Sudipto Saha

Sudipto Saha
Assistant Professor

Previous appointments:

Postdoctoral Fellow at Indiana University, School of Informatics, Indianapolis, USA from 2007-2008

Postdoctoral Fellow at Case Western Reserve University, School of Medicine, Cleveland, USA from 2008-20012

Research interests:

The overall goal of our lab is to improve diagnosis, prognosis, and treatment of lung diseases using bioinformatics and systems biology approaches


1. Clinical Biomarkers and Drug Targets for Lung Diseases
2. Identifying small chemical modulators of protein-protein interactions for drug discovery
3.
 Drug Resistance in MTB and other bacterial species
4. Regulatory networks in Pluripotent Stem cells and Lung Cancer Stem Cells (lCSCs)




Contact:

Address: Bioinformatics Centre
Centenary Campus
Bose Institute
P-1/12 C.I.T. Scheme VII-M
Kolkata - 700054, India
E-Mail: ssaha4[at]jcbose.ac.in
Phone: +91-33-25693333

Research:

R1: Systematic discovery of novel linear motifs mediating protein-protein interactions

Short linear motifs (LMs) are often present in disordered regions of proteins and are responsible for thousands of protein-protein interactions (PPIs). We have developed a relational database ( LMPID ) of linear motifs that mediate protein-protein interactions (PPIs). We have used these datasets and applied machine learning techniques to predict the linear motifs mediating Protein-Protein Interactions (PPIs) with SH3, WW and PDZ domains ( LMDIPred web server).


R2: Systematic discovery of biomarkers of asthma caused by common environmental allergens using human plasma proteomics, cytokine profiling and network biology - a systems approach to drug discovery

Study the integrated profile derived from plasma and cytokine assay among asthma patients. Our goal is to discover asthma related biomarkers and identify active networks based on protein-protein interactions and pathways affected and altered in asthma patients.


R3. Systematic identification of regulatory networks in pluripotent cells integrating coding and noncoding world

Identify the active subnetworks in pluripotent stem cells my merging the DNA, protein and regulatory noncoding RNA interactions.

Publications:

53. 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.  18(13):1123-1134(2018)

52. 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. 13(7):e0200430 (2018).

51. 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. 3(1). pii: e00135-17 (2018)

50. 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 164(1):99-110. (2018)

49. 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.1861(12):3190-3200. (2017)

48. 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. 7(6). pii:170024 (2017)

47. 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. 7(1):3942 (2017)

46. 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, 44(4):160501 (2017)

45. 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, 18(1):224 (2017) 

44. Mandal SD & Saha S*. PluriPred: AWeb server for predicting proteins involved in pluripotent network. J Biosci. 41(4):743-750 (2016)

43. 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. 291(34):18016-29 (2016)

42. Sarkar D & Saha S*. Computational Proteomics, Systems Biology Application in Synthetic Biology, Springer,  pp 11-20 (2016)

41. 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. 11(5):e0155911 (2016)

40. Barman RK, Jana T, Das S & Saha S* Prediction of Intra-species Protein-Protein Interactions in Enteropathogens Facilitating Systems Biology Study. PLoS One. 10(12):e0145648 (2015)

39. 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. 10(12):e0144547 (2015)

38. 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). 45(7):1259-61 (2015)

37. Sarkar D, Jana T & Saha S*. LMPID: A manually curated database of linear motifs mediating protein-protein interactions. Database (Oxford). pii: bav014 (2015)

36. Mandal RS, Saha S* & Das S. Metagenomic surveys of gut microbiota. Genomics Proteomics and Bioinformatics, 13(3):148-58 (2015)

35. 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,14 (3):1483-94 (2015)

34. 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. 33(2):298-321 (2015)

33. Barman RK, Saha S* & Das S. Prediction of interactions between viral and host proteins using supervised machine learning methods. PLoS One, 9(11):e112034 (2014)

32. Chakraborty S, Deb A, Maji RK, Saha S & Ghosh Z. LncRBase: An Enriched Resource for lncRNA Information. PloS One, 9(9):e108010 (2014)

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

30. 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. 289(36):25149-65 (2014)

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

28. Sircar G, Sarkar D, Bhattacharya SG & Saha S*. Allergen databases. Methods Mol Biol. 1184:165-81 (2014)

27. Sircar G, Saha B, Bhattacharya SG & Saha S*. In silico prediction of allergenic proteins. Methods Mol Biol. 1184:375-88 (2014)

26. 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, 6(5):519-23 (2014)

25. Sircar G, Saha B, Bhattacharya SG & Saha S*. Allergic asthma biomarkers using systems approaches. Front Genet. 4:308 (2014)

24. Saha S*. Systems Immunology. Encyclopedia of Systems Biology, 2073-2078 (2013)

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

22. 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,  287 (37), 31414-31426 (2012)

21. 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, 11(9):4476-87 (2012)

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

19. 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.  5(3-4):185-205 (2012)

18. 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. 186(3):1638-45 (2011)

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

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

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

14. 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, 1 (1), 12 (2008)

13. 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, 8 (1), 337 (2007)

12. S Saha & GPS Raghava. Predicting virulence factors of immunological interest. Methods Mol Biol.,409: 407-415 (2007)

11. S Saha & GPS Raghava. Searching and mapping of B-cell epitopes in Bcipep database. Methods Mol Biol., 409: 113-124 (2007)

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

9. S Saha & GPS Raghava. Prediction methods for B-cell epitopes. Methods Mol Biol., 409: 387-394 (2007)

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

7. 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 (2006)

6. 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, 4 (1), 42-47 (2006)

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

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

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

2. S Saha & GPS Raghava. BcePred: Prediction of continuous B-cell epitopes in antigenic sequences using physico-chemical properties. Artificial Immune Systems, LNCS, 3239, 197-204 (2004)

1. 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, 16 (3), 374-379 (2003)

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Recognition:

  • Ramalingaswami Re-entry Fellow, 2012-2017
  • European Respiratory Society Member, 2018-2019
  • CSIR-UGC JRF/SRF, 2002-2006

Teaching:

Ph.D Course Work

B12: Bioinformatics

B24: Proteomics


M.Sc-Ph.D Integrated Course

Proteomics

Statistical tools

Genetics and Genomics

Students:

Image Name Designation Department Campus Contact number Email
profile image Abhirupa Ghosh Junior Research Fellow Bioinformatics Centre Centenary 25693275 abhirupa
profile image Debangana Chakravorty Senior Research Fellow Bioinformatics Centre Centenary 25693349 debangana_c
profile image Krishnendu Banerjee Junior Research Fellow Bioinformatics Centre Centenary 25693275 krishnendu
profile image Saran N Senior Research Fellow Bioinformatics Centre Centenary 25693349 saran
profile image Shazia Firdous Junior Research Fellow Bioinformatics Centre Centenary 25693275
profile image Sreyashi Majumdar Senior Research Fellow Bioinformatics Centre Centenary 25693349 sreyashi91
profile image Tanmoy Jana Senior Research Fellow Bioinformatics Centre Centenary 25693275 tjana

Former:

Debasree Sarkar

Group News:

Papers recently accepted from our group

 ***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. doi: 10.2174/1568026618666180801092839. [Epub ahead of print] PMID: 30068279

 ***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 Jul 12;13(7):e0200430. doi: 10.1371/journal.pone.0200430. eCollection 2018. PMID: 30001346

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November 19-23, 2018: Krishnendu Banerjee, attended EMBL-EBI Workshop on "Analysis of genome scale data from bulk and single-cell sequencing" held in National Institute of Biomedical Genomics (NIBMG), Kalyani, India.

November 5-10, 2018: Debangana Chakravorty, attended EMBO Practical Course on "Computational analysis of protein-protein interactions: Sequences, networks, and diseases" held in Rome, Italy with EMBO Travel Grant award.

October 11-14, 2018: Sreyashi Majumdar attended and presented a poster titled “ DAAB-V2: An updated version of Database of Allergy and Asthma Biomarkers with SNPs, Protein Interactors and Drug Information." in the Joint Congress of the Asia Pacific Association of Allergy, Asthma and Clinical Immunology & the Asia Pacific Association of Pediatric Allergy Respirology and Immunology (APAAACI & APAPARI 2018 ), 2018, Bangkok, Thailand.

September 8-9, 2018: Sreyashi Majumdar attended and presented a poster titled “Improving diagnosis, prognosis, and treatment of lung diseases using bioinformatics and systems biology approaches” in Pulmocon, 2018, Kolkata. She won the best poster award for the said poster.

August 2, 2018: A paper titled "Prediction of half-maximal inhibitory concentration (IC50) for small chemical modulators targeting protein-protein interaction using support vector machine" accepted for oral presentation in International Conference on Bioinformatics (InCoB 2018), 2018, New Delhi

August 1, 2018: Shazia Firdous joined as Junior Research Fellow (UGC)

July 25, 2018: Debangana Chakravorty's poster abstract titled " FBXW7 and Skp2 mediated c-Myc degradation: An in silico approach" ' accepted in International Conference on Bioinformatics (InCoB 2018), 2018, New Delhi

July 25, 2018: Tanmoy Jana's poster abstract titled "PPIMdb: A database of small chemicals modulating (inhibiting) protein-protein interactions" accepted in International Conference on Bioinformatics (InCoB 2018), 2018, New Delhi

July 17-21,2018: Abhirupa Ghosh attended NIBMG Summer School 2018 on Systems Biology at National Institute of Biomedical Genomics (NIBMG), Kalyani, WB

February 25-27, 2018: Krishnendu Banerjee and Sudipto Saha attended and presented posters in India|EMBO symposia on "Big data in biomedicine", New Delhi

February 15, 2018: Sudipto Saha gave a lecture on the occasion of the Silver Jubilee of Machine Intelligence Unit at Indian Statistical Institute, Kolkata. Tittle of the talk was "Systematic discovery of novel linear motifs mediating protein-protein interactions"

January 18, 2018: Debasree Sarkar (SRF) submitted her Ph.D. thesis titled "Systematic discovery of linear motifs mediating protein-protein interactions"