Phase I

BI-201: FOUNDATION COURSE IN MODERN BIOLOGY

Cell as the basic unit of life; Cell aggregates: tissues, organs and organisms; Molecules of life: nucleic acids, proteins, carbohydrates and lipids, their structure and function; Genome organization and replication; Gene expression and regulation; Thermodynamics of biological systems; Biomolecular interactions; Immune system; Drug action and drug discovery; Biodiversity.

BI-202: INTRODUCTORY BIOMATHEMATICS & BIOSTATISTICS

Numbers and Algebra; Functions and equations; Trigonometry and Coordinate geometry; Limits and Discontinuities; Introductory Calculus: Differentiation and integration; Vectors and Matrices; Fourier and Laplace Transforms; Set theory and Group theory; Statistics and Probability: Distributions, Correlation and Regression; Principal Component Analysis; Clustering; Fractals; Applications

BI-203: BIOINFORMATICS –I

Role of computers in Biology and Medicine, Biological databases: Primary and secondary databases for Proteins, Nucleic acids (DNA/RNA), Metabolic pathways, Microbial and Cellular data bases, NCBI, EMBL, KEGG, DDBJ, SWISSPROT, PDB, PIR etc.; Tools for DNA sequence analysis, protein sequence analysis; Usage of sequence alignment and searching tools for Gene Identification, Genome Annotation, ORFs, ESTs, Codon biases, Redundancy, Search engines; Conserved motifs, patterns, blocks, domains, Secondary and tertiary Structure prediction tools; FASTA, BLAST, PSI-BLAST, CLUSTALW, Multalign, Dialign, GeneBee, MotifScan, TMPred, GOR, Chou-Fasman, NNPredict, Promoterfinder, NEBcutter, Genscan, ORF Finder, IntronExon finder etc

BI-204: COMPUTATIONAL BIOLOGY –I

Methods and algorithms for Biological data analysis and interpretation. Algorithms for Genome analysis & Gene finding: Markov models and Fourier Transform techniques; Theoretical models for Sequence Comparisons of Nucleic acids & Proteins. Sequence and structural, global and local, pairwise and multiple alignment techniques. Algorithms for homology based protein structure prediction with applications, their merits and limitations in protein folding. Practical Aspects of Homology Modeling. Approaches for protein structure prediction: Homology Modeling, Rosetta Stone. Importance of Parallelisation and clustering in computational biology, Introduction to biomolecular modeling and simulation.

Phase II

BI-301- BIOINFORMATICS –II

Using Biological databases; Structure visualization and Building; Protein Sequence Analysis; Genome Analysis; Protein Secondary and Tertiary structure prediction; Homology Modeling; Phylogenetic Analysis Software and Tools: Swiss PDB Viewer, Hyperchem, InsightII, Viewerlite, Rasmol, BLAST, Alibee, Phylip, CLUSTAL, GLIMMER, TCS Biosuite Special topics: Bioinformatics perspectives on human diseases; SNPs; DNA microarrays

BI-302- COMPUTATIONAL BIOLOGY-II

Methodologies and Algorithms for Analysis of DNA & Protein sequences. Probabilistic and Discriminative approaches with applications to genome and protein sequence analyses. Computational approaches to protein structure prediction: Threading and Homology based approaches, Experimental techniques for 3-D structure elucidation: X-ray crystallography, Gene prediction: Interpolated Markov Model, Hidden Markov Model, Dynamic programming, Significance of computational approaches in studying protein & DNA structure and function.

BI-303- MODELING AND SIMULATION

Introduction to ab-initio, semi-empirical & molecular mechanical methods, Theory and Practice of Energy minimization, Monte Carlo and Molecular Dynamics simulations. Generation of Electrostatic potential and field maps, Theoretical methods to calculate binding free energies and rate constants. Methods to model Nucleic Acids (DNA & RNA).

BI-304- GENOMICS AND PROTEOMICS

Structural Proteomics, Experimental techniques for protein structure elucidation X-Ray crystallography, 2-D Electrophoresis, MALDI-TOF, Mass spectrometry, Protein microarrays, Bioseparation, Structural, Functional and Comparative Genomics, Microbial Genomics

BI-305- DRUG DESIGN

Disease / disorder and Drug targets. Concept of receptor / target site. Concepts in molecular recognition. Drug-like properties and associated empirical rules. structure based drug design; Applications of QM methods; Molecular descriptors in QSAR studies, Small molecule force field parameters (charges), potentials, Active site identification algorithms, ligand docking algorithms, thermodynamics & kinetics of protein-drug binding. Drug stability, synthesizability and drug delivery.

BI-306- SYSTEMS BIOLOGY

Emerging new ideas on treating biological systems as systems of molecular networks. Elements of system modeling and mathematical methods to formulate system’s response to perturbations. New directions in metabolic pathways and cellomics to better understand organization of tissues, organs and organisms.