Publications

The faculty of IBAB publish their research and other thought pieces in some of the best journals, nationally and internationally. It has been a remarkable achievement in the short time since the institute was founded. This has allowed the institute to gain considerable recognition among its peers.

  • GNT indicates a publication by GANIT Labs
  • *” indicates research news, a book review, a general article or a letter to the editor
  • ST” 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.

 

  • ~ 2014 ~

    Chitturi N, Balagannavar G, Chandrashekar DS, Abinaya S, Srini VS and Acharya KK
    TIPMaP: a web server to establish Transcript Isoform Profiles from reliable Microarray Probes.
    BMC Genomics (in press)

    Bhagwat, S. et al.
    Acetylated alpha tubulin is reduced in individuals with poor sperm motility.
    Fertility and Sterility (in press)

    * Saberwal, G.
    On being a professional mutant
    Nature Biotechnology, 32, 106-107 (2014)

    Jaroslawski, S. and Saberwal, G.
    In eHealth in India today, the nature of work, the challenges and the finances: an interview based study.
    BMC Medical Informatics and Decision Making, 14, 1-12 (2014)

     

    ~ 2013 ~

    * Sundararajan, PR, Balaji, PV and Yathindra, N.
    Obituary: VSR Rao (1931–2013)
    Current Science, 105, 1303-1304 (2013)

    GNT Jain, P. , Krishnan, N.M. and Panda, B.
    Augmenting transcriptome assembly by combining de novo and genome-guided tools.
    Peer J., 1, e133 (2013)

    Ananth, P., Goldsmith, G. and Yathindra, N.
    An innate twist between Crick’s wobble and Watson & Crick base pairs. Its effect on RNA.
    RNA, 19, 1038-1053 (2013)

    Kumari, S. and Saberwal, G.
    Patent maintenance by Indian pharma and bio-pharma companies.
    Asian Biotechnology Development Review, 15, 69-77 (2013)

    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)

    Jaroslawski, S. and Saberwal, G.
    Case studies of innovative medical device companies from India: Barriers and enablers to development.
    BMC Health Services Research, 13, 199-207 (2013)

    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, pgs 773-777 (2013)

    Agrawal, S. and Rao, M. R. S.
    Biological disease mechanism networks
    Encyclopedia of Systems Biology, Springer Press, pgs 113-118 (2013)

     

    ~ 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)

    GNT Panda. B.
    Whither genomics diagnostics tests in India?
    Indian J. Med. Paediatr. Oncol., 33, 250-252 (2012)

    ST: Srinivasan, S, Patil, AH, Verma, M, Bingham, JL 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.G
    Novel Levamisole derivative induces extrinsic pathway of apoptosis in cancer cells and inhibits tumor progression in mice.
    PLoS One, 7(9), e43632 (2012)

    GNT 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, 7(10), e47812 (2012)

    * Saberwal, G
    Translating academic discoveries
    Current Science, 103, 767-769 (2012)

    GNT 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 (2012)

    ST: Vangala, R.K., Singh, L. and Gupta, R.P.
    Bioparishodhana: A novel graphical interface integrating BLAST, CLUSTALW, primer3 and restriction digestion tools. Bioinformation, 8, 639-643 (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)

    Akhilesh, K B, Davuluri, S, Chandrashekar, D S, Selvarajan, I, 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, e36776 (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)

    *, ST: 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)

    GNT: 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)

    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
    Medicinal Research Reviews, 31, 757-793 (2011)

    GNT: Krishnan, N et al.
    De novo sequencing and assembly of Azadirachta indica fruit transcriptome
    Current Science, 101, 1553-1561 (2011) (Cover page article)

    * Saberwal, G
    Caring for a severely disabled person
    Available at http://db.tt/bVuyIfN6

    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 Research, 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
    The Journal of Biological Chemistry, 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
    PLoS One, 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
    The Journal of Biological Chemistry, 284, 24453-24464 (2009)

    Saberwal, G
    Seeding a skilled workforce
    Nature Biotechnology, 27,773-775 (2009)

    * Acharya, K 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 K
    Mechanism of p300 specific histone acetyltransferase inhibition by small molecules
    Journal of Medicinal Chemistry, 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

    ST: Alva, V, Syamala Devi, D P and 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 Computational Biology, 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 B M, Mantelingu K, Agrawal, S, Reddy B A, Roy S, Rangappa K and Kundu T K
    Specific small-molecule activator of aurora kinase a induces autophosphorylation in a cell-free system
    Journal of Medicinal Chemistry, 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 and Reddi, P P
    cis-Requirement for the maintenance of round spermatid-specific transcription
    Developmental Biology, 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 Crystallographica, D61, 845-849 (2005)

    ST: Rajalalitha, P and Vali, S
    Molecular pathogenesis of oral submucos fibrosis – a collagen metabolic disorder
    Journal of Oral Pathology Medicine, 34, 321-328 (2005)

    * Saberwal, G
    English composition as a professional skill
    Current Science, 88, 848 (2005)

    ST: Kant, R
    Sweet proteins – Potential replacement for artificial low calorie sweeteners
    Nutrition Journal, 4, 5 (2005)

    ST: Sandhu, K S and Acharya, K K
    ExPrimer: To design primers from exon-exon junctions
    Bioinformatics, 21, 2091-2092 (2005)

    ST: 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 Electronic Journal of Molecular Design, 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)

    ST: 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 and 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
    Proceedings of the Indian Academy of Sciences, 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
    Proceedings 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 Crystallographica, 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)