Scientist F
Email: thomass[at]nirrh[dot]res[dot]in, susansherry[at]gmail[dot]com
Phone: +( 91-22) 2419 2107
Department: Biomedical Informatics Centre
- Ph.D guide for Life Sciences and Biotechnology, University of Mumbai
- Member of AdHoc Board Of Studies In Molecular Biology, University of Mumbai
Research Interests
- Machine learning algorithms for prediction and classification
- Sequence analysis, database creation and data mining
- Protein-protein interactions
- Disease informatics
Academic Background
- M.Sc. Tamil Nadu Agricultural University (Biotechnology; 1998)
- Ph.D Indian Institute of Technology , Bombay (Biotechnology; 2007)
Professional Experience
| Designation | Institute/Organization | FROM | TO |
| Scientist | NIRRH | 2006 | Till date |
| IUSSTF Post-doctorate Research Fellow | University of Miami, Florida, USA | 2011 | 2012 |
| DHR Fellow | University of Toronto, Canada | Sep 2018 | Feb 2019 |
| Queen Elizabeth Scholar | (QES), Center for Global Health Research, St. Michael’s hospital, Canada | May 2019 | Aug 2019 |
Present
- Ms. Indra Kundu (Ph.D student and Research Associate; 2019)
- Ms. Kshitija Rahate (Ph.D student; 2021)
- Ms. Ulka Gawde (Ph.D student and Project Associate; 2018)
- Ms. Karishma Desai (Ph.D student and Junior Research Fellow; 2019)
- Ms. Amisha Dalvi (Ph.D student; 2024)
- Ms. Nikita Manjhi (Ph.D student; 2025)
- Ms. Anam Arshi (Project Technical Officer – 2024)
- Ms. Ankita Murukesan (Scientific Administrative Assistant – 2023)
- Ms. Anchal Yadav (Scientific Administrative Assistant; 2024)
- Mr. Ishwar Patidar (Project Scientist – I; 2025)
- Ms. Grace Mathew (Intern;2025)
- Ms. Ishita Tandon (Project assistant; 2025)
- Mrs. Sheetal Gawade
Past
- Mr. Jitender Sakhreliya (M.Tech dissertation; 2007)
- Mr. Ashmit Hadke (M.Tech dissertation; 2007)
- Ms. Padma Nanaware (PA; 2007-2008)
- Ms. Archana Jagtap (PA/JRF/SRF; 2008-2015)
- Ms. Neha Srivastava (PA; 2008)
- Mr. Pravin Nilawe (PA; 2008-2010)
- Mr. Kapil Sharma (JRF; 2010-2011)
- Mr. Swapnil Patil (JRF; 2010-2011)
- Ms. Faiza Waghu (M.Sc. dissertation; 2011)
- Mr. Sarfaraz Niazi (SRF; 2011-2014)
- Mr. Lijin Gopi (SRF; 2011-2013)
- Mr. Pranay Ramteke (JRF; 2012-2013)
- Mr. Sahil Raje (JRF; 2017-2018)
- Ms. Faiza Waghu (Ph.D student; 2013-2019)
- Mr. Abhishek Tiwari (JRF, 2019)
- Ms. Pallavi Nakhawa (PA; 2013-2014)
- Mr. Bilal Nizami (M.Tech dissertation; 2013)
- Ms. Sapna Iyer (M.Sc. dissertation; 2013)
- Ms. Sonali Chauhan (SRF; 2014)
- Ms. Pratima Gurung (JRF; 2014-2015)
- Ms. Madhura Khare (M.Tech dissertation; 2014)
- Ms. Rasika Bhujbalrao (M.Sc. dissertation; 2014)
- Ms. Bhavana Sahu (PA; 2014-2015)
- Ms. Harshala Haldankar (M.Tech dissertation/PA; 2015- 2016)
- Mr. Mohammed Hussain (Research Scholar; 2015-2016)
- Ms. Sanchi Shah (M.Sc. dissertation; 2015)
- Ms. Khushboo Shroff (M.Tech dissertation; 2016)
- Ms. Abhipriya (JRF; 2015)
- Ms. Gauri Shende (SRF; 2016)
- Mr. Vinit Shetty (M.Sc. dissertation; 2016)
- Ms. Shrusti Raut (M.Sc. dissertation; 2016)
- Mr. Sanket Ghawali (JRF; 2016-2017)
- Ms. Ankita Dhamnaskar (PA; 2016-2017)
- Ms. Rachel Fernandes (Research Scholar; 2016-2017)
- Ms. Aishwarya Rane (M.Sc. dissertation; 2017)
- Mr. Raza Ali Jafri (JRF; 2018-2019)
- Mr. Ayan Mandal (M.Sc. dissertation; 2017)
- Ms. Karishma Desai (M.Sc. dissertation; 2018)
- Ms. Ritika Shah (M.Sc. dissertation; 2019)
- Ms. Tejaswani Puppala (M.Sc. dissertation; 2019)
- Mr. Kushal Pokar (Sr. Lab Assistant; 2018-2019)
- Dr. Muthu Sankar Aathi (ICMR-PDF; 2019-2021)
- Dr. Debangana Chakraborty (Project Scientist – I; 2021)
- Mr. Tanmay Shirshat (JRF; 2019-2021)
- Ms. Mridula Sharma (JRF; 2019-2021)
- Ms. Sameeksha Ratnakar Bhaye (Technical Assistant; 2018-2921)
- Mr. Aman Vishwakarma(Senior Lab Assistant; 2021-2022)
- Ms. Kaushiki Prabhudesai (Ph.D student; 2015-2022)
- Ms. Priyanka Hegde (Scientific Administrative Assistant-2021-2022)
- Mr. Ankit Kanojia (JRF-2022)
- Ms. Ashlesha Pande (Scientific Administrative Assistant-2022)
- Dr. Prayagraj Fandilolu (Project Scientist – I; 2022)
- Dr. Chandan Kumar (Project Scientist – I; 2021-2024)
- Mr. Pankajkumar Pandey (Scientific Administrative Assistant – 2024)
- Dr. Chandra Sekar P (Project Scientist – I; 2023-2024)
- Sonal Vishwakarma (Intern; 2023-2024)
- Sejal T. (Intern; 2024)
- Ms. Nirupma Singh (Project Scientist – I; 2024)
- Ms. Shuvechha Chakraborty (Ph.D student and Senior Research Fellow; 2017 – 2024)
- Dr. Anam Farooqui (Project Scientist – I; 2024 – 2025)
- Ms. Krisna Parab (Project Assistant – 2023 – 2025)
- Ms. Shazia Mirza (Scientific Administrative Assistant; 2024-2025)
- Ms. Ishita (Intern; 2024-2025)
- Ms. Anushka (Intern; 2025)
- Ms. Nidhi Mishra (Intern; 2025)
- Ms. Aneesha Shetty (Scientific Administrative Assistant – 2024-2025)
Awards & Achievements
- Scholarships/Fellowship
- SERB Science and Technology Award for Research (SERB-STAR) 2020
- Queen Elizabeth Scholar (QES), Center for Global Health Research, St. Michael’s hospital, Canada [May 2019-Aug 2019]
- Department of Health Research Overseas training fellowship (2018-2019)
- Indo-US Science and Technology Forum Research Fellowship (2011 – 2012)
- Fulbright PDR scholarship (selected but not availed)
- SERC Fast Track Scheme for Young Scientists (2010-2013)
- Junior & Senior Research Fellowship from CSIR (2001 – 2006)
- Junior Research Fellowship from ICAR (1996-1998)
- KAU merit scholarship (1991-1996)
- Achievements
- Gargi Vishnoi Memorial Award – Best Ph.D Thesis of BioSchool, IITB, 2007
- Finn Wold Travel Awardee of Protein Science Society, USA – 2006
- National Eligibility Test (NET) – 2001
- State Eligibility Test (SET) -2001
Publications
Predicting Toxicity of Insect Venom-Derived Antimicrobial Peptides Using MD Simulations: A Comparative Study of Multi-Component and Realistic Mammalian Membrane Models.
2025
Sekar, P. C., Gawde, U., Kumar, C., & Idicula-Thomas S.
The Journal of membrane biology, 2025
https://doi.org/10.1007/s00232-025-00363-2
EpiCandIn: An open online resource for epidemiology of Candida infections in India
2024
Rahate, K., Arshi, A., Barai, R.S., Chakraborty, S., & Idicula-Thomas S.
Indian Journal of Medical Research, 2024
http://dx.doi.org/10.25259/ijmr_886_23
Investigating role of positively selected genes and mutation sites of ERG11 in drug resistance of Candida albicans
2024
Fandilolu, P., Kumar, C., Palia, D., & Idicula-Thomas S.
Archives of microbiology, 2024
https://doi.org/10.1007/s00203-024-04159-1
Relation of mitochondrial DNA copy number and variants with the clinical characteristics of polycystic ovary syndrome
2024
Thariyal, S P, Rasal, S, Gawde, U, Mukherjee, S, Patil, A, Joshi, B, Idicula-Thomas S, & Shukla, P.
Molecular and Cellular Endocrinology, 2024
https://doi.org/10.1016/j.mce.2024.112386
Differential proteomics of circulating extracellular vesicles of placental origin isolated from women with early-onset preeclampsia reveal aberrant innate immune and hemostasis processes
2024
Rao A, Subedi R, Kundu I, Idicula-Thomas S, Shinde U, Bansal V, Balsarkar G, Mayadeo N, Das DK, Balasinor N, Madan T.
Am J Reprod Immunol, 2024
https://doi.org/10.1111/aji.13860
PBITV3: A robust and comprehensive tool for screening pathogenic proteomes for drug targets and prioritizing vaccine candidates
2024
Chakraborty, S., Askari, M., Barai, R.S. and Idicula-Thomas S
Protein Sciences, 2024
https://doi.org/10.1002/pro.4892
Genomic and computational analysis of four novel variants of MPL gene in Congenital Amegakaryocytic Thrombocytopenia
2023
CAMPR4: a database of natural and synthetic antimicrobial peptides.
2023
FSHR activation through small molecule modulators: Mechanistic insights from MD simulations
2023
GeDiPNet: Online resource of curated gene-disease associations for polypharmacological targets discovery.
2023
Mammalian cysteine-rich secretory proteins interact with plasma membrane Ca2+ exporter PMCA4b
2023
Ferroptosis mediators vary in metabolic syndrome, type-2 diabetes, and hypercholesterolemia: A meta-analysis report
2023
Ferroptosis mediators vary in metabolic syndrome, type-2 diabetes, and hypercholesterolemia: A meta-analysis report
2023
Kundu I, Pande A, Das T, Idicula-Thomas S
Genes & Diseases, 2023
https://doi.org/10.1016/j.gendis.2023.06.024
Mammalian cysteine-rich secretory proteins interact with plasma membrane Ca2+ exporter PMCA4b
2023
Miya V, Kumar C, Breed AA, Idicula-Thomas S, Pathak BR
Andrology, 2023
https://doi.org/10.1111/andr.13549
Genomic and computational analysis of four novel variants of MPL gene in Congenital Amegakaryocytic Thrombocytopenia
2023
Shah A, Kumar C, Shanmukhaiah C, Rajendran A, Mudaliar S, Idicula-Thomas S & Vundinti B R
Annals of Hematology 2023
https://doi.org/10.1007/s00277-023-05347-7
FSHR antagonists can trigger a PCOS-like state.
2022
Mapping of FSHR agonists and antagonists binding sites to identify potential peptidomimetic modulators
2022
Multimorbidity landscape of schizophrenia: Insights from meta-analysis of genome wide association studies
2022
Gawde U, Hegde P, Desai K, Barai R S, Shekhar B R, Das D K, Idicula-Thomas S
Schizophrenia Research, Volume 243, 2022, Pages 214-216, ISSN 0920-9964
https://doi.org/10.1016/j.schres.2022.03.013
Pathway Analysis of Genome Wide Association Studies (GWAS) Data Associated with Male Infertility
2022
GeDiPNet: Online resource of curated gene-disease associations for polypharmacological targets discovery
2022
Kundu I, Sharma M, Barai R S, Pokar K, Idicula-Thomas S
Genes & Diseases. 2022.
https://doi.org/10.1016/j.gendis.2022.05.034
Human Surfactant Protein D Facilitates SARS-CoV-2 Pseudotype Binding and Entry in DC-SIGN Expressing Cells, and Downregulates Spike protein Induced Inflammation
2022
Beirag N, Kumar C, Madan T, Shamji M.H, Bulla R, Mitchell D, Murugaiah V, Neto M.M, Temperton N.J, Idicula-Thomas S and Varghese P.M.
Frontiers in Immunology, Volume 13, 2022, ISSN 1664-3224
https://doi.org/10.3389/fimmu.2022.960733
N-linked glycosylation in Chinese hamster ovary cells is critical for insulin-like growth factor 1 signaling
2022
Human surfactant protein D facilitates SARS-CoV-2 pseudotype binding and entry in DC-SIGN expressing cells, and downregulates spike protein induced inflammation.
2021
FSHR antagonists can trigger a PCOS-like state
2021
Human Properdin Released By Infiltrating Neutrophils Can Modulate Influenza A Virus Infection
2021
Central residues of FSHβ (89-97) peptide are not critical for FSHR binding: Implications for peptidomimetic design
2021
Comparison of machine learning algorithms applied to symptoms to determine infectious causes of death in children: national survey of 18,000 verbal autopsies in the Million Death Study in India
2021
A Recombinant Fragment of Human Surfactant Protein D Binds Spike Protein and Inhibits Infectivity and Replication of SARS-CoV-2 in Clinical Samples
2021
Enrichment analyses of diseases and pathways associated with precocious puberty using PrecocityDB
2021
Exploring the druggable proteome of Candida species through comprehensive computational analysis
2021
PCOSKBR2: a database of genes, diseases, pathways, and networks associated with polycystic ovary syndrome.
2020
Membrane Interactome of a Recombinant Fragment of Human Surfactant Protein D Reveals GRP78 as a Novel Binding Partner in PC3, a Metastatic Prostate Cancer Cell Line
2020
A 5-mer peptide derived from hinge region of hFSHR can function as positive allosteric modulator in vivo
2020
Meta-analysis of gene expression profiles of lean and obese PCOS to identify differentially regulated pathways and risk of comorbidities
2020
A steady-state modeling approach for simulation of antimicrobial peptide-cell membrane interaction
2020
Identification and in vivo validation of a 9-mer peptide derived from FSHβ with FSHR antagonist activity
2020
A QSAR modeling approach for predicting myeloid antimicrobial peptides with high sequence similarity
2020
Collection of antimicrobial peptides database and its derivatives: Applications and beyond
2020
Effect of diversity in gp41 membrane proximal external region of primary HIV-1 Indian subtype C sequences on interaction with broadly neutralizing antibodies 4E10 and 10E8
2019
Discovery of small molecule binders of human FSHR(TMD) with novel structural scaffolds by integrating structural bioinformatics and machine learning algorithms
2019
Designing Antibacterial Peptides with Enhanced Killing Kinetics
2018
PBIT: Pipeline builder for identification of drug targets for infectious diseases.
2017
Tubulin acetylation: A novel functional avenue for CDYL in sperm.
2017
Protein-Protein interaction between surfactant protein D and DC-SIGN via C-type lectin domain can suppress HIV-1 transfer.
2017
Evaluation of 4-thiazolidinone derivatives as potential reverse transcriptase inhibitors against HIV-1 drug resistant strains.
2017
Leveraging family-specific signatures for AMP discovery and high-throughput annotation
2016
PCOSKB: A KnowledgeBase on genes, diseases, ontology terms and biochemical pathways associated with Poly Cystic Ovary Syndrome
2016
CAMPR3: A database on sequences, structures and signatures of antimicrobial peptides
2016
CAMP: Collection of sequences and structures of antimicrobial peptides
2014
Surfactant protein D inhibits HIV-1 infection of target cells via interference with gp120-CD4 interaction and modulates pro-inflammatory cytokine production
2014
Cervical cancer in Indian women reveals contrasting association among common sub-family of HLA class I alleles
2014
HPV16 E6 variants: Frequency, association with HPV types and in silico analysis of the identified novel variants
2014
A Chemical Proteomics Approach to Profiling the ATP-Binding Proteome of Mycobacterium tuberculosis
2013
In silico study on binding specificity of gonadotropins and their receptors: design of a novel and selective peptidomimetic for human follicle stimulating hormone receptor
2013
Imatinib resistance due to a novel tri-nucleotide insertion in the SH2/C lobe interface of BCR/ABL kinase domain between position K357 and N358
2012
Immunization with Ovarian Autoantigens leads to reduced fertility in mice following follicular dysfunction
2012
ClassAMP: a prediction tool for classification of antimicrobial peptides
2012
Anti-HSP90 autoantibodies in sera of infertile women identify a dominant, conserved epitope EP6 (380-389) of HSP90 beta protein
2011
CAMP: a useful resource for research on antimicrobial peptides.
2010
Molecular analysis of hereditary factor X (FX) deficiency cases from Western India
2010
ClotBase: A knowledgebase on proteins involved in blood coagulation
2010
A novel 9-bp insertion detected in steroid 21-hydroxylase gene (CYP21A2): prediction of its structural and functional implications by computational methods
2009
Projects Ongoing
- Machine learning algorithms trained on voice to predict psychological distress and postpartum depression. (ICMR, Government of India)
- Establishment of Bioinformatics and Computational Biology Centre (Centre for advanced research in bioinformatics and computational biology for woman and child health) – BIC at ICMR-National Institute for Research in Reproductive Health, Mumbai (Department of Biotechnology, Government of India)
- National Network Project of National Institute for Research in Reproductive and Child Health. (DBT, Government of India)
Projects Completed
- Integrated analyses of genomic scale metabolic models and omics profiles to capture the host-pathogen-environment interplay of Candida sp.(SERB, Government of India)
- Identification of enriched biochemical networks and polypharmacological targets in metabolic syndrome (SERB-STAR, Government of India )
- Identification of differentially expressed genes in lean and obese PCOS and validation using rat animal models (Department of Health Research, Government of India)
- Development and validation of multi-scale dynamic and steady state metabolic network models for PCOS using computational and wet-lab methods (Department of Biotechnology, Government of India)
- Identification and validation of potential drug targets for infectious diseases using in silico and wet lab methods (SERB, Government of India)
- Identification and preparation of radio-labeled modulators of hFSHR for therapeutic applications (BRNS, Department of Atomic Energy, Government of India)
- Exploring the hinge and transmembrane region of human FSHR for design of small molecule and peptidomimetic modulators (Department of Biotechnology, Government of India)
- Second phase of Task Force Biomedical Informatics Centres of ICMR (Indian Council of Medical Research)
- Analysis of the structures of known antimicrobial peptides using machine learning algorithms and molecular dynamics simulations. (Department of Science and Technology, Government of India)
- Studies on the binding specificities of gonadotropins and their receptors (Department of Biotechnology, Government of India)
- Studies to understand the tertiary structure-dependence on antimicrobial activity of 2 novel peptides (Department of Science and Technology, Government of India)
- Elucidation of the role of primary structure of proteins on their antimicrobial activity (Department of Science and Technology, Government of India)
- Introduction of electronic patient record systems in Indian government hospitals. (Department of Science and Technology, Government of India)