◊
Research
◊ Faculty
◊ Publications
◊ Supplementary
material
◊ Tools/Databases
◊ PhD students at IBAB
◊ Info for training/projects
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PUBLICATIONS
G
indicates a publication by GANIT Labs
* indicates research news, a book review, a general article or a letter
to the editor
S indicates a publication by an IBAB student. Either work
was done
mostly as a student of IBAB, or the student was part of IBAB when the
manuscript was being written.
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2013 |
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Jaroslawski, S. and Saberwal, G.
Case studies of innovative medical device companies from India: Barriers and enablers to development.
BMC Health Services Research (in press) |
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Ananth, P., Goldsmith, G. and Yathindra, N.
An innate twist between Crick's wobble and Watson & Crick base pairs. Its effect on RNA.
RNA (in press) |
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Bhagwat, S. et al.
Endometrial receptivity: A revisit to functional genomics studies on human endometrium and creation of HGEx-ERdb.
PLoS One 8, e58419 (2013) |
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Kumari, S. and Saberwal, G.
Patent maintenance by Indian pharma and bio-pharma companies.
Asian Biotechnology Development Review (in press) |
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Saberwal, G.
Giving voice to India's entrepreneurs.
Nature Biotechnology 31, 104-107 (2013) |
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Agrawal, S. and Rao, M. R. S.
Functional/signature network module for target pathway/gene discovery.
Encyclopedia of Systems Biology, Springer Press (in press)
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Agrawal, S. and Rao, M. R. S.
Biological network, disease mechanism network.
Encyclopedia of Systems Biology, Springer Press (in press)
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2012 |
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Srivastava, M. et al.
An inhibitor of nonhomologous end-joining abrogates double-strand break repair and impedes cancer progression.
Cell 151, 1474-1487 (2012) |
| * G |
Panda. B.
Whither genomics diagnostics tests in India?
Indian J. Med. Paediatr. Oncol., 33, 250-252 (2012) |
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Srinivasan, S., Patil, A.H., Verma, M., Bingham, J.L. and Srivatsan, R.
Genome-wide profiling of RNA splicing in prostate tumor from RNA-seq data using virtual microarrays.
J. Clinical Bioinformatics 2, 21-33 (2012) |
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Hegde, M. et al.
Novel Levamisole derivative induces extrinsic pathway of apoptosis in cancer cells and inhibits tumor progression in mice.
PLoS One, 7(9), e43632 (2012) |
| G |
Krishnan NM,
Gaur P, Choudhary R, Rao AA and Panda B
COPS: A sensitive and accurate tool for detecting somatic copy number alterations using short-read sequence data from paired samples.
PLoS One, doi 10.1371/journal.pone.0047812 (2012) |
| * |
Saberwal, G.
Translating academic discoveries
Current
Science, 103, 767-769 (2012) |
| G |
Krishnan NM, Pattnaik S, Jain P, Gaur P, Choudhary R, et al.
A draft of the genome and four transcriptomes of a medicinal and pesticidal angiosperm Azadirachta indica.
BMC Genomics, 13, 464. doi:10.1186/1471-2164-13-464 (2012) |
| S |
Vangala, R.K., Singh, L. and Gupta, R.P.
Bioparishodhana: A novel graphical interface integrating BLAST, CLUSTALW, primer3 and restriction digestion tools.
Bioinformation (in press) |
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Bajpai, A.K., Davuluri, S., Chandrashekar, D. S.,
Ilakya, S., Dinakaran, M.and Acharya, K.K.
MGEx-Udb: A Mammalian Uterus Database for Expression-Based Cataloguing
of Genes across Conditions, Including Endometriosis and Cervical Cancer
PLoS One, 7(5), e36776 (2012) |
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Chiruvella, K.K., Sebastian, R., Sharma, S., Karande, A.A., Choudhary, B. and Raghavan, S.C.
Time-dependent predominance of nonhomologous DNA end-joining pathways during embryonic development in mice.
J. Mol Biol., 417, 197-211 (2012) |
| * |
Venkatachalam, S . and Saberwal, G
Bio-business in brief: A case for new drugs at generic prices from
India
Current Science, 102, 1375-1381 (2012) |
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Jaroslawski, S. and Pai, M.
Why are inaccurate tuberculosis serological tests widely used in the
Indian private healthcare sector? A root-cause analysis.
Journal of
Epidemiology and Global Health, 2,
39-50 (2012) |
| * S |
Patil, A. H.
et al.
From data repositories to potential biomarkers: Application to prostate
cancer
Current Science, 102,
1111-1116 (2012) |
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Soby, S., Sebastian,
T.E. and Saberwal, G.
US patent holdings of Indian non-corporate entities
Asian Biotechnology Development Review, 14,
21-33 (2012) |
| * |
Soby, S., Kandasamy,
M. and Saberwal, G
Work outsourced to Indian biotech and pharma companies is not yet
significantly innovative.
Current Science, 102,
401-404 (2012) |
| G |
Pattnaik, S. et al.
Customisation of the exome data analysis pipeline using a combinatorial
approach.
PLoS One, 7(1), e30080 (2012) |
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Marimuthu, G., Kumari, S., Kandasamy, M.,
Raghunathan, S. and Saberwal, G.
Patents protecting
biologics or small molecule drugs are usually maintained.
Nature
Biotechnology, 30, 50-53
(2012) |
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2011 |
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Prakash, A.,
Yogeeshwari, S., Sircar, S. and Agrawal, S.
Protein domain of unknown function 3233 is a Translocation Domain of
Autotransporter Secretory Mechanism in Gamma proteobacteria
PLoS One, 6(1), e255570 (2011). |
| * |
Saberwal, G.
Caring for a severely disabled person
Available here. |
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Nambiar, M. et al.
Formation of a G-quadruplex at the BCL-2 major breakpoint region of the
t(14;18) translocation in follicular lymphoma.
Nucleic Acids Research, 39, 936-948 (2011). |
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Bateman, A. et al.
RNAcentral: a vision for an international database of RNA sequences
RNA, 17,
1941-1946 (2011) |
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Karthigeyan,
D., Prasad, S.B., Shandilya, J., Agrawal, S. and Kundu, T.K.
Biology of Aurora A
Kinase: Implications in cancer manifestation and therapy.
Med. Res. Rev., 31, 757-793 (2011) |
| G |
Krishnan, N. et al.
De novo sequencing and assembly of
Azadirachta indica fruit transcriptome.
Current Science,
101,
1553-1561 (2011) (Cover page article)
|
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Jaroslawski, S. and Toumi, M.
Market access agreements for pharmaceuticals in Europe: diversity of
approaches and underlying concepts.
BMC Health Services Research, 11, 259-265 (2011) |
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Sebastian, T.E.,
Pattnayak, J.P., Soby, S and Saberwal, G.
Patent holdings of Indian pharmaceutical and biotechnology companies in
international markets of different sizes.
Asian Biotechnology Development Review, 13, 17-37 (2011) |
| * |
Srinivasan, S.
Alternative splicing in eukaryotes: The norm, not an anomaly
Current Science, 100, 813-814 (2011) |
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2010 |
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Agrawal,
S., Nishant, K.T. and Rao, M R S.
Analysis of meiotic recombination hotspots: A bioinformatics approach
Book
chapter ISBN: 978-0-9807330-2-0 (Hard cover) |
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Sebastian,
A., Bender, A. and Ramakrishnan, V.
Virtual activity profiling of drug molecules by 1D fingerprinting.
Molecular Informatics, 29,
773-779 (2010) |
| * |
Yathindra, N.
Structure of an enzyme revealed 80 years after it was crystallized -
differential functional behaviour of plant and microbial ureases
uncovered.
Current Science, 99,
566-568 (2010) |
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Acharya, K., K. et
al.
A
novel tissue-specific meta-analysis approach for gene-expression
predictions, initiated with a mammalian gene expression testis database
BMC Genomics, 11, 467-476 (2010) |
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Ladha,
J. et al.
Glioblastoma-specific protein interaction network identifies PP1A and
CSK21 as connecting molecules between cell cycle-associated
genes.
Cancer. Res., 70, 6437-6447 (2010) |
| * |
Saberwal, G.
Bio-business in
brief: A bit about technology transfer
Current Science, 99, 177-180 (2010) |
| * |
Kapoor, M. and Saberwal, G.
The new crossroads
Biotech News, 5, 143-145 (2010) |
| * |
Saberwal, G.
Bio-business in
brief: The debate over biosimilars
Current Science, 98, 1575-1578 (2010) |
| * |
Saberwal, G.
Grants officers on
deputation to national research laboratories
Current Science, 98, 999 (2010) |
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Selvi,
B.R., Batta, K., Kishore, A.H., Mantelingu, K., Varier, R.A.,
Balasubramanyam, K., Pradhan, S.K., Dasgupta, D., Sriram, S. Agrawal,
S. and Kundu, T.K.
Identification of a
novel inhibitor of co-activator associated arginine methyl transferase
1 (CARM-1)-mediated methylation of histone H3-Arg 17.
J. Biol. Chem.,
285, 7143-7152 (2010) |
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Jeevitesh,
M.S., Behera, N., Jose, J., Kant, K. and Dey, A.
Higher accuracy
protein multiple sequence alignment by stochastic algorithm
Nature
Precedings |
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2009 |
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Sengupta,
U, Ukil, S., Dimitrova, N. and Agrawal, S.
Expression-based
network biology identifies alteration in key regulatory pathways of
Type 2 diabetes and associated risks/complications.
PLoSOne,
4 (12) e8100 (2009) |
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Saberwal, G.
Drug development in
India: What does the future look like?
Contemporary
Perspectives: History and Sociology of South Asia, Ed. N Tyabji,
3,
293-309 (2009) |
| * |
Saberwal, G.
A long march
Biotech
News, IV, 68-69, 75 (2009) |
| * |
Saberwal, G.
Bio-business in
brief: The paradox of being a drug company
Current Science, 97, 623-625 (2009) |
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Ravindra, K.C.,
Selvi, B.R., Arif, M. , Ashok Reddy, B.A., Thanuja, G.R., Agrawal, S.,
Pradhan, S.K., Nagashayana, N., Dasgupta, D. and Kundu, T.K.
Inhibition of Lysine Acetyltransferase KAT3B/p300 activity by a
naturally occurring hydroxynaphthoquinone, Plumbagin.
J. Biol.
Chem, 284,
24453-24464 (2009) |
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Saberwal, G.
Seeding a skilled workforce.
Nature
Biotechnology, 27,773-775
(2009) |
| * |
Acharya, K.
Book review:
Career development in bioengineering and biotechnology
By Madhavan, G., Oakley, B. and Ken, L. (eds)
Springer Science + Business Media (New York)
Current Science, 96, 293 (2009) |
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Sebastian, T.E., Chandra Bindu, Y. and
Saberwal, G.
Patent holdings of
US biotherapeutic companies in major markets.
Drug
Discovery Today,
14, 442-445
(2009) |
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Arif, M., Pradhan,
S.K., Thanuja G R, Vedamurthy, B.M., Agrawal, S., Dasgupta, D. and
Kundu, T.
Mechanism of p300 specific histone acetyltransferase inhibition by
small molecules.
J. Med. Chem.,
52, 267-277 (2009). |
| * |
Saberwal, G.
The proposed 4-year B.S. programme
Current Science, 96, 445-446 (2009) |
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Sundaramoorthy, S.,
Chandra Bindu, Y. , Mehdiratta, R. and Saberwal, G.
The US patent holdings of homegrown Indian biotech and pharma
companies.
Current Science, 96, 252-259 (2009) |
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2008 |
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Acharya, K.K.,
Kasliwal, G. and Haritha, H.
How do you choose your literature search tool(s)?
Nature
Precedings |
| S |
Alva, V., Syamala
Devi, D P, Sowdhamini, R.
COILCHECK: an interactive server for the analysis of interface regions
in coiled coils
Protein
and Peptide Letters,
15,
33-38 (2008) |
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Ramakrishnan, N. and
Bhalla, U.S.
Memory switches in chemical reaction space.
PLoS
Comp. Biol.,
4:
e1000122 (2008) |
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Agrawal, S.,
Dimitrova, N., Nathan, P., Udaykumar, K., Sailakshmi, S, Sriram, S,
Nair, M. and Sengupta, S.
T2D-Db: An integrated platform to study the molecular basis of Type 2
diabetes.
BMC Genomics, 9, 320-331 (2008) |
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Parida, D.K,
Mehdiratta, R. and Saberwal, G.
How many patents does a bio-therapeutics company need?
Nature
Biotechnology, 26, 763-766 (2008) |
| * |
Devaguptapu,
S, Mehdiratta, R and Saberwal, G
Bio-business in
brief: The case of Cytokinetics Inc.
Current Science, 94,
1576-1581 (2008) |
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Kishore
H, Vedamurthy
BM, Mantelingu
K, Agrawal,
S, Reddy
BA, Roy
S, Rangappa
K and Kundu TK.
Specific small-molecule activator of aurora kinase a induces
autophosphorylation in a cell-free system.
J Med Chem., 51, 792-797(2008). |
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Sai Lakshmi, S. and
Agrawal, S.
piRNABank: A web resource on classified and clustered piwi interacting
RNAs
Nucleic
Acids Research, 36, D173-177 (2008). |
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2007 |
| * |
Mehdiratta, R.,
Parida, D. K. and Saberwal, G.
Bio-business in brief: The challenges of clinical trials
Current Science, 93,
1367-1375 (2007) |
| * |
Mehdiratta, R. and
Saberwal, G.
Bio-business in brief: Many a monoclonal.
Current Science, 93,
789-796 (2007) |
| * |
Mehdiratta,
R. and Saberwal, G.
Bio-business in brief: The case of conotoxins.
Current Science, 92, 39-45 (2007) |
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2006 |
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Agrawal, S. , Chetan,
K. and Rao, M R S.
CREMOFAC - a database of chromatin remodelling factors
Bioinformatics, 22, 2940-2944 (2006). |
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Rathinavelan, T. and
Yathindra, N.
Base triplet nonisomorphism strongly influences DNA triplex
conformation: Effect of nonisomorphic G*GC and A*AT triplets and
bending of DNA triplexes.
Biopolymers,
82,
443-461 (2006) |
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Acharya, K.K.,
Govind, C.K., Shore, A.N., Stoler, M.H., Reddi, P.P.
cis-Requirement
for the maintenance of round spermatid-specific
transcription.
Dev.
Biol., 295,
781-790 (2006) |
| * |
Acharya
K. K.
The biotech-bioinfo
interface in the context of education and growth of
the biotechnology industry in India today.
Biovistas,
1, 7-13 (2006) |
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Saberwal, G
New pharma-biotech company formation in India
Nature
Biotechnology,
24,
499-501 (2006) |
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2005 |
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Rathinavelan,
T. and
Yathindra, N.
Molecular dynamics
structures of peptide nucleic acid DNA hybrid in the
wild-type
and mutated alleles
of Ki-ras proto-oncogene
FEBS
Journal, 272,
4055-4070 (2005) |
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Sreekumar, A., Acharya, K.K., Lalitha,
H.S., Indi, S.S., Bali, P. and Seshagiri, P.B.
Germ cell-specific localization of immunoreactive riboflavin carrier
protein in the male golden hamster: appearance during spermatogenesis
and role in sperm function.
Reproduction, 129, 577-587 (2005) |
*
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Yathindra, N.
M. Sundaralingam (1931-2004): a distinguished nucleic acid researcher.
Acta. Cryst., D61,
845-849 (2005) |
| S |
Rajalalitha, P and
Vali, S
Molecular pathogenesis of oral submucos fibrosis - a collagen metabolic
disorder
J. Oral Pathol.
Med., 34, 321-328 (2005) |
*
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Saberwal, G
English composition as a professional skill
Current Science, 88, 848 (2005) |
| S |
Kant, R
Sweet proteins - Potential replacement for artificial low
calorie
sweeteners
Nutrition
Journal, 4, 5 (2005) |
| S |
Sandhu, K S and
Acharya, K,
ExPrimer: To design primers from exon-exon junctions
Bioinformatics,
21,
2091-2092
(2005) |
| S |
Kant, R,
Rajasekaran,
M B and Suryanarayanarao, R
Sweet and taste
modifying proteins - Comparative modeling and docking
studies
of curculin,
mabinlin, miraculin with the T1R2-T1R3 receptor
Internet
Electron J.
Mol.Des., 4,
106-123 (2005) |
*
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Venkatesh, S and Bansal, M
Role of informatics in biodiversity conservation: overview of available
resources, In Biodiversity, Status
and Prospects (Eds. P. Tandon, M. Sharma and R. Swarup)
Narosa Publishing House, New Delhi, 134-145 (2005) |
S
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Rekha, N,
Machado, S
M, Narayanan, C, Krupa, A and Srinivasan, N
Interaction interfaces of protein
domains are not topologically
equivalent across
families within superfamilies: Implications for metabolic and
signalling pathways
Proteins,
58,
339-353 (2005) |
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2004 |
*
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Saberwal, G
Biotechnology incubation in India.
'Business
incubation: Initiatives in India' Ed. R. K. Lagu brought
out by NSTEDB, DST (2004) |
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Behera, N and Nanjundiah,V
Phenotypic plasticity can potentiate rapid evolutionary change
Journal of
Theoretical Biology, 226,
177-184 (2004) |
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Yamamura, Y, Higashi
M, Behera, N & Wakano, J Y
Evolution of mutualism through spatial effect
Journal of
Theoretical Biology, 226,
421-428 (2004) |
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Kanhere, A and Bansal, M
DNA bending and curvature: A turning point in DNA function
Proc. Indian
Acad. Sci., B70,
239-254 (2004) |
*
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Venkatesh, S and Bansal, M
Role of informatics in food biotechnology and safety
Indian Food
Industry, 23, 32-36
(2004) |
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2003 |
*
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Bansal, M
DNA structure: Revisiting the Watson-Crick double helix
Current Science,
85,
1556-1563 (2003) |
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Madhumalar, A and
Bansal, M
Sequence dependent structural features of A3T3 vs(AT)3 from molecular
dynamics study
Recent Trends
in Biophysical Research (ed. N. Maiti), Calcutta, pp. 10-16
(2003) |
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Madhumalar, A
and
Bansal, M
Structural insights into the effect of hydration and ions on
A-tract DNA: A molecular dynamics study
Biophysics
Journal, 85, 1805-1816
(2003) |
*
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Venkatesh, S
and
Bansal M
Role of informatics in biodiversity conservation: overview of available
resources
Proc. of
the 72nd Annual Session & National Symposium on Biodiversity
(2003) |
*
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Bansal, M and Sastri, S
Bioinformatics training - An Indian experience
Web03 Handbook
(2003) |
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Kanhere, A and
Bansal, M
An assessment of three dinucleotide parameters to predict DNA curvature
by
quantitative comparison to experimental data
Nucleic Acids
Research, 31, 2647-2658
(2003) |
*
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Ghosh, A and
Bansal,
M
A glossary of DNA structures from A to Z
Acta Cryst.,
D59,
620-626 (2003) |
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Behera, N
Book Review: Molecular Systematics and Evolution: Theory and Practice.
R. DeSalle, G. Giribet and W. Wheeler (eds)
Birkhauser Verlag, P.O. Box 133, CH-4010 Basel, Switzerland
Current Science,
84,
99-100 (2003) |
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2002 |
* |
Saberwal, G
Institute of Bioinformatics and Applied Biotechnology: Bioinformatics
training with a difference
Current Science,
83, 794
(2002) |
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