CHANDRA LAB
  • Publications

    2024

  1. Soncini D, Becherini P, Ladisa F, Ravera S, Chedere A, Gelli E, Giorgetti G, Martinuzzi C, Piacente F Dr, Mastracci L, Veneziano C Dr, Santamaria G Dr, Monacelli F, Ghanem MS, Cagnetta A, Guolo F Dr, Garibotto M, Aquino S, Passalacqua M, Bruzzone S, Bellotti A, Duchosal MA, Nahimana AA, Angelucci E, Nagasuma C Prof, Nencioni A, Lemoli RM, Cea M Prof. NAD+ METABOLISM RESTRICTION BOOSTS HIGH-DOSE MELPHALAN EFFICACY IN PATIENTS WITH MULTIPLE MYELOMA. Blood Adv,2024.
  2. Sakthivel NC., Chinmayi A, and Chandra N. Increased ‘selfness’ in the tumor emerges as a possible immune sculpting mechanism: A pan-cancer data analysis of 32 solid tumors in TCGA. bioRxiv,2024.
  3. Banerjee U., Borbora S. M., Guha M., Yadav V., Sanjay V., Singh A., Balaji K. N. and Chandra N. Inhibition of leukotriene-B4 signalling-mediated host response to tuberculosis is a potential mode of adjunctive host-directed therapy. Immunology,2024.
  4. Kavitha B., Srikanth K., Singh D., Gopi S., Mohan V., Chandra N. and Radha V. A novel stop-loss mutation in NKX2-2 gene as a cause of neonatal diabetes mellitus: molecular characterization and structural analysis. Acta diabetologica, 61(2),189–194,2024.
  5. Sankar S., Vasudevan S. and Chandra N. CRD: A de novo design algorithm for the prediction of cognate protein receptors for small molecule ligands. Structure,32(3),362-375.e4,2024.

    6. 2023

  6. Das M., Sreedharan S., Shee S., Malhotra N., Nandy M., Banerjee U., Kohli S., Rajmani R. S., Chandra N., Seshasayee A. S. N. Laxman S., and Singh, A. Cysteine desulfurase (IscS)-mediated fine-tuning of bioenergetics and SUF expression prevents Mycobacterium tuberculosis hypervirulence. Science advances,9(50),eadh2858,2023.
  7. Ravichandran S., Bhatt B., Shah A., Balaji KN and Chandra N. Knock-down of a regulatory barcode shifts macrophage polarization destination from M1 to M2 and increases pathogen burden upon S. aureus infection. eLife,12:RP91547,2023.
  8. Sankar S., Preeti P., Ravikumar K., Kumar A., Prasad Y., Pal S., Rao DN., Savithri HS. and Chandra N. Structural similarities between SAM and ATP recognition motifs and detection of ATP binding in a SAM binding DNA methyltransferase. Curr Res Struct Biol,6,2023.
  9. Banerjee U., Chedere A., Padaki R., Mohan A., Sambaturu N., Singh A. and Chandra N. PathTracer Comprehensively Identifies Hypoxia-Induced Dormancy Adaptations in Mycobacterium tuberculosis. J. Chem. Inf. Model.63(19),6156-6167,2023.
  10. Shee S., Veetil R. T. Mohanraj K., Das M., Malhotra N., Bandopadhyay D., Beig H., Birua S., Niphadkar S., Nagarajan S. N., Sinha V. K., Thakur C., Rajmani R. S., Chandra N., Laxman S., Singh M., Samal A., Seshasayee AN., and Singh A. Biosensor-integrated transposon mutagenesis reveals rv0158 as a coordinator of redox homeostasis in Mycobacterium tuberculosis. eLife 12,e80218,2023
  11. Banerjee, U., Chunchanur, S., Ambica R., Balaji KN., Singh A., Chakravortty D. and Chandra N. Systems-level profiling of early peripheral host-response landscape variations across COVID-19 severity states in an Indian cohort. Genes Immun,24,2023.
  12. Guttapadu R., Korla K., Safnaz Uk., Annam V., Ashok P., Chandra N. Identification of Probucol as a candidate for combination therapy with Metformin for Type 2 diabetes. NPJSyst Biol Appl.23,9(1),2023.
  13. Rao V., Banerjee U., Sambaturu N., Chuchanur S., Ambica R. and Chandra N. Pressured cytotoxic T cell epitope strength among SARS-CoV-2 variants correlates with COVID-19 severity HLA,2023
  14. Guttapadu R., Prakash N., Alka M., Chatterjee R, Mahantesh S., Jayranganath M., Sastry MK., Subramanyam JR., Chakravorthy D., Kalpana SR. and Chandra N. Profiling system-wide variations and similarities between Rheumatic Heart Disease and Acute Rheumatic Fever–A pilot analysis PLoS Negl Trop Dis, 17,4,2023.

    15. 2022

  15. Rao V. and Chandra N. In-silico study of influence of HLA heterogeneity on CTL responses across ethnicities to SARS-CoV-2. Hum. Imm.,83,12,2022.
  16. Chedere A., Mishra M., Kulkarni O., Sriraman S. and Chandra N. Personalized quantitative models of NAD metabolism in hepatocellular carcinoma identify a subgroup with poor prognosis. Front. Oncol.,30, 2022.
  17. Sankar S., Sakthivel N.C. and Chandra N. Fast Local Alignment of Protein Pockets (FLAPP): A System-Compiled Program for Large-Scale Binding Site Alignment. J. Chem. Inf. Model., 2022.
  18. Banerjee U., Rao P., Reddy M., Hussain M., Chunchanur S., Ambica R., Singh A. and Chandra N. A 9-gene biomarker panel identifies bacterial coinfections in culture-negative COVID-19 cases. Molecular Omics, 2022.
  19. Sankar S and Chandra N. SiteMotif: A graph-based algorithm for deriving structural motifs in Protein Ligand binding sites. Plos Computational Biology , 18, 2, e1009901.
  20. Thakur C., Tripathi A., Ravichandran S., Shivananjaiah A., Chakraborthy A., Varadappa S., Chikkavenkatappa N., Nagarajan D., Lakshminarasimhaiah S., Singh A. and Chandra N. A new blood-based RNA signature (R9), for monitoring effectiveness of tuberculosis treatment in a South Indian longitudinal cohort iScience, 2022, 25, 103745.

    21. 2021

  21. Ravichandran S., Banerjee U., DR Devi G., Kandukuru R., Thakur C., Chakravorthy D., Kithiganahalli B., Singh A. and Chandra N. VB10, a new blood biomarker for differential diagnosis and recovery monitoring of acute viral and bacterial infections EBioMedicine, 2021, 67, 103352.
  22. Banerjee U., Baloni P., Singh A. and Chandra N. Immune Subtyping in Latent Tuberculosis Front. Immunol., 2021, 12, 1048.

    23. 2020

  23. Banerjee U., Sankar S., Singh A. and Chandra N. A Multi-Pronged Computational Pipeline for Prioritizing Drug Target Strategies for Latent Tuberculosis Front. Chem., 2020, 8:593497.
  24. Sambaturu N., Pusadkar V., Hannenhalli S. and Chandra N. PathExt: a general framework for path-based mining of omics-integrated biological networks Bioinformatics, 2020, btaa941.
  25. Bhosle, A., Datey, A., Chandrasekharan, G., Singh, D., Chakravorthy, D. and Chandra, N. A strategic target rescues Trimethoprim sensitivity in Escherichia coli iScience, 2020, 23(4), 100986.

    26. 2019

  26. Nagarajan, D., Roy, N.,Kulkarni, O., Nanajkar, N., Datey, A., Ravichandran, S., Thakur, C., Sandeep, T., Aprameya, I.V., Sarma, S.P., Chakravortty, D. and Chandra, N. Ω76: A designed antimicrobial peptide to combat carbapenem-and tigecycline-resistant Acinetobacter baumannii Science advances, 2019, 5(7), p.eaax1946
  27. Nagarajan, D., Nagarajan, T., Nanajkar, N., and Chandra, N. A Uniform In Vitro Efficacy Dataset to Guide Antimicrobial Peptide Design MDPI Data, 2019, 4(1), 27.
  28. Ravichandran S and Chandra N, 2019. Interrogation of genome-wide networks in biology: comparison of knowledge-based and statistical methods. Int J Adv Eng Sci Appl Math

    29. 2018

  29. Mishra M, Jayal P, Karande AA, Chandra N, 2018. Identification of a co-target for enhancing efficacy of sorafenib in HCC through a quantitative modeling approach. FEBS J, 285(21), 3977-3992.
  30. Nagarajan D, Nagarajan T, Roy N, Kulkarni O, Ravichandran S, Mishra M, Chakravortty D, Chandra N, 2018. Computational antimicrobial peptide design and evaluation against multidrug-resistant clinical isolates of bacteria. Journal of Biological Chemistry, 293(10), 3492-3509.
  31. Gopalan A, Bhagavat R, Chandra N, Subbarao SH, Raja A, Bethunaickan R, 2018. Biophysical and biochemical characterization of Rv3405c, a tetracycline repressor protein from Mycobacterium tuberculosis. Biochem Biophys Res Commun, 496(3), 799-805.
  32. Nagarajan, D., Sukumaran, S., Deka, G., Krishnamurthy, K., Atreya, H.S. and Chandra, N., 2018. Design of a heme-binding peptide motif adopting a β-hairpin conformation. Journal of Biological Chemistry, pp.jbc-RA118.
  33. R Bhagavat, S Sankar, N Srinivasan, N Chandra, An Augmented Pocketome: Detection and Analysis of Small-Molecule Binding Pockets in Proteins of Known 3D Structure, Structure 26 (3), 499-512. e2.
  34. Narmada Sambaturu, Sumanta Mukherjee, Martín López-García, Carmen Molina-París, Gautam I Menon, Nagasuma Chandra, Role of genetic heterogeneity in determining the epidemiological severity of H1N1 influenza. PLoS computational biology 14 (3), e1006069

    35. 2017

  35. Sambarey A, Devaprasad A, Baloni P, Mishra M, Mohan A, Tyagi P, Singh A, Akshata JS, Sultana R, Buggi S and Chandra N Meta-analysis of host response networks identifies a common core in tuberculosis npj Systems Biology and Applications, 2017, Feb 10;3:4.
  36. Rahul Metri, Abhilash Mohan, Jérémie Nsengimana, Joanna Pozniak, Carmen Molina-Paris, Julia Newton-Bishop, David Bishop, and Nagasuma Chandra. "Identification of a gene signature for discriminating metastatic from primary melanoma using a molecular interaction network approach." Scientific Reports 7, no. 1 (2017): 17314.
  37. Rahul Metri, Shikhar Saxena, Madhulika Mishra, and Nagasuma Chandra. "Modelling metabolic rewiring during melanoma progression using flux balance analysis." Bioinformatics and Biomedicine (BIBM), 2017 IEEE International Conference on, pp. 134-137. IEEE, 2017.
  38. Raghu Bhagavat et. al. A genome-wide structure-based survey of nucleotide binding proteins in M. tuberculosis Scientific Reports, 2017, 7, article number: 12489.
  39. Bhaskarla C, Bhosale M, Banerjee P, Chandra N, Nandi D. Protein tagging, destruction and infection. Curr Protein Pept Sci. 2017 Jul 13. doi: 10.2174/1389203718666170713100627. [Epub ahead of print]
  40. Ramakrishnan G, Chandra N, Srinivasan N. Exploring anti-malarial potential of FDA approved drugs: an in silico approach. Malar J. 2017 Jul 18;16(1):290
  41. Bhagavat R, Srinivasan N and Chandra N. Deciphering common recognition principles of nucleoside mono/di/and tri-phosphates binding in diverse proteins via structural matching of their binding sites. Proteins, 2017 Sep;85(9):1699-1712.
  42. Korla K and Chandra N. A Systems Perspective of Signalling Networks in Host–Pathogen Interactions Journal of the Indian Institute of Science, 2017, Vol. 97:1, p 41-57
  43. Sahu U, Rajendra VKH, Kapnoor SS, Bhagavat R, Chandra N, Rangarajan PN. Methionine synthase is localized to the nucleus in Pichia pastoris and Candida albicans and to the cytoplasm in Saccharomyces cerevisiae. J Biol Chem. 2017 Sep 8;292(36):14730-14746.
  44. Mishra S, Shukla P, Bhaskar A, Anand K, Baloni P, Jha RK, Mohan A, Rajmani RS, Nagaraja V, Chandra N, Singh A. Efficacy of β-lactam/β-lactamase inhibitor combination is linked to WhiB4-mediated changes in redox physiology of Mycobacterium tuberculosis. Elife. 2017 May 26;6. pii: e25624. doi: 10.7554/eLife.25624. Z
  45. Mudgal R, Srinivasan N, Chandra N. Resolving protein structure-function-binding site relationships from a binding site similarity network perspective Proteins, 2017 Jul;85(7):1319-1335
  46. Sambarey A, Devaprasad A, Mohan A, Ahmed A, Nayak S, Swaminathan S, D'Souza G, Jesuraj A, Dhar C, Babu S, Vykarnam A, Chandra N. Unbiased Identification of Blood-based Biomarkers for Pulmonary Tuberculosis by Modeling and Mining Molecular Interaction Networks EBioMedicine, 2017, Vol. 15, page 112-126

    47. 2016

  47. Gilbert HJ, Chandra N. Editorial overview: Carbohydrate-protein interactions and glycosylation: integrating structural biology, informatics and systems modelling to understand glycan structure and glycan-protein interactions. Curr Opin Struct Biol. 2016 Oct;40:v-viii.
  48. Padiadpu J, Baloni P, Anand K, Munshi M, Thakur C, Mohan A, Singh A, Chandra N. Identifying and Tackling Emergent Vulnerability in Drug-Resistant Mycobacteria. ACS Infect Dis. 2016 Sep 9;2(9):592-607.
  49. Karyala P, Metri R, Bathula C, Yelamanchi SK, Sahoo L, Arjunan S, Sastri NP, Chandra N. DenHunt - A Comprehensive Database of the Intricate Network of Dengue-Human Interactions. PLoS Negl Trop Dis. 2016 Sep 12;10(9):e0004965.
  50. Ramakrishnan G, Jain A, Chandra N, Srinivasan N. Computational recognition and analysis of hitherto uncharacterized nucleotide cyclase-like proteins in bacteria. Biol Direct. 2016 May 31;11:27.
  51. Marathe SA, Balakrishnan A, Negi VD, Sakorey D, Chandra N, Chakravortty D. Curcumin Reduces the Motility of Salmonella enterica Serovar Typhimurium by Binding to the Flagella, Thereby Leading to Flagellar Fragility and Shedding. J Bacteriol . 2016 Jun 13;198(13):1798-811.
  52. Singh A, Bhagavat R, Vijayan M, Chandra N. (2016). A comparative analysis of the DNA recombination repair pathway in mycobacterial genomes. Tuberculosis (2016)
  53. Mukherjee S, Bhattacharyya C, and Chandra N. HLaffy: estimating peptide affinities for Class-1 HLA molecules by learning position-specific pair potentials. Bioinformatics (2016): btw156.
  54. Padiadpu J, Mishra M, Sharma E, Mala U, Somasundaram K, Chandra N. Probing the druggability limits for enzymes of the NAD biosynthetic network in glioma. Journal of Chemical Information and Modeling. 2016 Mar 9. PubMed PMID:26958865
  55. Dhar N, Mohan A, Thakur C, Chandra NR, Dighe RR. Dissecting the structural and functional features of the Luteinizing hormone receptor using receptor specific single chain fragment variables. Molecular and cellular endocrinology. 2016 Mar 3. PubMed PMID: 26940038
  56. Chandrashekara S, Anupama KR, Sambarey A, Chandra N. High IL-6 and low IL-15 levels mark the presence of TB infection: A preliminary study. Cytokine. 2016 May 31;81:57-62.26878649
  57. Bhosle A, and Chandra N. "Structural analysis of dihydrofolate reductases enables rationalization of antifolate binding affinities and suggests repurposing possibilities." FEBS Journal (2016).
  58. Shivashankar N, Patil S, Bhosle A, Chandra N, Natarajan V.MS3ALIGN: an efficient molecular surface aligner using the topology of surface curvature.BMC Bioinformatics. 2016 Jan 12;17(1):26. doi: 10.1186/s12859-015-0874-8.26753741

    59. 2015

  59. Sambaturu N, Mishra M, Chandra N. EpiTracer-an algorithm for identifying epicenters in condition-specific biological networks. InBioinformatics and Biomedicine (BIBM), 2015 IEEE International Conference on 2015 Nov 9 (pp. 177-182). IEEE
  60. Ghosh S, Chandra N, Vishveshwara S. "Mechanism of Iron-Dependent Repressor (IdeR) Activation and DNA Binding: A Molecular Dynamics and Protein Structure Network Study." PLoS Comput Biol. 2015 Dec 23;11(12):e1004500. doi: 10.1371/journal.pcbi.1004500. eCollection 2015 Dec.
  61. Mudgal R, Sandhya S, Chandra N, Srinivasan N. De-DUFing the DUFs: Deciphering distant evolutionary relationships of Domains of Unknown Function using sensitive homology detection methods. Biol Direct.2015 Jul 31;10:38. doi:10.1186/s13062-015-0069-2. PubMed PMID: 26228684; PubMed Central PMCID:PMC4520260.
  62. Ramakrishnan G, Chandra NR, Srinivasan N. Recognizing drug targets using evolutionary information: implications for repurposing FDA-approved drugs against Mycobacterium tuberculosis H37Rv. Mol Biosyst. 2015 Nov 10;11(12):3316-31. doi:10.1039/c5mb00476d. PubMed PMID: 26429199.
  63. Masood TB, Sandhya S, Chandra N, Natarajan V. CHEXVIS: a tool for molecular channel extraction and visualization. BMC Bioinformatics. 2015 Apr 16;16:119. doi: 10.1186/s12859-015-0545-9. PubMed PMID: 25888118; PubMed Central PMCID: PMC4411761.
  64. Mohan A, Bhosle A, Chandra N. Complete Genome Sequences of an Escherichia coli Laboratory Strain and Trimethoprim-Resistant (TMP32XR) Mutant Strains. Genome Announc. 2015 Dec 10;3(6). pii: e01434-15. doi: 10.1128/genomeA.01434-15. PubMed PMID: 26659679.
  65. Jose L, Ramachandran R, Bhagavat R, Gomez RL, Chandran A, Raghunandanan S, Omkumar RV, Chandra N, Mundayoor S, Kumar RA. Hypothetical protein Rv3423.1 of Mycobacterium tuberculosis is a histone acetyltransferase. FEBS J. 2015 Oct 17. doi: 10.1111/febs.13566. [Epub ahead of print] PubMed PMID: 26476134.
  66. Ghosh S, Chandra N, Vishveshwara S. 13 Influence of iron on iron dependent repressor (IdeR) activation and DNA binding. Journal of Biomolecular Structure and Dynamics. 2015 May 18;33(sup1):8- 26103225
  67. Metri R, Hariharaputran S, Ramakrishnan G, Anand P, Raghavender US, Ochoa-Montaño B, Higueruelo AP, Sowdhamini R, Chandra NR, Blundell TL, Srinivasan N. (2015) SInCRe—structural interactome computational resource for Mycobacterium tuberculosis. Database 2015 (2015): bav060.
  68. Jyothi Padiadpu, Priyanka Baloni, Nagasuma Chandra (2015) Gene expression profiles of wild-type and isoniazid-resistant strains of Mycobacterium smegmatis Data in Brief 4; Pages 186–189.
  69. Mukherjee S, Warwicker J, Chandra N. Deciphering complex patterns of class-I HLA-peptide cross-reactivity via hierarchical grouping. Immunol Cell Biol. 2015 Feb 24. doi: 10.1038/icb.2015.3. [Epub ahead of print]
  70. Anand P, Nagarajan D, Mukherjee S, Chandra N. ABS-Scan: In silico alanine scanning mutagenesis for binding site residues in protein-ligand complex. F1000Res. 2014 [revised 2014 Dec 1];3:214. doi: 10.12688/f1000research.5165.2.
  71. Mohan A, Padiadpu J, Baloni P, Chandra N. Complete Genome Sequences of a Mycobacterium smegmatis Laboratory Strain (MC2 155) and Isoniazid-Resistant (4XR1/R2) Mutant Strains. Genome Announc. 2015 Feb 5;3(1). doi:pii: e01520-14. 10.1128/genomeA.01520-14.
  72. Baloni P, Chandra N. Architectural plan of transcriptional regulation in Mycobacterium tuberculosis. Trends Microbiol. 2015 Mar;23(3):123-5. doi: 10.1016/j.tim.2015.02.002. Epub 2015 Feb 17.
  73. Raghunath, A., Sambarey, A., Sharma, N., Mahadevan, U., Chandra, N. . A molecular systems approach to modelling human skin pigmentation: identifying underlying pathways and critical components.BMC Res Notes. 2015 Apr 29;8(1):170
  74. Nagarajan D, et al. Design of symmetric TIM barrel proteins from first principles BMC Biochemistry. 2015 16:14

    75. 2014

  75. Bhosle, Amrisha, and Nagasuma Chandra. "Different cancer cell lines resistant to the same drug exhibit differences in folate pathway dynamics." Bioinformatics and Biomedicine (BIBM), 2014 IEEE International Conference on. IEEE, 2014.
  76. Ramakrishnan G, Chandra NR, Srinivasan N. From workstations to workbenches: Towards predicting physicochemically viable protein-protein interactions across a host and a pathogen. IUBMB Life. 2014 Nov;66(11):759-74. doi: 10.1002/iub.1331. Epub 2014 Dec 15.
  77. Mukherjee S, Chandra N. Grouping of large populations into few CTL immune 'response-types' from influenza H1N1 genome analysis. Clin Transl Immunology. 2014 Aug;3(8):e24. doi: 10.1038/cti.2014.17.
  78. Ramakrishnan G, Ochoa-Montaño B, Raghavender US, Mudgal R, Joshi AG, Chandra NR, Sowdhamini R, Blundell TL, Srinivasan N. Enriching the annotation of Mycobacterium tuberculosis H37Rv proteome using remote homology detection approaches: insights into structure and function. Tuberculosis (Edinb). 2015 Jan;95(1):14-25. doi: 10.1016/j.tube.2014.10.009. Epub 2014 Nov 6.
  79. Baloni P, Padiadpu J, Singh A, Gupta KR, Chandra N. Identifying feasible metabolic routes in Mycobacterium smegmatis and possible alterations under diverse nutrient conditions. BMC Microbiol. 2014 Nov 18;14(1):276. [Epub ahead of print]
  80. Mudgal R, Sandhya S, Kumar G, Sowdhamini R, Chandra NR, Srinivasan N. NrichD database: sequence databases enriched with computationally designed protein-like sequences aid in remote homology detection. Nucleic Acids Res. 2015 Jan;43(Database issue):D300-5. doi: 10.1093/nar/gku888. Epub 2014 Sep 27.
  81. Pentakota SK, Sandhya S, P Sikarwar A, Chandra N, Satyanarayana Rao MR. Mapping post-translational modifications of mammalian testicular specific histone variant TH2B in tetraploid and haploid germ cells and their implications on the dynamics of nucleosome structure. J Proteome Res. 2014 Dec 5;13(12):5603-17. doi: 10.1021/pr500597a. Epub 2014 Oct 6.
  82. Anand P, Chandra N. Characterizing the pocketome of Mycobacterium tuberculosis and application in rationalizing polypharmacological" target selection. Sci Rep. 2014 Sep 15;4:6356. doi: 10.1038/srep06356.
  83. Anand P, Nagarajan D, Mukherjee S, Chandra N."PLIC: protein-ligand interaction clusters. Database (Oxford). 2014 Apr 23;2014(0):bau029. doi: 10.1093/database/bau029. Print 2014.
  84. Mudgal R, Sowdhamini R, Chandra N, Srinivasan N, Sandhya S. Filling-in void and sparse regions in protein sequence space by protein-like artificial sequences enables remarkable enhancement in remote homology detection capability. J Mol Biol. 2014 Feb 20;426(4):962-79. doi: 10.1016/j.jmb.2013.11.026. Epub 2013 Dec 4.
  85. Bhagavat R, Chandra N. Common recognition principles across diverse sequence and structural families of sialic acid binding proteins. Glycobiology. 2014 Jan;24(1):5-16. doi: 10.1093/glycob/cwt063. Epub 2013 Sep 16.
  86. Ghosh, S., Baloni, P., Vishveshwara, S., Chandra, N. (2014). Weighting schemes in metabolic graphs for identifying biochemical routes. Systems and synthetic biology, 8(1), 47-57.

    87. 2013

  87. Nagarajan D., Chandra N. (2013, February). PocketMatch (version2.0): A parallel algorithm for the detection of structural similarities between protein ligand binding-sites. In Parallel Computing Technologies (PARCOMPTECH), 2013 National Conference on (pp. 1-6). IEEE.
  88. Ghosh S, Baloni P, Mukherjee S, Anand P, Chandra N. A multi-level multi-scale approach to study essential genes in Mycobacterium tuberculosis. BMC Syst Biol. 2013 Dec 5;7:132. doi: 10.1186/1752-0509-7-132.
  89. Sambarey A, Prashanthi K, Chandra N. Mining large-scale response networks reveals 'topmost activities' in Mycobacterium tuberculosis infection. Sci Rep. 2013;3:2302. doi: 10.1038/srep02302.
  90. Chandra N, Padiadpu J. Network approaches to drug discovery. Expert Opin Drug Discov. 2013 Jan;8(1):7-20. doi: 10.1517/17460441.2013.741119. Epub 2012 Nov 10. Review.

    91. 2012

  91. Mishra S, Bhagavat R, Chandra N, Vijayarangan N, Rajeswari H, Ajitkumar P. Cloning, expression, purification, and biochemical characterisation of the FIC motif containing protein of Mycobacterium tuberculosis. Protein Expr Purif. 2012 Nov;86(1):58-67. doi: 10.1016/j.pep.2012.08.020. Epub 2012 Sep 13.
  92. Vashisht R, Mondal AK, Jain A, Shah A, Vishnoi P, Priyadarshini P, Bhattacharyya K, Rohira H, Bhat AG, Passi A, Mukherjee K, Choudhary KS, Kumar V, Arora A, Munusamy P, Subramanian A, Venkatachalam A, Gayathri S, Raj S, Chitra V, Verma K, Zaheer S, et al. Crowd sourcing a new paradigm for interactome driven drug" target identification in Mycobacterium tuberculosis. PLoS One. 2012;7(7):e39808. doi: 10.1371/journal.pone.0039808. Epub 2012 Jul 11.
  93. Padiadpu J, Mukherjee S, Chandra N. Rationalization and prediction of drug resistant mutations in" targets for clinical anti-tubercular drugs. J Biomol Struct Dyn. 2013;31(1):44-58. doi: 10.1080/07391102.2012.691361. Epub 2012 Jul 18.
  94. Chandra N. Computational approaches for drug" target identification in pathogenic diseases. Expert Opin Drug Discov. 2011 Oct;6(10):975-9. doi: 10.1517/17460441.2011.611128. Epub 2011 Aug 22. No abstract available.
  95. Anand P, Yeturu K, Chandra N. PocketAnnotate: towards site-based function annotation. Nucleic Acids Res. 2012 Jul;40(Web Server issue):W400-8. doi: 10.1093/nar/gks421. Epub 2012 May 22.
  96. Ananthasubramanian S, Metri R, Khetan A, Gupta A, Handen A, Chandra N, Ganapathiraju M. Mycobacterium tuberculosis and Clostridium difficille interactomes: demonstration of rapid development of computational system for bacterial interactome prediction. Microb Inform Exp. 2012 Mar 21;2:4. doi: 10.1186/2042-5783-2-4.
  97. Padiadpu J, Vashisht R, Chandra N. Protein-protein interaction networks suggest different" targets have different propensities for triggering drug resistance. Syst Synth Biol. 2010 Dec;4(4):311-22. doi: 10.1007/s11693-011-9076-5. Epub 2011 Feb 20.
  98. Bhat AG, Vashisht R, Chandra N. Modeling metabolic adjustment in Mycobacterium tuberculosis upon treatment with isoniazid. Syst Synth Biol. 2010 Dec;4(4):299-309. doi: 10.1007/s11693-011-9075-6. Epub 2011 Feb 26.

    99. 2011

  99. Anand P, Sankaran S, Mukherjee S, Yeturu K, Laskowski R, Bhardwaj A, Bhagavat R; OSDD Consortium, Brahmachari SK, Chandra N. Structural annotation of Mycobacterium tuberculosis proteome. PLoS One. 2011;6(10):e27044. doi: 10.1371/journal.pone.0027044. Epub 2011 Oct 31.
  100. Chandra N, Bhagavat R, Sharma E, Sreekanthreddy P, Somasundaram K. Virtual screening, identification and experimental testing of novel inhibitors of PBEF1/Visfatin/NMPRTase for glioma therapy. J Clin Bioinforma. 2011 Jan 20;1(1):5. doi: 10.1186/2043-9113-1-5.
  101. Ghosh S, Prasad KV, Vishveshwara S, Chandra N. Rule-based modelling of iron homeostasis in tuberculosis. Mol Biosyst. 2011 Oct;7(10):2750-68. doi: 10.1039/c1mb05093a. Epub 2011 Aug 11.
  102. Bhardwaj A, Scaria V, Raghava GP, Lynn AM, Chandra N, Banerjee S, Raghunandanan MV, Pandey V, Taneja B, Yadav J, Dash D, Bhattacharya J, Misra A, Kumar A, Ramachandran S, Thomas Z; Open Source Drug Discovery Consortium, Brahmachari SK. Open source drug discovery--a new paradigm of collaborative research in tuberculosis drug development. Tuberculosis (Edinb). 2011 Sep;91(5):479-86. doi: 10.1016/j.tube.2011.06.004. Epub 2011 Jul 22. Review.
  103. Yeturu K, Chandra N. PocketAlign a novel algorithm for aligning binding sites in protein structures. J Chem Inf Model. 2011 Jul 25;51(7):1725-36. doi: 10.1021/ci200132z. Epub 2011 Jun 21.
  104. Arora A, Chandra NR, Das A, Gopal B, Mande SC, Prakash B, Ramachandran R, Sankaranarayanan R, Sekar K, Suguna K, Tyagi AK, Vijayan M. Structural biology of Mycobacterium tuberculosis proteins: the Indian efforts. Tuberculosis (Edinb). 2011 Sep;91(5):456-68. doi: 10.1016/j.tube.2011.03.004. Epub 2011 Apr 22. Review.
  105. Chandra N, Kumar D, Rao K. Systems biology of tuberculosis. Tuberculosis (Edinb). 2011 Sep;91(5):487-96. doi: 10.1016/j.tube.2011.02.008. Epub 2011 Apr 1. Review.

    106. 2010

  106. Chandra N, Anand P, Yeturu K. Structural bioinformatics: deriving biological insights from protein structures. Interdiscip Sci. 2010 Dec;2(4):347-66. doi: 10.1007/s12539-010-0045-6. Epub 2010 Dec 12. Review.
  107. Chaturvedi R, Bansal K, Narayana Y, Kapoor N, Sukumar N, Togarsimalemath SK, Chandra N, Mishra S, Ajitkumar P, Joshi B, Katoch VM, Patil SA, Balaji KN. The multifunctional PE_PGRS11 protein from Mycobacterium tuberculosis plays a role in regulating resistance to oxidative stress. J Biol Chem. 2010 Oct 1;285(40):30389-403. doi: 10.1074/jbc.M110.135251. Epub 2010 Jun 17.
  108. Yeturu K, Utriainen T, Kemp GJ, Chandra N. An automated framework for understanding structural variations in the binding grooves of MHC class II molecules. BMC Bioinformatics. 2010 Jan 18;11 Suppl 1:S55. doi: 10.1186/1471-2105-11-S1-S55.
  109. Raman K, Bhat AG, Chandra N. A systems perspective of host-pathogen interactions: predicting disease outcome in tuberculosis. Mol Biosyst. 2010 Mar;6(3):516-30. doi: 10.1039/b912129c. Epub 2009 Dec 14.
  110. Gupta P, Rajeswari H, Arumugam M, Mishra S, Bhagavat R, Anand P, Chandra N, Srinivasan R, Indi S, Ajitkumar P. Mycobacterium tuberculosis FtsZ requires at least one arginine residue at the C-terminal end for polymerization in vitro. Acta Biochim Biophys Sin (Shanghai). 2010 Jan;42(1):58-69.

    111. 2009

  111. Chandra N. Computational systems approach for drug" target discovery. Expert Opin Drug Discov. 2009 Dec;4(12):1221-36. doi: 10.1517/17460440903380422.
  112. Raman K, Vashisht R, Chandra N. Strategies for efficient disruption of metabolism in Mycobacterium tuberculosis from network analysis. Mol Biosyst. 2009 Dec;5(12):1740-51. doi: 10.1039/B905817F.
  113. Prabu JR, Thamotharan S, Khanduja JS, Chandra NR, Muniyappa K, Vijayan M. Crystallographic and modelling studies on Mycobacterium tuberculosis RuvA Additional role of RuvB-binding domain and inter species variability. Biochim Biophys Acta. 2009 Jul;1794(7):1001-9. doi: 10.1016/j.bbapap.2009.04.003. Epub 2009 Apr 15.
  114. Raman K, Chandra N. Flux balance analysis of biological systems: applications and challenges. Brief Bioinform. 2009 Jul;10(4):435-49. doi: 10.1093/bib/bbp011. Epub 2009 Mar 15.
  115. Bhadra S, Bhattacharyya C, Chandra NR, Mian IS. A linear programming approach for estimating the structure of a sparse linear genetic network from transcript profiling data. Algorithms Mol Biol. 2009 Feb 24;4:5. doi: 10.1186/1748-7188-4-5.
  116. Vani J, Chatterjee J, Shaila MS, Nayak R, Chandra NR. Structural basis for the function of anti-idiotypic antibody in immune memory. Mol Immunol. 2009 Mar;46(6):1250-5. doi: 10.1016/j.molimm.2008.11.019. Epub 2009 Jan 20.
  117. Das S, Laxminarayana SV, Chandra N, Ravi V, Desai A. Heat shock protein 70 on Neuro2a cells is a putative receptor for Japanese encephalitis virus. Virology. 2009 Mar 1;385(1):47-57. doi: 10.1016/j.virol.2008.10.025. Epub 2008 Dec 7.

    118. 2008

  118. Raman K, Chandra N. Mycobacterium tuberculosis interactome analysis unravels potential pathways to drug resistance. BMC Microbiol. 2008 Dec 23;8:234. doi: 10.1186/1471-2180-8-234.
  119. Raman K, Yeturu K, Chandra N." targetTB: a" target identification pipeline for Mycobacterium tuberculosis through an interactome, reactome and genome-scale structural analysis. BMC Syst Biol. 2008 Dec 19;2:109. doi: 10.1186/1752-0509-2-109.
  120. Yeturu K, Chandra N."PocketMatch: a new algorithm to compare binding sites in protein structures. BMC Bioinformatics. 2008 Dec 17;9:543. doi: 10.1186/1471-2105-9-543.
  121. Nagaraj VA, Arumugam R, Chandra NR, Prasad D, Rangarajan PN, Padmanaban G. Localisation of Plasmodium falciparum uroporphyrinogen III decarboxylase of the heme-biosynthetic pathway in the apicoplast and characterisation of its catalytic properties. Int J Parasitol. 2009 Apr;39(5):559-68. doi: 10.1016/j.ijpara.2008.10.011. Epub 2008 Nov 14.
  122. Prabu JR, Manjunath GP, Chandra NR, Muniyappa K, Vijayan M. Functionally important movements in RecA molecules and filaments: studies involving mutation and environmental changes. Acta Crystallogr D Biol Crystallogr. 2008 Nov;64(Pt 11):1146-57. doi: 10.1107/S0907444908028448. Epub 2008 Oct 18. Erratum in: Acta Crystallogr D Biol Crystallogr. 2012 Jul;68(Pt 7):871.

    123. 2007

  123. Damodaran D, Jeyakani J, Chauhan A, Kumar N, Chandra NR, Surolia A. CancerLectinDB: a database of lectins relevant to cancer. Glycoconj J. 2008 Apr;25(3):191-8. Epub 2007 Nov 24.
  124. Gangadhar V, Jeyakani JJ, Shaila MS, Nayak R, Chandra N. Perpetuation of immunological memory through common MHC-I binding modes of peptidomimic and antigenic peptides. Biochem Biophys Res Commun. 2007 Dec 14;364(2):308-12. Epub 2007 Oct 12.
  125. Kalidas Y, Chandra N. PocketDepth: a new depth based algorithm for identification of ligand binding sites in proteins. J Struct Biol. 2008 Jan;161(1):31-42. Epub 2007 Sep 15.
  126. Khodade P, Malhotra S, Kumar N, Iyengar MS, Balakrishnan N, Chandra N. Cytoview: development of a cell modelling framework. J Biosci. 2007 Aug;32(5):965-77. Review.
  127. Poddar A, Chandra N, Ganapathiraju M, Sekar K, Klein-Seetharaman J, Reddy R, Balakrishnan N. Evolutionary insights from suffix array-based genome sequence analysis. J Biosci. 2007 Aug;32(5):871-81.
  128. Singh DD, Chandran D, Jeyakani J, Chandra N. Scanning the genome of Mycobacterium tuberculosis to identify potential lectins. Protein Pept Lett. 2007;14(7):683-91.
  129. Sriharsha SN, Pai KS; Suhas, Shashikanth S, Chandra N, Prabhu KR. Synthesis, docking and anti-tumor activity of beta-L-1,3-thiazolidine pyrimidine nucleoside analogues. Med Chem. 2007 Sep;3(5):425-32.
  130. Verkhedkar KD, Raman K, Chandra NR, Vishveshwara S. Metabolome based reaction graphs of M. tuberculosis and M. leprae: a comparative network analysis. PLoS One. 2007 Sep 12;2(9):e881.
  131. Kanade SR, Suhas VL, Chandra N, Gowda LR. Functional interaction of diphenols with polyphenol oxidase. Molecular determinants of substrate/inhibitor specificity. FEBS J. 2007 Aug;274(16):4177-87. Epub 2007 Jul 25.
  132. Dash BP, Mukherjee S, Suhas VL, Chandra N. Interaction profiling of T-cell epitopes with MHC-class I molecules. Protein Pept Lett. 2007;14(6):557-64.
  133. Raman K, Rajagopalan P, Chandra N. Hallmarks of mycolic acid biosynthesis: a comparative genomics study. Proteins. 2007 Nov 1;69(2):358-68.
  134. Vani J, Justin J, Nagasuma RC, Nayak R, Shaila MS. Peptidomimics of antigen are present in variable region of heavy and light chains of anti-idiotypic antibody and function as surrogate antigen for perpetuation of immunological memory. Mol Immunol. 2007 Jul;44(13):3345-54. Epub 2007 Apr 3.
  135. Bhattacharya S, Bhattacharyya C, Chandra NR. Comparison of protein structures by growing neighborhood alignments. BMC Bioinformatics. 2007 Mar 6;8:77.

    136. 2006

  136. Konkimalla VB, Suhas VL, Chandra NR, Gebhart E, Efferth T. Diagnosis and therapy of oral squamous cell carcinoma. Expert Rev Anticancer Ther. 2007 Mar;7(3):317-29. Review.
  137. Bhattacharya S, Bhattacharyya C, Chandra NR. Projections for fast protein structure retrieval. BMC Bioinformatics. 2006 Dec 18;7 Suppl 5:S5.
  138. Ramesh S, Bharath MM, Chandra NR, Rao MR. A K52Q substitution in the globular domain of histone H1t modulates its nucleosome binding properties. FEBS Lett. 2006 Oct 30;580(25):5999-6006. Epub 2006 Oct 5.
  139. Vinod PK, Konkimalla B, Chandra N. In-silico pharmacodynamics: correlation of adverse effects of H2-antihistamines with histamine N-methyl transferase binding potential. Appl Bioinformatics. 2006;5(3):141-50.
  140. Prabu JR, Thamotharan S, Khanduja JS, Alipio EZ, Kim CY, Waldo GS, Terwilliger TC, Segelke B, Lekin T, Toppani D, Hung LW, Yu M, Bursey E, Muniyappa K, Chandra NR, Vijayan M. Structure of Mycobacterium tuberculosis RuvA, a protein involved in recombination. Acta Crystallogr Sect F Struct Biol Cryst Commun. 2006 Aug 1;62(Pt 8):731-4. Epub 2006 Jul 24.
  141. Chandra N. Common scaffolds, diverse recognition profiles. Structure. 2006 Jul;14(7):1093-4. No abstract available.
  142. Chandra NR, Kumar N, Jeyakani J, Singh DD, Gowda SB, Prathima MN. Lectindb: a plant lectin database. Glycobiology. 2006 Oct;16(10):938-46. Epub 2006 Jun 16.
  143. Krishna R, Manjunath GP, Kumar P, Surolia A, Chandra NR, Muniyappa K, Vijayan M. Crystallographic identification of an ordered C-terminal domain and a second nucleotide-binding site in RecA: new insights into allostery. Nucleic Acids Res. 2006 Apr 28;34(8):2186-95. Print 2006.

    144. 2005

  144. Raman K, Rajagopalan P, Chandra N. Flux balance analysis of mycolic acid pathway:" targets for anti-tubercular drugs. PLoS Comput Biol. 2005 Oct;1(5):e46. Epub 2005 Oct 14.
  145. Prasad T, Subramanian T, Hariharaputran S, Chaitra HS, Chandra N. Extracting hydrogen-bond signature patterns from protein structure data. Appl Bioinformatics. 2004;3(2-3):125-35.
  146. Chaitra MG, Hariharaputran S, Chandra NR, Shaila MS, Nayak R. Defining putative T cell epitopes from PE and PPE families of proteins of Mycobacterium tuberculosis with vaccine potential. Vaccine. 2005 Jan 26;23(10):1265-72.

    147. 2004

  147. Raval S, Gowda SB, Singh DD, Chandra NR. A database analysis of jacalin-like lectins: sequence-structure-function relationships. Glycobiology. 2004 Dec;14(12):1247-63. Epub 2004 Aug 25.
  148. Kumar P, Rao AG, Hariharaputran S, Chandra N, Gowda LR. Molecular mechanism of dimerization of Bowman-Birk inhibitors. Pivotal role of ASP76 in the dimerzation. J Biol Chem. 2004 Jul 16;279(29):30425-32. Epub 2004 Apr 28.
  149. Dhanasekaran S, Chandra NR, Chandrasekhar Sagar BK, Rangarajan PN, Padmanaban G. Delta-aminolevulinic acid dehydratase from Plasmodium falciparum: indigenous versus imported. J Biol Chem. 2004 Feb 20;279(8):6934-42. Epub 2003 Nov 24.

    150. 2003

  150. Konkimalla VB, Chandra N. Determinants of histamine recognition: implications for the design of antihistamines. Biochem Biophys Res Commun. 2003 Sep 19;309(2):425-31.
  151. Bharath MM, Chandra NR, Rao MR."Molecular modeling of the chromatosome particle. Nucleic Acids Res. 2003 Jul 15;31(14):4264-74.
  152. Ramachandraiah G, Chandra NR, Surolia A, Vijayan M. Computational analysis of multivalency in lectins: structures of garlic lectin-oligosaccharide complexes and their aggregates. Glycobiology. 2003 Nov;13(11):765-75. Epub 2003 Jul 8.
  153. Shobini J, Mishra AK, Chandra N."Conformation of gramicidin-A in CTAB micellar media. J Photochem Photobiol B. 2003 May-Jun;70(2):117-24.
  154. Datta S, Krishna R, Ganesh N, Chandra NR, Muniyappa K, Vijayan M. Crystal structures of Mycobacterium smegmatis RecA and its nucleotide complexes. J Bacteriol. 2003 Jul;185(14):4280-4.
  155. Datta S, Ganesh N, Chandra NR, Muniyappa K, Vijayan M. Structural studies on MtRecA-nucleotide complexes: insights into DNA and nucleotide binding and the structural signature of NTP recognition. Proteins. 2003 Feb 15;50(3):474-85.
  156. Prasad T, Prathima MN, Chandra N."Detection of hydrogen-bond signature patterns in protein families. Bioinformatics. 2003 Jan;19(1):167-8.

    157. 2002

  157. Bharath MM, Chandra NR, Rao MR. Prediction of an HMG-box fold in the C-terminal domain of histone H1: insights into its role in DNA condensation. Proteins. 2002 Oct 1;49(1):71-81.
  158. Bharath MM, Ramesh S, Chandra NR, Rao MR. Identification of a 34 amino acid stretch within the C-terminus of histone H1 as the DNA-condensing domain by site-directed mutagenesis. Biochemistry. 2002 Jun 18;41(24):7617-27.
  159. Ramachandraiah G, Chandra NR, Surolia A, Vijayan M. Re-refinement using reprocessed data to improve the quality of the structure: a case study involving garlic lectin. Acta Crystallogr D Biol Crystallogr. 2002 Mar;58(Pt 3):414-20. Epub 2002 Feb 21.