Scientific Publications  |  Chapters in the Books



Publications

2017

  1. Kadam K., Karbhal R., Jayaraman V. K., Sawant S., Kulkarni-Kale U. AllerBase: a comprehensive allergen knowledgebase. Database (2017) Vol. 2017.  doi:10.1093/database/bax066Database. [PDF]
     

  2. Rohan J. Meshram, Vijay B. Baladhye, Rajesh N. Gacche, Bhausaheb K. Karale, Rajendra B. Gaikar, Pharmacophore Mapping Approach for Drug Target Identification: A chemical synthesis and in silico study on novel thiadiazole compounds,  J. Clin.  Diag. Res., 11 (7):KF01-KF08, 2017. [PDF]
     

  3. Parulekar NN, Kolekar P, Jenkins A, Kleiven S, Utkilen H, Johansen A, Sawant  S, Kulkarni-Kale U, Kale M, Sæbø M. Characterization of bacterial community associated with phytoplankton bloom in a eutrophic lake in South Norway using 16SrRNA gene amplicon sequence analysis. PLoS One. 2017 Mar 10;12(3). [PDF]
     

  4. Waman VP, Kale MM, Kulkarni-Kale U. Genetic diversity and evolution of dengue virus serotype 3: A comparative genomics study. Infect Genet Evol. 2017 Apr; 49:234-240. [PDF]
     

  5. Augustine T, Chaudhary P, Gupta K, Islam S, Ghosh P, Santra MK, Mitra D. Cyclin F/FBXO1 Interacts with HIV-1 Viral Infectivity Factor (Vif) and Restricts Progeny Virion Infectivity by Ubiquitination and Proteasomal Degradation of Vif Protein through SCF(cyclin F) E3 Ligase Machinery. J Biol Chem. 2017 Mar 31;292(13):5349-5363. [PDF]
     

  6. Shrikant V Hese, Rohan J Meshram, Rahul D Kamble, Pratima P Mogle, Kapil K Patil, Sonali S Kamble, Rajesh N Gacche, Bhaskar S Dawane Antidiabetic and allied biochemical roles of new chromeno-pyrano pyrimidine compounds: synthesis, in vitro and in silico analysis. Medicinal Chemistry Research, 2017, 26: 4 : 805 - 818. [PDF]

2016

  1. Rajesh N. Gacche, Rohan J. Meshram, Ashwini A. Dawane, Sonali S. Kamble, Ganpat P. Shinde, Vivek N. Dhabadge and Kapil K. Patil. Modeling studies of arginase from Helicobacter pylori divulge novel inhibitor-protein interactions. Clinical Proteomics & Bioinformatics, 2016, 1:3: 54-61.

  2. Tidke P, Maurya D, Kulkarni A, Devasagayam T, Pal J. Radiation-induced Oxidative stress regulates protein synthesis by modulating the heme-regulated Eukaryotic initiation factor 2 alpha (eIF2a) kinase in human K562 cells. (Accepted in Indian J Biochem Biophys. In Press)

  3. Mathai J, Mittal SP, Alam A, Ranade P, Mogare D, Patel S, Saxena S, Ghorai S, Kulkarni AP, Chattopadhyay S.SMAR1 binds to T(C/G) repeat and inhibits tumor progression by regulating miR-371-373 cluster. Sci. Rep. 6, 33779; doi: 10.1038/srep33779 Sep 2016.

  4. Vijay B. Baladhye, Fawade M. M. Affinity Based Proteomic Profiling of Yeast in Response to Phenobaritone. Res J Pharm Biol Chem Sci, 7(5):94-104, 2016.

  5. Sengupta D, Joshi M, Athale CA, Chattopadhyay A.What can simulations tell us about GPCRs: Integrating the scales. Methods Cell Biol. 2016;132:429-52.

  6. Waman VP, Kolekar P, Ramtirthkar MR, Kale MM, Kulkarni-Kale U. Analysis of genotype diversity and evolution of Dengue virus serotype 2 using complete genomes. PeerJ. 2016 Aug 24;4:e2326. doi: 10.7717/peerj.2326. [Best Paper in the International Bioinformatics Conference (InCoB) held at Singapore during Sep 21-23, 2016.]

  7. Kolekar P, Pataskar A, Kulkarni-Kale U, Pal J, Kulkarni A. IRESPred: Web Server for Prediction of Cellular and Viral Internal Ribosome Entry Site (IRES). Sci Rep. (2016) 6:27436. doi: 10.1038/srep27436.

  8. Waman VP, Kasibhatla SM, Kale MM, Kulkarni-Kale U. Population genomics of dengue virus serotype 4: insights into genetic structure and evolution. Arch Virol. 2016 Aug;161(8):2133-48. doi: 10.1007/s00705-016-2886-8. Epub 2016 May 12.
  9. Gaikwad PS, Panicker L, Mohole M, Sawant S, Mukhopadhyaya R, Nath BB. Differential sensitivity of Chironomus and human hemoglobin to gamma radiation. Biochemical and Biophysical Research Communications 476 (2016) 371-378.

  10. Agrawal S, Kulabhusan PK, Joshi M, Bodas D, Paknikar KM. A high affinity phage-displayed peptide as a recognition probe for the detection of Salmonella Typhimurium. J Biotechnol. 2016 May 21;231:40-45.

  11. Tandale A, Joshi M, Sengupta D. Structural insights and functional implications of inter-individual variability in ß2-adrenergic receptor. Sci Rep. 2016 Apr 14;6:24379.

  12. Kulkarni AP, Mittal SP. Sequence data mining in search of hookworm (Necator americanus) microRNAs. Gene. 2016 May 31. pii: S0378-1119(16)30434-6. doi: 10.1016/j.gene.2016.05.039.

  13. Kolekar PS, Waman VP, Kale MM, Kulkarni-Kale U. RV-Typer: A Web Server for Typing of Rhinoviruses Using Alignment-Free Approach. PLoS One. 2016 Feb 12;11(2):e0149350. doi: 10.1371/journal.pone.0149350.


  14. Joshi M, Rajpathak SN, Narwade SC, Deobagkar D. Ensemble-Based Virtual Screening and Experimental Validation of Inhibitors Targeting a Novel Site of Human DNMT1. 
    Chem Biol Drug Des. 2016 Jul;88(1):5-16. doi: 10.1111/cbdd.12741.  
  15. Margaret Susan Winchester, Rhonda BeLue, Tolu Oni, Ursula Wittwer-Backofen, Deepti Deobagkar*, Hans Onya, T. Alafia Samuels, Stephen A Matthews,  Connor Stone, BA; Collins O. Airhihenbuwa. The Pan-University Network for Global Health: Framework for collaboration and review of global health needs. Globalization and Health (2016) 12:13 DOI: 10.1186/s12992-016-0151-2

  16. Gawade RL, Chakravarty DK,  Debgupta J,  Sangtani E, Narawade S, Gonnade RG,   Puranik VG, Deobagkar DD*. Comparative Study of dG Affinity vs.DNA Methylation Modulating Properties of Side Chain Derivatives of Procainamide: Insight into its DNA Hypomethylating Effect. Royal Soceity of Chemistry (RSC) Advances 2016, DOI: 10.1039/C5RA20012A Accepted 04 Jan 2016 First published online 07 Jan 2016. [PDF]

  17. Mane A, Vidhate P, Kusro C, Waman V, Saxena V, Kulkarni-Kale U, Risbud A. Molecular mechanisms associated with Fluconazole resistance in clinical Candida albicans isolates from India. Mycoses. 2016 Feb;59(2):93-100. doi:10.1111/myc.12439. [PDF]

  18. Sandhu V, Bowitz Lothe IM, Labori KJ, Skrede ML, Hamfjord J, Dalsgaard AM, Buanes T, Dube G, Kale MM, Sawant S, Kulkarni-Kale U, Børresen-Dale AL, Lingjærde OC, Kure EH. Differential expression of miRNAs in pancreatobiliary type of periampullary adenocarcinoma and its associated stroma. Mol Oncol. 2016 Feb;10(2):303-16. doi:10.1016/j.molonc.2015.10.011


2015

  1. Karbhal R, Sawant S, Kulkarni-Kale U. BioDB extractor: customized data extraction system for commonly used bioinformatics databases. BioData Min. 2015 Oct 28;8:31. doi: 10.1186/s13040-015-0067-z. eCollection 2015. [PDF]
    Karbhal R, Sawant S, Kulkarni-Kale U. Erratum to: BioDB extractor: customized data extraction system for commonly used bioinformatics databases. BioData Min. 2016 Feb 2;9:8. doi: 10.1186/s13040-016-0081-9.

  2. Panikar CS, Rajpathak SN, Abhyankar V, Deshmukh S, Deobagkar DD*. Presence of  DNA methyltransferase activity and CpC methylation in Drosophila melanogaster. Mol Biol Rep. 2015 Dec;42(12):1615-1621. doi:10.1007/s11033-015-3931-5.

  3. Chavan SG, Deobagkar DD*. An In Silico Insight into Novel Therapeutic Interaction of LTNF Peptide-LT10 and Design of Structure Based Peptidomimetics for Putative Anti-Diabetic Activity. PLoS One. 2015 Mar 27;10(3):e0121860. doi:10.1371/journal.pone.0121860.

  4. Kulkarni RR, Shaiwale NS, Deobagkar DN, Deobagkar DD. Synthesis and extracellular accumulation of silver nanoparticles by employing radiation-resistant Deinococcus radiodurans, their characterization, and determination of bioactivity. Int J Nanomedicine. 2015 Jan 29;10:963-974. doi: 10.2147/IJN.S72888.


  5. Roy SV, Hajare SN, Gautam S, Deobagkar DD*,  Sharma A. Sporulation associated mother cell lysis in Bacillus displays markers of programmed cell death. 2015 Current Science. 109:1283-1294. [PDF]


  6. Shaiwale NS, Basu B, Deobagkar DD*, Deobagkar DN, Apte SK. DNA adenine hypomethylation leads to metabolic rewiring in Deinococcus radiodurans. J Proteomics. 2015 Aug 3;126:131-9. doi: 10.1016/j.jprot.2015.05.036.

  7. Gupta S, Chavan S, Deobagkar DN, Deobagkar DD*. Bio/chemoinformatics in India: an outlook. Brief Bioinform. 2015 Jul;16(4):710-731. [PDF]

2014

  1. Kulkarni-Kale U, Raskar-Renuse S, Natekar-Kalantre G, Saxena SA. Antigen-Antibody Interaction Database (AgAbDb): a compendium of antigen-antibody interactions. Methods Mol Biol. 2014;1184:149-164. [Abstract]

  2. Desai DV, Kulkarni-Kale U. T-cell epitope prediction methods: an overview. Methods Mol Biol. 2014;1184:333-364. [Abstract] 
  3. Waman VP, Kolekar PS, Kale MM, Kulkarni-Kale U. Population structure  and evolution of rhinoviruses. PLoS One. 2014;  9(2):e88981. doi:10.1371/journal.pone.0088981.
  4. Kolekar P, Hake N, Kale M, Kulkarni-Kale U. WNV Typer: a server for genotyping of West Nile viruses using an alignment-free method based on a return time distribution. 
    J Virol Methods. 2014 Mar;198:41-55. [PDF]
  5. Mittal SP, Kulkarni AP, Mathai J, Chattopadhyay S, Pal JK. Dose-dependent differential response of mammalian cells to cytoplasmic stress is mediated through the heme-regulated eIF2α kinase. 
    Int J Biochem Cell Biol. 2014; 54:186-197. [PDF]
  6. Agrawal MR, Ozarkar AD, Gupta S, Deobagkar DN, Deobagkar DD. Comparative study of Plasmodium falciparum erythrocyte membrane protein 1-DBLα domain variants with respect to antigenic variations and docking interaction analysis with glycosaminoglycans. Mol Biosyst. 2014 Jul 29;10(9):2466-2479. doi: 10.1039/c4mb00274a.

  7. Chavan SG, Deobagkar DD*. In silico molecular interaction analysis of LTNF peptide-LT10 with snake venom enzymes. Protein Pept Lett. 2014 Jul;21(7):646-56. [Abstract]

  8. Shahane G, Parsania C, Sengupta D, Joshi M. Molecular Insights into the Dynamics of Pharmacogenetically Important N-Terminal Variants of the Human β2-Adrenergic Receptor. PLoS Comput Biol. 2014 Dec 11;10(12):e1004006
  9. Rajpathak SN, Vellarikkal SK, Patowary A, Scaria V, Sivasubbu S, Deobagkar DD. Human 45,X fibroblast transcriptome reveals distinct differentially expressed genes including long noncoding 
    RNAs potentially associated with the pathophysiology of Turner syndrome. PLoS One. 2014 Jun 16;9(6):e100076. doi:10.1371/journal.pone.0100076.
  10. Rajpathak SN, Deobagkar DD. Evidence for epigenetic alterations in Turner syndrome opens up feasibility of new pharmaceutical interventions. Current Pharmaceutical Design. 2014;20(11):1778-1785. [Abstract]
    
  11. Mukherjee S, Sainis KB, Deobagkar DD*. F1 hybrids of BALB/c and C57BL/6 mouse strains respond differently to low-dose ionizing radiation exposure. J Genet. 2014 Dec;93(3):667-682.  [PDF]
  12. Khandeparkar R., R. M Meena, Deobagkar DD*.  Bacterial diversity in deep-sea sediments from Afanasiy–Nikitin seamount, equatorial Indian Ocean. Geomicrobiology Journal 2014 31:10, 942-949. [PDF] 
  13. Nath A., Bharathi L, Deobagkar DD. Insights in to the structural and functional aspects of Rel a by molecular modelling and docking calculations. 
    International Journal of Pharmacy and Pharmaceutical Sciences, 2014; 6:958-967. [PDF]
  14. Anjali D. Apte-Deshpande, Mandar S. Paingankar, Mangesh D. Gokhale  & Dileep N. Deobagkar. Serratia odorifera mediated enhancement in susceptibility of Aedes aegypti for chikungunya virus. 
    Indian J Med Res, 2014; 139: 762-768. [PDF]

 

2013

  1. Balakrishnan L, Soman S, Patil YB, Advani J, Thomas JK, Desai DV, Kulkarni-Kale U, Harsha HC, Prasad TS, Raju R, Pandey A, Dimitriadis E,Chatterjee A. IL-11/IL11RA receptor mediated signaling: a web accessible knowledgebase. Cell Commun Adhes. 2013; 20: 81-86. doi: 10.3109/15419061.2013.791683

  2. Joshi M, Kulkarni A, Pal JK. Small molecule modulators of eukaryotic initiation factor 2a kinases, the key regulators of protein synthesis. Biochimie. 2013 Nov;95(11):1980-1990. [PDF]

  3. Mittal SP, Mathai J, Kulkarni AP, Pal JK, Chattopadhyay S. miR-320a regulates erythroid differentiation through MAR binding protein SMAR1. Int J Biochem Cell Biol. 2013 Nov;45(11):2519-2529.  [Abstract]

  4. Kolhi S. and Kolaskar A.S, Metabolic Network Analysis: Current Status and Way Forward. Current Bioinformatics Vol. 8, 2013.

  5. Ponnusamy S, Zinjarde S, Bhargava S, Kulkarni-Kale U, Sawant S, and Ravikumar A. Deciphering the inactivation of Human Pancreatic a-Amylase, an anti-diabetic target, by Bisdemethoxycurcumin, a small molecule inhibitor, isolated from Curcuma longa. Natural Products Journal. 2013; 3: 15-25.

  6. Yadav A, Jayaraman VK, Kale MM, Kulkarni-Kale U. Phylogenetic clustering of protein sequences using Recurrence Quantification Analysis. Advanced Science Letters. 2013; 19: 1336-1339.
  7. Sonali P. Patil, Abhay N. Salve, Vijay B. Baladhye. Proteomic Profiling of Caralluma fimbriata Cell Wall During Drought Condition. Int J Pharm Bio Sci 2013 July; 4(3): (B) 385 – 395.
  8. Biradar V, Narwade S, Paingankar M, Deobagkar D.D. White Spot Syndrome Virus infection in Penaeus monodon is facilitated by housekeeping molecules. J Biosci. 2013; 38: 917-924.
  9. Basu S, Deobagkar DD, Matondkar SG, Furtado I. Culturable bacterial flora associated with the dinoflagellate green Noctiluca miliaris during active and declining bloom phases in the Northern Arabian Sea. Microbial Ecology. 2013; 65: 934-54.

 

2012

  1. Kulkarni-Kale, U., Waman V., Raskar S., Mehta S., & Saxena S. (2012). Genome To Vaccinome: Role of Bioinformatics, Immunoinformatics & Comparative Genomics. Current Bioinformatics (CBIO). Volume 7, Number 4, 454-466. [Invited review article in a special Hot Topic issue titled “Contemporary Trends in Bioinformatics Relevant for Some Important Biomedical Problems”.

  2. Mallipeddi, P. L.*, Joshi, M., Briggs, J. M. Pharmacophore-based virtual screening to aid in the identification of unknown protein function. Chem. Biol. Drug Des. 2012 Dec;80(6):828-42

  3. Kolhi S. and Kolaskar A. S., Categorization of metabolome in bacterial systems. Bioinformation, 2012;8:309-15.

  4. Kolekar P., Kale M., Kulkarni-Kale U., Alignment-free distance measure based on return time distribution for sequence analysis: Applications to clustering, molecular phylogeny and subtyping, Molecular Phylogenetics and Evolution, (2012) 65(2), 510-522.

  5. Deobagkar DD*, Panikar C, Rajpathak SN, Shaiwale NS, Mukherjee S. An immunochemical method for detection and analysis of changes in methylome.Methods. 2012 Feb;56(2):260-267. doi: 10.1016/j.ymeth.2011.10.003.

  6. Deshmukh S., Panniker C. Deobagkar DD*. Exposure to heat stress modulates DNA methyltransferase activity in S2 cell line of Drosophila melanogaster. (2012) Drosophila Information service, 95, 89-91

  7. Tanu, Deobagkar, D.D., Khandeparker, R., Sreepada, R.A., Sanaye, S.V., Pawar, H.B. A study on bacteria associated with the intestinal tract of farmed yellow seahorse, Hippocampus kuda (Bleeker, 1852): Characterization and extracellular enzymes. Aquaculture Research, 2012;  vol.43(3); 386-394. [PDF]

  8. Radhakrishnan A, Raju R, Tuladhar N, Subbannayya T, Thomas JK, Goel R, Telikicherla D, Palapetta SM, Rahiman BA, Venkatesh DD, Urmila KK, Harsha HC, Mathur PP, Prasad TS, Pandey A, Shemanko C, Chatterjee A. A pathway map of prolactin signaling. J Cell Commun Signal. 2012 Aug;6(3):169-73. doi:10.1007/s12079-012-0168-0.

  9. Banerji A., Magarkar A.; "How happy is your web browsing? A model to quantify satisfaction of an Internet user searching for desired information"; Physica A: Statistical Mechanics and its Applications, 391 (2012) : 4215-4224 [Abstract]

  10. Using Pig on Hadoop for data analysis in Bioinformatics, Smita Saxena, International Journal of Advanced Research in computer Science, Vol. 3(7),  2012, pp 240-245.

 

2011

  1. Kolaskar A. S. and Shweta Kolhi. Pune University Metabolic Pathway Engineering (PuMPE) Resource.  Journal of Emerging Trends in Computing and Information Sciences. 2011; 2: 325-331

  2. Kolekar PS, Kale M, Kulkarni-Kale U: Genotyping of Mumps viruses based on SH gene: Development of a server using alignment-free and alignment-based methods. Immunome Res. 2011. 7(3):1-7.

  3. Singh P.,  Banerji A. (2011). Case for an RNA-prion world: a hypothesis based on conformational diversity. J Biol Phys, 37:185-188, DOI 10.1007/s10867-011-9219-7. [Abstract]

  4. Banerji A, Ghosh I. (2011). Fractal symmetry of protein interior: what have we learned? Cell Mol Life Sci.  DOI 10.1007/s00018-011-0722-6. [Abstract]

  5. Khandeparker, R. ,Verma, P., Meena, R., Deobagkar, D.D*. Phylogenetic diversity of carbohydrate degrading culturable bacteria from Mandovi and Zuari estuaries, Goa, west coast of India.  Estuarine, Coastal and Shelf Science. 2011, 95; 359-366.

  6. Khandeparker R, Verma P, Deobagkar D*. A novel halotolerant xylanase from marine isolate Bacillus subtilis cho40: gene cloning and sequencing. New Biotechnology 2011 Oct;28(6):814-21.

  7. Sanjay Mukherjee, K. B. Sainis, Deepti Deobagkar*, Identification of methylated genes in BALB/c mice lever using monoclonal antibody combined with the high throughput cDNA microarray approach. Current Science, 2011,  101, 66-72.

 

2010

  1. Banerji A., Ghosh I. , Mathematical criteria to observe mesoscopic emergence of protein biochemical properties. Journal of Mathematical Chemistry, Nov. 2010, Volume 49, Number 3, 643-665, DOI: 10.1007/s10910-010-9760-9. [Abstract]

  2. Dey S., Jejurikar S., Bhattacharya S.K. , Banerji A., Adhi K.P., Dharmadhikari C.V., Electrical characterization of zinc oxide/aluminum nitride thin film precursor field effect transistor structures: A conducting atomic force microscopy and density functional theoretical study. J. Appl. Phys. 108, 094510 (2010); doi:10.1063/1.3471815 [Abstract]

  3. Kolekar PS, Kale MM, Kulkarni-Kale U: `Inter-Arrival Time' Inspired Algorithm and its Application in Clustering and Molecular Phylogeny. AIP Conference Proceedings 2010, 1298(1):307-312. [Abstract]

  4. Kulkarni-Kale U, Sawant S., Chavan V. Bioinformatics education in India. Briefings in Bioinformatics. Advance Access published on August 12, 2010.doi:10.1093/bib/bbq027.  [Abstract]

 

2009

  1. Banerji A, Ghosh I (2009);  Revisiting the Myths of Protein Interior: Studying Proteins with Mass-Fractal Hydrophobicity-Fractal and Polarizability-Fractal Dimensions. PLoS ONE 4(10): e7361. doi:10.1371/journal.pone.0007361 [PDF]

  2. Banerji A, Ghosh I (2009); A new computational model to study mass inhomogeneity and hydrophobicity inhomogeneity in proteins; Eur. Biophys J 38: 577–587.[PDF]

  3. S.M. Kotwal, V. Shankar(2009);  Immobilized invertase; Biotechnol Adv. 2009 Jul-Aug;27(4):311-22   [PDF]

  4. Vinekar R, Ghosh I. Determination of phosphorylation sites for NADP-specificisocitrate dehydrogenase from mycobacterium tuberculosis. J Biomol Struct Dyn. 2009 Jun;26(6):741-54.  

 

2008

  1. Hosseini Ashraf , Ranade Suvidya H. , Ghosh Indira, Khandekar Pramod (2008). Simple sequence repeats in different genome sequences of Shigella and comparison with high GC and AT-rich genomes. DNA Sequence. , 19, 167-76 [PDF]

 

2007

  1. Rahim F*, Deshpande A**, Hosseini A***. Fuzzy Expert System For Fluid Management In General Anaesthesia. Journal of Clinical and Diagnostic Research [Serial Online] August 2007, 1:256-267. [PDF]

  2. Chaitanya N. Hiremath (2007) Abbreviated Profile of Drugs (A-POD): A unique numerical and graphical representation for compound properties and its use in ADMET prediction,  IJIB,  1(1), 44-50.

  3. Greenbaum, J. A., Andersen, P. H., Blythe, M., Bui, H. H., Cachau, R. E., Crowe, J., Davies, M., Kolaskar, A. S., Lund, O., Morrison, S., Mumey, B., Ofran, Y., Pellequer, J. L., Pinilla, C., Ponomarenko, J. V., Raghava, G. P., Van Regenmortel, M. H., Roggen, E. L. , Sette, A., Schlessinger, A., Sollner, J., Zand, M., Peters, B.(2007). Towards a consensus on datasets and evaluation metrics for developing B-cell epitope prediction tools. J. Mol. Recognit.  20(2), 75-82.

  4. Kulkarni-Kale, U., Ojha, J., Manjari, S., Deobagkar, D. D., Mallya, A.D., Dhere, R. M. & Kapre, S. V. (2007).  Mapping antigenic diversity & strain-specificity of mumps virus: a bioinformatics approach. Virology. 359, 436-446.

  5. A. Kumar and I. Ghosh  (2007). Mapping Selectivity and Specificity of Active Site of Plasmepsins from Plasmodium falciparum Using Molecular Interaction Field Approach. Protein & Peptide Letters , 14(6), 569-574.

  6. A.D. Ghate, B.U. Bhagwat, S.G. Bhosle, S.M. Gadepalli and U. D. Kulkarni-Kale(2007). Characterization of Antibody-Binding Sites on Proteins: Development of a Knowledgebase and Its Applications in Improving Epitope Prediction. Protein & Peptide Letters, 14(6),  531-535.

 

2006

  1. Ghosh, I. (2006).  Target based High Throughput Screening and lead designing in pharmaceutical drug industry. Indian Journal of Chemistry. 45 A; 63-73.

  2. Kulkarni-Kale, U., Bhosle,  S.,  Manjari, S.,  Joshi,  M., Bansode, S. & Kolaskar, A. S.,  (2006). Curation of viral genomes: Challenges, applications and the way forward. BMC Bioinformatics. 7(Suppl 5): S12. 

  3. Om Prakash , Ghosh Indira (2006)  Developing an antituberculosis compounds database and data mining in the search of a motif responsible for the activity of a diverse class of antituberculosis agents. J Chem Inf Model. , 46(1), 17-23. 

  4. Singh, V. K. & Ghosh, I. (2006). Kinetic modeling of tricarboxylic acid cycle and glyoxylate bypass in Mycobacterium tuberculosis, and its application to assessment of drug targets. Theoretical Biology and Medical Modelling, 3,27.

  5. Gaur, R. K. (2006). Helicase: Mystery of progression” in Molecular Biology reports. [PDF]
          
 2005

  1. Urmila Kulkarni-Kale, Shriram Bhosle and A. S. Kolaskar (2005)
    CEP: a conformational epitope prediction server Nucleic Acids Research.33,W168–W171 [PDF]
       
 2004
  1. Urmila Kulkarni Kale, Shriram Bhosle, G. Sunitha Manjari and A. S. Kolaskar. (2004) VirGen: A comprehensive viral genome resource. Nucleic Acids Research., 32,289-292.[PDF]

  2. Sarkar, D., Ghosh, I. & Datta, S. (2004). Biochemical characterization of Plasmodium falciparum HGXPRTase:role of histidine in substrate selectivity, Molecular & Biochemical Parasitology.  137, 267-276.

  3. Raychaudhury, C. & Ghosh, I. (2004). An Information-Theoretical Measure of Similarity and a Topological Shape and Size Descriptor for Molecular Similarity Analysis.  Internet Electron. J. Mol. Des. 3, 350-360.

2003
  1. Kulkarni-Kale, U. and Kolaskar, A. S., 2003
    Prediction of 3D structure of envelope glycoprotein of Sri Lanka strain of Japanese encephalitis virus. In Yi-Ping Phoebe Chen (ed.), Conferences in research and practice in information technology. 19, 87-96. [PDF]

  2. Sangeeta Sawant, A.S. Kolaskar.,2003
    Multiple Molecular Dynamics Simulations Of A 28mer Oligopeptide
    Reveal Enhanced Sampling of Conformational Space.In Yi-Ping Phoebe Chen (ed.), Conferences in research and practice in information technology.19,97-105. [PDF]

  3. Amit Awasthi, Ramkumar Mathur,Aslam Khan,Bimba N. Joshi,Nitya Jain, Sangeeta Sawant, Ramanamurthy Boppana,Debashis Mitr and Bhaskar Saha
    CD40 Signaling Is Impaired in L. major–infected Macrophages and Is Rescued by a p38MAPK Activator Establishing a Host-protective Memory T Cell Response.., Journal of Experimental Medicine. 197,8,1037-1043.[PDF]
2002
  1. Sakharkar MK, Kangueane P, Petrov DA, Kolaskar AS, Subbiah S.,2002,
    SEGE: A database on 'intron less/single exonic' genes from eukaryotes.
    Bioinformatics,18(9),1266-67. [PDF]

2001

  1. Mazumder, R., Kolaskar, A.S. and Seto, D., 2001, GeneOrder: comparing the order of genes in small genomes, Bioinformatics, 17, 2, 162-166.[PDF]

2000

  1. A. S. Kolaskar, P. S. Naik, June, 2000, Online identification of viruses J. Microbiol Immunol Infect, 33,2,69-78. [PDF]

  2. E. E. Abola, A. Bairoch, W. C. Barker, S. Beck, D. A. Benson, H. Berman, G. Cameron, C. Cantor, S. Doubet, T. J. P. Hubbard, T. A.  Jones, G. J. Kleywegt, A. S. Kolaskar, A. Van Kuik, A. M. Lesk,Mewes, D. Neuhaus, F. Pfeiffer, L. F. TenEyck, R. J. Simpson, G. Stoesser, J. L. Sussman, Y. Tateno, A. Tsugita, E. L. Ulrich, J.F.G. Vliegenthart, 2000,
    Quality control in databanks for molecular biology, BioEssays, 22, 1024-1034. [PDF]

1999

  1. A.S. Kolaskar and Urmila Kulkarni-Kale, 1999 - Prediction of three-dimensional structure and mapping of conformational epitopes of envelope glycoprotein of japanese encephalitis virus,Virology, 261, 31-42.
    [PDF]

1998

  1. A.S. Kolaskar and R.R. Joshi, 1998 - Molecular Dynamics Simulation of a 13-mer Duplex - DNA: A PvuII Substrate, Biomol. Struct. Dyn., 15, 1155-1165.
    [PDF]
  2. A.S. Kolaskar and P.S. Naik, 1998 - Computer-aided virus identification on the World Wide Web, Arch. of Virology, 143, 1513-1521.
     [PDF]
  3. Jacquelyn A. Davis, Elisabeth Peen, Ralph C. Williams, Jr., Shane Perkins, Christine C. Malone, Wayne T. McCormack, Elena Csernok, W.L. Gross, A.S. Kolaskar and Urmila Kulkarni-Kale, 1998 - Determination of Primary Amino Acid Sequence and Unique Three-Dimensional Structure of WGH-1, WGH1, a Monoclonal Human IgM Antibody with Anti- PR3 Specificity, Clinical Immunology and Immunopathology, 89 , 35-43.
     [PDF]
  4. A.S. Kolaskar, R.R. Joshi, 1998 - Role of Tata in Prokaryotic Promoters, Research Communications in Biochem, Cell & Molecular Biology, 2, 371-380.
1997
  1. Ralph C. Williams, Jr. Christine C. Malone, A.S. Kolaskar and Urmila Kulkarni-Kale, 1997 – Antigenic determinants reacting with rheumatoid factor: Epitopes with different primary sequences share similar conformation, Molecular Immunology, 34, 543-556.
    [PDF]
1996
  1. A.S. Kolaskar and Sangeeta Sawant, 1996 - Prediction of conformational states of amino acids using Ramachandran plot, Int. J. Pept. Prot. Res., 47, 110-116.
    [PDF]
  2. V. Sundararajan and A.S. Kolaskar, 1996 – Conformation of Biomolecules : A search by Genetic Algorithms, Computer Science and Informatics, 26, 22-29.
    [PDF]

1995

  1. A.S. Kolaskar, Bharati Joshi and B.V.B. Reddy, 1995 - Contextual Constraints in the choice of synonymous codons, Indian Journal of Biochemistry and Biophysics, 32, 417-423.
    [PDF]
1993
  1. Shashank Date, Rajendra Kulkarni, Bhavana Kulkarni, Urmila Kulkarni-Kale and A.S. Kolaskar, 1993 - Multiple Alignment of Sequences on Parallel Computers, CABIOS, 9, 397-402.
    [PDF]
  2. M. Kutubuddin, M.M. Gore, K. Banerjee, S.N. Ghosh and A.S. Kolaskar 1993 - Analysis of computer-predicted antibody inducing epitope on Japanese Encephalitis virus, Acta Virol. , 37, 417- 428.
     [PDF]
  3. Rajendra Kulkarni, Shashank Date, Bhavna Kulkarni, Urmila Kulkarni and A.S. Kolaskar, 1993 - PRAS: Parallel Alignment of Sequences Algorithm, Parallel Processing Letters, 3, 243-252.
     [PDF]
1992
  1. A.S. Kolaskar and U. Kulkarni-Kale, 1992 - Sequence alignment approach to pick up conformationally similar protein fragments, J. Mol. Biol., 223, 1053-1061.
     [PDF]
  2. A.S. Kolaskar, 1992 - Outline of Activities as Distributed Bioinformation Centre, University of Poona, Bioinformatics, 1, 3-5.
      [PDF]
  3. A.S. Kolaskar and P.S. Naik, 1992 - Computerization of Animal Virus Data - An Indian Attempt, Bioinformatics, 1, 6-10.
  4. A.S. Kolaskar and P.S. Naik, 1992 - Computerization of virus data and its usefulness in virus classification, Intervirology, 34, 133-141.
    [PDF]

1991

  1. M. Kutubuddin, A.S. Kolaskar, S.Galande, M.M.Gore, S.N.Ghosh and K. Banerjee, 1991 - Recognition of helper T Cell epitopes in envelope (E) Glycoprotein of Japanese Encephalitis, West Nile and Dengue viruses, Mol. Immunology, 28, 149-154.
     [PDF]
  2. Hiromi Suzuki, A. S. Kolaskar, Steven Samuel, Akira Tsugita, 1991 - A protein secondary structure database (PSS), Prot. Seq. Data Anal., 4, 97-104.
    [Full Paper in MS Word Format]
  3. A. S. Kolaskar and S.L. Samuel, 1991 - Analysis of Inverted Repeats in primary structure of proteins, Prot. Seq. Data Anal., 4, 105-110.
     [PDF]
1990
  1. A.S. Kolaskar and Prasad Tongaonkar, 1990 - A semi-empirical method for prediction of antigenic determinants on protein antigens, FEBS Letters, 276, 172-174.
    [PDF]
  2. P.S. Naik and A.S. Kolaskar, 1990 - Distributed Information Centre and The Animal Virus Information System, Indian J. Virol., 6, 32-37.
    [Full Paper in MS Word Format]
1989
  1. T.A. Thanaraj, A.S. Kolaskar and M.W. Pandit, 1989 - An extension of the graph theoretical approach to predict the secondary structure of large RNAs: the complex of 16S and 23S rRNAs from E.coli as a case study, CABIOS, 3, 211-218.
    [Full Paper in MS Word Format]
  2. A. Sharada Devi, T. Rehana, A.S. Kolaskar and M.W. Pandit, 1989 - Hydrophilicity and antigenicity of proteins - A case study of myoglobin and hemoglobin, J. Biosci., 14, 133-142.
    [PDF]
1988
  1. T.A. Thanaraj, A.S.Kolaskar and M.W.Pandit, 1988 - Prediction of the recognition sites on 16S and 23S rRNAs from E.coli for the formation of 16S-23S rRNA Complex., J.Biomol. Struct Dyn., 6 , 587-592.
    [PDF]
1986
  1. A. S. Kolaskar and B.V.B.Reddy, 1986 - Contextual constraints on codon pair usage: Structural and biological implications, J. Biomol. Struct Dyn., 3 , 725-738.
  2. M.W.Pandit, A. S. Kolaskar, T.A.Thanaraj and P.M.Bharghava, 1986 - Analysis of repeating oligonucleotide sequences in ribonucleic acids using an Apple II microcomputer, CABIOS, 2, 189-194.

1985

  1. A. S. Kolaskar and B.V.B.Reddy, 1985 - A method to locate protein coding sequences in DNA of prokaryotic systems, Nucleic Acids Res., 13, 185-194.
    [PDF]
  2. A. S. Kolaskar and B.V.B.Reddy, 1985 - Complimentary DNA sequence data analysis of prokaryotic systems., J.Biosci., 7, 49-59.
     [PDF]
  3. A. S. Kolaskar, T.A.Thanaraj and M.W.Pandit., 1985 - Prediction of secondary structures of 16S and 23S rRNA from Escherichia coli, Proc. Int. Symp. Biomol. Struct. Interactions, Suppl. J. Biosci., 8 , 791-798.
     [PDF]
1984
  1. A. S. Kolaskar, K.R.Naidu,Y.Seethambaram and V.S.Rama Das, 1984 - Photoacoustic characterisation of the in vivo levels of chlorophyll a in the adaxial and abaxial sides of the leaf, Proc. Indian Acad.Sci. (Plant Sci) 93, 275-279.
     
  2. A. S. Kolaskar and V.Ramabrahmam, 1984 - Are Secondary structures secondary?, Int.J.Peptide and Prot.Res. 24, 392-401.
     [PDF]
1983
  1. A. S. Kolaskar and V.Ramabrahmam, 1983 - Conformational properties of pairs of amino acids, Int.J.Pept. and Prot. Res., 22, 83-91.
    [PDF]
1982
  1. A. S. Kolaskar and V.Ramabrahmam, 1982 - Side chain characteristic main chain conformations of amino acid residues, Int.J.Pept. Prot. Res., 19, 1-9.
     [PDF]
  2. A. S. Kolaskar and V.Ramabrahmam, 1982 - Nature of amino acid substitutions in homologous proteins during evolution, Int.J.Biol.Macromol., 4, 150-154.
    [PDF]
  3. A. S. Kolaskar and V.Ramabrahmam, 1982 - Obligatory amino acids in primitive proteins, BioSystems 15, 105-109.
    [PDF]
1981
  1. A. S. Kolaskar and V.Ramabrahmam,1981-Conformational similarity among amino acid residues:1. Analysis of protein crystal structure data, Int.J.Biol.Macromol., 3, 171-178.
     [PDF]
1980
  1. A. S. Kolaskar and K.P.Sarathy, 1980 - The non-planar peptide unit IV Geometry and non-planar distortions of the cis-peptide unit, Biopolymers, 19, 1345-1355.
    [PDF]
  2. A. S. Kolaskar, V.Ramabrahmam and K.V.Soman, 1980 - Reversals of polypeptide chain in globular proteins, Int.J.Pept. Prot. Res., 16, 1-11.
    [PDF]
1979
  1. A. S. Kolaskar and D.Prashanth, 1979 - Empirical torsional potential functions from protein structure data.Phi- and Psi-Potentials for Nonglycyl Amino Acid residues, Int.J. Pept. and Prot. Res., 14, 88-98.
    [PDF]
  2. A. S. Kolaskar and K.V.Soman, 1979 - A common factor in in vivo synthesised polypeptides, Curr.Sci., 48, 928-931.
    [PDF]
1977
  1. A. S. Kolaskar and D.Prashanth, 1977 - Torsional potentials from observed dipeptide conformations in protein structure data, Curr.Sci., 46, 543-546.
     [PDF]
1975
  1. A. S. Kolaskar, A.V. Lakshminarayanan, K.P.Sarathy and V. Sasisekharan, 1975 - The non-planar peptide unit III. Quantum chemical calculations for related compounds and experimental X- ray diffraction data, Biopolymers, 14, 1081-1094.
  2. A. S. Kolaskar, K.P.Sarathy and V.Sasisekharan, 1975 - The need for a modified psi-potential in the dipeptide model, Curr.Sci., 44, 35-38.
     [PDF]
  3. A. S. Kolaskar, V.Sasisekharan, and K.P.Sarathy, 1975 - A note on the torsional potential function V(f ) in the dipeptide model, Theoret. Chim. Acta(Berl), 38 109-114.
1974
  1. G.N. Ramachandran, A.S.Kolaskar and Ramesh Narayan, 1974 - A new type of dihedral angle for the description of Biomolecular structures - Curr.Sci., 43, 197-199.
     [PDF]
  2. G.N. Ramachandran, A.S.Kolaskar, C. Ramakrishnan, V. Sasisekharan, 1974 - The mean geometry of the peptide unit from crystal structure data., Biochim. Biophys. Acta., 359, 298-302.
     [PDF]

1973

  1. G.N.Ramachandran, A.V. Lakshminarayanan and A.S.Kolaskar, 1973 - Theory of the Non-planar Peptide Unit, . Biochim. Biophys. Acta, 303, 8-13.
     [PDF]
  2. G.N.Ramachandran and A.S.Kolaskar, 1973, - The non-planar peptide unit II. Comparison of theory with crystal structure data. Biochim. Biophys. Acta, 303, 385-388.    
     [PDF]
  3. G.N.Ramachandran, K.P.Sarathy and A.S.Kolaskar, 1973 - Interatomic potential functions and crystal packing, Z.fur Kristallographie, Bd., 138, 299-312.    
  4. G.N.Ramachandran, K.P.Sarathy and A.S.Kolaskar, 1973 - Molecular packing of the crystal, N-methyl acetamide, Z. Naturforsch, 28 a, 643-646.    

     

Chapters in the Books

2016

  1. Sengupta, D., Joshi, M., Athale, C.A., Chattopadhyay, A. (2016). What can simulations tell us about GPCRs: Integrating the scales. In A.K. Shukla(Ed.), G Protein-Coupled Receptors-Signaling,Trafficking and Regulation(Series in Methods in Cell Biology: Volume 132) (pp.429-452). Netherland: Academic Press.
     

  2. Kadam K, Sawant S, Jayaraman VK. & Kulkarni-Kale U. (2016).  “Databases & Algorithms in Allergen Informatics” in the Book titled Bioinformatics", Editor: Dr. Ibrokhim  Abdurakhmanov, Center of Genomics and Bioinformatics, Uzbekistan. ISBN 978-953-51-4682-7. Publisher: InTech Publishers. Croatia. [PDF]  

2015

  1. Sunitha M Kasibhatla, Vaishali Waman, Mohan M Kale, Urmila Kulkarni-Kale. ‘Analysis of Next Generation Sequencing Data in Virology: Opportunities and Challenges" in the Book titled ‘Next Generation Sequencing’ Editor: J. K. Kulski, The University of Western Australia, Australia;. Publisher: InTech publishers, Croatia (2015) p. 173-203.[PDF]

2014

  1. Deobagkar DD*, “Epigenetics” Chapter 70 in the “Text Book of Biochemistry, Biotechnology, Allied and Molecular Medicine” by Talwar and Husnain 2014 (in Press)

  2. Kadam K, Sawant S, Kulkarni-Kale U & Jayaraman VK. “Prediction of Protein Function Based On Machine Learning Methods: An Overview” in the book “Introduction to Sequence and Genome Analysis” iConcept Press Ltd. (2014) p. 125-162.  [PDF]

  3. Mandar Paingankar and Dileep Deobagkar “Vector Competance in Mosquitoes – Role of receptor and non-receptor molecules”  in the book “Major Tropical Diseases –Public Health Perspective” (2014) edited by Aswani Kumar, Savio Rodrigues and Amit Dias published by Broadway Publishing House..

  4. Desai DV and Kulkarni-Kale U. (2014) “T-cell epitope prediction methods: an overview” in a book “Immunoinformatics (2nd Edition)” Eds: De RK & Tomar N, published by Springer Printer & Business Media. Methods in molecular biology (Clifton, N.J.) (2014) Vol. 1184, p. 333-364 [Abstract]

  5. Kulkarni-Kale U, Raskar-Renuse S, Natekar-Kalantre G & Saxena SA.  “Antigen-Antibody Interaction Database (AgAbDb): A compendium of antigen-antibody interactions” in the book Immunoinformatics (2nd Edition)” Eds: De RK & Tomar N, published by Springer Printer & Business Media, Methods in molecular biology (Clifton, N.J.) (2014) Vol. 1184,  p. 149-164. [Abstract]

2012

  1. Deepti Deobagkar* (2012)  "DNA methylation and Toxicogenomics"   in a book  Toxicology and Epigenetics,  Edited by Saura C. Sahu., Published  by John Wiley & Sons, Ltd.

2011

  1. Pandurang Kolekar, Mohan Kale and Urmila Kulkarni-Kale (2011). Molecular Evolution & Phylogeny: What, When, Why & How?, Computational Biology and Applied Bioinformatics, Heitor Silverio Lopes and Leonardo Magalhães Cruz (Ed.), ISBN: 978-953-307-629-4, InTech, Available from: http://www.intechopen.com/articles/show/title/molecular-evolution-phylogeny-what-when-why-how-

2007

  1. Subhash Choudhary, Ananta Paine & Indira Ghosh,  "Application of Bioinformatics in Drug designing in Antimalarial Drug Targets” published  as a chapter in  the book “ Current Trends in Pharmacology” ed. A.Ray & K.Gulati, IK publishing house, New Delhi. 2007 

 

1999

  1. Vijayan, M., Yatindra, N. Kolaskar, A. S., Perspectives in structural biology: a volume in honour of G.N.Ramachandran, Universities Press (India) Limited, Hyderabad , ISBN: 81-7371-254-9, Pages: 746 (1999).

1997

  1. A.S. Kolaskar and P.S. Naik, 1997 - Computerised Virus Database and its usefulness in identification and classification -   Chapter in a book entitled `Species Diversity : Global Data System', Ed. Karen Wilson and Frank Bisby, Springer.
    
  2. V. Sundararajan and A.S. Kolaskar, 1997 - Migrating Genetic Algorithms on PARAM for Conformational Search, 
    a chapter in the book `Computational Paradigm for Synthesizing Models and Simulations of Complex Biological Systems', Edited by S.S. Iyengar, CRC Press.
    

1995

  1. A.S. Kolaskar and P.S. Naik, 1995 - Concerted Use of Multiple Databases for Taxonomic Insights, a Chapter in a book "The Information Revolution : Impact on Science and Technology", Ed. J.E. Dubois and N. Gershon, 263-270, Springer.

1992

  1. A. S. Kolaskar, 1992 - Bioinformatics in India - Past, present and future, Growth of Biotechnology in India - A Tribute to Dr. S. Ramachandran, (Ed. G.P. Talwar and Sandip K. Basu) 157-165.