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.

	2013
	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)
	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)
	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)
	Kumari, S. and Saberwal, G. Patent maintenance by Indian pharma and bio-pharma companies. Asian Biotechnology Development Review (in press)
	Saberwal, G. Giving voice to India's entrepreneurs. Nature Biotechnology 31, 104-107 (2013)
	Agrawal, S. and Rao, M. R. S. Functional/signature network module for target pathway/gene discovery. Encyclopedia of Systems Biology, Springer Press (in press)
	Agrawal, S. and Rao, M. R. S. Biological network, disease mechanism network. Encyclopedia of Systems Biology, Springer Press (in press)
	2012
	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)
	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)
	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)
	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)
	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)
	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)
	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)
	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)
	2011
	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.
	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).
	Bateman, A. et al. RNAcentral: a vision for an international database of RNA sequences RNA, 17, 1941-1946 (2011)
	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)
	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)
	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)
	2010
	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)
	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)
	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)
	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)
	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)
	Jeevitesh, M.S., Behera, N., Jose, J., Kant, K. and Dey, A. Higher accuracy protein multiple sequence alignment by stochastic algorithm Nature Precedings
	2009
	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)
	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)
	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)
	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)
	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)
	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)
	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)
	2008
	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)
	Ramakrishnan, N. and Bhalla, U.S. Memory switches in chemical reaction space. PLoS Comp. Biol., 4: e1000122 (2008)
	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)
	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)
	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).
	Sai Lakshmi, S. and Agrawal, S. piRNABank: A web resource on classified and clustered piwi interacting RNAs Nucleic Acids Research, 36, D173-177 (2008).
	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)
	2006
	Agrawal, S. , Chetan, K. and Rao, M R S. CREMOFAC - a database of chromatin remodelling factors Bioinformatics, 22, 2940-2944 (2006).
	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)
	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)
	Saberwal, G New pharma-biotech company formation in India Nature  Biotechnology, 24, 499-501 (2006)
	2005
	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)
	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)
*	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)
*	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)
*	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	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)
	2004
*	Saberwal, G Biotechnology incubation in India. 'Business incubation: Initiatives in India' Ed. R. K. Lagu brought out by NSTEDB, DST (2004)
	Behera, N and Nanjundiah,V Phenotypic plasticity can potentiate rapid evolutionary change Journal of Theoretical Biology, 226, 177-184 (2004)
	Yamamura, Y, Higashi M, Behera, N & Wakano, J Y Evolution of mutualism through spatial effect Journal of Theoretical Biology, 226, 421-428 (2004)
	Kanhere, A and Bansal, M DNA bending and curvature: A turning point in DNA function Proc. Indian Acad. Sci., B70, 239-254 (2004)
*	Venkatesh, S and Bansal, M Role of informatics in food biotechnology and safety Indian Food Industry, 23, 32-36 (2004)
	2003
*	Bansal, M DNA structure: Revisiting the Watson-Crick double helix Current Science, 85, 1556-1563 (2003)
	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)
	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)
*	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)
*	Bansal, M and Sastri, S Bioinformatics training - An Indian experience Web03 Handbook (2003)
	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)
*	Ghosh, A and Bansal, M A glossary of DNA structures from A to Z Acta Cryst., D59, 620-626 (2003)
*	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)
	2002
*	Saberwal, G Institute of Bioinformatics and Applied Biotechnology: Bioinformatics training with a difference Current Science, 83, 794 (2002)