REVISED BINC SYLLABUS for Paper-III
BINC BioInformatics Syllabus : Basic
Major Bioinformatics Resources: NCBI, EBI, ExPASy, RCSB:
  • The knowledge of various databases and bioinformatics tools available at these resources, organization of databases: data contents and formats, purpose and utility in Life Sciences
Open access bibliographic resources and literature databases:
  • Open access bibliographic resources related to Life Sciences viz., PubMed, BioMed Central, Public Library of Sciences (PloS)
Sequence databases:
  • Formats, querying and retrieval
  • Nucleic acid sequence databases: GenBank, EMBL, DDBJ;
  • Protein sequence databases: Uniprot-KB: SWISS-PROT, TrEMBL, PIR-PSD
  • Repositories for high throughput genomic sequences: EST, STS GSS, etc.;
  • Genome Databases at NCBI, EBI, TIGR, SANGER
  • Viral Genomes
  • Archeal and Bacterial Genomes;
  • Eukaryotic genomes with special reference to model organisms (Yeast, Drosophila, C. elegans, Rat, Mouse, Human, plants such as Arabidopsis thaliana, Rice, etc.)
3D Structure Database: PDB, NDB
  • Chemical Structure database: Pubchem
  • Gene Expression database: GEO, SAGE
Derived Databases:
  • Knowledge of the following databases with respect to: basic concept of derived databases, sources of primary data and basic principles of the method for deriving the secondary data, organization of data, contents and formats of database entries, identification of patterns in given sequences and interpretation of the same
  • Sequence: InterPro, Prosite, Pfam, ProDom, Gene Ontology
  • Structure classification database: CATH,SCOP, FSSP
  • Protein-Protein interaction database: STRING
Compilation of resources:
  • NAR Database and Web server Issues and other resources published in Bioinformatics related journals
Sequence Analysis:

File formats:
  • Various file formats for bio-molecular sequences: GenBank, FASTA, GCG, MSF etc
Basic concepts:
  • Sequence similarity, identity and homology, definitions of homologues, orthologues, paralogues
Scoring matrices:
  • Basic concept of a scoring matrix, Matrices for nucleic acid and proteins sequences, PAM and BLOSUM series, principles based on which these matrices are derived
Pairwise sequence alignments:
  • Basic concepts of sequence alignment: local and global alignments, Needleman and Wunsch, Smith and Waterman algorithms for pairwise alignments, gap penalties, use of pairwise alignments for analysis of Nucleic acid and protein sequences and interpretation of results.
Multiple sequence alignments (MSA):
  • The need for MSA, basic concepts of various approaches for MSA (e.g. progressive, hierarchical etc.). Algorithm of CLUSTALW and PileUp and their application for sequence analysis (including interpretation of results), concept of dandrogram and its interpretation
Database Searches:
  • Keyword-based searches using tools like ENTREZ and SRS
  • Sequence-based searches: BLAST and FASTA
Sequence patterns and profiles:
  • Basic concept and definition of sequence patterns, motifs and profiles, various types of pattern representations viz. consensus, regular expression (Prosite-type) and sequence profiles; profile-based database searches using PSI-BLAST, analysis and interpretation of profile-based searches
Taxonomy and phylogeny:
  • Basic concepts in systematics, taxonomy and phylogeny; molecular evolution; nature of data used in Taxonomy and Phylogeny, Phylogenetic tree and its reconstruction.
Protein and nucleic acid properties:
  • Computation of various parameters using proteomics tools at the ExPASy server and EMBOSS
Comparative genomics:
  • Basic concepts and applications, whole genome alignments: understanding significance. Artemis as an example
Structural Biology:

3-D structure visualization and simulation:
  • Visualization of structures using Rasmol or SPDBV or CHIME or VMD
  • Basic concepts in molecular modeling: different types of computer representations of molecules. External coordinates and Internal Coordinates
  • Non-Covalent Interactions and their role in Biomolecular structure and function
  • Fundamentals of Receptor-ligand interactions.
Proteins:
  • Principles of protein structure; Peptide bond, phi, psi and chi torsion angles, ramachandran map, anatomy of proteins-Hierarchical organization of protein structure-Primary. Secondary, Super secondary, Tertiary and Quaternary structure; Hydrophobicity of amino acids, Packing of protein structure, Structures of oligomeric proteins and study of interaction interfaces
DNA and RNA:
  • Types of base pairing Watson-Crick and Hoogsteen; types of double helices (A, B, Z), triple and quadruple stranded DNA structures, geometrical as well as structural features; structural and geometrical parameters of each form and their comparison; various types of interactions of DNA with proteins, small molecules
  • RNA secondary and tertiary structures, t-RNA tertiary structure
Carbohydrates:
  • The various building blocks (monosaccharides), configurations and conformations of the building blocks; formations of polysaccharides and structural diversity due to the different types of linkages
  • Glyco-conjugates: various types of glycolipids and glycoproteins
Classification and comparison of protein 3D structures:
  • Purpose of 3-D structure comparison and concepts, Algorithms : CE, VAST and DALI, concept of coordinate transformation, RMSD, Z-score for structural comparision
  • Databases of structure-based classification; CATH, SCOP and FSSP
Secondary structure prediction:
  • Algorithms viz. Chou Fasman, GOR methods; nearest neighbor and machine learning based methods, analysis of results and measuring the accuracy of predictions.
Tertiary Structure prediction:
  • Fundamentals of the methods for 3D structure prediction (sequence similarity/identity of target proteins of known structure, fundamental principles of protein folding etc.) Homology/comparative Modeling, fold recognition, threading approaches, and ab initio structure prediction methods
BINC BioInformatics Syllabus : Advanced
Sequence analysis: Scoring matrices:
  • Detailed method of derivation of the PAM and BLOSUM matrices
Pairwise sequence alignments:
  • Needleman and Wuncsh, Smith and Waterman algorithms and their implementation
Multiple sequence alignments (MSA):
  • Use of HMM-based Algorithm for MSA (e.g. SAM method)
Sequence patterns and profiles:
  • Repeats: Tandem and Interspersed repeats, repeat finding, Motifs, consensus, position weight matrices
  • Algorithms for derivation of and searching sequence patterns: MEME, PHI-BLAST, SCanProsite and PRATT
  • Algorithms for generation of sequence profiles: Profile Analysis method of Gribskov, HMMer, PSI-BLAST
Protein and nucleic acid properties: e.g. Proteomics tools at the ExPASy server and EMBOSS Taxonomy and phylogeny:
  • Phylogenetic analysis algorithms such as maximum Parsimony, UPGMA, Transformed Distance, Neighbors-Relation, Neighbor-Joining, Probabilistic models and associated algorithms such as Probabilistic models of evolution and maximum likelihood algorithm, Bayesian inference algorithm, Bootstrapping methods, use of tools such as Phylip, Mega, PAUP
  • Analysis of regulatory RNAs: Databases and tools
Structural Biology:
  • Experimental methods for Biomolecular structure determination:X-ray and NMR
  • Identification/assignment of secondary structural elements from the knowledge of 3-D structure of macromolecule using DSSP and STRIDE methods
  • Prediction of secondary structure: PHD and PSI-PRED methods
Tertiary Structure prediction:
  • Fundamentals of the methods for 3D structure prediction (sequence similarity/identity of target proteins of known structure, fundamental principles of protein folding etc.) Homology Modeling, fold recognition, threading approaches, and ab-initio structure prediction methods
Structure analysis and validation:
  • Pdbsum, Whatcheck, Procheck,Verify3D and ProsaII
  • Critical assesment of Structure prediction(CASP)
  • Structures of oligomeric proteins and study of interaction interfaces
Molecular modeling and simulations:
  • Macro-molecular force fields, salvation, long-range forces
  • Geometry optimization algorithms: Steepest descent, conjugate gradient
  • Various simulation techniques: Molecular mechanics, conformational searches, Molecular Dynamics, Monte Carlo, genetic algorithm approaches, Rigid and Semi-Flexible Molecular Docking
Genomics:
  • Large scale genome sequencing strategies
  • Genome assembly and annotation
  • Genome databases of Plants, animals and pathogens
  • Metagenomics
  • Gene networks: basic concepts, computational model such as Lambda receptor and lac operon
  • Prediction of genes, promoters, splice sites, regulatory regions: basic principles, application of methods to prokaryotic and eukaryotic genomes and interpretation of results
  • Basic concepts on identification of disease genes, role of bioinformatics-OMIM database, reference genome sequence, integrated genomic maps, gene expression profiling; identification of SNPs, SNP database (DbSNP). Role of SNP in Pharmacogenomics, SNP arrays
  • DNA microarray: database and basic tools, Gene Expression Omnibus (GEO), ArrayExpress, SAGE databases
  • DNA microarray: understanding of microarray data, normalizing microarray data, detecting differential gene expression, correlation of gene expression data to biological process and computational analysis
  • Next Generation sequencing & assembly: Elements of big data analysis, NGS Platforms based on pyrosequencing, sequencing by synthesis, emulsion PCR approach with small magnetic beads and single molecule real time (SMRT) sequencing; Genome assembly algorithms, De-novo assembly algorithms, Sequence Alignment formats: Sequence Alignment/Map (SAM) format, Binary Alignment/Map (BAM) format.
Comparative genomics:
  • Basic concepts and applications, BLAST2, MegaBlast algorithms, PipMaker, AVID, Vista, MUMmer, applications of suffix tree in comparative genomics, synteny and gene order comparisons
  • Comparative genomics databases: Clusters of Orthologous Groups (COGs), Ensembl
Functional genomics:
  • Application of sequence based and structure-based approaches to assignment of gene functions e.g. sequence comparison, structure analysis (especially active sites, binding sites) and comparison, pattern identification, etc. Use of various derived databases in function assignment, use of SNPs for identification of genetic traits
  • Gene/Protein function prediction using Machine learning tools: supervised/unsupervised learning, Neural network, SVM etc.
Proteomics:
  • Protein arrays: basic principles
  • Computational methods for identification of polypeptides from mass spectrometry
  • Protein arrays: bioinformatics-based tools for analysis of proteomics data (Tools available at ExPASy Proteomics server); databases (such as InterPro) and analysis tools
  • Protein-protein interactions: databases such as STRINGS, DIP, PPI server and tools for analysis of protein-protein interactions
Modeling biological systems
  • Systems biology-Topology of biological networks: Random vs Scale-Free networks. Use of computers in simulation of cellular subsystems:Simulation and analysis of biochemical networks and their dynamics using ODEs and stochastic algorithm, Flux Balance Analysis (FBA), Boolean network simulations.
  • Metabolic networks, or network of metabolites and enzymes, Signal transduction networks, Gene regulatory networks, Metabolic pathways: databases such as KEGG, EMP , MetaCyc, AraCyc
Drug design:
  • Drug discovery process
  • Role of Bioinformatics in drug design
  • Target identification and validation and lead optimization
  • Different systems for representing chemical structure of small molecules like SMILES etc
  • Generation of 3D coordinates of small molecules
  • Structure-based drug design: Identification and Analysis of Binding sites and virtual screening
  • Ligand based drug design: Structure Activity Relationship-QSARs and QSPRs, QSAR Methodology, Pharmacophore mapping
  • In silico prediction ADMET properties for Drug Molecules
Vaccine design:
  • Reverse vaccinology and immunoinformatics
  • Databases in Immunology
  • Principles of B-cell and T-cell epitope prediction
Suggested Books for Reading:
  • David W Mount, Bioinformatics: Sequence And Genome Analysis, 2nd Edition, cold Spring Harbor Press
  • Durbin et al (2007) Biological Sequence Analysis: Probabilistic models of protein and Nucleic acids Cambridge University Press.
  • Stuart M.Brown (2013) Next-generation DNA sequencing Informatics. Cold Spring Harbor Press
  • M.E.J. Newman (2010) Networks: An Introduction, Oxford University Press
  • Thomas E. Creighton, Proteins: structures and molecular properties
  • Chemoinformatics Edited by Johann Gasteiger and Thomas Engel
  • Structural Bioinformatics, Edited Philip E. Bourne and Helge Weissig
  • Lee A Segel (2008), Biological Kinetics, Cambridge University Press Cambridge
  • Cornish-Bowden (2012), Fundamentals of Enzyme Kinetics ,Wiley-Blackwell
  • Alberghina L (2005), System Biology : Definitions and Perspectives, Springer-Verlag Berlin Heidelberg
  • Najarian K, Najarian S, Gharibzadeh S, Eichelberger CN (2009) Systems Biology and Bioinformatics: A Computational Approach, CRC Press
  • Klipp E, Liebermeister W, Wierling C, Kowald A, Lehrach H, Herwig R (2009) Systems Biology : A Text Book, Wiley-Blackwell
  • Integrative approaches for finding modular structure in biological networks, NATURE REVIEWS , GENETICS, VOLUME 14, OCTOBER 2013
  • BIOINFORMATICS, Vol. 19 no. 2, 2003
  • Nucleic Acids Research (2014), Vol. 42, Database issue D199-D205 doi:10.1093/nar/gkt1076
  • Nucleic Acids Research (2012), Vol. 40, Database issue D109-D114 doi:10.1093/nar/gkr988
  • An extended bioreaction database that significantly improves reconstruction and analysis of genome-scale metabolic networks (2011), Integrative Biology, 2011.3, 1071-1086
  • Computational Systems Bioinformatics-Methods and Biomedical Applications ByXiaobo Zhou (Harvard Medical School and Brigham & Women's Hospital, USA), Stephen T C Wong (Harvard Medical School and Brigham & Women's Hospital, USA)
  • Bioinformatics for Systems Biology (2009) by Stephen Krawetz, Published by Humana Press
BINC Iinformation Technology Syllabus : Basic
  • Fundamentals in Computing
  • Types of Processing: Batch, Real-Time, Online, Offline.
  • Types of modern computing: Workstations, Servers, Parallel Processing Computing, Cluster computing, Grid computing
  • Memory and Storage Devices, Network, Internet-Basics
  • Introduction to operating systems: Operating System concept, UNIX/LINUX.
  • Basic Programming Concepts sequential, conditional and loop constructs, Arrays, Strings, Object Oriented Programming Concepts- Classes, Objects, Inheritance, Polymorphism; File Handling
  • Introduction to Database Systems-SQL Queries
BINC Information Technology Syllabus : Advanced
  • Data Structures and Algorithm
  • Arrays, Link Lists, Stacks, Queues, Graphs, Trees, Sorting, Searching, string comparison&$45Programs to be implemented using eith C or Python or Java
  • Databases-SQL, indexing and Hashing.
  • Elements of scripting languages
  • Elements of NoSQL
Suggested Books for Reading:
  • Database Management System Ramakrishnan and Gehrke
  • Data Structure : Andrew S Tannenbaum
  • Complete Reference to C
  • Complete Reference to Java
  • Complete Reference to Perl
  • Complete Reference to Python