Publications

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

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

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

2016
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

2014

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.

2014
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

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