Dr. Susan Thomas
Scientist-E
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
Academic Background
- M.Sc. Tamil Nadu Agricultural University (Biotechnology; 1998)
- Ph.D Indian Institute of Technology , Bombay (Biotechnology; 2007)
Professional Experience
| 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
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(QES), Center for Global Health Research, St. Michael’s hospital, Canada | May 2019 – Aug 2019 |
Research Interests
- Machine learning algorithms for prediction and classification
- Sequence analysis, database creation and data mining
- Protein-protein interactions
- Disease informatics
Present
- Ms. Kaushiki Prabhudesai (Ph.D student; 2015)
- Ms. Shuvechha Chakraborty (Ph.D student; 2017)
- Ms. Ulka Gawade (PA; 2018)
- Ms. Sameeksha Ratnakar Bhaye (Technical Assistant; 2018)
- Ms. Indra Kundu (Ph.D student; 2019)
- Ms. Mridula Sharma (JRF; 2019)
- Dr. Muthu Sankar Aathi (ICMR-PDF)
- Ms. Karishma Desai (Technician-C; 2019)
- Mr. Tanmay Shirshat (JRF; 2019)
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)
Awards & Achievements
- Scholarships/Fellowship
- SERB Science and Technology Award for Research (SERB-STAR) 2020
- 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
Exploring the druggable proteome of Candida species through comprehensive computational analysis
2021
Shuvechha Mukherjee, Indra Kundu, Mehdi Askari, Ram Shankar Barai, K.V. Venkatesh, Idicula-Thomas S
Genomics Volume 113, Issue 2, March 2021, Pages 728-739
Enrichment analyses of diseases and pathways associated with precocious puberty using PrecocityDB
2021
Sharma M, Kundu I, Barai RS, Bhaye S, Desa Ki, Pokar K and Idicula-Thomas S
Scientific Reports 11, 4203 (2021). https://doi.org/10.1038/s41598-021-83446-z
A Recombinant Fragment of Human Surfactant Protein D Binds Spike Protein and Inhibits Infectivity and Replication of SARS-CoV-2 in Clinical Samples
2021
Madan T, Biswas B, Varghese PM, Subedi R, Pandit H, Idicula-Thomas S, Kundu I, Rooge S, Agarwal R, Tripathi DM, Kaur S, Gupta E, Gupta SK, Kishore U
Am J Respir Cell Mol Biol. 2021 Mar 30. doi: 10.1165/rcmb.2021-0005OC. Epub ahead of print. PMID: 33784482
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
Idicula-Thomas S, Gawde U & Jha P
BMC Public Health 21, 1787
Central residues of FSHβ (89-97) peptide are not critical for FSHR binding: Implications for peptidomimetic design
2021
Prabhudesai KS, Raje S, Desai K, Modi D, Dighe V, Contini A, Idicula-Thomas S
Bioorg Med Chem Lett. 2021 Jul 15;44:128132
Collection of antimicrobial peptides database and its derivatives: Applications and beyond
2020
Waghu FH, Idicula-Thomas S
Protein Sci. 2020 Jan;29(1):36-42. doi: 10.1002/pro.3714
A QSAR modeling approach for predicting myeloid antimicrobial peptides with high sequence similarity
2020
Waghu FH, Gawde U, Gomatam A, Coutinho E, Idicula-Thomas S
Chem Biol Drug Des. 2020;10.1111/cbdd.13749. doi:10.1111/cbdd.13749
Identification and in vivo validation of a 9-mer peptide derived from FSHβ with FSHR antagonist activity
2020
Prabhudesai KS, Raje S, Dhamanaskar A. Modi D. Dighe V. Contini A. Idicula-Thomas S.
Peptides. 2020;132:170367. doi:10.1016/j.peptides.2020.170367
A steady-state modeling approach for simulation of antimicrobial peptide-cell membrane interaction
2020
Srinivasan S, Waghu FH, Idicula-Thomas S, Venkatesh KV.
Biochim Biophys Acta Biomembr. 2020;1862(4):183242. doi:10.1016/j.bbamem.2020.183242
Meta-analysis of gene expression profiles of lean and obese PCOS to identify differentially regulated pathways and risk of comorbidities
2020
Idicula-Thomas S, Gawde U, Bhaye S, Pokar K, Bader G D
Computational and Structural Biotechnology Journal
A 5-mer peptide derived from hinge region of hFSHR can function as positive allosteric modulator in vivo
2020
Prabhudesai KS, Aathi MS, Dighe V, Idicula-Thomas S
Biochimica et Biophysica Acta (BBA)-Biomembranes, 183492
PCOSKBR2: a database of genes, diseases, pathways, and networks associated with polycystic ovary syndrome.
2020
Sharma, M, Barai, RS, Kundu, I, Bhaye S., Pokar K, Idicula-Thomas S
Sci Rep 10, 14738
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
Thakur G, Sathe G, Kundu I, Biswas B, Gautam P, Alkahtani S, Idicula-Thomas S, Sirdeshmukh R, Kishore U, Madan T
Front Immunol. 2021 Jan 19;11:600660. doi: 10.3389/fimmu.2020.600660. PMID: 33542717
Discovery of small molecule binders of human FSHR(TMD) with novel structural scaffolds by integrating structural bioinformatics and machine learning algorithms
2019
Sahu B, Shah S, Prabhudesai K, Contini A, Idicula-Thomas S
J Mol Graph Model Jun;89:156-166. doi: 10.1016/j.jmgm.2019.02.001.
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
Sutar J, Padwal V, Sonawani A, Nagar V, Patil P, Kulkarni B, Hingankar N, Deshpande S, Idicula-Thomas S, Jagtap D, Bhattacharya J, Bandivdekar A, Patel V.
Virus Res. 2019 Nov;273:197763. doi: 10.1016/j.virusres.2019.197763.
Designing Antibacterial Peptides with Enhanced Killing Kinetics
2018
Waghu FH, Joseph S, Ghawali S, Martis EA, Madan T, Venkatesh KV, Idicula- Thomas S
Front Microbiol. 2018 Feb 23;9:325. doi: 10.3389/fmicb.2018.00325
Evaluation of 4-thiazolidinone derivatives as potential reverse transcriptase inhibitors against HIV-1 drug resistant strains.
2017
Suryawanshi R, Jadhav S, Makwana N, Desai D, Chaturbhuj D, Sonawani A, Idicula-Thomas S, Murugesan V, Katti SB, Tripathy S, Paranjape R, Kulkarni S
Bioorg Chem. 2017, 71:211-218, doi: 10.1016/j.bioorg.2017.02.007.
Protein-Protein interaction between surfactant protein D and DC-SIGN via C-type lectin domain can suppress HIV-1 transfer.
2017
Dodagatta-Marri E, Mitchell DA, Pandit H, Sonawani A, Murugaiah V, Idicula-Thomas S, Nal B, Al-Mozaini MM, Kaur A, Madan T, Kishore U.
Front Immunol 31: 8:834, doi: 10.3389/fimmu.2017.00834, 2017.
Tubulin acetylation: A novel functional avenue for CDYL in sperm.
2017
Parab S, Dalvi V, Mylavaram S, Kishore A, Idicula-Thomas S, Sonawane S, Parte P.
Cytoskeleton 74: 331-342, 2017.
PBIT: Pipeline builder for identification of drug targets for infectious diseases.
2017
Shende G, Haldankar H, Barai RS, Bharmal MH, Shetty V, Idicula-Thomas S.
Bioinformatics 33: 929-931, 2017
PCOSKB: A KnowledgeBase on genes, diseases, ontology terms and biochemical pathways associated with Poly Cystic Ovary Syndrome
2016
Joseph S, Barai RS, Bhujbalrao R, Idicula-Thomas S
Nucleic Acids Res 44(D1):D1032-5, 2016
CAMPR3: A database on sequences, structures and signatures of antimicrobial peptides
2016
Waghu FH, Barai RS, Gurung P, Idicula-Thomas S
Nucleic Acids Res, 4;44(D1):D1094-7, 2016
Leveraging family-specific signatures for AMP discovery and high-throughput annotation
2016
Waghu FH, Barai RS, Idicula-Thomas S
Sci Rep, 6:24684, 2016
HPV16 E6 variants: Frequency, association with HPV types and in silico analysis of the identified novel variants
2014
Gokhale PS, Sonawani A, Idicula-Thomas S, Kerkar S, Tongaonkar H and Mania-Pramanik J
J Med Virol 86: 968-974, 2014
Cervical cancer in Indian women reveals contrasting association among common sub-family of HLA class I alleles
2014
Gokhale PS, Mania-Pramanik J, Sonawani A, Idicula-Thomas S, Kerkar S, Tongaonkar H, Chaudhari H, Warke H and Salvi V
Immunogenetics 66: 683-691
Surfactant protein D inhibits HIV-1 infection of target cells via interference with gp120-CD4 interaction and modulates pro-inflammatory cytokine production
2014
Pandit H, Gopal S, Sonawani A, Yadav AK, Qaseem AS, Warke H, Patil A, Gajbhiye, R, Kulkarni V, Al-Mozaini MA, Idicula-Thomas S, Kishore U and Madan T
PLoS One 9(7):e102395, 2014
CAMP: Collection of sequences and structures of antimicrobial peptides
2014
Waghu FH, Gopi L, Barai RS, Ramteke P, Nizami B and Idicula-Thomas S
Nucleic Acids Res 42: D1154-D1158, 2014
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
Sonawani A, Niazi S, Idicula-Thomas S
PLoS One 8:e64475, 2013
A Chemical Proteomics Approach to Profiling the ATP-Binding Proteome of Mycobacterium tuberculosis
2013
Wolfe LM, Veeraraghavan U, Idicula-Thomas S, Schurer S, Wennerberg K, Reynolds R, Besra GS, Dobos KM
Mol Cell Proteomics 12:1644-1660, 2013
ClassAMP: a prediction tool for classification of antimicrobial peptides
2012
Joseph S, Karnik S, Nilawe P, Jayaraman VK, Idicula-Thomas S
IEEE/ACM Trans Comput Biol Bioinform 9: 1535-8, 2012
Immunization with Ovarian Autoantigens leads to reduced fertility in mice following follicular dysfunction
2012
Mande P, Thomas S, Khan S, Jadhav S, Khole V
Reproduction 143:309-23, 2012
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
Vaidya S, Sonawani A, Idicula-Thomas S, Vundinti BR, Ghosh K
Leuk Res. 36(5) :e110-2, 2012
Anti-HSP90 autoantibodies in sera of infertile women identify a dominant, conserved epitope EP6 (380-389) of HSP90 beta protein
2011
Pires ES, Choudhury AK, Idicula-Thomas S, Khole V
Reprod Biol Endocrinol 27: 9-16, 2011
ClotBase: A knowledgebase on proteins involved in blood coagulation
2010
Sonawani A, Nilawe P, Barai RS, Idicula-Thomas S
Blood 116: 855-856, 2010
Molecular analysis of hereditary factor X (FX) deficiency cases from Western India
2010
Mota L, Shetty S, Idicula-Thomas S, Ghosh K
Haemophilia 16: 693-697, 2010
CAMP: a useful resource for research on antimicrobial peptides.
2010
Joseph S, Karnik S, Barai RS, Jayaraman VK, Idicula-Thomas S.
Nucleic Acids Res. 2010 Jan;38(Database issue):D774-80. doi: 10.1093/nar/gkp1021. Epub 2009 Nov 18. PubMed PMID: 19923233; PubMed Central PMCID: PMC2808926.
A novel 9-bp insertion detected in steroid 21-hydroxylase gene (CYP21A2): prediction of its structural and functional implications by computational methods
2009
Dubey S, Idicula-Thomas S, Anwaruddin M, Saravanan C, Varma R and Maitra A
J Biomed Sci 16:3, 2009
Hereditary basis of protein C deficiency (PCD) in thrombosis patients: First report from India
2009
Pai N, Shetty S, Idicula-Thomas S, Kulkarni B and Ghosh K
Thromb Haemost 101: 785-787, 2009
Projects Ongoing
- 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)
- 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)
Projects Completed
- 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)
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Analysis of the structures of known antimicrobial peptides using machine learning algorithms and molecular dynamics simulations. (Department of Science and Technology, Government of India)
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Studies to understand the tertiary structure-dependence on antimicrobial activity of 2 novel peptides (Department of Science and Technology, Government of India)
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Elucidation of the role of primary structure of proteins on their antimicrobial activity (Department of Science and Technology, Government of India)
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Introduction of electronic patient record systems in Indian government hospitals. (Department of Science and Technology, Government of India)