Dr. S. K. M. Habeeb, Ph.D

Associate Professor
Phone:27417813 Extn: 1151
Email id: habeebm@srmist.edu.in
Area: Applied Bioinformatics, Bioinformatics, Bio-programming languages, Genomics, Molecular Modeling, NGS Data Analysis
Affiliation: Department of Biotechnology, School of Bioengineering, Kattankulathur Campus, SRM Institute of Science and Technology

Education

Other Details:

Courses

• Bioinformatics, Pharmacogenomics & Personalized Medicine, Functional Genomics & Proteomics

Research Interest

• Bioinformatics, Applied Bioinformatics (Health & Agricultural Sciences), Next Generation Sequencing, Structural and Functional Bioinformatics, Application Development & Entomoinformatics

Selected Publications

• Akash S, Shyam R, Sakthivel S, Habeeb SKM. Insights from the Molecular Modelling and Docking Analysis of AIF-NLS complex to infer Nuclear Translocation of the Protein. Bioinformation. 2018;14(3).
• Sakthivel S, Habeeb SKM, Raman C. Screening of broad spectrum natural pesticides against conserved target Arginine Kinase in Cotton pests by molecular modeling. J. Biomol Struct Dyn. 2018.
• Sakthivel S, Habeeb SKM. Combined pharmacophore, virtual screening and molecular dynamics studies to identify Bruton’s Tyrosine Kinase inhibitors. J Biomol Struct Dyn.2017.
• Sureshan CS, Sakthivel S and Habeeb SKM. Structure-Based Virtual Screening, Docking and Molecular Dynamics Simulation Studies on Human Telomerase Reverse Transcriptase (hTERT) Inhibitors. Current Biotechnology. 2017. p. 1–10
• Madar IH, Kathirvel P, Subramanian S, Ssadh H AL, Desai A, Tayubi IA, et al. Modelling & Docking Studies of Wild and Mutant Rubisco Enzyme in Dunaleila salina. Int J Pharma Biosci. 2017;8(3):210–6.
• Thambidurai Y, D S, Habeeb SKM, Ashok Kumar T. Free Radical Scavenging Activity of Marine Sponges Collected from Kovalam, Chennai. Asian J Pharm Clin Res.2017;10(6):321–7.
• Thambidurai Y, Habeeb SKM, Kizhakudan J, D S. Screening of Bioactive Compounds from Marine Sponges Collected from Kovalam, Chennai. Asian J Pharm Clin Res.2017;10(5):231–6.
• Ramachandra HG, Sakthivel S, Madar IH, Tayubi IA, Habeeb SKM. Ductal Carcinoma in situ and Invasive Breast Cancer Based Differential Gene Expression Study for Therapeutic Development. Asian J Pharm Clin Res. 2016;0(0):48–51.
• Sakthivel S, Habeeb SKM. SeeHaBITaT: A server on bioinformatics applications for Tospoviruses and other species. Appl Transl Genomics. 2016;9:30–2.
• Sureshan CS, Habeeb SKM. Identification and conformational analysis of putative microRNAs in Maruca vitrata (Lepidoptera: pyralidae). Appl Transl genomics. 2015;7:2–12.
• Habeeb SKM, Sanjayan KP. Molecular Docking and Enzymatic Analysis of Annonin-I, Against the Dusky Cotton Bug Oxycarenus laetus Kirby. Curr Bioinform. 2015;10(1):91–6.
• Sakthivel S, Habeeb SKM. NNvPDB: Neural Network based Protein Secondary Structure Prediction with PDB Validation. Bioinformation. 2015;11(8):416–21.
• Anuradha V, Praveena A, Habeeb SKM, others. Identification of Drug Targets through Mutational Analysis of Drug Resistance Genes in Candida albicans. Res J Pharm Technol. 2013;6(3):267–77.
• Kesavan S, Habeeb SKM. Molecular Modeling and Drug Discovery of Potential Inhibitors for Anticancer Target Gene Melk (Maternal Embryonic Leucine Zipper Kinase). Int Res J Pharm. 2011;2(12):141.
• Habeeb SKM, Kumar S, Sanjayan KP, Anuradha V, Praveena A. Comparative evolutionary analysis of insects using mitochondrial genes. Int J Curr Res.2011;3(11):66–73.
• Praveena A, Sindhuja R, Anuradha V, Habeeb SKM. Putative Drug Target Identification for Chlamydia Trachomatis: an insilico proteome analysis. Int J Biomed Res.2011;2(2):151–60.
• Anuradha V, Habeeb SKM, Praveena A, Priya A. A New GC Based HMM Algorithm for Disease Classification. Int J Comput Appl. 2011;16(5):19–22.
• Habeeb SKM, Sanjayan KP. Sequencing and phylogenetic analysis of the mitochondrial Cytochrome C Oxidase subunit 1 of Oxycarenus laetus (Hemiptera: Lygaeidae). Intl JPlant Anim Environ Sci. 2011;1:85–91.
• Praveena A, Anuradha V, Habeeb SKM, Aruna P. Docking Studies on Plant Proteinase Inhibitors in Control of Cotton Bollworm, Helicoverpa armigera. Adv Comput SciTechnol. 2011;4(1):61–71.
• Habeeb SKM, Anuradha V, Parveena A. Comparative molecular modeling of insect glutathione S-transferases. In: IJCA. 2011. p. 16–22.

Book Chapters

• Entomoinformatics – A prelude to the concepts in Bioinformatics In book: Short Views on Insect Biochemistry and Molecular Biology, Edition: First Edition Chapter: 28 Publisher: International Book Mission, Academic Publisher, Manhattan, KS, USA (ISBN No. 978-1-63315-205-2)
• Focus on Physiological Vital Proteins from Silkworm Bombyx mori – CRC Press – In Press

Funded Projects

• Habeeb. SKM. “Comparative Resistance Study to Identify Molecular Markers for the Control of Dusky cotton Bug Oxycarenus laetus (Kirby) (Hemiptera: Lygaeidae) across Habitats using Mitochondrial DNA and Transcriptomics approaches“ funded by DST-SERB Young Scientist Scheme, Government of India (INR 25 Lakh) 2015 – 2018
• Habeeb. SKM. (Mentor). “Host Pest Interaction of Oxycarenus laetus and its Biocontrol (Kirby)” DBT – BINC fellowship funded by Govt. of India., 2017 – 2019

Bioinformatics Applications Developed

• SEEHABITAT – A Bioinformatics Workbench & Server (http://bit.srmuniv.ac.in/)
• TOAGRIBASE – Tospovirus Agricultural Database (http://bit.srmuniv.ac.in/bit/togribase/index.php)
• MOLBIT – Tools to Analyze Genome Data of Tosposvirus (http://bit.srmuniv.ac.in/bit/molbit/index.php)
• SRMBIT – Bioinformatics Tools for Sequence Manipulation (http://bit.srmuniv.ac.in/bit/srmbit/index.php)
• NNvPDB – Neural Network Based Secondary Structure Prediction With Automated Validation (http://bit.srmuniv.ac.in/cgi-bin/bit/cfpdb/nnsecstruct.pl)
• DCP – Bioinformatics Database on Cotton Pests (http://bit.srmuniv.ac.in/bit/dcp/)
• miRCal – A tool to differentiate miRNA from other RNAs (http://bit.srmuniv.ac.in/bit/dcp/mfei_calculator.pl)

Sequencing Data Submitted

• Habeeb. S. K. M. Generated RNAseq data of the Dusky Cotton Bug Oxycarenus laetus (Kirby).
• Habeeb. S. K. M. Generated Small RNAseq data of the Dusky Cotton Bug Oxycarenus laetus (Kirby).
• Habeeb. S. K. M. Generated Mitochondrial DNA data of the Dusky Cotton Bug Oxycarenus laetus (Kirby).
• Sewali Ghosh & Habeeb S. K. M. Submitted an RNAseq data of the Tea Mosquito Bug Helopeltis theivora (Waterhouse) to NCBI SRA database.
• Sewali Ghosh & Habeeb S. K. M. Submitted a Small RNAseq data of the Tea Mosquito Bug Helopeltis theivora (Waterhouse) to NCBI SRA database.
• Shama Uzmi & Habeeb S. K. M. Submitted a V3 – V4 16s rRNA Metagenomics Amplicon sequencing to study Gut Microbiota of Dysdercus cingulatus to NCBI SRA database.
• Habeeb S. K. M. & Sanjayan KP. Submitted a nucleotide sequence of Mitochondrial Cytochrome Oxidase Subunit-1 partial CDS from Oxycarenus laetus to NCBI Genbank.

Papers & Posters Presented

• “Gene Expression Profiling of Dusky Cotton Bug Oxycarenus laetus from different locations” at Nextgen Genomics, Biology, Bioinformatics & Technology International Conference held in October 2018 at Jaipur.
• “Small RNA sequencing of Oxycarenus laetus Kirby (Hemiptera: Lygaeidae) for identifying microRNA based biomarkers” at Nextgen Genomics, Biology, Bioinformatics & Technology International Conference held in October 2018 at Jaipur.
• “Enhancing Apoptosis Inducing Factor-Importin Interaction by Nuclear Localization Signal Modification to Facilitate Nuclear Translocation of the Protein” at the Recent Trends in Genetic Engineering and Biotechnology conference in September 2017 at the SRM University in Chennai.
• “Identification of Gut Microbiota of the Dusky Cotton Bug Oxycarenus laetus” at the Research Symposium in April 2017 at the SRM University in Chennai.
• “Identification of miRNAs from the tea mosquito bug Helopeltis theivora using Small RNA-Seq” at the Nextgen Genomics, Biology, Bioinformatics & Technology Conference held in October 2016 at Kochi.
• “Structure Based Virtual Screening, Docking and Molecular Dynamic Simulation Studies on Human Telomerase Reverse Transcriptase (hTERT) Inhibitors” at the Nextgen Genomics, Biology, Bioinformatics & Technology Conference held in October 2016 at Kochi.
• “Identification of potential target genes to design broad spectrum cotton insecticide using Bioinformatics techniques” at the Nextgen Genomics, Biology, Bioinformatics & Technology Conference held in October 2016 at Kochi.
• “Identification of microbial community colonizing the gut of Dysdercus cingulatus Fabricius (Hemiptera:Pyrrhocoridae)” at the Nextgen Genomics, Biology, Bioinformatics & Technology Conference held in October 2016 at Kochi.
• “Inhibition of the Biosynthesis of Epicatechin in tea, Camellia sinensis (L. Kuntze) by insecticides deployed for the control of the tea mosquito bug, Helopeltis theivora (Waterhouse) at the National Conference on Emerging Trends in Management of Infectious Diseases and Public Health held in February 2016 at Mohammed Sathak College of Arts & Science at Chennai.
• “Seehabitat” at the Research Day held at SRM University in February 2013 at Chennai.
• “Efficacy of Anosom on the growth characteristics of Dusky Cotton Bug Oxycarenus laetus” at the International Conference on Next Generation Bioinformatics held in February 2013 at the SRM University in Chennai.
• “Annonin as a candidate drug against hepatocarcinoma HCT 116 cell lines” at the International Conference on Next Generation Bioinformatics held in February 2013 at the SRM University in Chennai.
• “DNA Barcoding of the dusky cotton bug Oxycareus laetus kirby (Hemiptera: Lygaeidae)” at the National Congress on Biosciences held at Eithiraj College, Chennai.
• “Impact of Phytochemical Anosom on the Feeding and Growth of the Dusky Cotton Bug Oxycarenus laetus Kirby (Hemiptera: Lygaeidae)” in the National conference on Environment Production and Management held at Loyola college, Chennai.
• “Confirmation Analysis of DNA Holiday Junction at Insights’ 06 a state level symposium held at Guru Nanak College, Chennai.
• Poster Presentation on Proteomics at Motif’ 05 a national level symposium held at the Bharathiyar University, Coimbatore.

Work in Progress

• Identification of biomarkers in cotton bug Oxycarenus laetus using NGS transcriptomics, Mitochondrial DNA and Microarray approaches.
• Gossypol tolerance in Oxycarenus laetus using NGS transcriptomics, Metagenomics approaches.
• Gene expression profiling and microRNA identification from tea mosquito bug Helopeltis theivora using NGS RNAseq & Small RNAseq.
• Novel inhibitors against Bruton Tyrosine Kinase using Molecular Modeling approaches.

Academic Experience

• Assistant Professor, Department of Genetic Engineering at SRM University, Kattankulathur Campus, Chennai (June 2016 – December 2017)
• Assistant Professor, Department of Bioinformatics at SRM University Kattankulathur Campus, Chennai (June 2012 – May 2016)
• Assistant Professor, Department of Bioinformatics at Guru Nanak College, Chennai (June 2007 – May 2011)
• Visiting Professor, Department of Biochemistry at T.S. Narayanasamy College of Arts & Science, Chennai (January 2010 – April 2012) 

Editorial Boards / Reviewers

• Journal of Biomolecular & Structural Design
• SAR and QSAR in Environmental Research
• Journal of Microbiology, Biotechnology and Food Sciences
• Iranian Journal of Science & Technology
• Letters in Drug Design & Discovery
• Asian Journal of Pharmaceutical Research
• Current Bioactive Compounds
• Research & Reviews: A Journal of Bioinformatics
• Proteomics & Bioinformatics: Current Research
• PeerJ
• Journal of Microbiology, Biotechnology and Food Sciences

Organized National /International workshop/ Conference

• Organized IDENTITY – Hands-on Workshop on NGS Based Identification of Microbes on 15th February 2018 at the Dept. of Genetic Engineering, SRM University, Chennai.
• Organized IDENTITY – Hands-on Workshop on NGS Based Identification of Microbes on 16th February 2017 at the Dept. of Genetic Engineering, SRM University, Chennai.
• Organized a Knowledge sharing workshop session Biology for Computer Scientists on 12th November 2015 at the Dept. of Bioinformatics, SRM University, Chennai.
• Organized three day National Conference and Workshop on Genome Informatics on January 21st – 23rd 2015 at the Dept. of Bioinformatics, SRM University, Chennai.
• Organized an International Conference on Next Generation Bioinformatics on 25-27 February, 2013 at the Dept. of Bioinformatics, SRM University, Chennai.
• Organized Insights – National Conference and Workshop on Bioinformatics on March 2009 at the Dept. of Bioinformatics, Guru Nanak College, Chennai.

Guest Lectures Delivered & Recognitions

• Delivered an invited lecture on “Role of Bioinformatics in Oral Pathological Research” at the Watson & Crick Hall, Department of Biochemistry, Saveetha Dental College, Chennai (October 2018)
• Delivered an Invited Keynote address at the 1st Sari Mutiara Indonesia International Conference on Health (SaMICoH) on  “Natural Pesticides for Conserved Target across Cotton Pests by Molecular Modeling” held at Grand Mercure Hotel, Medan, Indonesia (October 2018).
• Delivered an Invited guest lecture on “ Role of Bioinformatics in Drug Discovery & Development and Pharmacogenomics” at the Sari Mutiara University, Medan, Indonesia (October 2018).
• Delivered a guest lecture on Drug Discovery through Bioinformatics (CADD) at a state level seminar “e-Medicina” (March 2012) conducted by the department of Bioinformatics, Acharya College of Arts and Science, Pondichery.
• Awarded the Best young scientist award at a National conference on Environment Production and Management held at Loyola College (Sep 2012), Chennai.
• Delivered a Guest Lecture on Phylogenetic Analysis at a workshop conducted (Oct 2011) by the Department of Biochemistry, D.G. Vaishnava College, Chennai.
• Delivered a Guest lecture on Bioinformatics at a state level symposium (Sep 2010) organized by the Dept. of Biochemistry, D.G. Vaishnava College, Chennai.
• Judged the paper presentation competition at the inter-collegiate fest CHIMERA’11, organized by the Dept of Biochemistry, T.S. Narayanasamy College of Arts & Science, Navalur. Chennai.

Achievements and Awards

• Best posters presentation award for “Gene Expression Profiling of Dusky Cotton Bug Oxycarenus laetus from different locations” at Nextgen Genomics, Biology, Bioinformatics & Technology International Conference held in October 2018 at Jaipur.
• Won the second best paper presentation award for “Seehabitat” at the Research Day held at SRM University in February 2013 at Chennai.
• Won the best paper presentation award for “Inhibition of the Biosynthesis of Epicatechin in tea, Camellia sinensis (L. Kuntze) by insecticides deployed for the control of the tea mosquito bug, Helopeltis theivora (Waterhouse) at the National Conference on Emerging Trends in Management of Infectious Diseases and Public Health held in February 2016 at Mohammed Sathak College of Arts & Science at Chennai.
• Won the best paper presentation award and best young scientist award at National conference on Environment Production and Management held at Loyola College (Sep 2012), Chennai.

Memberships

• Member in Indian Science Congress Association (ISCA) , 2012