jun 6 2006. (Invited presentation)
8.
Principles of transcription
factor co-regulation in yeast transcriptional regulatory network, NCBI, NLM,
NIH, Oct 2005. (Seminar series)
9.
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,
10.
A survey of Structural
Classification of Proteins, Protein folding society, Indian Institute of
Science, Bangalore, India, 21 Oct 2001. (Invited Presentation)
11.
Application of J0
technique for optical interference based characterization of materials,
Department of Physics, Indian
12. “Dissecting the dynamics of
yeast transcription factors” is accepted
and has been selected for poster presentation in 5th Annual RECOMB
Satellite Conference on Regulatory Genomics/4th Annual RECOMB Satellite
Conference on Systems Biology/3rd DREAM Conference. Broad Institute of MIT and Harvard, Boston. Oct 28-Nov 2 2008.
13.
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 boards: Editorial board of Biology Direct (discovery notes
section)
Journal Reviews: Ad hoc Reviewer for: Nucleic Acids Res.,
Trends in Genetics, BMC Systems Biology, BMC Evolutionary Biology, BMC
genomics, BMC Bioinformatics, Briefings in Bioinformatics, Bioinformatics, Biology
Direct, 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
Bethesda, MD 20894, USA
Phone:
1-301-594-2445, Fax: 1-301-435-7794 or 1-301-480-9241
Email: aravind@ncbi.nlm.nih.gov
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
Group Leader / Investigator
MRC-Laboratory
of Molecular Biology,
University
of Cambridge
Hills
Road, Cambridge CB2 2QH, United Kingdom.
Phone:
44-1223-402 208, Fax: 44-1223-213556
Email: madanm@mrc-lmb.cam.ac.uk
4. Dr. Teresa Przytycka (Collaborator)
Investigator, National
Center of Biotechnology Information
National
Library of Medicine (NLM)
National
Institutes of Health (NIH)
BLDG 38A,
Room 5N505, 8600 Rockville Pike
Bethesda, MD
20894, Phone: 301-402-1723
E-mail:
Przytyck@mail.nih.gov