Prof. Manju Bansal Lab, MBU, IISc, Bangalore, India.
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Prof. Manju Bansal Lab, MBU, IISc, Bangalore, India.
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List of publications of Prof. Manju Bansal (Updated: 10 July., 2019): The wwPDB Consortium, EMDB-the Electron Microscopy Data Bank,(2024) Nucleic Acids Research, Volume 52, Issue D1,D456-D465 , DOI:10.1093/nar/gkad1019 (Link to paper at publisher's site) Hidden modes of DNA binding by human nuclear receptors, D Bhimsaria, JA Rodríguez-Martínez, J Méndez, D Ghoshdastidar, A Varadarajan, M Bansal, DL Daniels, P Ramanathan, AZ Ansari (2023) Nat Comm 14:4179, DOI : 0.1038/s41467-023-39577-0 (Link to paper at publisher's site) Flexibility of flanking DNA is a key determinant of transcription factor affinity for the core motif, D.Ghoshdastidar and M.Bansal (2022) Biophysical J 121(20), 3987-4000, DOI: 10.1016/j.bpj.2022.08.015 (Link to paper at publisher's site) The effect of mutation in the stem of the MicroROSE thermometer on its thermosensing ability, S Halder and M Bansal (2022) RSC Advances 12, 11853-11865, DOI : 10.1039/d2ra00169a (Link to paper at publisher's site) RNA-mediated translation regulation in viral genomes: computational advances in the recognition of sequences and structures, A.Gupta and M.Bansal (2019) Briefings in Bioinformatics. , DOI:10.1093/bib/bbz054 Link to paper at publisher's site) Variation of gene expression in plants is influenced by gene architecture and structural properties of promoters, S.Das and M.Bansal (2019)Plos One. 14, DOI:10.1371/journal.pone.0212678 Link to paper at publisher's site) Flexibility and structure of flanking DNA impact transcription factor affinity for its core motif, V.R Yella, D.Bhimsaria, D.Ghoshdastidar, J A.Rodríguez-Martínez , A Z.Ansari M.Bansal (2018)Nucleic Acids Research DOI:10.1093/nar/gky1057(In Press).(Link to paper at publisher's site) Towards a universal structural and energetic model for prokaryotic promoters, A.Mishra, P.Siwach, P.Misra, B.Jayaram, M.Bansal , W.K.Olson, K.M.Thayer, and D.L. Beveridge (2018)Biophysical journal. 115, 1180-1189, DOI:doi.org/10.1101/348854.(Link to paper at publisher's site) Dynamics of physiologically relevant noncanonical DNA structures: an overview from experimental and theoretical studies, D.Ghoshdastidar M.Bansal (2018)Briefings in Functional Genomics. DOI:10.1093/bfgp/ely026.(Link to paper at publisher's site) Biomolecular Structures: Prediction,Identification and Analyses, P.Kumar,S.Halder and M.Bansal (2018) Encyclopedia of Bioinformatics and Computational Biology. 504-534.(Link to paper at publisher's site) Identification of putative promoters in 48 eukaryotic genomes on the basis of DNA free energy, V.R.Yella, A.Kumar and M.Bansal (2018) Scientific Reports. 8,4520: DOI:10.1038/s41598-018-22129-8.(Link to paper at publisher's site) RNAHelix: computational modeling of nucleic acid structures with Watson-Crick and non-canonical base pairs, D.Bhattacharyya, S.Halder, S.Basu, D.Mukherjee, P.Kumar and M.Bansal (2017) J Comput Aided Mol Des. 33,219-235.(Link to paper at publisher's site) DNA structural features of eukaryotic TATA-containing and TATA-less promoters, V.R.Yella and M.Bansal (2017) FEBS Openbio. 7,324-334. (Link to paper at publisher's site) Data on diverse roles of helix perturbations in membrane proteins, A.Shelar and M.Bansal (2016) Data in Brief. 9, 781-802. (Link to paper at publisher's site) Unveiling DNA structural features of promoters associated with various types of TSSs in prokaryotic transcriptomes and their role in gene expression, A.Kumar and M.Bansal (2016) DNA Res. DOI:10.1093/dnares/dsw045 (Link to paper at publisher's site) The Role of Sequence in Altering the Unfolding Pathway of an RNA Pseudoknot: A Steered Molecular Dynamics Study, A.Gupta and M.Bansal (2016) Phys. Chem. Chem. Phys. 18, 28767-28780 (Link to paper at publisher's site) Structural and functional analyses of PolyProline-II helices in globular proteins, P.Kumar and M.Bansal (2016) J.Structural Biology, 196(3),414-425. (Link to paper at publisher's site) Structural features of DNA are conserved in the promoter region of orthologous genes across different strains of H. pylori, A.Kumar, V.Manivelan, and M.Bansal (2016)FEMS Microbiology Letters , 363, 1-10. (Link to paper at publisher's site) Helix perturbations in membrane proteins assist in inter-helical interactions and optimal helix positioning in the bilayer. A.Shelar, and M.Bansal (2016) Biochimica et Biophysica Acta (BBA)-Biomembranes. 1858(11) 2804-2817. (Link to paper at publisher's site) Genome-wide targets regulated by OsMADS1 in rice florets reveal its DNA recognition properties. I.Khanday, S.Das, G. Chongloi, M.Bansal U. Grossniklaus and U.Vijayraghavan (2016) Plant Phys, 172(1), 372-388. (Link to paper at publisher's site) Insights into the Structural Dynamics of Nucleocytoplasmic Transport of tRNA by Exportin-t. A.Gupta,S.Kailasam and M.Bansal (2016) Biophysical journal, 110(6), 1264-1279. (Link to paper at publisher's site) New insight into the architecture of oxy-anion pocket in unliganded conformation of GAT domains: A MD-simulation study Hridoy R. Bairagya and M.Bansal, (2016) Proteins, 84(3),360-73. (Link to paper at publisher's site) Conformational stabilities of iminoallantoin and its base pairs in DNA: implications for mutagenicity. N.R Jena, M.Bansal and PC Mishra. (2016)Phys. Chem. Chem. Phys., , 18(18),12774-12783.(Link to paper at publisher's site) Dissecting π-helices: Sequence, Structure and Function. P.Kumar and M.Bansal, (2015) FEBS J, 282, 4415-4432. (Link to paper at publisher's site) Identification of local variations within secondary structures of proteins. P.Kumar and M.Bansal, (2015) Acta Crystallogr. Sec.D, 71, 1077-1086. (Link to paper at publisher's site) Ligand 5,10,15,20-Tetra(N-methyl-4-pyridyl)porphine (TMPyP4) Prefers the Parallel Propeller-Type Human Telomeric G-Quadruplex DNA over Its Other Polymorphs. A.Ali, M.Bansal,and S.Bhattacharyaa (2015) J. Phys. Chem. B119(1),5-14. (Link to paper at publisher's site) Stacking Interactions in RNA and DNA: Roll-Slide Energy Hyperspace for Ten Unique Dinucleotide Steps, S.Mukherjee, S.Kailasam, D.Bhattacharyya, M.Bansal (2015) Biopolymers, 103,134-147. (Link to paper at publisher's site) Local Structural and Environmental Factors Define the Efficiency of an RNA Pseudoknot Involved in Programmed Ribosomal Frameshift Process, A.Gupta and M.Bansal (2014)J. Phys. Chem. B, 118 (41), pp 11905-11920 (Link to paper at publisher's site) Sequence and conformational preferences at termini of α-helices in membrane proteins: Role of the helix environment, A. Shelar, M.Bansal (2014) Proteins: Structure, Function, and Bioinformatics, DOI: 10.1002/prot.24696 (Link to paper at publisher's site) MolBridge: A program for identifying non-bonded interactions in small molecules and biomolecular structures, P.Kumar, S.Kailasam, S.Chakraborty and M.Bansal (2014) J Appl Crystallogr, 47,5, 1772-1776 (Link to paper at publisher's site) Sequence dependent variations in RNA duplex are related to non-canonical hydrogen bond interactions in dinucleotide steps, S.Kailasam, D.Bhattacharyya, M.Bansal (2014) BMC Research Notes, 7,1,83 (Link to paper at publisher's site) Role of DNA sequence based structural features of promoters in transcription initiation and gene expression, M.Bansal, A.Kumar, V.R.Yella (2014) Current Opinion in Structural Biology, 25,77-85 (Link to paper at publisher's site) Energy hyperspace for stacking interaction in AU/AU dinucleotide step: Dispersion-corrected density functional theory study, S.Mukherjee, S.Kailasam, M.Bansal, D.Bhattacharyya (2014) Biopolymers, 101,1,107-120 (Link to paper at publisher's site) DNA structural features and architecture of promoter regions play a role in gene responsiveness of S. cerevisiae, V.R.Yella and M.Bansal (2013) Journal of Bioinformatics and Computational Biology, 11,6,1343001. (Link to paper at publisher's site) HELANAL-Plus: a web server for analysis of helix geometry in protein structures. P.Kumar and M.Bansal, (2012) J Biomol Struct Dyn., 30, 773-783. (Link to paper at publisher's site) Characterization of structural and free energy properties of promoters associated with Primary and Operon TSS in Helicobacter pylori genome and their orthologs. A.Kumar and M.Bansal (2012)Journal of Biosciences.,37,423-431.(PDF) PROMBASE: A webresource for various genomic features and predicted promoters in prokaryotice genomes. V.Rangannan and M.Bansal (2011)BMC Research Notes. 4:257.(PDF) Intrinsic structural variability of DNA allows multiple genomic encoding for nucleosomes. A.Marathe and M.Bansal (2011) Phys Life Review. 69-72. (PDF) An ensemble of B-DNA dinucleotide geometries lead to characteristic nucleosomal DNA structure and provide plasticity required for gene expression. A.Marathe and M.Bansal (2011) BMC Struct Biol. 11(1).(PDF) DNA free energy based promoter prediction and comparative analysis of Arabidopsis and rice genomes C.Morey, S.Mookherjee, G.Rajasekaran and M.Bansal (2011) Plant Physiology 156:1300-1315. (PDF) Mutagenicity associated with O6-methylguanine-DNA damage and mechanism of nucleotide flipping by AGT during repair N.R.Jena and M.Bansal (2011) Phys. Biol. 8(4)046007. (PDF) The 5-methyl group in thymine dynamically influences the structure of A-tracts in DNA at the local and global level. A.Marathe and M.Bansal (2010) J Phys Chem B 114(16):5534-46 (PDF) High-quality annotation of promoter regions for 913 bacterial genomes, V.Rangannan, M.Bansal (2010) Bioinformatics 26 (24): 3043-3050.(PDF) Relative stability of DNA as a generic criterion for promoter prediction: whole genome annotation of microbial genomes with varying nucleotide base composition, V.Rangannan and M.Bansal (2009) Mol. BioSyst. 5:1758-1769.(PDF). Small local variations in B-form DNA lead to a large variety of global geometries which can accommodate most DNA-binding protein motifs, A.Marathe, D.Karandur and M.Bansal (2009) BMC Struct. Biol. 9: 24 (doi:10.1186/1472-6807-9-24). (PDF) Identification and annotation of promoter regions in microbial genome sequences on the basis of DNA stability, V.Rangannan and M.Bansal (2007) J. Biosci 32, 851-862. (PDF) Conformational specificity of non-canonical base pairs and higher order structure in nucleic acids: crystal structure database analysis. S.Mukherjee, M.Bansal (2006) D.Bhattacharyya. J Comput Aided Mol Des. 20:629-645. (PDF)
Structural properties of promoters: similarities and differences between
prokaryotes and eukaryotes, A. Kanhere and M.Bansal (2005) Nucleic Acids Res.
33, 3165-3175.
(PubMed)
(PDF) Collagen Structure: The Madras Triple Helix and the Current Scenario. A.Bhattacharjee and M.Bansal (2005). IUBMB Life, 57(3): 161-172. (PDF)
DNA Bending and Curvature: A Turning Point in DNA Function, A. Kanhere and
M.Bansal (2004) Proc. Indian Natl. Sci. Acad. B70, 239-254. (PDF)
Modelling studies on neurodegenerative disease causing triplet repeat sequences
d(CGG/GCC) and d(CAG/CTG): Duplexes vs Quadruplexes, S. Chowdhury and M.Bansal
(2001) J. Biosci. 26, 649-665.
(PDF)
A nanosecond molecular dynamics study of antiparallel d(G)7 quadruplex
structures: Effect of the coordinated cations, S. Chowdhury and M.Bansal (2001)
J. Biomol. Struct. Dynam. 18, 647-669. A standard reference frame for the description of Nucleic Acid Base-Pair Geometry. Wilma K. Olson, M.Bansal (2001), Stephen K. Burley Richard E. Dickerson, Mark Gerstein, Stephen C. Harvey Udo Heinemann, Xiang-Jun Lu, Stephen Neidle, Zippora Shakked Heinz Sklenar, Masashi Suzuki, Chang-Shung Tung, Eric Westhof Cynthia Wolberger and Helen M. Berman. J. Mol. Biol. 313, 229-237 .(PDF)
Effect of coordinated ions on structure and flexibilty of parallel G-quadruplexes:
A molecular dynamics study, S. Chowdhury and M.Bansal (2000) J. Biomol. Struct.
Dynam. 18, 11-28. (PDF) A semi-empirical SCF-MO study on the base-pairing properties of 8-oxopurines: significance for mutagenicity Divi Venkateswarlu, R. H. Duncan Lyngdoh and M.Bansal (1997). J. Chem. Soc., Perkin Trans. 2, 621-625. (PDF)
Structural and Sequence Characteristics of Long Alpha Helices in Globular
Proteins, S. Kumar and M.Bansal (1996) Biophys. J. 71, 1574-1586.
(PDF) CA\TG Sequence at the 5'end of Oligo(A)-tracts Strongly Modulates DNA Curvature, A. K. Nagaich, D. Bhattacharyya, S. K. Brahmachari and M.Bansal (1994) J. Biol. Chem., 269, 7824-7833. (PDF)
Conformational
Polymorphism in G-tetraplex Structures: Strand Reversal by Base Flipover or
Sugar Flipover, D. Mohanty and M.Bansal (1993) Nucleic Acids Res., 21,
1767-1774. (PubMed)
(PDF)
Local variability and base sequence effect
in DNA crystal structures. M.Bansal, D.Bhattacharyya (1990).
J. Biomol. Struct. Dynam 8(3), 539-72.
(PubMed)
Energetic of
left and right handed models of DNA, D.Bhattacharyya and M.Bansal (1987)
J. Biomol. Struct. Dynam. 4, 1027-1040.
(PubMed)
Comparison of
inter-proton distances in DNA models with nOe data, B.Gopalakrishnan and M.Bansal (1985)
Jl. Biosci. (supplement Part II) pp. 603-614.
(PDF)
Structural
investigations on poly-4-hydroxy-L-proline, I. Theoretical studies, M.Bansal,
S.K.Brahmachari and V.Sasisekharan (1979) Macromolecules, 12, 23-28.
(PDF)
Stereochemistry of the pyrrolidine rings in the collagen structure,
G.N.Ramachandran and M.Bansal (1976) Curr. Sci. 45, 647-649.
b) Scientific Reviews:
Collagen Structure: The Madras
triple helix and the current scenario, A. Bhattacharjee and M.Bansal (2005)
IUBMB Life 57, 161-172.
(PDF)
DNA structure: Revisiting the
Watson-Crick double helix, M.Bansal (2003) Current Sci. 85, 1556-1563.
(PDF)
The Madras Triple Helix:
Origins and Current Status, M.Bansal (2001) Resonance 6, 38-47.
(PDF)
The structure of collagen, M.Bansal
(1979), in `Vistas in Molecular, Solid State and Bio-physics', (Eds.
A.S.N.Murty and V.Kumar) , 317-322.
Role of Informatics in
biodiversity conservation: Overview of available resources, S. Venkatesh and M.Bansal in
'Biodiversity: Status and Prospects' (Eds. P.Tandon, M. Sharma, R.
Swarup) Narosa Publishing House, New Delhi, 2005, pp.134-145.
Role of Informatics in Food
Biotechnology and Safety, S. Venkatesh and M.Bansal, (2004) Indian Food
Industry 23.2, 32-36.
Structural Variations Observed
in DNA Crystal Structures and Their Implications for Protein-DNA Interaction, M.Bansal in 'Biological Structure and Dynamics' (Eds. Sarma, R.H. and Sarma, M.)
Adenine Press, New York, 1996, Vol.1, 121-134.
Sequence-Structure Correlation
in DNA: A Database cum Computer Modelling Study, M.Bansal, in Proceedings of
Discussion Meeting on Computational Biology, I.I.Sc., Bangalore, 1995.
Local structural features of
DNA as revealed by single- crystal x-ray diffraction methods, U.Heinemann, C.
Alings, M.Bansal and M. Hahn in 'Advances in Life Sciences: Structural Tools
for the Analysis of Protein-Nucleic Acid Complexes', Birkhauser Verlag Basel,
1992, pp. 53-61
Parameterization of Empirical Energy Functions for Biopolymers,
M.Bansal in
Proceedings of Discussion Meeting on 'Molecular Dynamics Simulation of
Biological Macromolecules', I.I.Sc., Bangalore, 1992.
Real and
apparent curvature in oligonucleotides, M.Bansal and D. Bhattacharyya, in
'Structure & Methods Vol.3: DNA & RNA' (Eds. R.H. Sarma & M.H. Sarma)
Adenine
Press, New York, 1990, pp. 139-153.
Structures of
DNA: A case study of right and left handed duplexes in the B-form,
V.Sasisekharan, M.Bansal and G.Gupta in `Nucleic Acids - Vectors of Life' (Ed.
B.Pullman and D.Jortner) Reidel Press, Dordrecht, 1983, pp. 101-110.
Structure of
DNA re-examined, V.Sasisekharan, M.Bansal and G.Gupta in `Structural aspects of
recognition and assembly in Biological macromolecules' (Ed. M. Balaban) Balaban
International Science Services, Rehovot, 1981, 501-521.
Conformational
flexibility of DNA: A theoretical formalism, V.Sasisekharan, M.Bansal,
S.K.Brahmachari and G.Gupta in `Biomolecular Stereodynamics' (Ed. R.H.Sarma)
Adenine Press, New York, 1981, 123-150.
d) Chapters in books
Modulation of Gene Expression by Gene Architecture and Promoter Structure, A.Kumar* and M.Bansal in 'Bioinformatics in the Era of Post Genomics and Big Data' (Ed. I.Abdurakhmov),pp,37-53 IntechOpen, 2018.
.(PDF)
In silico identification of eukaryotic promoters VR Yella and M.Bansal in 'Synthetic and System Biology' (Eds. V.Singh and P.Dhar)Springer Pubs 63-75, 2015 (Book chapter).(PDF)
DNA structure and promoter engineering VR.Yella, A.Kumar and M.Bansal in 'Synthetic and System Biology' (Eds. V.Singh and P.Dhar)Springer Pubs 241-254, 2015 (Book chapter).(PDF)
Defining α-helix geometry by Cα atom trace vs (φ-ψ) torsion angles: a comparative analysis, A. Shelar*, P.Kumar* and M.Bansal in 'Biomolecular Forms and Functions' (Ed. M. Bansal and N.Srinivasan) IISc, Bangalore, 2013,
pp.116-127.(PDF)
Sequence
dependent structural features of A3T3 vs (AT)3 from Molecular Dynamics study, A.
Madhumalar and M.Bansal in 'Recent Trends in Biophysical Research' (Ed. N.
Maiti, G. Suresh Kumar and S. Das) Double A Work Station, Kolkata, 2003,
pp.10-16.
Cross-strand
C-H..O and N-H..N Interactions in B-DNA Duplex Structure: Hydrogen Bonds or
Short Contacts? M.Bansal and A. Ghosh in
'Perspectives in
Structural Biology' (Eds. M. Vijayan, N. Yathindra and A. S. Kolaskar)
University Press, Hyderabad, 1999, pp. 602-613. (PDF)
Exploring the
Structural Repertoire of Guanine Rich DNA Sequences: Computer Modelling Studies,
M.Bansal, M. Ravikiran and S. Chowdhury in
in 'Recent Trends in
Biophysical Research' (Ed. J. Leszczynski) Elsevier Science, Amsterdam,
1999, pp. 279-323.
New
Theoretical Models for DNA Structure, M.Bansal and V.Sasisekharan in 'Landolt-Bornstein
Numerical Data and Functional Relationships', New Series, Vol.VII/1 d on Nucleic
Acids (Ed. W.Saenger) Springer-Verlag, Berlin, 1991, pp.455-486.
DNA Bending: A
natural consequence of base sequence dependent variability, M.Bansal, D.
Bhattacharyya and D. Mohanty in 'Biomolecular Structure and Interactions' (Eds.
S. Ramaseshan and P. Balaram), Indian Academy of Sciences, Bangalore, 1991, pp.
347-362.
Straight and
Curved DNA : Structural Variability Revisited, M.Bansal and V.Sasisekharan in
'Theoretical Methods in Biological Chemistry', (Eds. D.L.Beveridge and R.Lavery)
Adenine Press, New York, 1990, pp.329-342.
Molecular
Model-building of DNA: Constraints and Restraints, M.Bansal and V.Sasisekharan
in `Theoretical Chemistry of Biological Systems', (Ed. Naray-Szabo) Elsevier
Scientific Publishing Co., Amsterdam,1986, pp.127-218.
Twists and Turns on the path to DNA. M.Bansal, (2012)
Women and society THE ROAD TO CHANGE., 40-47.
Nucleic acids in disease and disorder: Understanding the language of life emerging from the 'ABC' of DNA. M.Bansal, B.Jayaram and M.Aditya (2012)
Journal of Biosciences.,37,375-378.(PDF)
BioSuite: A comprehensive bioinformatics
package (A unique industry academia collaboration ) The NMTTLI- Biosuite Team: (2007) Curr. Sci. 92, 29-38.(PDF)
Classics in Indian Medicine: Structure of
collagen, M.Bansal (2007) Natl. Med. Jl. India, 19, 348-352.
Research News: DNA Structure: Yet Another
Avatar? M.Bansal (1999), Curr. Sci, 76, 1178-1181.
(PDF)
Book Review: " Computer Modeling in
Molecular Biology" (Ed. J. Goodfellow), M.Bansal (1995) Ind. Jl.
Biochem. Biophys, 33, 237-238.
Studies on Structure of Fibrous Proteins,
Nucleic Acids and Macromolecular Assemblies, M.Bansal in 'Research and
Development in Biological Sciences'. Platinum Jubilee Volume, IISc, Bangalore,
1984, pp.113
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Copyright © 2008
Prof. Manju Bansal
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