, Bioinformatics Centre
PhD: Jawarharlal Nehru University, work done at CSIR-IMTECH, 2007
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
The overall goal of our lab is to improve diagnosis, prognosis, and treatment of lung diseases using bioinformatics and systems biology approaches
Current Research Focus
Lung mitochondrial dysfunction and lung microbiome dysbiosis can cause chronic asthma and lung cancer. We are interested to dissect the mitochondrial proteins and their networks/pathways in disease mice model and identify the key targets for therapeutics. We are also interested in studying the lung microbiome, gut-lung axis and antimicrobial drug-resistant gene mutation patterns in asthma and tuberculosis.
Human 3D genome architecture plays a significant role in transcription and translation. We are interested in modeling chromatin spatial reorganization of the genome in T and B cells, which are important players of adaptive immunity. We want to integrate DNA-protein (CTCF, RNAPOL2), Protein-Protein and DNA-DNA interactions (using HiC, ChIA-PET assays in B-cells) to model and predict the 2D interactome of chromatin looping.
P-1/12 C.I.T. Scheme VII-M
Kolkata - 700054, India
We work on the following topics:
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.
R4: Identifying small chemical modulators of protein-protein interactions for drug discovery
Small chemical inhibitors are targeted in interface regions of protein-protein interactions (for e,g., IL33/ST2), for identifying novel drug(s).
61. Saha S and Ewing RM. Editorial: Integrated Omics for Defining Interactomes, Frontiers in Physiology DOI: 10.3389/fphys.2020.00081 (2020)
60. Chakravorty D, Ghosh A, Saha S. Computational approach to target USP28 for regulating Myc. Comput Biol Chem. 85:107208. (2020)
59. Mohammed S, Vineetha NS, James S, Aparna JS, Babu Lankadasari M, Maeda T, Ghosh A, Saha S, Li QZ, Spiegel S, Harikumar KB. Regulatory role of SphK1 in TLR7/9-dependent type I interferon response and autoimmunity. FASEB J. doi: 10.1096/fj.201902847R. [Epub ahead of print] (2020)
58. Banerjee SK, Lata S, Sharma AK, Bagchi S, Kumar M, Sahu SK, Sarkar D, Gupta P, Jana K, Gupta UD, Singh R, Saha S, Basu J, Kundu M. The sensor kinase MtrB of Mycobacterium tuberculosis regulates hypoxic survival and establishment of infection. J Biol Chem. pii: jbc.RA119.009449 (2019)
57. Bhowmik M, Majumdar S, Dasgupta A, Gupta Bhattacharya S, Saha S. Pilot-Scale Study Of Human Plasma Proteomics Identifies ApoE And IL33 As Markers In Atopic Asthma. J Asthma Allergy. 12:273-283. (2019)
56.Sarkar D, Saha S. Machine-learning techniques for the prediction of protein-protein interactions. J Biosci. 44(4). pii: 104. (2019)
55. Chakravorty D, Banerjee K, Mapder T, Saha S. In silico modeling of phosphorylation dependent and independent c-Myc degradation. BMC Bioinformatics. 20(1):230 (2019)
54. Chakravorty D, Banerjee K and Saha S. Integrative Omics for Interactomes, In book: Synthetic Biology, S. Singh (ed.), Springer Nature Singapore Pte Ltd, pp 39-49 (2018)
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)View More
- Ramalingaswami Re-entry Fellow, 2012-2017
- European Respiratory Society Member, 2018-2019
- CSIR-UGC JRF/SRF, 2002-2006
Ph.D Course Work
M.Sc-Ph.D Integrated Course
Genetics and Genomics
|Sreyashi Majumdar||Senior Research Fellow||Bioinformatics Centre||Centenary||25693349||sreyashi91|
Debasree Sarkar, Ph.D. awarded, University of Calcutta, 2019
Tanmoy Jana, Ph.D. awarded, Maulana Abul Kalam Azad University of Technology, West Bengal, 2019
Debangana Chakravorty submitted her Ph.D. thesis to University of Calcutta, 2019 (2nd December 2019)
Papers recently accepted from our group
***Chakravorty D, Ghosh A, Saha S. Computational approach to target USP28 for regulating Myc. Comput Biol Chem. 85:107208. (2020)
*** Bhowmik M, Majumdar S, Dasgupta A, Gupta Bhattacharya S, Saha S. Pilot-Scale Study Of Human Plasma Proteomics Identifies ApoE And IL33 As Markers In Atopic Asthma. J Asthma Allergy. 12:273-283. (2019)
February 11-15, 2020 : Saran N presented a poster entitled “Genome sequencing of Fluoroquinolone resistant M.smegmatis identifies key mutations in few genes associated with drug resistance” in India|EMBO Symposium on “Mycobacterial heterogeneity and host tissue tropism”, held at National Institute of Immunology(NII) and International Centre for Genetic Engineering and Biotechnology (ICGEB), New Delhi, India.
December 2, 2019: Debangana Chakravorty submitted her Ph.D. thesis titled "Bioinformatics based knowledge map of c-MYC regulatory networks and modulators".
November 21, 2019: Tanmoy Jana was awarded a Ph.D. degree from Maulana Abul Kalam Azad University of Technology, West Bengal.
November 9-12, 2019: Abhirupa Ghosh presented a poster entitled “Towards identifying drug-resistant gene-mutation signatures in lung microbiome of antibiotic exposed individual” in India|EMBO symposium on “Human microbiome: Resistance and Disease”, held at National Institute of Biomedical Genomics (NIBMG), Kalyani, India.
November 9-12, 2019: Sudipto Saha presented a poster entitled “Meta-analysis for identifying relationship of Human Gut-Lung Microbiome to lung function of Asthma using GLMdb” in India|EMBO symposium on “Human microbiome: Resistance and disease”, held at National Institute of Biomedical Genomics (NIBMG), Kalyani, India.
September 20-21, 2019: Shazia Firdous attended the “1st TCGA conference and workshop in India” held at IISER Pune and presented a poster entitled “Biomarkers of Cancer Stem Cells (BCSCs) database”.
September 10-12, 2019: Abhirupa Ghosh presented a poster entitled “Prediction of drug resistance in MTB using machine learning algorithms” and won the best poster bronze award in InCoB 2019 held at Universitas YARSI, Jakarta, Indonesia.
September 10-12, 2019: Debangana Chakravorty gave a short talk on “Computational approach to target USP28 for regulating Myc” in InCoB 2019 held at Universitas YARSI, Jakarta, Indonesia.
June 19, 2019: Sudipto Saha gave an invited talk at the National Workshop and Hands-on Training on Computational Biology with Modern Tools, MAKAUT, WB on "Big data in Network Biology".
March 25-26, 2019: Sudipto Saha gave an invited talk at the National Conference on Emerging Trends
in Disease Model systems, organized by NCCS Pune on “Systematic discovery of biomarkers and drug
targets of atopic asthma using proteomics approach “
February 14, 2019: Sudipto Saha gave an invited talk at Indian Institute of Technology Jodhpur
lung diseases using bioinformatics and systems biology approaches“
January 26-28, 2019: Bishnupur visit by the lab members
January 9, 2019: Debasree Sarkar was awarded Ph.D. degree from University of Calcutta.
January 6, 2019: Debangana Chakravorty, Sreyashi Majumdar, Abhirupa Ghosh, and Sudipto Saha completed Kolkata 5K Marathon Race, organized by Kolkata Police Force.
December 27, 2018: Debasree Sarkar defended her Ph.D. thesis titled "Systematic Discovery Of Linear Motifs Mediating Protein-Protein Interactions".
December 13-15, 2018: Sudipto Saha gave an invited talk at VIBCON-2018, Dimapur, Nagaland on "Predicting small chemical modulators of protein-protein interactions for drug discovery in lung diseases".
November 19-23, 2018: Krishnendu Banerjee and Debasree Sarkar 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"