My 25 Years in CSIR and in Bioinformatics My 25 Years in CSIR and in Bioinformatics G P S Raghava Institute of Microbial Technology Sector 39A, Chandigrah,

Slides:

Advertisements

Similar presentations

1 Computer-aided Vaccine and Drug Discovery G.P.S. Raghava Understanding immune system Breaking complex problem Adaptive immunity Innate Immunity Vaccine.

Advertisements

1 Support Vector Machine and its Appliactions G P S Raghava Institute of Microbial Technology Sector 39A, Chandigrah, India

Genomics: READING genome sequences ASSEMBLY of the sequence ANNOTATION of the sequence carry out dideoxy sequencing connect seqs. to make whole chromosomes.

Introduction and Importance of Bioinformatics: Application in Drug/Vaccine Design G. P. S. Raghava Web:

CENTER FOR BIOLOGICAL SEQUENCE ANALYSIS Department of Systems Biology Technical University of Denmark Immunological Bioinformatics Introduction to the.

BIOINFORMATICS Ency Lee.

The European Bioinformatics Institute (EBI) Toolbox Julie Pellegrini Introduction to Bioinformatics.

Protein databases Morten Nielsen. Background- Nucleotide databases GenBank, National Center for Biotechnology Information.

The Cell, Central Dogma and Human Genome Project.

Introduction to Bioinformatics Presented By Dr G. P. S. Raghava Co-ordinator, Bioinformatic Centre, IMTECH, Chandigarh, India & Visiting Professor, Pohang.

Epitope Selection Rational Vaccine design. Why? Therapeutic vaccines Therapeutic vaccines Treatment of viral infections (e.g., HIV, HCV), and resistant.

Institute of Microbial Technology, Chandigarh, India

Signaling Pathways and Summary June 30, 2005 Signaling lecture Course summary Tomorrow Next Week Friday, 7/8/05 Morning presentation of writing assignments.

Computer Programs for Biological Problems: Is it Service or Science ? G. P. S. Raghava G. P. S. Raghava G. P. S. Raghava  Simple Computer Programs Immunological.

ExPASy - Expert Protein Analysis System The bioinformatics resource portal and other resources An Overview.

Computer-Aided Protein Structure Prediction Dr. G.P.S. Raghava, F.N.A. Sc. Bioinformatics Centre Institute of Microbial Technology Institute of Microbial.

Institute of Microbial Technology, Chandigarh, India

Bioinformatics Jan Taylor. A bit about me Biochemistry and Molecular Biology Computer Science, Computational Biology Multivariate statistics Machine learning.

Overview of Bioinformatics A/P Shoba Ranganathan Justin Choo National University of Singapore A Tutorial on Bioinformatics.

Bioinformatics for biomedicine Protein domains and 3D structure Lecture 4, Per Kraulis

Bioinformatics.

Tips for Research in Bioinformatics

Institute of Systems Biology (INBIOSIS)/ School of Biosciences & Biotechnology (Faculty of Science & Technology), Bioinformatics Development in Malaysia.

Methods MHC class-I T cell epitope prediction for Nef Consensus and ancestral sequences of the Nef protein for the different HIV-1 subtypes were obtained.

Overview of the Immune System Immune System Innate (Nonspecific) Cellular Components Humoral Components Adaptive (Specific) Cell- Mediated Humoral (Ab)

Bioinformatics and medicine: Are we meeting the challenge?

Secondary Databases Ansuman sahoo Roll: Y Bioinformatics Class Presentation 30 Jan 2013.

Institute of Microbial Technology, Chandigarh, India

Gary Stormo by Andrew Bardee. History Born 1950 in South Dakota Undergraduate in Biology from Caltech PhD in Molecular Biology from University of Colorado.

1 Computer-aided Subunit Vaccine Design G.P.S. Raghava, Institute of Microbial Technology, Chandigarh  Understanding immune system  Breaking complex.

1 G. P. S. Raghava Institute of Microbial Technology, Chandigarh.

What is Genetic Research?. Genetic Research Deals with Inherited Traits DNA Isolation Use bioinformatics to Research differences in DNA Genetic researchers.

1 Computer-aided Drug Discovery G.P.S. Raghava  Annotation of genomes  Searching drug targets  Properties of drug molecules  Protein-chemical interaction.

Biological Databases Biology outside the lab. Why do we need Bioinfomatics? Over the past few decades, major advances in the field of molecular biology,

Web Servers for Predicting Protein Secondary Structure (Regular and Irregular) Dr. G.P.S. Raghava, F.N.A. Sc. Bioinformatics Centre Institute of Microbial.

Bioinformatics Core Facility Guglielmo Roma January 2011.

Biological Signal Detection for Protein Function Prediction Investigators: Yang Dai Prime Grant Support: NSF Problem Statement and Motivation Technical.

Antigen Receptors of Lymphocytes. Recognition: molecular patterns Recognition : molecular details (antigenic determinants) Innate immunity Aquired immunity.

1 Web Site: Dr. G P S Raghava, Head Bioinformatics Centre Institute of Microbial Technology, Chandigarh, India Prediction.

BioinformaticsDrug InformaticsVaccine Informatics Chemoinformatics

Motif discovery and Protein Databases Tutorial 5.

Bioinformatics and Computational Biology

AP Biology Immune Systems Part 2. Important concepts from previous units: 1) Three parts to the Signal Transduction Pathway – Reception, transduction,

Chapter 12 B-Cell Activation and Differentiation Dr. Capers

Career Opportunities in IT Presented By Dr G P S Raghava, Scientist Head, Bioinformatic Centre IMTECH, Chandigarh Web:

BIOINFORMATICS Ayesha M. Khan Spring 2013 Lec-8.

Bioinformatics Centre Instittute of Microbial Technology, Chandigarh Infrastructure for Protein Modelling and Engineering IT related services (Facilities.

The National Science Foundation Independent Federal Agency Support for all fields of fundamental science and engineering.

BLAST: Basic Local Alignment Search Tool Robert (R.J.) Sperazza BLAST is a software used to analyze genetic information It can identify existing genes.

Bioinformatics Overview

Protein databases Henrik Nielsen

T Cell Receptor (TCR) & MHC Complexes-Antigen Presentation

Computer-aided Vaccine and Drug Discovery G. P. S

Intracellular Pathogens Extracellular Pathogens

7.3 Translation udent_view0/chapter3/animation__how_translation_work s.html.

Genomes and Their Evolution

Figure 1 CTLA-4 and PD-1–PD-L1 immune checkpoints

PABIO 590B Advanced Topics in Bioinformatics

Introduction to Bioinformatics II

KEY CONCEPT Entire genomes are sequenced, studied, and compared.

Geneomics and Database Mining and Genetic Mapping

Experimental methods in classic epitope discovery

BSC1010: Intro to Biology I K. Maltz Chapter 21.

Computer-Aided Protein Structure Prediction

Computer-Aided Protein Structure Prediction

Evolution of Genomes Chapter 21.

KEY CONCEPT Entire genomes are sequenced, studied, and compared.

Computer-Aided Protein Structure Prediction

KEY CONCEPT Entire genomes are sequenced, studied, and compared.

A schematic presentation of secreted, endocytic, and signaling pattern-recognition receptors. A schematic presentation of secreted, endocytic, and signaling.

Presentation transcript:

My 25 Years in CSIR and in Bioinformatics My 25 Years in CSIR and in Bioinformatics G P S Raghava Institute of Microbial Technology Sector 39A, Chandigrah, India Web:

My 25 Years in Bioinformatics IMTECH is one of original DIC’s started by DBT IMTECH is one of original DIC’s started by DBT I start my carrier in 1986 as computer scientist I start my carrier in 1986 as computer scientist My first task was to support DIC at IMTECH My first task was to support DIC at IMTECH : Infrastructure ( , NICNET, Medline) : Infrastructure ( , NICNET, Medline) : Services with development of computer programs : Services with development of computer programs : Data based discovery, protein structure, web : Data based discovery, protein structure, web : Drug/Vaccine targets and genome annotation : Drug/Vaccine targets and genome annotation : Integration of tools & collaboration : Integration of tools & collaboration ?: Drug/Vaccine in real life ?: Drug/Vaccine in real life

: Infrastructure & Services Literature search Literature search DIALOG search via Telex DIALOG search via Telex MicroVax II (First powerful computer) MicroVax II (First powerful computer) Nucleotide and Sequence data on tapes Nucleotide and Sequence data on tapes NICNET connectivity and databases searches NICNET connectivity and databases searches -Facility via ERNET (UUCP) -Facility via ERNET (UUCP) via NICNET to other DICs via NICNET to other DICs EMBL data and software via Servers EMBL data and software via Servers

: Advance level of service Software development for biological problems Software development for biological problems First research publication (1991) First research publication (1991) Number of publications Number of publications Establishment of INTERNET Establishment of INTERNET Completed Ph.D. (1996) Completed Ph.D. (1996)

: International Presence Methods developed for protein structure prediction Methods developed for protein structure prediction Participated in International competition CASP Participated in International competition CASP Worked at Oxford University, UK ( ) Worked at Oxford University, UK ( ) Mirror-Sites of software archieves Mirror-Sites of software archieves Web based applications launched Web based applications launched

: Drug/Vaccine targets and genome annotation Adaptive Immunity (Cellular Response) : T helper Epitopes Adaptive Immunity (Cellular Response) : CTL Epitopes Adaptive Immunity (Humoral Response) :B-cell Epitopes Innate Immunity : Pathogen Recognizing Receptors and ligands Signal transduction in Immune System Propred: for promiscuous MHC II binders MMBpred:for high affinity mutated binders MHC2pred: SVM based method MHCBN: A database of MHC/TAP binders and non-binders Pcleavage: for proteome cleavage sites TAPpred: for predicting TAP binders Propred1: for promiscuous MHC I binders CTLpred: Prediction of CTL epitopes Cytopred: for classification of Cytokines BCIpep: A database of B-cell eptioes; ABCpred: for predicting B-cell epitopes ALGpred: for allergens and IgE eptopes HaptenDB: A datbase of haptens PRRDB: A database of PRRs & ligands Antibp: for anti-bacterial peptides

: Drug/Vaccine targets and genome annotation Genome Annotation FTGpred: Prediction of Prokaryotic genes EGpred: Prediction of eukaryotic genes GeneBench: Benchmarking of gene finders SRF: Spectral Repeat finder Comparative genomics GWFASTA: Genome-Wide FASTA Search: GWBLAST: Genome wide BLAST search COPID: Composition based similarity search LGEpred: Gene from protein sequence Subcellular Localization Methods PSLpred: localization of prokaryotic proteins ESLpred: localization of Eukaryotic proteins HSLpred: localization of Human proteins MITpred: Prediction of Mitochndrial proteins TBpred: Localization of mycobacterial proteins Prediction of drugable proteins Nrpred: Classification of nuclear receptors GPCRpred: Prediction of G-protein-coupled receptors GPCRsclass: Amine type of GPCR VGIchan: Voltage gated ion channel Pprint: RNA interacting residues in proteins GSTpred: Glutathione S-transferases proteins Protein Structure Prediction APSSP2: protein secondary structure prediction Betatpred: Consensus method for  -turns prediction Bteval: Benchmarking of  -turns prediction BetaTurns: Prediction of -turn types in proteins Turn Predictions: Prediction of  /  /  -turns in proteins GammaPred: Prediction of-turns in proteins BhairPred: Prediction of Beta Hairpins TBBpred: Prediction of trans membrane beta barrel proteins SARpred: Prediction of surface accessibility (real accessibility) PepStr: Prediction of tertiary structure of Bioactive peptides

Important Points for CSIR Scientists 1.Why we join CSIR? (survival, Job, Recognition, service) 2.Are we lucky persons? ( Job security, environment) 3.Can anybody force us to work or not to work? 4.What is ultimate goal? (getting promotion on time, director) 5.What is level of competition? (lab, national, international) 6.Is scientist loyal to boss/director, institute, country, science? 7.Do we feel pride in front of our kids? 8.Are we liability on our institute/country? 9.Can I survive in competitive world (private, abroad) 10.Am I enjoying my life?

URLs: & & bic.uams.edu/