Enrichment analyses of diseases and pathways associated with precocious puberty using PrecocityDB


Sharma M, Kundu I, Barai RS, Bhaye S, Desa Ki, Pokar K and Idicula-Thomas S
Scientific Reports 11, 4203 (2021).

A Recombinant Fragment of Human Surfactant Protein D Binds Spike Protein and Inhibits Infectivity and Replication of SARS-CoV-2 in Clinical Samples


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

Collection of antimicrobial peptides database and its derivatives: Applications and beyond


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


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


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


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


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


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.


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


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


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


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


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.


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.


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.


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.


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


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


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


Waghu FH, Barai RS, Idicula-Thomas S
Sci Rep, 6:24684, 2016

A triad of telomerase, androgen receptor and early growth response 1 in prostate cancer cells.

Jacob S, Nayak S, Kakar R, Chaudhari UK, Joshi D, Vundinti BR, Fernandes G, Barai RS, Kholkute SD, Sachdeva G
Cancer Biol Ther. 2016 Apr 2;17(4):439-48. 
PMID: 27003515

HPV16 E6 variants: Frequency, association with HPV types and in silico analysis of the identified novel variants


Gokhale PS, Sonawani A, Idicula-Thomas S, Kerkar S, Tongaonkar H and Mania-Pramanik J
J Med Virol 86: 968-974, 2014

Androgen receptor as a regulator of ZEB2 expression and its implications in epithelial-to-mesenchymal transition in prostate cancer.

Jacob S, Nayak S, Fernandes G, Barai RS, Menon S, Chaudhari UK, Kholkute SD, Sachdeva G
Endocr Relat Cancer. 2014 May 8;21(3):473-86. 
PMID: 24812058

Cervical cancer in Indian women reveals contrasting association among common sub-family of HLA class I alleles


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


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


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


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


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


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


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


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


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


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


Mota L, Shetty S, Idicula-Thomas S, Ghosh K
Haemophilia 16: 693-697, 2010

CAMP: a useful resource for research on antimicrobial peptides.


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


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


Pai N, Shetty S, Idicula-Thomas S, Kulkarni B and Ghosh K
Thromb Haemost 101: 785-787, 2009