Sudipto Saha
Associate Professor
Sudipto Saha
Associate Professor, Biological Sciences
PhD: Jawarharlal Nehru University, work done at CSIR-Institute of Microbial Technology, 2007
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 the diagnosis, prognosis, and treatment of lung diseases using bioinformatics and systems biology approaches
Current Research Focus
Life Science:
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 the disease mice models 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.
Understand the interaction between the lung microbiome, its metabolites, and host innate immune cells in obstructive pulmonary diseases. The study of the association between the lung microbiome and its metabolites and immune cells like macrophages and neutrophils shall shed light on a new direction in asthma pathogenesis and management. We plan to use asthmatic patient sputum samples and generate proteomics/genomics/metabolomics data and perform integrative OMICS analysis for drug discovery.
Contact:
| Address: |
Biological Sciences Unified Academic Campus Bose Institute EN-80, Sector V Bidhan Nagar Kolkata - 700 091, India |
| E-Mail: | ssaha4[at]jcbose.ac.in |
| Phone: | +91-33-25693216 |
Research:
Current ongoing research work
Projects Completed:
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 by 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).
Publications:
85. Ghosh A and Saha S. Meta-analysis of sputum microbiome studies identifies airway disease-specific taxonomic and functional signatures. Journal of Medical Microbiology,72(12) DOI: 10.1099/jmm.0.001617 (2022)
84. N Saran and Saha S. Survey of mycobacterial fluoroquinolone resistance protein conservon (mfp conservon) in Mycobacteriaceae and identification of its promoter activity. Gene Reports, 29(1):101684 DOI: 10.1016/j.genrep.2022.101684 (2022)
83. Pati S, Mukherjee S, Dutta S, Guin A, Roy D, Bose S, Paul S, Saha S, Bhattacharyya S, Datta P, Chakraborty J, Sarkar DK, Sa G. Tumor-associated CD19+CD39- B regulatory cells deregulate class-switch recombination to suppress antibody responses. Cancer Immunol Res. CIR-21-1073. doi: 10.1158/2326-6066.CIR-21-1073 (2022)
82. Gaur D, Kumar N, Ghosh A, Singh P, Kumar P, Guleria J, Kaur S, Malik N, Saha S, Nystrom T, Sharma D. Ydj1 interaction at nucleotide-binding-domain of yeast Ssa1 impacts Hsp90 collaboration and client maturation. PLoS Genet.18(11):e1010442. doi: 10.1371/journal.pgen.1010442. (2022)
81. Bhattacharjee S, Saha B, Bhattacharyya P and Saha S. Classification of obstructive and non-obstructive pulmonary diseases on the basis of spirometry using machine learning techniques. Journal of Computational Science, 63:101768, DOI: 10.1016/j.jocs.2022.101768 (2022)
80. Sircar G, Ghosh N, Saha S. Designing Next-Generation Vaccines Against Common Pan-Allergens Using In Silico Approaches. Monoclon Antib Immunodiagn Immunother.41(5):231-242. doi: 10.1089/mab.2021.0033. (2022)
79. Firdous S, Ghosh A, Saha S. BCSCdb: a database of biomarkers of cancer stem cells. Database (Oxford). 2022:baac082. doi: 10.1093/database/baac082. (2022)
78. Chaudhary D, Singh A, Marzuki M, Ghosh A, Kidwai S, Gosain TP, Chawla K, Gupta SK, Agarwal N, Saha S, Kumar Y, Thakur KG, Singhal A, Singh R. Identification of small molecules targeting homoserine acetyl transferase from Mycobacterium tuberculosis and Staphylococcus aureus. Sci Rep.12(1):13801. doi: 10.1038/s41598-022-16468-w. (2022)
77. Mahatha AC, Banerjee SK, Ghosh A, Lata S, Saha S, Basu J, Kundu M. A systems approach to decipher a role of transcription factor RegX3 in the adaptation of Mycobacterium tuberculosis to hypoxic stress. Microbiology (Reading).168(8). doi: 10.1099/mic.0.001229.(2022)
76: Bhattacharjee S, Saha B, Bhattacharyya P, Saha S. LHSPred: A web based application for predicting lung health severity. Biomed Signal Process Control. 77:103745. doi: 10.1016/j.bspc.2022.103745. (2022)
75. S Bhattacharjee, B Saha, S Saha. Classification of Lung Diseases Using Machine Learning Techniques. In Book: Artificial Intelligence Technologies for Computational Biology, pp 75-94, CRC Press (2022)
74. S Firdous, SK Srivastava, S Saha. Cancer Biomarkers in the Era of Systems Biology. In Book: Systems Biomedicine Approaches in Cancer Research, pp 51-70, Springer, Singapore (2022)
73. S Bhattacharjee, A Ghosh, B Saha, S Saha. In Book: Machine Learning in Genomics. Machine Learning and Systems Biology in Genomics and Health, pp 69-90, Springer, Singapore (2022)
72. Majumdar S, Bhattacharjee S, Jana T, Saha S. DAAB-V2: Updated database of allergy and asthma biomarkers. Allergy. 76(12):3829-3832. doi: 10.1111/all.15100. (2021)
71. Bhowmik M, Biswas Sarkar M, Kanti Sarkar R, Dasgupta A, Saha S, Jana K, Sircar G, Gupta Bhattacharya S. Cloning and immunobiochemical analyses on recombinant chymopapain allergen Cari p 2 showing pollen-fruit cross-reaction. Mol Immunol.137:42-51. doi: 10.1016/j.molimm.2021.06.010.(2021)
70. Joardar N, Shit P, Halder S, Debnath U, Saha S, Misra AK, Jana K, Sinha Babu SP. Disruption of redox homeostasis with synchronized activation of apoptosis highlights the antifilarial efficacy of novel piperine derivatives: An in vitro mechanistic approach. Free Radic Biol Med.169:343-360. doi: 10.1016/j.freeradbiomed.2021.04.026. Epub 2021 Apr 23.PMID: 33895288 (2021)
69. Majumdar S, Verma R, Saha A, Bhattacharyya P, Maji P, Surjit M, Kundu M, Basu J, Saha S. Perspectives About Modulating Host Immune System in Targeting SARS-CoV-2 in India. Front Genet.12:637362. doi: 10.3389/fgene.2021.637362. (2021)
68. Roy D, Bose S, Pati S, Guin A, Banerjee K, Saha S, Singhal AK, Chakraborty J, Sarkar DK, Sa G. GFI1/HDAC1-axis differentially regulates immunosuppressive CD73 in human tumor-associated FOXP3+ Th17 and inflammation-linked Th17 cells. Eur J Immunol. 51(5):1206-1217. doi: 10.1002/eji.202048892. (2021)
67. Ghosh N, Sharma N, Saha I, Saha S. Genome-wide analysis of Indian SARS-CoV-2 genomes to identify T-cell and B-cell epitopes from conserved regions based on immunogenicity and antigenicity. Int Immunopharmacol.91:107276. doi: 10.1016/j.intimp.2020.107276. Epub 2020 Dec 16. (2021)
66. Ghosh A, Firdous S, Saha S. Bioinformatics for Human Microbiome, In Book: Advances in Bioinformatics, S. Singh (ed.) Springer Singapore, pp 333-350 (2021)
65. Mishra A, Behura A, Kumar A, Ghosh A, Naik L, Mawatwal S, Mohanty SS, Mishra A, Saha S, Bhutia SK, Singh R, Dhiman R. Soybean lectin induces autophagy through P2RX7 dependent activation of NF-κB-ROS pathway to kill intracellular mycobacteria. Biochim Biophys Acta Gen Subj.1865(2):129806. doi: 10.1016/j.bbagen.2020.129806. Epub 2020 Nov 28. (2021)
64. Majumdar S, Saha S. Systems Immunology Approach in
Understanding the Association of Allergy and Cancer, In Book: Systems and Synthetic Immunology, S. Singh (ed.) Springer Singapore, pp
53-72 (2020)
63. Ghosh N, Sircar G, Asam C, Wolf M, Hauser M, Saha S, Ferreira F, Bhattacharya SG. Purification and biochemical characterization of Hel a 6, a cross-reactive pectate lyase allergen from Sunflower (Helianthus annuus L.) pollen. Sci Rep. 10(1):20177. doi: 10.1038/s41598-020-77247-z.(2020)
63. Mahatha AC, Mal S, Majumder D, Saha S, Ghosh A, Basu J, Kundu M. RegX3 Activates whiB3 Under Acid Stress and Subverts Lysosomal Trafficking of Mycobacterium tuberculosis in a WhiB3-Dependent Manner. Front Microbiol. 11:572433. doi: 10.3389/fmicb.2020.572433. (2020)
62. Ghosh A, N S, Saha S. Survey of drug resistance associated gene mutations in Mycobacterium tuberculosis, ESKAPE and other bacterial species. Sci Rep. 10(1):8957. doi: 10.1038/s41598-020-65766-8. (2020)
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 MoreRecognition:
- Ramalingaswami Re-entry Fellow, 2012-2017
- European Respiratory Society Member, 2018-2022
- 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 | |
|---|---|---|---|---|---|---|
 |
Dibakar Roy | Junior Research Fellow | Bioinformatics Centre | Centenary | droy7329@gmail.com | |
 |
Jagannath | Senior Research Fellow | Bioinformatics Centre | Centenary | jagannath.zoology@gmail.com | |
 |
Paramita Roy | Senior Research Fellow | Bioinformatics Centre | Centenary | royparamita95@gmail.com | |
 |
Shazia Firdous | Senior Research Fellow | Bioinformatics Centre | Centenary | sazfirdaus03@gmail.com | |
 |
Stuti Ghosh | Junior Research Fellow | Bioinformatics Centre | Centenary | stutighosh50@gmail.com |
Former:
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, Ph.D. awarded, University of Calcutta, 2021
Sreyashi Majumdar, Ph.D. awarded, University of Calcutta, 2022
Group News:
Papers recently accepted from our group
*** Ghosh A and Saha S. Meta-analysis of sputum microbiome studies identifies airway disease-specific taxonomic and functional signatures. Journal of Medical Microbiology,72(12) DOI: 10.1099/jmm.0.001617 (2022)
*** Bhattacharjee S, Saha B, Bhattacharyya P, Saha S. LHSPred: A web-based application for predicting lung health severity. Biomed Signal Process Control. 77:103745. DOI: 10.1016/j.bspc.2022.103745. (2022)
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December 18, 2022: Sudipto Saha gave an invited talk at the workshop under the "Accelerate Vigyan' scheme of SERB (Ministry of Science and Technology, Govt of India) on "Machine learning based approach for the identification of biomarkers and for drug discovery" held by the Department of Biotechnology, National Institute of Technology Durgapur entitled "Machine learning based classification of lung diseases using different types of biomarkers".
December 2, 2022: Saran N submitted his Ph.D. thesis titled "The Role Of Mycobacterial Fluroquinolone Pentapaptide (Mfp) Proteins Conferring Drug Resistance in Mycobacteria".
October 31- November 2, 2022: Dibakar Roy presented a poster entitled “MDPD: Microbiome Database of Pulmonary Diseases” at the 4th IBSE International Symposium on "Microbiomes in Environment, Space and Human Health", held at IIT Madras, India.
August 13, 2022: Sudipto Saha gave an invited talk at the webinar "Microbial Technology: Present and Future" held by the Deptt. of Microbiology of Vidyasagar University on "The role of Lung Microbiome in Airway Diseases".
August 5, 2022, Sreyashi Majumdar was awarded a Ph.D. degree from the University of Calcutta.
March 9, 2021: Debangana Chakravorty was awarded a Ph.D. degree from the University of Calcutta.
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 the relationship of Human Gut-Lung Microbiome to the 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 the Indian Institute of Technology Jodhpur
on “Understanding
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 a Ph.D. degree from the 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 at the 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 the 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." at 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" was accepted for oral presentation at 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 at 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 at the International Conference on Bioinformatics (InCoB 2018), 2018, New Delhi
July 17-21,2018: Abhirupa Ghosh attended NIBMG Summer School 2018 on Systems Biology at the 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 the Machine Intelligence Unit at the Indian Statistical Institute, Kolkata. The title 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"