Hello sir I want Bioinformatics Syllabus from Pune University. Will you please provide me PDF of Bioinformatics Syllabus Pune University?

Pune University is invites for MSC admission in Bioinformatics. The Pune University is also provides syllabus for MSC in Bioinformatics.

The M.Sc. in Bioinformatics is a full time course of two year duration, consisting of four semesters.

The hands-on-training component is given more importance and is an integral part of the course.

The course will include training in the major areas of Bioinformatics such as

Basic Biology
Basic Mathematics
Biological Chemistry
Statistical Techniques
Genetic Information Flow & Processing
Concepts in Computing & Computer Programming
Introduction to Database Systems
Biodiversity Informatics
Structural Biology
Cell Biology, Genetics & Immunology
Chemoinformatics
Computer Graphics and Visualization
Programming in Object Oriented Languages
Biological Databanks, Data Mining and Data Security
Taxonomy & Phylogeny
Comparative Genomics and Proteomics

Bioinformatics Syllabus Pune University
Present Course Structure of M. Sc. (Bioinformatics)
Semester – I
Course No. Course Name Total
Credits
BIM 101 (T)* Basic Biology 2.5+0
BIM 102 (T+P)* Mathematics For Bioinformatics 2+0.5
BIM 103 (T+P) Statistical Techniques 2+0.5
BIM 104 (T) Biological Chemistry 3+0
BIM 105 (T) Genetic Information Flow & Processing 3+0
BIM 106 (T+P) Basic Concepts in Computing 1+2
BIM 107 (T+P) Introduction to Database Systems 2+2
BIM 108 (T+P) Biological Databases and Data Analysis 2+2
BIM 109 (P) Programming in Perl 0+3
15+10
Total credits 25
* Students from Mathematics Stream will take BIM 101(T), while those from the
Biology Stream will take BIM 102(T)
Semester – II
Course No. Course Name Total
Credits
T+P
BIM 201 (T) Cell Biology, Genetics & Genomics 3+0
BIM 202 (T) Structural Biology & Bioinformatics 3+0
BIM 203 (T+P) Chemoinformatics 2+1
BIM 204 (T+P) Immunology and Bioinformatics 2+1
BIM 205 (T+P) Programming in Object Oriented Languages 2+2
BIM 206 (P) Programming in C 0+3
BIM 207 (P) Computational Structural Biology 0+2
BIM 208 (P) Laboratory Techniques in Modern Biology 0+2
BIM 209 (P) UNIX & Linux Commands & Scripting 0+1
12+12
Total credits 24
Syllabus draft: BoS April 26, 2010 Dr. Urmila Kulkarni-Kale 3
Semester – III
Course No. Course Name Total
Credits
BIM 301 (T+P) Molecular Phylogenetics 1+1
BIM 302 (T+P) Genome to Drug and Vaccine 3+2
BIM 303 (T+P) Comparative Genomics and Proteomics 2+2
BIM 304 (T+P) Molecular Modeling & Simulations 2+2
BIM 305 (P) Database design & web-implementation 0+1
BIM 306 (T+P) Scientific Data Visualization 1+2
BIM 307 (T+P) Tools & Techniques for Biological Data Mining 2+2
BIM 308 (T) Project (Phase I) & Review 2+0
13+12
Total credits 25
Semester – IV
Course No. Course Name Total Credits
BIM 401 (T+P) Advanced Techniques for Sequence and Structure
Analysis
2+2
BIM 402 (T+P) Metabolic Engineering & Systems Biology 3+1
BIM 403 (T) Emerging Areas in Bioinformatics 1+0
BIM 404 (P) Project work 0+16
Any one of the following
BIM 405 (T+P) Seminars on Applications of Bioinformatics in
Agriculture
1
BIM 406 (T+P) Seminars on Applications of Bioinformatics in Human
Health
1
BIM 407 (T+P) Seminars on Applications of Bioinformatics in
Environment
1
BIM 408 (T+P) Seminars on Applications of Bioinformatics in
Biotechnology
1
BIM 409 (T+P) Seminars on Applications of Bioinformatics Molecular
Biology
1
BIM 410 (T+P) Seminars on Applications of Bioinformatics in
Neurobiology
1
BIM 411 (T+P) Seminars on Applications of Bioinformatics Drug
Designing
1
BIM 412 (T+P) Seminars on Applications of Bioinformatics in Veterinary
Sciences
1+0
7+19
Total credits 26
(Numbers in the brackets indicate total credits for respective courses and also indicates
number of hours of classroom teaching for respective theory courses per week. Credits for
practical courses indicate number of laboratory sessions per week (each session is of 3
hours).
Syllabus draft: BoS April 26, 2010 Dr. Urmila Kulkarni-Kale 4
Semester – I
BIM 101 (T): Basic Biology 1 (2.5 credits)
Objectives:
This course will enable the students to:
• appreciate the basic nature and diversity of microbial, plant and animal life.
• understand the classification of organisms, their structure and function.
Theory
• Origin of life: an introduction (2)
• Viruses: Biology of viruses; bacteriophages, plant and animal viruses (2)
• Level of organization: prokaryotic and eukaryotic cells, multicelluarity (2)
• Five kingdom classification: salient features and outline classification
with examples
o Monera (3)
o Protista (2)
o Mycota (3)
o Plantae (7)
o Animalia (9)
References:
• Wallace Robert A., Sanders Gerald P., Ferl Robert J. The science of life. Publisher:
New York, NY : Harper Collins, 1991. ISBN: 0673380440.
• Solomon Eldra P., Berg Linda R., Martin Diana W. Biology 6th edition. Publisher:
Pacific Grove, CA, Brooks/Cole Thomson Learning, 2002. ISBN: 0030335035.
BIM 102 (T+P) : Mathematics for Bioinformatics1 (2T+0.5P credits)
Objectives:
This course will enable the students to:
• achieve skills in mathematics that are essential for application in bioinformatics.
Theory
• Trigonometry: (4)
Trigonometric Functions, Series Expansion, Inverse, General Values, Graphs,
Taylor series
• Calculus: (10)
Limits, Continuity, Analysis, Differentiation (1D & Partial), Reimann
Integration, Definite Integrals.
1 Students from Mathematics Stream will take BIM 101(T), while those from the Biology
Stream will take BIM 102(T)
Syllabus draft: BoS April 26, 2010 Dr. Urmila Kulkarni-Kale 5
• Ordinary & Partial Differential Equation (5)
1’st Order & 2’nd Order Ordinary Differential Equations. Self Adjoint
Equations, Method of Separation of Variables
• Vector & Matrices (3)
Vector Algebra, Vector Calculus, Basic Computations, Matrices
• Introduction to Set Theory (2)
• Integral transform (6)
Fourier Series, Fourier Transform, Laplace Transform
Practicals
Objectives:
This course will enable the students to:
• achieve skills in mathematics that are essential for application in bioinformatics.
Syllabus:
• Assignments/Tutorials based on theory topics as listed above: 8 (+2) sessions of 2
hours each (6th week onwards)
References:
• Isaev Alexander. Introduction to Mathematical Methods in Bioinformatics. Publisher:
Berlin; New York: Springer, 2004. ISBN: 3540219730
• Raman K. V. & Pal Sourav. Mathematics in Chemistry. New Delhi, Vikas Publishing
House Pvt Ltd., 2004. ISBN: 8125912886
• Jones D.S., Sleeman B.D.. Differential Equations and Mathematical Biology
Publisher : Chapman & Hall. 2003. ISBN:1584882964
• Bracewell Ronald. The Fourier transform and it’s applications 3rd edition. Publisher:
New Delhi : McGraw Hill, 2000. ISBN: 0073039381.
• Stephenson G., Radmore P. M.. Advanced Mathematical Methods for Engineering and
Science Students Cambridge: Cambridge University Press, 1990.
• Arfken George. Mathematical methods for physicists. Publisher: Orlando : Academic
Press 1985. ISBN: 0120598205.
BIM 103 (T+P): Statistical Techniques (2T+0.5P credits)
Objectives:
This course will enable the students to:
• understand and apply statistical techniques that are essential to process and interpret
biological data.
Theory
Syllabus:
• Introduction to principles of statistical sampling from a population (2)
• Frequency Distributions and Statistical Measures: mean, mode, median,
variance, standard deviation, coefficient of variation, measures of skewness
and kurtosis (6)
• Introduction to theory of Probability, Conditional Probability, Bayesian Rules,
Random variable, Distributions of random variables, Binomial, Poisson, Geometric,
Normal and extreme value distribution, Vector valued Random Variables (8)
Syllabus draft: BoS April 26, 2010 Dr. Urmila Kulkarni-Kale 6
• Hypothesis testing: (10)
o Test of significance viz. Z test, t test, pair t test, chi2 test of goodness of fit
o Non parametric tests: median test, sign test, Kruscal-Wallis test
• Basic of Cluster Analysis (4)
o Search using stem numbers
o Search using text signatures
Practicals
Objectives:
This course will enable the students to:
• understand and apply statistical techniques that are essential to process and interpret
biological data
• Assignments/Tutorials based on topics listed below: 8 (+2) sessions of 2 hours each
(6th week onwards)
• Using any of the software like R programming/SAS etc. exercises will be done on -
o Computation of Statistical Measures using given data (2)
o Fitting distributions to given data (3)
o PAM, BLOSUM, Substitution Rates etc. (1)
o Standard parametric tests (1)
o Non parametric tests (1)
References:
• Mathur Sunil K. Statistical bioinformatics with R. Publisher : Academic Press, 2010
ISBN: 9780123751041.
• Pal Nabendu, Sarkar Sahadeb. Statistics: Concepts and Applications. Publisher: PHI
Learning Pvt. Ltd., 2005. ISBN: 8120326792.
• Gentle, James E.; Härdle, Wolfgang K. Mori, Yuichi (Eds.). Handbook of
Computational Statistics Concepts and Methods. Publisher Springer 2004. ISBN:
354040464.
• Lange Kenneth. Mathematical and statistical methods for genetic analysis. Publisher:
New York, Springer, 2002. ISBN: 8181281136.
• Joseph Glaz, Joseph Naus, Sylvan Wallenstein. Scan Statistics. Publisher: New York;
Springer, 2001. ISBN: 038798819X.
• Murray R. Spiegel, Larry J. Stephens Schaum's Outline of Statistics 3rd edition
Publisher: McGraw-Hill New Delhi 3rd edition 2000. ISBN:0070435103.
• Schaum's Outline of Introduction to Probability and Statistics. Publisher: McGraw-
Hill, 1999. ISBN: 0071164936.
• Schaum's Outline of Statistics.
• Bilal M. Ayyub, McCuen Richard H.. Probability, statistics, & reliability for
engineers. Publisher: Boca Raton : CRC Press, 1997. ISBN: 0849326907.
• Frank Harry, Althoen Steven C.. Statistics: Concepts and Applications. Publisher:
Cambridge University Press. 1995. ISBN : 052144554X.
• Colin Richard Campbell Statistics for biologists. Publisher: Cambridge University
Press, 1989 ISBN: 0521369320.
Syllabus draft: BoS April 26, 2010 Dr. Urmila Kulkarni-Kale 7
BIM 104 (T): Biological Chemistry (3T credits)
Objectives:
This course will enable the students to:
• be familiar with the chemistry of different classes of biomolecules and their
interactions in an aqueous environment
• understand the structure-function relationships of macromolecules, the principles of
enzyme catalysis and regulation,
• understand organization of metabolic systems with an in-depth account of the
pathways for the complete oxidation of glucose.
Theory
• Water as the universal biological solvent; concepts of pH, buffer and
osmolarity (2)
• Carbohydrates: monosaccharides, oligosaccharides, polysaccharides,
glycosaminoglycans, proteoglycans and glycoproteins (3)
• Lipids: fatty acids, acylglycerols; phospholipids, sphingolipids, cholesterol
and membranes; Isoprenoids, icosanoids and their biological importance. (4)
• Nucleic acids: bases, nucleotides, RNA and DNA; different structural forms
of DNA; different types of RNA. (3)
• Proteins: amino acids and peptides; primary, secondary, tertiary and
quaternary structures; structure, function and evolutionary relationships;
protein – protein interactions, protein folding; allosteric proteins. (8)
• Enzymes: enzyme nomenclature and classification; units of
enzyme activity; specificity; coenzymes and metal cofactors; temperature and pH
effects; Michaelis-Menten kinetics; Inhibitors and activators; active site and catalytic
mechanisms; covalent and non-covalent regulations; isoenzymes. (15)
• Organization of metabolic systems: enzyme chains, multi-enzyme complexes and
multifunctional enzymes; anaplerotic sequences and amphibolic pathways; pacemaker
enzymes and feedback control of metabolic pathways; shuttle pathways; energy
charge. (3)
• Oxidation of glucose in cells: high energy bond, glycolysis, citric acid cycle and
oxidative phosphorylation. (7)
References:
• Nelson David L., Cox Michale. Lehninger Principles of Biochemistry 5th Edition.
Publisher: New York. W. H. Freeman. 2008. ISBN 978 0716771081.
• Berg, Jeremy M, Tymoczko, John L. Stryer, Lubert. Biochemistry 6th Edition.
Publisher: New York : W.H. Freeman. 2007.ISBN: 071676766X.
• Hames David, Hooper Nigel. Instant Notes in Biochemistry 3rd Edition. Publisher .
Nodia, Taylor & Francis. 2007. ISBN: 185996 2491.
• Voet, Donald, Voe Judith, Pratt, Charlotte W. Fundamentals of Biochemistry: Life at
the molecular Level 2nd Edition. Publisher: Asia, John Wiley & Sons. 2006. ISBN:
0471753416.
• Horton, Robert, Moran, Laurence A, Scrimgeour, Perry Gray Marc, Rawn.David.
Principles of biochemistry. Publisher: New Jersey, Pearson Prentice Hall, 2006.
ISBN: 0131453068.
Syllabus draft: BoS April 26, 2010 Dr. Urmila Kulkarni-Kale 8
• Mathews, Christopher K. van Holde, K. E., Ahern Kevin G. Biochemistry. Publisher:
San Francisco, Pearson Education 2000.ISBN: 81 29702150.
• Zubay,Geoffrey.Biochemistry 4th Edition, Publisher: Boston,Wm C. Brown, 1998,
ISBN 0697219003.
• Garrett, Reginald H. , Grisham, Charles M. Principles of biochemistry: with a human
focus. Publisher: Australia Brooks/Cole, Thomson Learning, 1997.
ISBN:0030973694.
BIM105 (T): Genetic Information Flow & Processing (3T credits)
Objectives:
This course will enable the students to:
• understand the current concepts in gene organization, transcription, translation and
regulation of gene function
• know biotechnological implications of recent developments in cloning and genome
sequencing.
Theory
• Introduction: DNA as a genetic material – Experiments done to prove this (1)
• Nucleic acid structure: single stranded & double stranded; denaturation, renaturation
and hybridization of DNA; secondary structures in single stranded molecules;
alternative double helical structures in double stranded DNA; Closed DNA as
supercoiled molecule (2)
• Genome organization: Prokaryotic and eukaryotic genomes – C value paradox,
repetitive and non-repetitive DNA., transposons and retroposons; Exons and introns –
organization of interrupted genes, one DNA sequence may code for multiple proteins;
Gene numbers – essential genes and total gene number, gene clusters, pseudogenes;
Gene families – globin and rDNA gene families; Organelle genome – mitochondrial
and chloroplast. (6)
• Packaging of genome – Bacterial genome as nucleoid; Eukaryotic genome –
nucleosomes, chromatin, solenoids, loops, domains, scaffolds, chromosomes. (3)
• Perpetuation of DNA: Prokaryotic DNA replication – DNA polymerases, origin of
replication, initiation, elongation and termination of replication. Rolling circle model
of replication; Eukaryotic DNA polymerases – multiple origins of replication, process
of replication; Regulation of replication in both prokaryotes and eukaryotes. (5)
• DNA damage, repair and recombination: Different types of DNA damages; Variety of
DNA repair systems in prokaryotes and eukaryotes – Base excision repair system,
Nucleotide excision repair system, Mismatch repair system, Recombination repair
system; Recombination – homologous and non-homologous recombination. (3)
• Gene Expression – Transcription and Translation: Transcription in prokaryotes – RNA
polymerase, initiation, elongation and termination of transcription; regulation of
transcription – operon concept, lactose and tryptophan operons (6)
• Transcription in eukaryotes: Different RNA polymerases – requirement of promoters
by these RNA polymerases, initiation, elongation and termination by these
polymerases; Processing of transcripts – 5’ capping, 3’ polyadenylation, splicing
Syllabus draft: BoS April 26, 2010 Dr. Urmila Kulkarni-Kale 9
and editing; Regulation of transcription – response elements, enhancers and
silencers,protein-nucleic acid interaction, HLH, leucine zipper proteins, noncoding
RNA (7)
• Translation in prokaryotes: protein synthesis machinery – mRNA, tRNA and rRNA
molecules; initiation, elongation and termination of translation; Genetic code –
interpreting genetic code; Accuracy of translation. (3)
• Eukaryotic translation: protein synthesis – initiation, elongation and termination; Posttranslational
modifications of proteins; protein degradation; Regulation of translation -
mRNA stability, 5’ and 3’ UTRs, mRNA localization (5)
• Gene regulation by post-translational modifications of proteins (acetylation,
methylation, ribosylation, phosphorylation etc.) and different intermediate RNAs

Address:

University of Pune,
Ganeshkhind Road,
Pune - 411 007
Maharashtra State,
India.


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