Publications in Pubmed

2018

• Chakravorty D, Banerjee K and Saha S. Integrative Omics for Interactomes. , In book: Synthetic Biology, S. Singh (ed.), Springer Nature Singapore Pte Ltd, 2018 pp 39-49

• Majumdar S, Ghosh A, Saha S. Modulating Interleukins and their receptors interactions with small chemicals using in silico approach for asthma. Curr Top Med Chem., 2018, 18(13):1123-1134

• Sarkar D, Jana T, Saha S. LMDIPred: A web-server for prediction of linear peptide sequences binding to SH3, WW and PDZ domains. PLoS One, 2018, 13(7):e0200430

• Subramani C, Nair VP, Anang S, Mandal SD, Pareek M, Kaushik N, Srivastava A, Saha S, Shalimar, Nayak B, Ranjith-Kumar CT, Surjit M. Host-Virus Protein Interaction Network Reveals the Involvement of Multiple Host Processes in the Life Cycle of Hepatitis E Virus. mSystems, 2018, 3(1). pii: e00135-17

• Chatterjee A, Sharma AK, Mahatha AC, Banerjee SK, Kumar M, Saha S, Basu J, Kundu M. Global mapping of MtrA-binding sites links MtrA to regulation of its targets in Mycobacterium tuberculosis. Microbiology 2018 Jan;164(1):99-110.

2017

• Mawatwal S, Behura A, Ghosh A, Kidwai S, Mishra A, Deep A, Agarwal S, Saha S , Singh R, Dhiman R. Calcimycin mediates mycobacterial killing by inducing intracellular calcium-regulated autophagy in a P2RX7 dependent manner. Biochim Biophys Acta. 2017 Dec;1861(12):3190-3200.

• Mustfa SA, Singh M, Suhail A, Mohapatra G, Verma S, Chakravorty D, Rana S, Rampal R, Dhar A, Saha S , Ahuja V, Srikanth CV. SUMOylation pathway alteration coupled with downregulation of SUMO E2 enzyme at mucosal epithelium modulates inflammation in inflammatory bowel disease. Open Biol. 2017 Jun;7(6). pii:170024

• Subramani E, Rameshbabu AP, Jothiramajayam M, Subramanian B, Chakravorty D, Bose G, Joshi M, Ray CD, Lodh I, Chattopadhyay R, Saha S , Mukherjee A, Dhara S, Chakravarty B, Chaudhury K.. Mycobacterial heat shock protein 65 mediated metabolic shift in decidualization of human endometrial stromal cells. Sci Rep.2017 Jun 21;7(1):3942

• Jana T, Ghosh A, Mandal SD, Banerjee R, Saha S*. PPIMpred: a web server for high-throughput screening of small molecules targeting protein–protein interaction. Royal Society Open Science, 2017 April, 4(4):160501

• Chakravorty D,Jana T, Mandal SD, Seth A, Bhattacharya A, Saha S*. MYCbase: A database of functional sites and biochemical properties of Myc in both normal and cancer cells. BMC Bioinformatics, 2017 Apr 28;18(1):224.

2016

• Mandal SD, Saha S*. PluriPred: A web server for predicting proteins involved in pluripotent network. J Biosci. 2016 Dec;41(4):743-750. PMID: 27966493

• Sircar G, Jana K, Dasgupta A, Saha S, Gupta Bhattacharya S. Epitope mapping of Rhi o 1 and generation of a hypoallergenic variant: a candidate molecule for fungal allergy vaccines. J Biol Chem. 2016 Aug 19;291(34):18016-29. PMID: 27358405

• Sarkar D and Saha S* Computational Proteomics Systems Biology Application in Synthetic Biology,Springer, 2016, pp 11-20

• Sarkar D, Patra P, Ghosh A, Saha S* Computational framework for prediction of peptide sequences that may mediate multiple protein interactions in cancer-associated hub proteins. PLoS One. 2016 May 24; 11(5):e0155911. PMID: 27218803

2015

• Barman RK, Jana T, Das S, Saha S* Prediction of Intra-species Protein-Protein Interactions in Enteropathogens Facilitating Systems Biology Study. PLoS One. 2015 Dec 30; 10(12):e0145648 doi: 10.1371/journal.pone.0145648

• Sircar G, Saha B, Mandal RS, Pandey N, Saha S, Gupta Bhattacharya S Purification, Cloning and Immuno-Biochemical Characterization of a Fungal Aspartic Protease Allergen Rhi o 1 from the Airborne Mold Rhizopus oryzae. PLoS One. 2015 Dec 16;10(12):e0144547.doi:10.1371/journal.pone.0144547.PMID:26672984

• Sircar G, Saha B, Jana T, Dasgupta A, Gupta Bhattacharya S, Saha S*. DAAB: A manually curated database of Allergy and Asthma Biomarkers. Clinical & Experimental Allergy (Wiley). 2015 Jul;45(7):1259-61. doi: 10.1111/cea. PMID:25973645.

• Sarkar D, Jana T, Saha S*. LMPID: A manually curated database of linear motifs mediating protein-protein interactions. Database (Oxford). 2015, pii: bav014. doi: 10.1093/database/bav014. PMID:25776024.

• Mandal RS, Saha S* and Das S. Metagenomic surveys of gut microbiota. Genomics Proteomics and Bioinformatics, 2015 June; 13(3):148-58. doi: 10.1016/j.gpb.2015.02.005.

• Vukoti K, Yu X, Sheng Q, Saha S, Feng Z, Hsu AL, Miyagi M. Monitoring Newly Synthesized Proteins over the Adult Life Span of Caenorhabditis elegans. Journal Proteome Research 2015 Mar 6;14(3):1483-94. doi:10.1021/acs.jproteome.5b00021.Epub 2015 Feb 25. PMID:25686393.

• Maity A, Majumdar S, Priya P, De P, Saha S, Ghosh Dastidar S. Adaptability in protein structures: structural dynamics and implications in ligand design. J Biomol Struct Dyn. 2015; 33(2):298-321.doi:10.1080/07391102.PMID:24433438.

2014

• Barman RK, Saha S*, Das S. Prediction of interactions between viral and host proteins using supervised machine learning methods. PLoS One. 2014 Nov 6;9(11):e112034. doi: 10.1371/journal.pone.0112034.

• Chakraborty S, Deb A, Maji RK, Saha S and Ghosh Z. LncRBase: An Enriched Resource for lncRNA Information. PloS One. 2014.18;9(9):e108010.doi:10.1371/journal.pone.0108010. PMID:25233092

• Dhal PK, Barman RK, Saha S*, Das S. Dynamic modularity of host protein interaction networks in salmonella typhi infection. PLoS One, 2014. 9(8):e104911

• Arora G, Tiwari P, Mandal RS, Gupta A, Sharma D, Saha S, Singh R. High Throughput Screen Identifies Small Molecule Inhibitors Specific for Mycobacterium tuberculosis Phosphoserine Phosphatase. J Biol Chem. 2014, 289(36):25149-65.

• Sarkar A, Maji RK, Saha S, Ghosh Z. piRNAQuest: searching the piRNAome for silencers. BMC Genomics. 2014 Jul 4;15(1):555.

• Sircar G, Sarkar D, Bhattacharya SG, Saha S*. Allergen databases. Methods Mol Biol. 2014; 1184:165-81. doi:10.1007/978-1-4939-1115-8_9

• Sircar G, Saha B, Bhattacharya SG, Saha S*. In silico prediction of allergenic proteins. Methods Mol Biol.2014;1184:375-88. doi: 10.1007/978-1-4939-1115-8_21. 2014

• Chakraborty J, Jana T, Saha S , Dutta TK. Ring-Hydroxylating Oxygenase database: a database of bacterial aromatic ring-hydroxylating oxygenases in the management of bioremediation and biocatalysis of aromatic compounds, Environ Microbiol Rep, 2014 Oct;6(5):519-23.

• Sircar G, Saha B, Bhattacharya SG, Saha S*. Allergic asthma biomarkers using systems approaches. Front Genet. 2014 Jan 8;4:308. eCollection 2014.

2013

• Saha S*. Systems Immunology. Encyclopedia of Systems Biology, 2073-2078

2012

• J Song, S Saha, G Gokulrangan, PJ Tesar, RM Ewing. DNA and chromatin modification networks distinguish stem cell pluripotent ground states. Molecular & Cellular Proteomics. 2012, 11 (10), 1036-1047

• Y Yuan, CS Kadiyala, TT Ching, P Hakimi, S Saha, H Xu, C Yuan, V Mullangi. Enhanced energy metabolism contributes to the extended life span of calorie-restricted Caenorhabditis elegans. Journal of Biological Chemistry. 2012, 287 (37), 31414-31426

• S Saha, JE Dazard, H Xu, RM Ewing. A computational framework for analysis of prey-prey associations in interaction proteomics identifies novel human protein-protein interactions and networks. Journal of Proteome Research, 2012 11(9):4476-87. doi: 10.1021/pr300227y.

• JE Dazard, S Saha, RM Ewing. ROCS: a Reproducibility Index and Confidence Score for Interaction Proteomics Studies. BMC Bioinformatics, 2012, 13 (1), 128

• S Saha, T Roman, A Galante, M Koyutürk, RM Ewing. Network–based approaches for extending the Wnt signalling pathway and identifying context–specific sub–networks., Int J Comput Biol Drug Des. 2012, 5(3-4):185-205. doi: 10.1504/IJCBDD.2012.049203.

2011

• Dhiman R, Bandaru A, Barnes PF, Saha S, Tvinnereim A, Nayak RC, Paidipally P,  Valluri VL, Rao LV, Vankayalapati R. c-Maf-dependent growth of Mycobacterium tuberculosis in a CD14(hi) subpopulation of monocyte-derived macrophages. J Immunol. 2011 Feb 1;186(3):1638-45.

• S Saha, R Ewing. Systematic discovery of condition specific Wnt signaling subnetworks, IEEE BIBM Integrative Data Analysis in Systems biology (IDASB) workshop, 2011, pp. 229-234

2010

• S Saha, P Kaur, RM Ewing. The bait compatibility index: computational bait selection for interaction proteomics experiments. Journal of Proteome Research, 2010, 9 (10), 4972-4981

2009

• S Saha, SH Harrison, JY Chen. Dissecting the human plasma proteome and inflammatory response biomarkers. Proteomics,2009, 9 (2), 470-484

2008

• S Saha, SH Harrison, C Shen, H Tang, P Radivojac, RJ Arnold, X Zhang, JY Chen. HIP2: an online database of human plasma proteins from healthy individuals. BMC Medical Genomics,2008, 1 (1), 12

2007

• M Rashid, S Saha, GPS Raghava. Support Vector Machine-based method for predicting subcellular localization of mycobacterial proteins using evolutionary information and motifs. BMC bioinformatics, 2007, 8 (1), 337

• S Saha, GPS Raghava. Predicting virulence factors of immunological interest. Methods Mol Biol., ,Immunoinformatics 2007, 407-415.

• S Saha, GPS Raghava. Searching and mapping of B-cell epitopes in Bcipep database. Methods Mol Biol., , Immunoinformatics, 2007, 113-124.

• S Saha, GPS Raghava. BTXpred: prediction of bacterial toxins. In silico biology, 2007, 7 (4-5), 405-412.

• S Saha, GPS Raghava. Prediction methods for B-cell epitopes. Methods Mol Biol.,Immunoinformatics, 2007, 387-394.

• S Saha, GPS Raghava. Prediction of neurotoxins based on their function and source. In silico biology, 2007, 7 (4), 369-387.

2006

• S Saha, J Zack, B Singh, GPS Raghava. VGIchan: prediction and classification of voltage-gated ion channels. Genomics, Proteomics & Bioinformatics, 2006, 4 (4), 253-258.

• S Saha, GPS Raghava. VICMpred: an SVM-based method for the prediction of functional proteins of Gram-negative bacteria using amino acid patterns and composition. Genomics, Proteomics & Bioinformatics, 2006, 4 (1), 42-47.

• S Saha, GPS Raghava. Prediction of continuous B‐cell epitopes in an antigen using recurrent neural network. Proteins: Structure, Function, and Bioinformatics, 2006, 65 (1), 40-48.

• S Saha, GPS Raghava. AlgPred: prediction of allergenic proteins and mapping of IgE epitopes. Nucleic Acids Research, 2006, 34 (suppl 2), W202-W209.

2005

• S Saha, M Bhasin, GPS Raghava. Bcipep: a database of B-cell epitopes. BMC Genomics, 2005, 6 (1), 79.

2004

• S Saha, GPS Raghava. BcePred: Prediction of continuous B-cell epitopes in antigenic sequences using physico-chemical properties. Artificial Immune Systems, LNCS, 2004, 197-204.

2003

• DN Kamra, S Saha, N Bhatt, LC Chaudhary, N Agarwal. Effect of diet on enzyme profile, biochemical changes and in sacco degradability of feeds in the rumen of buffalo. Asian Australasian Journal Of Animal Sciences, 2003, 16 (3), 374-379.