Oommen K. Mathew

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A comparative study of Bisulphite-seq analysis pipeline

Rashmi Kumari, Chaithra Pradeep, Dharam Nandan, 2019 .

RStrucFam: a web server to associate structure and cognate RNA for RNA-binding proteins from sequence information

Ramanathan Sowdhamini, Pritha Ghosh, Oommen K. Mathew, 2016, BMC Bioinformatics.

Pipeline to upgrade the genome annotations

Oommen K. Mathew, Dhinoth Kumar, Lijin K. Gopi, 2017 .

PASS2 database for the structure-based sequence alignment of distantly related SCOP domain superfamilies: update to version 5 and added features

Ramanathan Sowdhamini, Pritha Ghosh, Sridhar Hariharaputran, 2015, Nucleic Acids Res..

A comparative study of Bisulphite-seq analysis pipeline

Rashmi Kumari, Dharam Nandan, Baskar Viswanathan, 2017 .

DOCKSCORE: a webserver for ranking protein-protein docked poses

Ramanathan Sowdhamini, Oommen K. Mathew, Sony Malhotra, 2015, BMC Bioinformatics.

PASS2 version 6: a database of structure-based sequence alignments of protein domain superfamilies in accordance with SCOPe

Ramanathan Sowdhamini, Pritha Ghosh, Oommen K. Mathew, 2019, Database J. Biol. Databases Curation.

LenVarDB: database of length-variant protein domains

Ramanathan Sowdhamini, Oommen K. Mathew, Eshita Mutt, 2013, Nucleic Acids Res..

STIFDB2: An Updated Version of Plant Stress-Responsive TranscrIption Factor DataBase with Additional Stress Signals, Stress-Responsive Transcription Factor Binding Sites and Stress-Responsive Genes in Arabidopsis and Rice

Khader Shameer, Ramanathan Sowdhamini, Oommen K. Mathew, 2013, Plant & cell physiology.

STIFDB 2 : An Updated Version of Plant Stress-Responsive TranscrIption Factor DataBase with Additional Stress Signals , Stress-Responsive Transcription Factor Binding Sites and Stress-Responsive Genes in Arabidopsis and Rice

Oommen K. Mathew, R. Sowdhamini, K. Shameer, 2013 .

Genome sequencing of herb Tulsi (Ocimum tenuiflorum) unravels key genes behind its strong medicinal properties

Oommen K. Mathew, R. Sowdhamini, S. Malhotra, 2015, BMC Plant Biology.

Draft Genome Sequence of Plant Growth-Promoting Endophytic Microbacterium hydrothermale BPSAC84, Isolated from the Medicinal Plant Mirabilis jalapa

Oommen K. Mathew, A. Hashem, M. Dharne, 2019, Microbiology Resource Announcements.

Draft Genome Sequence of Streptomyces thermocarboxydus BPSAC147, a Potentially Plant Growth-Promoting Endophytic Bacterium

Oommen K. Mathew, A. Hashem, M. Dharne, 2019, Microbiology Resource Announcements.

A knowledge-driven protocol for prediction of proteins of interest with an emphasis on biosynthetic pathways

Oommen K. Mathew, R. Sowdhamini, Anshul Sukhwal, 2020, MethodsX.

The Indian cobra reference genome and transcriptome enables comprehensive identification of venom toxins

Markus S. Schröder, Brendan K Faherty, Oommen K. Mathew, 2020, Nature Genetics.

Near-chromosomal de novo assembly of Bengal tiger genome reveals genetic hallmarks of apex-predation

Oommen K. Mathew, S. Seshagiri, U. Ramakrishnan, 2022, bioRxiv.

Network Modules Driving Plant Stress Response, Tolerance and Adaptation: A case study using Abscisic acid Induced Protein-protein Interactome of Arabidopsis thaliana

Oommen K. Mathew, R. Sowdhamini, K. Shameer, 2016, bioRxiv.

Sepsis in the era of data-driven medicine: personalizing risks, diagnoses, treatments and prognoses

Lakshminarayanan Subramanian, Kipp W. Johnson, Khader Shameer, 2019, Briefings Bioinform..

An Approach to Function Annotation for Proteins of Unknown Function (PUFs) in the Transcriptome of Indian Mulberry

Oommen K. Mathew, R. Sowdhamini, R. S. Sajeevan, 2016, PloS one.

Near-chromosomal de novo assembly of Bengal tiger genome reveals genetic hallmarks of apex predation

Oommen K. Mathew, S. Seshagiri, U. Ramakrishnan, 2022, bioRxiv.

Draft Genome Sequence of Freshwater-Derived Streptomyces sp. Strain BPSDS2, Isolated from Damte Stream, Northeast India

Oommen K. Mathew, A. Hashem, M. Dharne, 2019, Microbiology Resource Announcements.

Dataset for the combined transcriptome assembly of M. oleifera and functional annotation

Oommen K. Mathew, R. Sowdhamini, Anshul Sukhwal, 2020, Data in brief.

The transcriptome enables the identification of candidate genes behind medicinal value of Drumstick tree (Moringa oleifera).

Oommen K. Mathew, R. Sowdhamini, Anshul Sukhwal, 2019, Genomics.

Bioinformatics and Biology Insights

Ramanathan Sowdhamini, Khader Shameer, Mahantesha BN Naika, 2022 .

Genome sequencing of herb Tulsi (Ocimum tenuiflorum) unravels key genes behind its strong medicinal properties

Oommen K. Mathew, R. Sowdhamini, S. Malhotra, 2015, BMC Plant Biology.

DOCKSCORE: a webserver for ranking protein-protein docked poses

Oommen K. Mathew, R. Sowdhamini, S. Malhotra, 2015, BMC Bioinformatics.

RStrucFam: a web server to associate structure and cognate RNA for RNA-binding proteins from sequence information

Oommen K. Mathew, R. Sowdhamini, Pritha Ghosh, 2016, BMC Bioinformatics.

Genome sequencing of herb Tulsi (Ocimum tenuiflorum) unravels key genes behind its strong medicinal properties

Oommen K. Mathew, R. Sowdhamini, S. Malhotra, 2015, BMC Plant Biology.

The sequence and de novo assembly of the genome of the Indian oil sardine, Sardinella longiceps

Oommen K. Mathew, P. Rohit, A. Gopalakrishnan, 2023, Scientific data.

CNN-LSTM based classification of polo like kinase family of Proteins: An emerging cancer drug target

Oommen K. Mathew, Jayakrushna Sahoo, Chinju John, 2022, Materials Today: Proceedings.

PIMADb: A Database of Protein–Protein Interactions in Huge Macromolecular Assemblies

Oommen K. Mathew, R. Sowdhamini, 2016, Bioinformatics and biology insights.