M.Sc. Bioinformatics Syllabus

Swami Ramanand Teerth Marathwada
University
Nanded
School of Technology
Sub Centre, Latur
Syllabus For the

M.Sc. Bioinformatics (CGPA)
School of Technology,
SRTMUN Sub-Centre, Latur
Academic Year 2010-11

M.Sc. Bioinformatics (CGPA) degree builds the student for higher studies in Bioinformatics and
to be competent with the current race with the development of new computational technologies.
The duration of the study is four semesters, which is normally completed in two years. The
primary goal of bioinformatics is to increase our understanding of biological processes. What
sets it apart from other approaches, also, it is focus on developing and applying computationally
intensive techniques (e.g., computer aided drug design, systems biology, pattern recognition, data
mining, machine learning algorithms, and visualization) to achieve this goal. Major research
efforts in the field include sequence alignment, gene finding, genome assembly, drug design,
drug discovery, protein structure alignment, protein structure prediction, prediction of gene
expression and protein-protein interactions, genome-wide association studies and the modeling
of evolution.
CGPA system
Presently the School conducts M.Sc. Bioinformatics (CGPA) Post-Graduate Courses as per
CGPA = CUMULATIVE GRADE POINT AVERAGE
A Cumulative Grade Point Average (CGPA) is the mean Grade Point Average (GPA) from all
academic terms within a given academic year, whereas the GPA may only refer to one term.
Courses
Sr. No Name of the Program Duration Intake
I M. Sc. [Bioinformatics]- CGPA 2 Years 30 (Seat)
Eligibility and Fees

Any science graduate is eligible for seeking admission to both of the courses. More details of
admission procedure and fees structure can be seen from the prospectus of Campus Schools of
the University.
Feature of CGPA System
Master Degree would be of 112 Credits each

Each semester shall have five theory courses, Four practical courses
Five theory courses = 20 Credits
Four practical courses= 8 Credits
Total 28 credits per semester
Total 700 marks per semester
Every student shall complete 112 credits in a minimum of four semesters. All semester will have
28 credits each.
Four semester X 28 credits = 112 credits
Total 2800 marks for Master Degree program
One Credit = 25 marks
Two Credits = 50 Marks
Four Credits = 100 Marks
Theory Course = 100 Marks
Practical Course = 50 Marks
Theory Course = 100 Marks
Internal Exam External Exam

50 Marks = 2 Credits 50 Marks = 2 Credits
Break up internal exam marks for Theory
Theory Test-1 Theory Test-2 Home Assignments Total Marks
15 marks 15 marks 20 marks 50 Marks = 2 Credits
Practical Course = 50 Marks

25 Marks = 1 Credit 25 Marks = 1 Credit
Break up internal exam marks for Practical
Practical Test-1 Practical Test-2 Total Marks
10 marks 15 marks 25 Marks = 1 Credit

Project Course = 200 Marks

100 Marks = 4 Credits 100 Marks = 4 Credits
Break up internal exam marks for Project

Synopsis Project work Total Marks
25 marks 75 marks 100 Marks = 4 Credits
Semester I
CODE NO NAME OF PAPER INTERNAL EXAM / INTERNA TO
DEPARTMENT LEVEL L EXAM TA
CREDIT CREDITS L
CR
EDI
TS
BIM-101 (T) Genetics and Molecular 2 2 4

Biology
BIM-102 (T) Bioinformatics 2 2 4

BIM-103 (T) Biostatistics 2 2 4
BIM-104 (T) Data Base Managements 2 2 4
Systems Oracle
BIM-105 (T) Linux 2 2 4
BIM-102 (P) Bioinformatics 1 1 2

BIM-103 (P) Biostatistics 1 1 2
BIM-104 (P) Data Base Managements 1 1 2
Systems Oracle
BIM-105 (P) Linux 1 1 2

14 14 28
Total Credits in I Semester = 28

Semester II
CODE NO NAME OF PAPER INTERNAL INTERNAL TO
EXAM / EXAM TA
DEPARTMENT CREDITS L
LEVEL CREDIT CR
ED
IT
S
BIM-201 (T) Advanced Molecular Biology 2 2 4
BIM-202 (T) Computational Biology 2 2 4

BIM-203 (T) Immunoinformatics 2 2 4
BIM-204 (T) Chemoinformatics 2 2 4
BIM-205 (T) Machine Intelligence in 2 2 4
Bioinformatics
BIM-203 (P) Immunoinformatics 1 1 2

BIM-204 (P) Chemoinformatics 1 1 2
BIM-205 (P) Machine Intelligence in 1 1 2
Bioinformatics
BIM-206 (P) Numerical Methods and 1 1 2

Optimization Techniques
14 14 28
Total Credits in II Semester = 28

Semester III
CODE NO NAME OF PAPER INTERNAL INTERNA TO
EXAM / L EXAM TA
DEPARTMENT CREDITS L
LEVEL CREDIT CR
ED
ITS
BIM-301 (T) Computer Aided Drug Design 2 2 4

BIM-302 (T) Object Oriented Programming 2 2 4
(OOPS) JAVA
BIM-303 (T) Microbial Genomics 2 2 4

BIM-304 (T) Principle of Drug Action 2 2 4
BIM-305 (T) Molecular Modeling 2 2 4
BIM-301 (P) Computer Aided Drug design 1 1 2

BIM-302 (P) Object oriented Programming 1 1 2
(OOPS) JAVA
BIM-303 (P) Microbial Genomics 1 1 2

BIM-304 (P) Perl for Bioinformatics 1 1 2
14 14 28
Total Credits in III Semester = 28
Semester IV
CODE NO NAME OF PAPER INTERNAL EXAM / INTERNAL TOTAL
DEPARTMENT EXAM CREDITS
LEVEL CREDIT CREDITS
BIM-401 (T) Plant Genomics 2 2 4

BIM-402 (T) Metabolomics and Metabolic 2 2 4
Engineering
BIM-403 (T) Oncogenomics and Cell 2 2 4

Signaling
BIM-404 (T) IPR and Industrial Psychology 2 2 4

BIM-405 (PJ) Project 4 4 8
BIM-401 (P) Plant Genomics 1 1 2

BIM-402 (P) Metabolomics and Metabolic 1 1 2
Engineering
14 14 28
Total Credits in IV Semester = 28

University
Nanded
Sub Centre, Latur
Syllabus For the

Semester -I
Genetics and Molecular Biology
Sub. Code: BIM-101 (T)
Course Objectives: To enable the students to gain knowledge about the fundamentals concepts
and basic principles such as structure of DNA / RNA, transcription, translation gene regulation,
and RNA splicing and also the Mendelian genetics
Total: 45L Total Credits: 4
Unit -I: Structure of Nucleic Acid (9L)

Structure of DNA
Different forms of DNA and RNA
Identification of DNA as genetic material by Griffith –Avery,
McLeod and McCarty
Frankel and Singer
Hershey and Chase
Messelson and Stahl experiment
Unit -II: DNA Replication and Mutation (9L)

Semi-Conservative replication
Replication of DNA in Eukaryotes
Molecular basis of Mutation
Classification of mutation
Unit -III: Gene Expression and Regulation (9L)

Genetic code
Transcription
Prokaryotes and Eukaryotes
Post transcriptional modification
Translation in prokaryotes and Eukaryotes
Post translational modification
Gene Regulation
Lac operon model
Unit -IV: Mendelian Genetics (9L)

Mendel’s laws
Monohybrid
Dihybrid inheritance
Multiple alleles
Structure and organization of chromosome in Prokaryote and Eukaryotes
Unit -V: Crossing Over and Linkage (9L)

Linkage
Types of linkage
Crossing over and their types
Recombination mapping
Two point and three point text cross mapping in bacteria
Text Books:
Molecular Genetics: Structure of Life, Virendra Gomase and Aravind Tripathi, VDM Verlag Dr.
Müller, Germany, ISBN:978-3-639-25001-5, (2010).
Genetechnology, Virendra Gomase and Shruti Gomase, VDM Verlag Dr. Müller, Germany,
ISBN: 978-3-639-13467-4, (2010).
Molecular biology of the Cell, Bruce Alberts, Alexander Johnson, Alexander Johnson, Julian
Lewis, Martin Raff, keith Roberts, Peter Walter; Garland Science, Taylor & Francis
group,4th Edition (2002)
Essential Cell Biology, Bruce Alberts Dennis Bray, Karen Hopkins, Alexander Johnson Julian
Lewis, Martin Raff, Keith Roberts, Peter Walter; Garland Science; Taylor & Francis
Group,4th Edition (2004)
Cell Molecular Biology, E. D. P. De Robertis, E. M. F. De Robertis, Jr, Lippinwt William &
Wilkins (2001)
Molecular biology, David Freifelder, Narosa Publishing House, 1st Edition(2004)
Genes, VIII Benjamin Lewin; Pearson Education International,8th Edition (2004)
Principles of Gene Manuplation, S. B. Primrose R. M. Twyman & R. W. old, Blackwell
Science,6th Edition (2001)
Advanced Molecular Biology, R. M. Twyman, 1st Edition , (2003)
Instant Notes on Molecular Biology; P.C. Turner, A. G. Mclennan, A. D. Bates & M. R. H.
White, 2nd Edition (2002)
Molecular Biology, David Freifelder, Narosa Publishing House,2nd edition (2004)
Microbial Genetics, David Freifelder, Narosa Publishing House, 2nd edition(2004)
Essential Molecular Biology (volume I & II) Practical Approach; Edited By T. A. Brown; Oxford
University Press, 2nd Edition (2001)
Bioinformatics
Course Objectives: To enable the students to gain knowledge about Bioinformatics.
Unit -I: Biological Database Design and Management (9L)

DBMS, RDBMS
Sources of biological data
Database Design and Data Mining
Database Management Security & Architecture
Unit -II: Genomics Database (9L)

Human Genome Project
Database of Model Species : Drosophila melanogaster , Arabidopsis thaliana, C. elegans,
Saccharomyces cerevisiae, Danio rerio
Plasmodium Falsiparum Genome Project
The Arabidopsis Genome Project
Unit -III: Biological Databanks (9L)

NCBI, DDBJ, EMBL, PDB, SRS,
BRENDA, TrEMBL, UniProt,
KEGG, MIAME, OMIM
Unit -IV: Bioinformatics database & repositories (9L)

Protein database – GenBank
Nucleotide & Gene database – GenBank
Microarray Database & analysis
Gene Expression Profile Database – GEO
Metabolic Pathway – PathDB
Enzyme Database – KEGG
Ion Transport Database
Unit -V: Genome Analysis (9L)

Genome Analysis
Genome Anatomy
a. Prokaryotic Genome –E coli Mycoplasma
b. Eukaryotic Genome- Human, Rat, Arabidopsis, Soybean, Mungbean, Rice
Comparative genomics
c. Proteomics analysis, horizontal gene transfer
Functional classification of gene
Gene order on chromosome
Text Books:
Bioinformatics- Theory and Practice, N.J. Chikhale and V.S. Gomase, Himalaya Publication
House, India; 1 edition, 2007, ISBN-13: 978-81-8318-831-9
BLAST, Ian Korf, Mark Yandell, Joseph Bedell, 2003, O'Reilly
Sequence Analysis in a Nutshell: A Guide to Common Tools and Databases, Scott Markel, Darryl
Leon, 2003, O'Reilly
Bioinformatics for Geneticists, Michael Barnes, Ian C Gray (Editors), 2003, John Wiley & Sons
Bioinformatics for Dummies, Jean-Michel Claverie, Cedric Notredame, 2003, John Wiley &
Sons
Mathematics of Genome Analysis, Jerome K. Percus, 2002, Cambridge Univ Press
Bioinformatics Computing, Bryan P. Bergeron, 2002, Prentice Hall
Proteomics- Theory and Practice, V.S. Gomase and N.J. Chikhale, Himalaya Publication House,
India,1-edition, 2009, IBSN: 978-81-8488-313-8
Introduction to Bioinformatics, Teresa Attwood, David Parry-Smith, 2001, Prentice Hall
Bioinformatics: Sequence and Genome Analysis, David W. Mount, 2001, Cold Spring Harbor
Laboratory Press
Fundamental Concepts of Bioinformatics, Dan E. Krane, Michael L. Raymer, Michaeel L.
Raymer, Elaine Nicpon Marieb, 2002, Benjamin/Cummings
Essentials of Genomics and Bioinformatics, C. W. Sensen (Editor), 2002, John Wiley & Sons
Current Topics in Computational Molecular Biology (Computational Molecular Biology), Tao
Jiang, Ying Xu, Michael Zhang (Editors), 2002, MIT Press
Biostatistics
Course Objectives: To enable the students to gain knowledge about Biostatistics.
Unit -I: Introduction (9L)

Methods of collection of data
Classifications and graphical representation of data
Binomial and normal probability distribution
Polygon, histogram, measure of central tendency
Significance of statistical methods
Probability
Degree of freedom, measures of variation
Standard deviation, Standard error
Unit -II: Statistical Sampling (9L)

Sampling, sample size and power
Statistical inference and hypothesis
Tests for statistical significance: student t-test
Chi-square test, confidence level
Null hypothesis
Unit -III: Statistical Analysis (9L)

Linear regression and correlation
Analysis of Variance (one way and two way)
Factorial designs (including fraction factorial design)
Theory of probability
Permutation and Combination
Ratios, Percentage and Proportion
Two way ANOVA and Multiple comparison procedures
Unit -IV: Experimental design and trials (9L)

Non-parametric tests,
Experimental design in clinical trials
Statistical quality control, Validation
Optimization techniques and Screening design
Correlation and regression, least square method
Significance of coefficient of correlation
Nonlinear regression
Unit -V: Bioassays-calculations (9L)

Bioassays-calculations of doses response relationships
LD50, ED50, probit analysis
Applications of software for statistical calculation viz. SPSS, foxtron
Application of computers in Pharmaceutical sciences
Textbook:
The Biostatistics Cookbook: The Most User-Friendly Guide for the Bio/Medical Scientist, S.
Michelson and T. Schofield, Springer; 1 edition, ISBN-13: 978-0792338840, (1996).
Intuitive Biostatistics: A Nonmathematical Guide to Statistical Thinking, Harvey Motulsky,
Oxford University Press, USA, ISBN-13: 978-0199730063, (2010).
Biostatistics: The Bare Essentials 3/e (with SPSS), Norman, Geoffrey Norman, David Streiner,
BC Decker Inc; 3 edition, ISBN-13: 978-1550094008, (2008).
Biostatistics, Second Edition: A Guide to Design, Analysis and Discovery. Ronald N. Forthofer,
Eun Sul Lee, Mike Hernandez , Academic Press; 2 edition, ISBN-13: 978-0123694928,
(2006).
Fundamentals of Biostatistics, Bernard Rosner, Duxbury Press; 6 edition, ISBN-13: 978-
0534418205, (2005).
Biostatistics for the Biological and Health Sciences with Statdisk, Marc M. Triolaand and Mario
F. Triola, Addison Wesley, ISBN-13: 978-0321194367, (2005).
Introduction to Biostatistics: Second Edition, Robert R. Sokal and F. James Rohlf, Dover
Publications; 2 edition, ISBN-13: 978-0486469614, (2009).
Basic & Clinical Biostatistics (LANGE Basic Science), Beth Dawson, Robert Trapp, Robert
Trapp , McGraw-Hill Medical; 4 edition, ISBN-13: 978-0071410175, (2004).
Biostatistics, Tarum Rawat, Samuel Devlin, Kõva köide,Kirjastus: Sarup & Son, ISBN-13:
9788176258050 (2008).
Pharmaceutical Statistics: Practical and Clinical Applications, Revised and Expanded (Drugs and
the Pharmaceutical Sciences), Sanford Bolton and Charles Bon , Informa Healthcare; 4
edition, ISBN-13: 978-0824746957, (2003)
Statistical Methods in Biology , Norman T. J. and Bailey M.A., Cambridge University Press; 3
edition, ISBN-13: 978-0521469838, (1995).
Primer of Applied Regression Analysis and Analysis of Variance, 2nd edition, Glantz S.A.,
Slinker B.K., New York: McGraw-Hill, (2001)
Data Base Managements Systems Oracle
Course Objectives: To enable the students to gain knowledge about Data Base Managements
Systems Oracle.
Unit -I: Basic concepts (9L)

Database & database users,
Characteristics of the database, database systems,
Concepts and architecture, date models, schemas & instances,
DBMS architecture & data independence,
Database languages & interfaces,
Data modeling using the entity-relationship approach. Overview of hierarchical,
Network & Relational Data Base Management Systems
Unit -II: Relational model, languages & systems (9L)

Relational data model & relational algebra
Relational model concepts
Relational model constraints, relational algebra
SQL- a relational database language
Date definition in SQL, view and queries in SQL
Specifying constraints and indexes in SQL
Relational database management systems
DB2, Oracle PL/SQL
Programming Language / Structure Query Language- DDL, DML
Unit -III: Data Structure (9L)

DB2 Architecture
Logical Data Structures Physical Data Structure
Instances, Table Spaces, Types of Tablespaces
Internal Memory Structure
Background Processes
Data Types, Roles & Privileges
Stored Procedures
User Defined Functions
Packages, Cursors, Error Handling, Triggers, collectors
Unit -IV: Relational data base design (9L)

Function dependencies & normalization for relational databases:
Functional dependencies,
Normal forms based on primary keys, (1NF, 2NF, 3NF & BCNF),
Lossless join and dependency preserving decomposition
Unit -V: Concurrency control & recovery techniques (9L)

Concurrency control techniques
Locking techniques, time stamp ordering
Granularity of data items, recovery techniques
Recovery concepts, database backup and recovery from catastrophic failures
Text Books:
Oracle Data Guard 11g Handbook (Osborne ORACLE Press Series), Larry Carpenter, Joseph
Meeks, Charles Kim, Bill Burke, Sonya Carothers, Joydip Kundu, Mike Smith, Nitin
Vengurlekar, McGraw-Hill Osborne Media; 1 edition, ISBN-13: 978-0071621113, (2009)
Oracle General Ledger Guide: Implement a Highly Automated Financial Processing System,
Melanie Cameron, McGraw-Hill Osborne Media; 1 edition, ISBN-13: 978-0071622295,
(2009)
Database System Concepts, Avi Silberschatz, Henry F. Korth, S. Sudarshan, McGraw-Hill, ISBN
0-07-295886-3
Database Management Systems By Raghu Ramakrishnan, Johannes Gehrke, McGraw-Hill ,
ISBN: 0072465638 / 9780072465631
Fundamentals of Database Management Systems by Mark L. Gillenson, John Wiley & Sons,
ISBN-13: 9780471262978, 978-0471262978
Relational Database Management: A Systems Programming Approach, M. Papazoglou and W.
ValderPrentice Hall, ISBN-10: 0137718667
Oracle Database 11g, A Beginner's Guide, Ian Abramson, Michael Abbey, Michael Corey,
McGraw-Hill Osborne Media, ISBN-10: 0071604596
An Introduction to Database Systems, C. J. Date, Addison Wesley Longman, ISBN-10:
0201385902
Linux
Course Objectives: To enable the students to gain knowledge about Linux.
Unit –I: Introduction to Linux (9L)

OS and Linux, History of Linux and Unix
Linux Software
Linux Documentation, Distribution
Installation of Linux
Linux and Interfaces
Genome Desktop, KDE
Unit –II: Linux Environments (9L)

KDE - desktop, help system, KDE configuration
Genome - Interface, file manager, Panel, Applets, configurations
The shell – command line, file name, encapsulation, standards output/ input, shell variables,
pipes
Linux File Structure
Shell configuration
Unit –III: System and network Configuration (9L)

System configuration
Distribution administration tools
Read Hat administration tools
Configuring users
Mapping CD Rom, Floppy, CD-R/W Drivers
Printer, Update tools
Install softwares packages
Unit –IV: Client Applications and Server managements (9L)

Client Applications
Mails and News clients
Web, FTP and JAVA clients
Networks tools, Office applications
DBMS, Graphic tools, editors
Server managements
FTP Servers, Web servers, Domain Name Services
Mail Servers, SMTP, POP, IMAP
Unit –V: System Administration and Network administration (9L)

Basic of system administration
Boot management tools
Managing users
Software managements
File system administration
Devices and Printers
Kernel Administration
Configuration of Network connection
NFS, NIS, Applets Table
Samba, Administrating TCP / IP Networks
Network Security, Firewalls, and authentications
Text Books:
Practical Guide to Fedora and Red Hat Enterprise Linux, A (5th Edition) by Mark G. Sobell,
( 2010).
Linux Bible 2010 Edition: Boot Up to Ubuntu, Fedora, KNOPPIX, Debian, openSUSE, and 13
Other Distributions, Christopher Negus, Wiley; Pap/Dvdr/C edition, ISBN-13: 978-
0470485057, (2009)
Practical Guide to Linux Commands, Editors, and Shell Programming, A (2nd Edition), Mark G.
Sobell, Prentice Hall; 2 edition, ISBN-13: 978-0131367364, (2009).
Linux Administration: A Beginner's Guide, Fifth Edition , Wale Soyinka, McGraw-Hill Osborne
Media; 5 edition, ISBN-13: 978-0071545884, (2008).
Linux Pocket Guide, Daniel J. Barrett, O'Reilly Media; 1st edition, ISBN-13: 978-0596006280,
(2004).
Linux in a Nutshell, Ellen Siever, Stephen Figgins, Robert Love, Arnold Robbins, O'Reilly
Understanding the Linux Kernel, Third Edition, Daniel P. Bovet and Marco Cesati, O'Reilly
Linux For Dummies, 9th Edition, Richard Blum, For Dummies; 9 edition, ISBN-13: 978-
0470467015, (2009).
Practical UNIX/Linux, Eugene Khmelevsky, Amazon Digital Services, ASIN: B001SERN5W.
Running Linux, Matthias Kalle Dalheimer and Matt Welsh, (2005).
Beginning Linux Programming by Neil Matthew and Richard Stones, (2007).
Bioinformatics Practical
Sub. Code: BIM-102 (P)
Course Objectives: To enable the students to gain knowledge about Bioinformatics.
Total Credits: 2
List of experiments
Database Searching
Nucleotide Databases -NCBI, DDBJ, EMBL, PDB, BRENDA, TrEMBL, KEGG, Microarray –
MIAME. GEO
Diseases -OMIM Database
Protein databases- PIR, UniProt
Search Engines- SRS, Entrez
BLAST, PHI-PSI- BLAST, FASTA
Sequence alignments
Local Alignments
Global Alignments
Dynamic Programming, Dot Plot
Smith-Waterman, Needleman- Wunch Algorithms,
Day Hoff Matrix, Blossum, PAM Matrices,
GAP Penalties
Multiple Sequence alignments- ClustalW, DALI
Text Books:
Algorithms on Strings, Trees, and Sequences: Computer Science and Computational Biology,
Dan Gusfield, 1997, Cambridge University Press
Sons
Laboratory Press
Structural Bioinformatics, Philip E. Bourne, Helge Weissig (Editors), 2003, John Wiley & Sons
Protein Structure Prediction: Bioinfomatic Approach, I.F. Tsigelny, 2002, International
University Line
Introduction to Protein Architecture: The Structural Biology of Proteins, Arthur M. Lesk, 2001,
Oxford University Press
Protein Structure Prediction: Methods and Protocols, David M. Webster (Editor), 2000, Humana
Press
Introduction to Protein Structure, Carl-Ivar Branden, John Tooze, 1999, Garland Publishing
Structure and Mechanism in Protein Science: A Guide to Enzyme Catalysis and Protein Folding,
Alan Fersht, 1999, Freeman
Biostatistics Practical
Course Objectives: To enable the students to gain knowledge about Biostatistics, or the use of
numerical techniques to extract information from data and facts.
Total Credits: 2
List of experiments
Biostatistical Design of Medical Studies.
Descriptive Statistics.
Descriptive Methods for Categorical Data.
Descriptive Methods for Continuous Data.
Probability and Probability Models.
Random Variables and Distributions
Estimation of Parameters.
Introduction to Statistical Tests of Significance.
Comparison of Population Proportions.
Comparison of Population Means.
Correlation and Regression.
Logistic Regression.
Methods for Count Data.
Analysis of Survival Data and Data from Matched Studies.
Study Designs
Likelihood Ratios, Bayesian Methods and Multiple Hypotheses
Textbook:
The Biostatistics Cookbook: The Most User-Friendly Guide for the Bio/Medical Scientist, S.
Michelson and T. Schofield, Springer; 1 edition, ISBN-13: 978-0792338840, (1996).
Intuitive Biostatistics: A Nonmathematical Guide to Statistical Thinking, Harvey Motulsky,
Oxford University Press, USA, ISBN-13: 978-0199730063, (2010).
Biostatistics: The Bare Essentials 3/e (with SPSS), Norman, Geoffrey Norman, David Streiner,
BC Decker Inc; 3 edition, ISBN-13: 978-1550094008, (2008).
Biostatistics, Second Edition: A Guide to Design, Analysis and Discovery. Ronald N. Forthofer,
Eun Sul Lee, Mike Hernandez , Academic Press; 2 edition, ISBN-13: 978-0123694928,
(2006).
Fundamentals of Biostatistics, Bernard Rosner, Duxbury Press; 6 edition, ISBN-13: 978-
0534418205, (2005).
Biostatistics for the Biological and Health Sciences with Statdisk, Marc M. Triolaand and Mario
F. Triola, Addison Wesley, ISBN-13: 978-0321194367, (2005).
Introduction to Biostatistics: Second Edition, Robert R. Sokal and F. James Rohlf, Dover
Publications; 2 edition, ISBN-13: 978-0486469614, (2009).
Basic & Clinical Biostatistics (LANGE Basic Science), Beth Dawson, Robert Trapp, Robert
Trapp , McGraw-Hill Medical; 4 edition, ISBN-13: 978-0071410175, (2004).
Biostatistics, Tarum Rawat, Samuel Devlin, Kõva köide,Kirjastus: Sarup & Son, ISBN-13:
9788176258050 (2008).
Pharmaceutical Statistics: Practical and Clinical Applications, Revised and Expanded (Drugs and
the Pharmaceutical Sciences), Sanford Bolton and Charles Bon , Informa Healthcare; 4
edition, ISBN-13: 978-0824746957, (2003)
Statistical Methods in Biology , Norman T. J. and Bailey M.A., Cambridge University Press; 3
edition, ISBN-13: 978-0521469838, (1995).
Primer of Applied Regression Analysis and Analysis of Variance, 2nd edition, Glantz S.A.,
Slinker B.K., New York: McGraw-Hill, (2001)
Data Base Managements Systems Oracle Practical
Course Objectives: To enable the students to gain knowledge about Data Base Managements
Systems Oracle.
Total Credits: 2
List of experiments
Oracle Database Administration
Installing Oracle Database Software
Creating and Controlling Oracle Databases
Administering Users
Managing Schema Objects and Data
Implementing Oracle Security Features
Monitoring Performance
Performing Database Backup and Recovery
Basic PL/SQL Concepts.
Laying the Groundwork: PL/SQL Fundamentals.
Controlling Program Flow.
Handling Exceptions.
Standards and Structures.
Creating Naming Standards.
Creating Coding Standards.
PL/SQL Data Manipulations.
Basic Datatypes.
Advanced Datatypes.
Transaction Control.
Dynamic SQL and PL/SQL.
Text Books:
Oracle Data Guard 11g Handbook (Osborne ORACLE Press Series), Larry Carpenter, Joseph
Meeks, Charles Kim, Bill Burke, Sonya Carothers, Joydip Kundu, Mike Smith, Nitin
Vengurlekar, McGraw-Hill Osborne Media; 1 edition, ISBN-13: 978-0071621113, (2009)
Oracle General Ledger Guide: Implement a Highly Automated Financial Processing System,
Melanie Cameron, McGraw-Hill Osborne Media; 1 edition, ISBN-13: 978-0071622295,
(2009)
Database System Concepts, Avi Silberschatz, Henry F. Korth, S. Sudarshan, McGraw-Hill, ISBN
0-07-295886-3
Database Management Systems By Raghu Ramakrishnan, Johannes Gehrke, McGraw-Hill ,
ISBN: 0072465638 / 9780072465631
Fundamentals of Database Management Systems by Mark L. Gillenson, John Wiley & Sons,
ISBN-13: 9780471262978, 978-0471262978
Relational Database Management: A Systems Programming Approach, M. Papazoglou and W.
ValderPrentice Hall, ISBN-10: 0137718667
Oracle Database 11g, A Beginner's Guide, Ian Abramson, Michael Abbey, Michael Corey,
McGraw-Hill Osborne Media, ISBN-10: 0071604596
An Introduction to Database Systems, C. J. Date, Addison Wesley Longman, ISBN-10:
0201385902
Linux Practical
Course Objectives: To enable the students to gain knowledge about Linux.
Total Credits: 2
List of experiments
Working with Linux.
Toolchains, Portability.
Software Configuration Management.
Network Programming.
Databases.
Kernel Development.
Kernel Interfaces.
Linux Kernel Modules.
The shell – command line, file name, encapsulation, standards output/ input, shell variables,
pipes
Linux File Structure
Shell configuration
Client Applications and Server managements
Basic of system administration
Boot management tools,
Managing users,
Software managements,
File system administration,
Devices and Printers
Kernel Administration,
Configuration of Network connection
NFS, NIS, Applets Table,
Samba, Administrating TCP / IP Networks,
Network Security, Firewalls, authentications
Text Books:
Practical Guide to Fedora and Red Hat Enterprise Linux, A (5th Edition) by Mark G. Sobell,
( 2010).
Linux Bible 2010 Edition: Boot Up to Ubuntu, Fedora, KNOPPIX, Debian, openSUSE, and 13
Other Distributions, Christopher Negus, Wiley; Pap/Dvdr/C edition, ISBN-13: 978-
0470485057, (2009)
Practical Guide to Linux Commands, Editors, and Shell Programming, A (2nd Edition), Mark G.
Sobell, Prentice Hall; 2 edition, ISBN-13: 978-0131367364, (2009).
Linux Administration: A Beginner's Guide, Fifth Edition , Wale Soyinka, McGraw-Hill Osborne
Linux Pocket Guide, Daniel J. Barrett, O'Reilly Media; 1st edition, ISBN-13: 978-0596006280,
(2004).
Linux in a Nutshell, Ellen Siever, Stephen Figgins, Robert Love, Arnold Robbins, O'Reilly
Understanding the Linux Kernel, Third Edition, Daniel P. Bovet and Marco Cesati, O'Reilly
Linux For Dummies, 9th Edition, Richard Blum, For Dummies; 9 edition, ISBN-13: 978-
0470467015, (2009).
Practical UNIX/Linux, Eugene Khmelevsky, Amazon Digital Services, ASIN: B001SERN5W.
Running Linux, Matthias Kalle Dalheimer and Matt Welsh, (2005).
Beginning Linux Programming by Neil Matthew and Richard Stones, (2007).
Swami Ramanand Teerth
Marathwada University
Nanded
Sub Centre, Latur
Syllabus For the

Semester -II
Advanced Molecular Biology
Course Objectives: To enable the students to gain knowledge about Advanced Molecular Biology
and genetics.
Unit -I: Central Dogma of Molecular Biology (9L)

DNA, RNA, Protein
Replication
Transcription
Translation
Unit -II: Split genes and overlapping genes (9L)

Evolution of one cistron one polypeptide theory,
Genetic complementation –cis-trans test of genetic functions.
Plasmids
Mobile elements in prokaryotes and eucaryotes-Insertion sequences, transposons, transposable,
elements and their properties, detection and significance, retroposons,
Shapiro’s model of replicative transposition
Gene transfer in bacteria
Restriction and modification of DNA
Recombination and enzymes involved.
Unit -III: Recombinant DNA Technology (9L)

Debate over the technology
General strategy of gene cloning
Tools in rDNA technology
Methods of construction of rDNAs
Methods of transplantation of rDNA
Screening of r DNA clones, scope and significance
Unit -IV: Techniques (9L)

PCR, LCR, RFLP
DNA foot and fingerprinting
Chromosome walking, blotting techniques human genome project
Nick translation hybrid release and arrested translation
Colony hybridization, enzyme and protein engineering
Unit -V: Metabolic engineering (9L)

Essence of metabolic engineering examples of pathway manipulation
Metabolic engineering in practice
Fluxomics, Metabolic flux analysis and its applications
Synthesis low molecular wt. compounds
Text Books:
Molecular Genetics: Structure of Life, Virendra Gomase and Aravind Tripathi, VDM Verlag Dr.
Müller, Germany, ISBN:978-3-639-25001-5, (2010).
Genetechnology, Virendra Gomase and Shruti Gomase, VDM Verlag Dr. Müller, Germany,
ISBN: 978-3-639-13467-4, (2010).
Molecular biology of the Cell, Bruce Alberts, Alexander Johnson, Alexander Johnson, Julian
Lewis, Martin Raff, keith Roberts, Peter Walter; Garland Science, Taylor & Francis
group,4th Edition (2002)
Essential Cell Biology, Bruce Alberts Dennis Bray, Karen Hopkins, Alexander Johnson Julian
Lewis, Martin Raff, Keith Roberts, Peter Walter; Garland Science; Taylor & Francis
Group,4th Edition (2004)
Cell Molecular Biology, E. D. P. De Robertis, E. M. F. De Robertis, Jr, Lippinwt William &
Wilkins (2001)
Metabolomics, Virendra Gomase and Shruti Gomase, VDM Verlag Dr. Müller, Germany,
ISBN:978-3-639-24991-0, (2010).
Molecular biology, David Freifelder, Narosa Publishing House, 1st Edition(2004)
Genes, VIII Benjamin Lewin; Pearson Education International,8th Edition (2004)
Principles of Gene Manuplation, S. B. Primrose R. M. Twyman & R. W. old, Blackwell
Science,6th Edition (2001)
Advanced Molecular Biology, R. M. Twyman, 1st Edition , (2003)
Instant Notes on Molecular Biology; P.C. Turner, A. G. Mclennan, A. D. Bates & M. R. H.
White, 2nd Edition (2002)
Molecular Biology, David Freifelder, Narosa Publishing House,2nd edition (2004)
Microbial Genetics, David Freifelder, Narosa Publishing House, 2nd edition(2004)
Essential Molecular Biology (volume I & II) Practical Approach; Edited By T. A. Brown; Oxford
University Press, 2nd Edition (2001)
Computational Biology
Course Objectives: To enable the students to gain knowledge about Computational Biology.
Unit -I: Database Searching (9L)

Nucleotide Databases -NCBI, DDBJ, EMBL, PDB, BRENDA, TrEMBL, KEGG Microarray –
MIAME, GEO
Diseases -OMIM Database
Protein databases- PIR, UniProt
Search Engines- SRS, Entrez
BLAST, PHI-PSI- BLAST, FASTA
Unit -II: Sequence alignments (9L)

Local Alignments
Global Alignments
Dynamic Programming, Dot Plot
Smith-Waterman, Needleman- Wunch Algorithms,
Day Hoff Matrix, Blossum, PAM Matrices,
GAP Penalties
Multiple Sequence alignments
ClustalW, DALI
Unit -III: Pattern identification (9L)

Pattern matching function,
Repeat analysis
Invert repeats
Domain
Motif
Restriction enzyme cleavage sites
Unit -IV: Protein analysis (9L)

Primary structure analysis –Protparam, COILS
Topology Prediction -TMHMM
Secondary structure prediction -GOR, SOPMA, PHD
Tertiary structure prediction-CPHModels
Antigenic predictions
Isoelectric points
Unit -V: Phylogenic tree constructions (9L)

General-purpose packages
Parsimony programs
Distance matrix methods
Computation of distances
Maximum likelihood and Bayesian methods
Artificial-intelligence and genetic algorithms methods
Invariants (or Evolutionary Parsimony) methods
Consensus trees, subtrees, supertrees, distances between trees
Tree-based alignment
Description or prediction of data from trees
Text Books:
Sons
Laboratory Press
Immunoinformatics
Course Objectives: To enable the students to gain knowledge about Immunoinformatics is an

emerging sub discipline of bioinformatics.
Unit -I: Introduction to Immunoinformatics (9L)

Introduction
Immunity
Immune system
Immunoinformatics is an emerging sub discipline of bioinformatics
Immunology and informatics
Genomics immunological methods
Proteomics and immunological methods
Networks regulating the immune system
Unit -II: Applied data-driven strategies (9L)

MHC
TCR
Peptide-MHC and allergen research
Epitope prediction
De-immunization of therapeutic proteins
Host-pathogen interactions
Modeling of immune responses to pathogens
Large-scale chemical mutagenesis-driven genetic analyses systems
Unit -III: Immunological Supertypes (9L)

Defining HLA Supertypes
supertypes of GRID/CPCA
Hierarchical clustering methods
Hla-Ad supertypes
MHC supertypes, and Class I Hla Alleles
Unit -IV: Immunoinformatics databases (9L)

IMGT/HLA
IPD
SYEPEITHI
MHCBN database
JenPep database
Unit -V: Immunoinformatics Methods (9L)

MHC Prediction
Predicting Peptide-MCH Binding
MCH binders
TAP binding
MHC similarities, and predicting virulence factors
B-cell epitopes
T-Cell epitopes
Class I and II MHC
HLA-peptide binding
Text Books:
Immunobiotechnology, Virendra Gomase and Sunilkumar Dwivedi, VDM Verlag Dr. Müller,
Germany, ISBN: 978-3-639-25017-6, (2010).
Immunoinformatics: Shoba Ranganathan, Vladimir Brusic, Christian Schonbach, ISBN:
0387729674, Springer, (2007).
Immunoinformatics: Darren R Flower, ISBN: 1588296997, Humana Press, (2007).
Immunology: Richard A. Goldsby, Thomas J. Kindth, Barbara A, Osborne, Janis Kuby, W. H.
Freeman & Company, 5th Edition (2003).
Roitt’s Essential Immunology: Ivan M. Roitt, Peter J. Delves Blackwell Science Ltd., 10th
Edition (2001)
An Introduction to Immunology: C.V. Rao; Narosa Publishing House,1st Edition (2004)
Instant Notes in Immunology; P.M. Lydyard, A. Whelan, M.W. Fanger BIOS Scientific
Publishers Ltd, 1st Edition (2003)
Textbook of Microbiology: R. Ananthnarayan, C. K. J. Panicker, Orient Longman , 6th Edition
(2003)
Immunology: Introductory Textbook; Nandini Shetty, New Age International pvt. Ltd. 1st
Edition (2003)
Chemoinformatics
Course Objectives: To enable the students to gain knowledge about Computers in Chemical
Research.
Unit -I: Introduction to Chemoinformatics (9L)

Introduction to Chemoinformatics
Computers in Chemical Research
Data analysis and data management tools in preclinical development
Impact of bioinformatics on preclinical drug and vaccine discovery
Statistical modeling in pharmaceutical research
Drug discovery from Medicinal Plants
Unit –II: Pharmaceutical Information (9L)

Pharmaceutical Information Management
Strategies for using information effectively in early stage drug discovery
Pharmacophore Modeling
Computer aided drug design
Ligand Libraries and Screening
High Throughput Screening for Pharmacogenetics
Clinical data collection and management
New paradigm for analyzing adverse drug events
Unit –III: Drug Databases and Data Banks (9L)

Drug information data bases
Type of Drug Data
Databases of Chemical Structures
Databases on Chemical Reactions
Spectroscopic Databases
Chemistry in the Internet
Computers and protein crystallography
Protein-ligand free energy predictions for drug discovery
Molecule libraries for synthesis
Unit –IV: Data Collection and Simulation Strategies (9L)

Pharmacogenomics and Pharmacoproteomics
Computer methods for predicting drug metabolism
Toxicogenomics and Toxicoinformatics
Computational optimization of biopharmaceutical properties
Computer simulations in pharmacokinetics and pharmacodynamics
MicroRNA, RNAinterference for Drug targets
Computational Biology of microRNAs
Unit –V: Legal and Ethical Aspects (9L)
Legal and Ethical Aspects of Chemoinformatics
Chemical formulation informatics
The ethics of computing in pharmaceutical and chemical research
An expert system for contextual hyper linking in knowledge management
Intellectual property protection, Copyright and Copyleft
Information infrastructure regulations
Text Books:
Encyclopedia of Drug Design (11 Volumes), Virendra Gomase and Shruti Gomase, ISBN:978-9-
380-02632-9, IK International Publishing House Pvt. Ltd
Computer Applications in Pharmaceutical Research and Development, Wang, Binghe, ISBN-10:
0-471-73779-8, John Wiley and Sons India Pvt. Ltd.
Quantitative molecular pharmacology and informatics in drug discovery, Michael Lutz and Jerry
Kenatin, ISBN-10: 0471988618, John Wiley and Sons India Pvt. Ltd.
RNA Interference Technology- From Basic Science to Drug Development, Krishnarao Appasani,
ISBN: 13:9780521836777, Cambridge University Press India Private Limited
microRNAs: From Basic Science to Disease Biology, Krishnarao Appasani, ISBN-13:
9780521865982, Cambridge University Press India Private Limited
Microarray Bioinformatics, Dov Stekel, ISBN:13:9780521525879, Cambridge University Press
India Private Limited
Medical Informatics & Telemedicine: Recent Advances, J Mukhopadhyay,
ISBN:9780230630185, Macmillan India Limited
Nanotechnology in Biology and Medicine Methods, Devices, and Applications, Tuan Vo-Dinh,
ISBN: 0849329494, I.K. International Publishing House Pvt. Ltd
Molecular pharmacology a short course, Jerry Kenatin, ISBN-10: 086542540X, John Wiley and
Sons India Pvt. Ltd.
Pharmaceutical Drug Analysis, Ashutosh Kar, ISBN:9788122415827, New Age International (P)
Ltd., Publishers
Stereochemistry of Organic Compounds, Ernest L. Eliel, Samuel H. Wilen, ISBN: 978-0-471-
01670-0, John Wiley and Sons India Pvt. Ltd.
Organic Chemistry, T. W. Graham Solomons, Craig B. Fryhle, ISBN: 978-0-471-68496-1, John
Wiley and Sons India Pvt. Ltd.
Stereochemistry, David G. Morris, ISBN: 978-0-471-22477-8, John Wiley and Sons India Pvt.
Ltd.
Machine Intelligence in Bioinformatics
Course Objectives: To enable the students to gain knowledge about Machine Intelligence.
Unit -I: Introduction to Biological Data Mining (9L)

Data Mining in Genomics
Gene Expression Data Mining
Data Mining in Proteomics
Data Mining Preparatory Activities
Data cleaning, data preprocessing, and semantic integration of heterogeneous, distributed
biomedical databases
RNA Data Mining
Unit -II: 3. Optimization Techniques (9L)

Steepest descent
Conjugate gradient
Newton Raphson
Simulated annealing and biomolecular structure optimization
Genetic algorithms
Unit -III: Machine Learning Techniques (9L)

Neural Network based biological applications
HMM based biological applications
Dynamic programming and biological applications
Sequences alignments
Structure alignments
Unit -IV: Monte Carlo and Bayesian approaches in data mining (9L)
Data mining models and data streams
Bayesian techniques and current biological research
Statistical alignment MCMC workbench
Models of computational analysis
Markov Chain Monte Carlo
Bayesian phylogenetics
RNA substitution model and early mammalian evolution
Advantages of Bayesian applications
Unit -V: Clustering algorithms and applications (9L)

Hierarchical and non-hierarchical clustering
Grid Based clustering, Microarray analysis
Microarray and automatic segmentation
Protein array data analysis
Text Books:
Sons
Laboratory Press
Structural Bioinformatics, Philip E. Bourne, Helge Weissig (Editors), 2003, John Wiley & Sons
Protein Structure Prediction: Bioinfomatic Approach, I.F. Tsigelny, 2002, International
University Line
Introduction to Protein Architecture: The Structural Biology of Proteins, Arthur M. Lesk, 2001,
Oxford University Press
Protein Structure Prediction: Methods and Protocols, David M. Webster (Editor), 2000, Humana
Press
Introduction to Protein Structure, Carl-Ivar Branden, John Tooze, 1999, Garland Publishing
Structure and Mechanism in Protein Science: A Guide to Enzyme Catalysis and Protein Folding,
Alan Fersht, 1999, Freeman
Immunoinformatics Practical
Course Objectives: To enable the students to gain knowledge about Immunoinformatics is an

Total Credits: 2
List of experiments
Information retrieval and analysis of database i.e. IMGT/HLA IPD, SYEPEITHI
Information retrieval and analysis of database i.e. MHCBN, JenPep
Immunoinformatics Methods
MHC Prediction
Predicting Peptide-MCH Binding
MCH binders prediction
TAP binders prediction
MHC similarities, and predicting virulence factors
B-cell epitopes prediction
T-Cell epitopes prediction
Class I and II MHC prediction methods
HLA-peptide binding
Text Books:
Immunobiotechnology, Virendra Gomase and Sunilkumar Dwivedi, VDM Verlag Dr. Müller,
Germany, ISBN: 978-3-639-25017-6, (2010).
Immunoinformatics: Shoba Ranganathan, Vladimir Brusic, Christian Schonbach, ISBN:
0387729674, Springer, (2007).
Immunoinformatics: Darren R Flower, ISBN: 1588296997, Humana Press, (2007).
Immunology: Richard A. Goldsby, Thomas J. Kindth, Barbara A, Osborne, Janis Kuby, W. H.
Freeman & Company, 5th Edition (2003).
Roitt’s Essential Immunology: Ivan M. Roitt, Peter J. Delves Blackwell Science Ltd., 10th
Edition (2001)
An Introduction to Immunology: C.V. Rao; Narosa Publishing House,1st Edition (2004)
Instant Notes in Immunology; P.M. Lydyard, A. Whelan, M.W. Fanger BIOS Scientific
Publishers Ltd, 1st Edition (2003)
Textbook of Microbiology: R. Ananthnarayan, C. K. J. Panicker, Orient Longman , 6th Edition
(2003)
Immunology: Introductory Textbook; Nandini Shetty, New Age International pvt. Ltd. 1st
Edition (2003)
Chemoinformatics Practical
Sub. Code: BIM -204 (P)
Course Objectives: To enable the students to gain knowledge about Chemoinformatics is an
Total Credits: 2
List of experiments
Data analysis and data management tools in preclinical development

Statistical modeling in chemical research
Study of Secondary metabolites from Medicinal Plants
Pharmacophore Modeling
Ligand Libraries and Screening
High Throughput Screening for Pharmacogenetics
Clinical data collection and management
Databases of Chemical Structures
Databases on Chemical Reactions
Protein-ligand free energy predictions for drug discovery
Molecular libraries for synthesis
Computational optimization of biopharmaceutical properties
Computer simulations in pharmacokinetics and pharmacodynamics
Molecular analysis for drug design
Text Books:
Computer Applications in Pharmaceutical Research and Development, Wang, Binghe, ISBN-10: 0-471-
Quantitative molecular pharmacology and informatics in drug discovery, Michael Lutz and Jerry Kenatin,
ISBN-10: 0471988618, John Wiley and Sons India Pvt. Ltd.
RNA Interference Technology- From Basic Science to Drug Development, Krishnarao Appasani, ISBN:
13:9780521836777, Cambridge University Press India Private Limited
microRNAs: From Basic Science to Disease Biology, Krishnarao Appasani, ISBN-13: 9780521865982,
Cambridge University Press India Private Limited
Microarray Bioinformatics, Dov Stekel, ISBN:13:9780521525879, Cambridge University Press India
Private Limited
Medical Informatics & Telemedicine: Recent Advances, J Mukhopadhyay, ISBN:9780230630185,
Macmillan India Limited
Nanotechnology in Biology and Medicine Methods, Devices, and Applications, Tuan Vo-Dinh, ISBN:
0849329494, I.K. International Publishing House Pvt. Ltd
Molecular pharmacology a short course, Jerry Kenatin, ISBN-10: 086542540X, John Wiley and Sons
India Pvt. Ltd.
Pharmaceutical Drug Analysis, Ashutosh Kar, ISBN:9788122415827, New Age International (P) Ltd.,
Publishers
Stereochemistry of Organic Compounds, Ernest L. Eliel, Samuel H. Wilen, ISBN: 978-0-471-01670-0,
John Wiley and Sons India Pvt. Ltd.
Organic Chemistry, T. W. Graham Solomons, Craig B. Fryhle, ISBN: 978-0-471-68496-1, John Wiley and
Machine Intelligence in Bioinformatics Practical
Course Objectives: To enable the students to gain knowledge about Machine Intelligence
techniques, algorithms in bioinformatics.
Total Credits: 2
List of experiments
Data mining in genomics
Gene expression data mining
Data mining in proteomics
RNA secondary structure comparison and alignment
Minimum free-energy method for RNA secondary structure prediction
Gene mapping by pattern discovery
Data mining: predicting protein folding pathways
Data mining methods for a systematic of protein subcellular location
Sequence homology
Sequences alignments
Structure alignments
Motif involve in protein targeting
Ab initio method prediction from sequence
Mining chemical compounds
Text Books:
Bioinformatics- Theory and Practice, N.J. Chikhale and V.S. Gomase, Himalaya Publication House, India;
1 edition, 2007, ISBN-13: 978-81-8318-831-9
Algorithms on Strings, Trees, and Sequences: Computer Science and Computational Biology, Dan
Gusfield, 1997, Cambridge University Press
Sequence Analysis in a Nutshell: A Guide to Common Tools and Databases, Scott Markel, Darryl Leon,
2003, O'Reilly
Bioinformatics for Dummies, Jean-Michel Claverie, Cedric Notredame, 2003, John Wiley & Sons
Proteomics- Theory and Practice, V.S. Gomase and N.J. Chikhale, Himalaya Publication House, India,1-
edition, 2009, IBSN: 978-81-8488-313-8
Bioinformatics: Sequence and Genome Analysis, David W. Mount, 2001, Cold Spring Harbor Laboratory
Press
Fundamental Concepts of Bioinformatics, Dan E. Krane, Michael L. Raymer, Michaeel L. Raymer, Elaine
Nicpon Marieb, 2002, Benjamin/Cummings
Current Topics in Computational Molecular Biology (Computational Molecular Biology), Tao Jiang,
Ying Xu, Michael Zhang (Editors), 2002, MIT Press
Numerical Methods and Optimization Techniques Practical
Sub. Code: BIM -206 (P)
Course Objectives: To enable the students to gain knowledge about Numerical Methods and
Optimization Techniques Practical, algorithms in bioinformatics.
Total Credits: 2
List of experiments
Engineering Optimization Methods and Principles
Optimization and Programming
Optimization Techniques
Numerical Analysis
Application of Optimization Techniques
Numerical Methods & Optimization
Coordinate descent and subgradient method
Optimization and Cutting Plane Methods
Babylonian, Restricted step methods and Non linear equations
Linearly Constrained Optimization Techniques
Text Books:
Gilat Amos (2004) MATLAB: An Introduction with Applications (2nd edition ed.). John Wiley
& Sons. ISBN 0-471-69420-7.
Hildebrand F. B. (1974) Introduction to Numerical Analysis (2nd edition ed.). McGraw-Hill.
ISBN 0-070-28761-9.
Leader Jeffery J. (2004) Numerical Analysis and Scientific Computation. Addison Wesley. ISBN
0-201-73499-0.
Trefethen Lloyd N. (2006) "Numerical analysis", 20 pages. In: Timothy Gowers and June
Barrow-Green (editors), Princeton Companion of Mathematics, Princeton University
Press
Marti K. (2002) Stochastic Optimization Techniques: Numerical Methods And Technical
Applications, ISBN: 3540428895, Springer
Emmanuel Le Tallec Patrick, Numerical Methods In Sensitivity Analysis And Shape
Optimization, {with Cd-rom}, ISBN: 0817643222, (2003), Birkhauser
University
Nanded
Sub Centre, Latur
Syllabus For the

Semester -III
Computer Aided Drug Design
Course Objectives: To enable the students to gain knowledge about Computer Aided Drug Design
Unit-I: Introduction to CADD (9L)

Introduction to CADD, SBDD
Representation of Molecular Structures
Chemical Nomenclature and Structure Representation
Processing Constitutional Information
Representation of 3D Structures
Molecular Shape Analysis
Representation of Chemical Reactions
Unit-II: Virtual Screening (9L)

Virtual Screening
Chemoinformatics in Lead Discovery
Computational Chemistry,
Molecular Complexity and Screening Set Design
Algorithmic Engines in Virtual Screening
Strengths and Limitations of Pharmacophore-Based Virtual Screening
Unit-III: Lead Discovery (9L)

High Throughput Screening
Hit and Lead Discovery
Enhancing Hit Quality and Diversity within Assay Throughput Constraints
Molecular Graphics, Molecular Dynamics and Simulation of Lead
Molecular Diversity in Lead Discovery: From Quantity to Quality
In Silico Lead Optimization
Unit-IV: Databases and Libraries (9L)

Databases and Libraries
PubChem, PubEchm-BioAssay, Pharma Project, DrugBank
WOMBAT: World of Molecular Bioactivity
Cabinet - Chemical and Biological Informatics Network
Structure Modification in Chemical Databases
Rational Design of GPCR-specific Combinational Libraries Based on the Concept of Privileged
Substructures
Unit-V: CADD Applications (9L)

CADD Applications
A Practical Strategy for Directed Compound Acquisition
Efficient Strategies for Lead Optimization
Chemoinformatics Tools for Library Design
Hit-to-Lead Process: A User's Perspective
Application of Predictive 3DQSAR Models to Database Mining
Drug Discovery - Case Study
Text Book:
0-471-73779-8, John Wiley & Sons India Pte. Ltd.
Engineering Chemistry, R.V. Gadag and A. Nityananda Shetty, ISBN: 8188237833, I.K.
International Publishing House Pvt. Ltd
Quantum Chemistry and Spectroscopy, Engel, ISBN: 9788131712856, Pearson Education
Quantum Chemistry, Ira N. Levine, ISBN: 8120330641, Prentice-Hall of India
An Introduction to Drug Design, S.N. Pandeya, New Age International (P) Ltd., Publishers
Pharmaceutical Organic Chemistry, Rama Rao Nadendla, ISBN: 9781403924957, Macmillan
India Limited
Virtual Screening in Drug Discovery, Juan Alvarez and Brian Shoichet, ISBN-13: 978-
0824754792, CRC Press
Biological Thermodynamics, Donald T. Haynie, ISBN:9780521704045, Cambridge University
Press India Private Limited
Chemoinformatics, Gasteiger, Johann / Engel, Thomas (eds.), ISBN-13: 978-3-527-30681-7,
John Wiley & Sons India Pte. Ltd.
Chemoinformatics in Drug Discovery, Tudor I. Oprea, Raimund Mannhold, Hugo Kubinyi, Gerd
Folkers, ISBN: 978-3-527-30753-1, John Wiley & Sons India Pte. Ltd.
Handbook of Chemoinformatics: From Data to Knowledge, Johann Gasteiger, ISBN: 978-3-527-
30680-0, John Wiley & Sons India Pte. Ltd.
An Introduction to Computational Biochemistry, C. Stan Tsai, ISBN: 978-0-471-40120-9, John
Wiley & Sons India Pte. Ltd.
Object oriented Programming (OOPS) JAVA
Course Objectives: To enable the students to gain knowledge about Object oriented Programming
(OOPS) JAVA.
Unit-I: Introduction to Computing (9L)

Introduction to Programming, Computer Organization
Evolution of Operating Systems
Personal – Distributed and Client/Server Computing
Machine Languages – Assembly Languages and High level Languages
Structured Programming, Object Technology
Unit-II: Backbone of OOPS (9L)

Abstract Data Type (ADT), Encapsulation
Object, Message, Method, Class, Inheritance
Late Binding Polymorphism, Virtual Functions
Abstract Classes, Interface, Generic Classes and Interfaces
Constructors & Destructors, Overloading & Overriding, Copy Constructor
Unit-III: JAVA Basics (9L)

Importance and features of java,
Modifiers, Access Controls, Data types, Expressions, Declarations,
Statements & Control Structures,
Program Structures, String handling, Packages,
Interfaces, Working with java.util Package, Garbage Collection, Object Class
Exception Handling, I/O & JDBC
Exception Handling:
Fundamentals exception types, uncaught exceptions, throw, throw final, built in exception,
creating your own exceptions.
Input Stream & Output Stream:
Streams, Byte and Character stream,
Predefined streams, Reading and Writing from Console and Files,
Buffered Reader & Writer, Serialization,
Data Compression, Using Standard Java Packages (lang, util, io, net)
Database: JDBC Architecture, JDBC Basics,
JDBC Drivers, Connecting to Database and accessing databases
Unit-IV: AWT & Event Handling (9L)

Creating User interface with AWT
Applets, Applet Life Cycle
Simple Graphics, Fonts and Colors
Events, Listeners, Components
Containers, Working with Layouts
Image Processing, AWT Exceptions
Delegation Event Model, Event Classes
Event Listener Interfaces, Adapter and Inner Classes
Unit-V: Multithreading & Communication (9L)

Java Thread Model: Priorities, Synchronization
Messaging, Life Cycle of Thread, Thread class
Runnable interface, Interthread Communication
Suspending, Resuming and Stopping threads
Multithreading, Synchronization
Scheduling and Priority of Threads
Sockets, Types of Sockets
Working with URLs, Web browsers and Handlers
Text Books:
Java How to Program (How to Program (Deitel), Harvey & Paul, Deitel & Deitel, Prentice Hall,
ISBN-10: 0131483986
Java In A Nutshell, David Flanagan, O'Reilly Media; ISBN-10: 0596007736
Programming With Java A Primer by Balagurusamy, TMH, ISBN: 0074625425
Java 2: The Complete Reference, Herbert Schildt, McGraw-Hill Osborne Media, ISBN-10:
0070495432
Mastering Java 2, J2se 1.4 by Zukowski, BPB Publication, ISBN: 8176566187
Microbial Genomics
Course Objectives: To enable the students to gain knowledge about Microbial Genomics.
Unit-I: Introduction (9L)

History- Bioinformatics and microbial pathogenesis
Bacteriophage Bioinformatics
New methods of gene sequencing
Unit-II: Genome Analysis (9L)

Comparative Microbial Metabolism
Genomic Analysis of Membrane Transport
Analysis of the Bacterial Cell Cycle
Unit-III: Bacterial Biodiversity (9L)

Concepts of Bacterial Biodiversity for the age of Genomics
Coevolution of symbionts and pathogens with their hosts
Unit-IV: Pathogenic Genomes (9L)

Plant pathogen genomes
Parasite genomics
Genomes of pathogenic enterobacteria and thermophiles
Unit-V: Application (9L)

Application of Genomics to Biocatalysis and Biodegradation
Microbial proteomics
Text Books:
Microbial Genomes, Fraser, Claire M, Read, Timothy, Nelson, Karen E., Humana Press, (2004).
Microbial Genome Methods, Kenneth W. Adolph, CRC Press, (1996).
Microbial Functional Genomics, Jizhong Zhou, Wiley-IEEE, (2004).
Microbial Genomics and Drug Discovery, Thomas John Dougherty, Steven J. Projan, CRC Press,
(2003).
Microbial Biodegradation: Genomics and Molecular Biology, Eduardo Diaz, Caister Academic
Press; 1 edition, ISBN:978-1904455172 (2008).
Computing for Comparative Microbial Genomics: Bioinformatics for Microbiologists
(Computational Biology), David W. Ussery, Trudy M. Wassenaar, Stefano Borini,
Springer; 1 edition, ISBN:978-1848002548, (2008).
Functional Microbial Genomics, Volume 33 (Methods in Microbiology), Brendan Wren, Nick
Dorrell, Academic Press; 1 edition, ISBN:978-0125215336, (2002).
Microbial Genomics and Drug Discovery, Thomas J. Dougherty, Steven J. Projan, CRC Press; 1
edition, ISBN:978-0824740412, (2003).
Principle of Drug Action

Course Objectives: To enable the students to gain knowledge about Principle of Drug Action.
Unit-I: Principle of Drug Action (9L)

Basic Principles Drug Action, Drug Interactions
Pharmacodynamics
Pharmacokinetics
Drug Metabolism
Drug Evaluation and Regulation
Introduction to Autonomic Pharmacology
Cholinoceptor-Activating and Cholinesterase-Inhibiting Drugs
Cholinoceptor Blockers and Cholinesterase Regenerators
Sympathomimetics, Adrenoceptor Blockers
Unit-II: Cardiovascular and Bronchodilators (9L)

Cardiovascular Drugs
Drugs Used in Hypertension
Vasocilators & the Treatment of Angina
Drugs Used in Congestive Heart Failure
Antiarrhythmic Drugs
Diuretic Agents
Histamine, Serotonin, and the Ergot Alkaloids
Vasoactive Peptides
Prostaglandins and Eicosanoids
Nitric Oxide, Donors, and Inhibitors
Bronchodilators
Unit-III: CNS (9L)

Drugs That Act in the Central Nervous System
Sedative-Hypnotic Drugs, Alcohols
Antiseizure Drugs
General Anesthetics, Local Anesthetics
Skeletal Muscle Relaxants
Drugs Used in Parkinsonism & Other Movement Disorders
Antipsychotic Drugs & Lithium,
Antidepressants
Opioid Analgesics & Antagonists
Drugs of Abuse
Unit-IV: NSAIDS and Hormones (9L)

Agents Used in Anemia and Hematopoietic Growth Factors
Drugs Used in Coagulation Disorders
Drugs Used in the Treatment of Hyperlipidemias
Nonsteroidal Anti-Inflammatory Drugs
Hypothalamic and Pituitary Hormones
Thyroid and Antithyroid Drugs
Corticosteroids and Antagonists
Gonadal Hormones and Inhibitors
Pancreatic Hormones, Antidiabetic Agents and Hyperglycemic Drugs
Drugs that Affect Bone Mineral Homeostasis
Unit-V: Chemotherapeutic Agents (9L)

Beta-Lactam Antibiotics and Cell Wall Synthesis Inhibitors
Aminoglycosides
Antimycobacterial Drugs, Antifungal Agents
Antiviral Chemotherapy and Prophylaxis
Antiparasitic Chemotherapy, Antiprotozoal Drugs
Anthelmintic Drugs
Cancer Chemotherapy
Immunopharmacology
Vaccines, Immune Globulins, and Complex Biologic Products
Vitamins, Heavy Metals and Chelating Agents
Text Books
Medical Pharmacology at a Glance, Michael J. Neal, ISBN: 978-1-4051-3360-9, John Wiley and
Pharmacology: From Drug Development to Gene Therapy, Robert A. Meyers, ISBN: 978-3-527-
Essentials of Pharmacotherapeutics, Barar FSK, ISBN: 8121904447, S Chand & Company Ltd
Current Trends in Pharmacology, Arunabha Ray and Kavita Gulati, ISBN:8188237779, I.K.
The Textbook of Pharmaceutical Medicine, John P. Griffin, New Age International (P) Ltd.,
Publishers
An Introduction to Drug Design, S.N. Pandeya, ISBN : 978-81-224-0943-7, New Age
International (P) Ltd., Publishers
Medical Pharmacology at a Glance, M.J. Neal, New Age International (P) Ltd., Publishers
Katzung and Trevor's Review of Pharmacology, Anthony Trevor, Bertram Katzung, Susan
Masters, ISBN13: 9780071488693, McGraw-Hill
Modern Pharmacology with Clinical Applications, Charles R Craig and Robert E Stitzel, ISBN-
13: 978-0-7817-3762-3, Lippincott Williams & Wilkins
Lippincott's Illustrated Reviews: Pharmacology, ISBN-10: 0-7817-7155-2, Lippincott Williams
& Wilkins
Molecular Modeling
Course Objectives: To enable the students to gain knowledge about Molecular Modeling.
Unit-I: Introduction Molecular Structure (9L)

Molecules Electronic States and Coordinates patterns
Rotation, Vibration, and Potential Curves of Diatomic Molecules
Spectra of Diatomic Molecules
Molecule Symmetries and Group Theory
Rotation and Vibrations of Polyatomic Molecules
Electronic States of Polyatomic Molecules
Spectra of Polyatomic Molecules
Molecules in External Fields
Van der Waals Molecules and Clusters
Unit-II: Molecular Mechanics (9L)

Electric charges and their properties
The Forces between Molecules
The dipole-dipole interaction
Balls on Springs
Modeling the solvent
Modern Force Fields
The Molecular Potential Energy Surface (PES)
Order Methods
Geometry Optimization
Conformation Searches
Flexible Molecules QSAR
Unit-III: The energy Sharing (9L)

The Boltzmann Probability
A two-level quantum system
Lindemann's Theory of Melting
Statistical Thermodynamics
The Internal Energy Uth
Equation of state and pressure
The Virial of Clausius
Monte Carlo Simulations
MC Simulation of Rigid Molecules
Unit-IV: Molecular Dynamics (9L)

Molecular Dynamics Methodology
Algorithms for time dependence
Introduction to quantum modeling
The Schrödinger equation
Particles in potential wells
Vibrational Motion
The Maxwell Boltzmann distribution of atomic kinetic energies
Fermions and Bosons
The Pauli Exclusion Principle
Unit-V: Quantum modeling (9L)

The orbital model
The LCAO model
The HF-LCAO model
The Unrestricted Hartree Fock (UHF) model
Hückel ã-electron Theory
All Valence Electron ZDO models
CNDO, INDO, MINDO
AM1, PM3, SAM1, ZINDO
The Kohn-Sham LCAO equations
IMOMM, IMOMO, ONIOM
Text Book
Molecular Modelling for Beginners, Alan Hinchliffe, ISBN: 978-0-470-51313-2, John Wiley
and Sons India Pvt. Ltd.
Molecular Physics: Theoretical Principles and Experimental Methods, Wolfgang Demtröder,
ISBN: 978-3-527-40566-4, John Wiley and Sons India Pvt. Ltd.
Biophysical Chemistry -Principles and Techniques, Upadhyay, Upadhyay and Nath, ISBN: 978-
81-8318-865-4, Himalaya Publication House
Perspective In Structural Biology , Vijayan, ISBN:978-81-7371-254-8, Orient Blackswan Private
Limited (University Press)
Fundamental of Crystal Chemistry, Tarren, ISBN:978-81-7371-297-5, Orient Blackswan Private
Limited (University Press)
Electrostatic of Atoms and Molecules, Gadre, ISBN:978-81-7371-296-8, Orient Blackswan
Private Limited (University Press)
Organic Chemistry of Natural Products-I, Gurdeep R. Chatwal, ISBN:81-8318-307-7, Himalaya
Publication House
The Art of Molecular Dynamics Simulation, 2nd Edition, D. C. Rapaport,
ISBN:13:9780521825689, Cambridge University Press India Private Limited
Molecular Reaction Dynamics, Raphael D. Levine, ISBN:9780521842761, Cambridge
University Press India Private Limited
Molecular Structure and Spectroscopy, G. Aruldhas, ISBN:9788120332157, Prentice-Hall of
India
Molecular Spectroscopy, Jeanne L. McHale, ISBN: 9788131720592, Pearson Education
Physical Chemistry, Peter Atkins and Julio De Paula, ISBN: 9780195685220, Oxford University
Press
Computer Aided Drug Design
Course Objectives: To enable the students to gain knowledge about Computer Aided Drug Design.
Total Credits: 2
List of experiments
Representation of Molecular Structures, Molecular Shape Analysis
Chemical Nomenclature and Structure Representation
Virtual Screening, 3DQSAR Models
Molecular Dynamics and Simulation of Lead
Molecular Diversity in Lead Discovery: In Silico Lead Optimization
Databases and Libraries
Combinational Libraries Based on the Concept of Privileged Substructures
Hit-to-Lead Process: A User's Perspective
Text Book
0-471-73779-8, John Wiley & Sons India Pte. Ltd.
Engineering Chemistry, R.V. Gadag and A. Nityananda Shetty, ISBN: 8188237833, I.K.
Quantum Chemistry and Spectroscopy, Engel, ISBN: 9788131712856, Pearson Education
Quantum Chemistry, Ira N. Levine, ISBN: 8120330641, Prentice-Hall of India
An Introduction to Drug Design, S.N. Pandeya, New Age International (P) Ltd., Publishers
Pharmaceutical Organic Chemistry, Rama Rao Nadendla, ISBN: 9781403924957, Macmillan
India Limited
Virtual Screening in Drug Discovery, Juan Alvarez and Brian Shoichet, ISBN-13: 978-
0824754792, CRC Press
Biological Thermodynamics, Donald T. Haynie, ISBN:9780521704045, Cambridge University
Press India Private Limited
Chemoinformatics, Gasteiger, Johann / Engel, Thomas (eds.), ISBN-13: 978-3-527-30681-7,
John Wiley & Sons India Pte. Ltd.
Chemoinformatics in Drug Discovery, Tudor I. Oprea, Raimund Mannhold, Hugo Kubinyi, Gerd
Folkers, ISBN: 978-3-527-30753-1, John Wiley & Sons India Pte. Ltd.
Handbook of Chemoinformatics: From Data to Knowledge, Johann Gasteiger, ISBN: 978-3-527-
An Introduction to Computational Biochemistry, C. Stan Tsai, ISBN: 978-0-471-40120-9, John
Wiley & Sons India Pte. Ltd.
Object oriented Programming (OOPS) JAVA
Course Objectives: To enable the students to gain knowledge about Object oriented Programming
(OOPS) JAVA.
Total Credits: 2
List of experiments
Installing BioJava, Symbols,
Basic Sequence Manipulation (DNA to RNA, Reverse Complement, motif as regular
expression),
Translation (DNA to Protein, Codon to amino acid, Six frame translation),
Proteomics (Calculate the mass and pI of a peptide),
Sequence I/O (File Formats conversions),
Locations and Features (PointLocation, RangeLocation, Feature modifications),
BLAST and FASTA (Blast and FastA Parser, extract information from parsed results), Counts
and Distributions,
Weight Matrices and Dynamic Programming,
User Interfaces
Text Books:
Java How to Program (How to Program (Deitel), Harvey & Paul, Deitel & Deitel, Prentice Hall,
ISBN-10: 0131483986
Java In A Nutshell, David Flanagan, O'Reilly Media; ISBN-10: 0596007736
Programming With Java A Primer by Balagurusamy, TMH, ISBN: 0074625425
Java 2: The Complete Reference, Herbert Schildt, McGraw-Hill Osborne Media, ISBN-10:
0070495432
Mastering Java 2, J2se 1.4 by Zukowski, BPB Publication, ISBN: 8176566187
Laboratory Press
Microbial Genomics
Course Objectives: To enable the students to gain knowledge about Microbial Genomics .
Total Credits: 2
List of experiments
Microbial Bioinformatics
Microbial metabolism
Genomics-Based Analysis of the Bacterial Cell Cycle
Plant pathogens
Comparative Microbial Metabolism
Microbial Genomic Analysis of Membrane Transport
Analysis of the Bacterial Cell
Plant -Microbial interaction
Text Books:
Microbial Genomes, Fraser, Claire M, Read, Timothy, Nelson, Karen E., Humana Press, (2004).
Microbial Genome Methods, Kenneth W. Adolph, CRC Press, (1996).
Microbial Functional Genomics, Jizhong Zhou, Wiley-IEEE, (2004).
Microbial Genomics and Drug Discovery, Thomas John Dougherty, Steven J. Projan, CRC Press,
(2003).
Microbial Biodegradation: Genomics and Molecular Biology, Eduardo Diaz, Caister Academic
Press; 1 edition, ISBN:978-1904455172 (2008).
Computing for Comparative Microbial Genomics: Bioinformatics for Microbiologists
(Computational Biology), David W. Ussery, Trudy M. Wassenaar, Stefano Borini,
Springer; 1 edition, ISBN:978-1848002548, (2008).
Functional Microbial Genomics, Volume 33 (Methods in Microbiology), Brendan Wren, Nick
Dorrell, Academic Press; 1 edition, ISBN:978-0125215336, (2002).
Microbial Genomics and Drug Discovery, Thomas J. Dougherty, Steven J. Projan, CRC Press; 1
edition, ISBN:978-0824740412, (2003).
Perl for Bioinformatics
Course Objectives: To enable the students to gain knowledge about Perl for Bioinformatics.
Total Credits: 2
List of experiments
Installing Perl on Your Computer
Text Editors, Individual Approaches to Programming
Sequences and Strings, Representing Sequence Data
A Program to Store a DNA Sequence
Concatenating DNA Fragments
Transcription: DNA to RNA
Using the Perl Documentation
Calculating the Reverse Complement in Perl
Proteins, Files, and Arrays
Reading Proteins in Files
Motifs and Loops, Finding Motifs
Counting Nucleotides
Exploding Strings into Arrays
Command-Line Arguments and Arrays
Mutations and Randomization
Program Using Randomization
Program to Simulate DNA Mutation, Generating Random DNA
Data Structures and Algorithms for Biology
Translating DNA into Proteins
Reading DNA from Files in FASTA Format
Restriction Maps and Restriction Enzymes
GenBank Files
Parsing PDB Files
Obtaining BLAST
String Matching and Homology, Web Programming
Algorithms and Sequence Alignment
Microarrays and XML
Graphics Programming
Text Books:
Perl Programming for Bioinformatics & Biologists, Lab Manual D. Curtis Jamison, John Wiley
& Sons, INC., 2004.
Perl Programming for Bioinformatics, Harshawardhan P Bal, Tata McGraw Hill, 2003.
James Tisdall, Mastering Perl for Bioinformatics, O’Reilly, 2003.
Perl Programming for Bioinformatics & Biologists, D. Curtis Jamison, John Wiley & Sons,
INC., 2004.
Bioinformatics Biocomputing and Perl, Michael Moorhouse, Paul Barry, Wiley, 2004.
University
Nanded
Sub Centre, Latur
Syllabus For the

Semester -IV
Plant Genomics
Course Objectives: To enable the students to gain knowledge about Plant Genomics
Unit-I: Plant Genome Databases (9L)

Nucleotide database- NCBI (GenBank), DDBJ, EMBL,
Protein structure Databank - PDB,
Search Engine - SRS, Entrez
Enzyme databases- BRENDA, , KEGG
Protein database - TrEMBL, UniProt, PIR
Index to Plant Chromosome Numbers database - IPCN
Unit-II: The Arabidopsis Genome Project (9L)

History of Plant, Arabidopsis Genome study, Entrez Records, Phylogenetic relationship, Model
Plant Arabidopsis Thaliana, TAIR, TIGR
Cytogenetics - A cytogenetic resource of FISH-mapped, sequence-tagged clones;
dbSNP- Database of SNPs and other genetic variation;
Entrez- Gene Focal point for genes and associated information;
RefSeq - Reference Sequence collection: genomic DNA, transcripts, and proteins;
UniGene -Non-redundant gene-oriented clusters;
UniSTS- STS markers;
Protein coding gene
Repeat Sequences- RNA
Advantages as a model organism
Unit-III: Genome organization and evolution (9L)

Plant genomics and Proteomics
Transmission of genetic information – Mapping, High resolution maps, Horizontal gene transfer
Genome Analysis
Eukaryotic Genome- Arabidopsis, Soybean, Mungbean, Rice, Cotton, Withania, Maize,
Plant viruses study – Coat protein study, TMV, PMV, PAMV
Unit-IV: Protein function and biochemical pathways (9L)

BRITE- Biomolecular Relations in Information Transmission and Expression
EcoCyc/MetaCyc- Encyclopedia of E. coli genes and metabolism; Metabolic encyclopedia
EMP- Metabolic pathways
KEGG -Kyoto encyclopedia of genes and genomes
Biochemical Pathways -Enzyme database and link to biochemical pathway map
Metabolic Pathway- Metabolic pathways of biochemistry
aMAZE- Protein function and biochemical pathways project at EBI
PathDB- Metabolic pathway information
Secondary metabolites,
Pathway analysis,
Phytochemicals
Unit-V: Application of Plant Genomics (9L)
Transgenic Plants
Metabolomics
Functional genomics- Arabidopsis thaliana
Metabolic profiling and fingerprinting
New drug developments
Phylogenetic analysis
Gene expression analysis
Microarray techniques
Text Books:
Plant Biotechnology: Green Revolution, Virendra Gomase and Anant Sherkhane, VDM Verlag
Dr. Müller, Germany, ISBN:978-3-639-03208-6, (2010).
Encyclopedia of Agricultural Sciences (5 Vol. Set), Virendra Gomase, Shruti Gomase, Serial
Publication, India, ISBN:978-8-183-87339-0, (2010).
Toxicogenomics, Virendra Gomase and Shruti Gomase, VDM Verlag Dr. Müller, Germany,
ISBN:978-3639249958, (2010).
Plant Genomics: Methods and Protocols (Methods in Molecular Biology), Daryl J. Somers, Peter
Langridge, J.P. Gustafson, Humana Press; 1 edition, ISBN-13: 978-1588299970, (2009).
Principles and Practices of Plant Genomics, Volume 3: Advanced Genomics, Chittaranjan Kole,
Albert G. Abbott, Science Publishers; 1 edition, ISBN-13: 978-1578086832, (2010).
Plant Stress Biology: From Genomics to Systems Biology, Heribert Hirt, Wiley-VCH, ISBN-13:
978-3527322909, (2009).
Genetics and Genomics of Soybean (Plant Genetics and Genomics: Crops and Models), Gary
Stacey, B. Goldberg, Springer; 1 edition, ISBN-13: 978-0387722986, (2008).
Plant Pathogenic Bacteria: Genomics and Molecular Biology, Robert W. Jackson, Caister
Academic Press; illustrated edition edition, ISBN-13: 978-1904455370, (2009).
Metabolomics and Metabolic Engineering
Course Objectives: To enable the students to gain knowledge about metabolomics and the
metabolic engineering in post genomic era.
Unit-I: Introduction to Metabolomics (9L)

Overview of Metabolomics
Metabolomics in Arabidopsis thaliana
Metabolic pathway databases
EcoCyc, MetaCyc, LIGAND, ENZYME, BRENDA, KEGG
Unit-II: Metabolome Informatics (9L)

Introduction to the ARM Database
The Genome-Based E-CELL Modeling (GEM) System
Large-Scale Simulation of Metabolism
Metabolomics and Medical Sciences
Unit-III: Introduction to Metabolic Engineering (9L)

Importance of metabolic engineering
Comprehensive models for cellular reactions
Material balances & Data Consistency
Metabolic pathway synthesis
Metabolic pathway and disease interaction
Secondary metabolites and new drug approach
System Biology approach
Network Engineering
Unit-IV: Metabolic Flux Analysis and its Application (9L)

Theory-determination of flux by isotope labeling
Metabolic control analysis
Control coefficients and summation theorems, FCC determination
Grouping of reactions, gFCC, identification of independent pathways
Unit-V: Flux Analysis of Metabolic Networks (9L)

Bottom up and Top down approaches
Case study-optimization of flux amplification
Consistency tests and experiment validation
Supervised and unsupervised approach
Machine learning techniques
Cluster analysis for pathways
Textbooks:
ISBN:978-3-639-24991-0, (2010).
Metabolomics- The Frontier of Systems Biology, M. Tomita, T. Nishioka, Springer Publications,
(2003).
Metabolic Engineering- Principles and Methodologies, Gregory N. Stephanopoulos, Academic
press, First Edition, (1998).
An Introduction to Metabolic and Cellular Engineering, S. Cortassa, World scientific public
company Ltd., (2002).
Metabolomics: Methods And Protocols, Wolfram Weckwerth, Humana Press, (2007).
Oncogenomics and Cell Signaling
Course Objectives: To enable the students to gain knowledge about Oncogenomics and Cell
Signaling.
Unit- I: Introduction to Oncology and Chemotherapy (9L)

Cancer: Terminology and classification
Introduction to anti-cancer drugs
Side effects of chemotherapy and radiotherapy
New developments in cancer therapy
Introduction to: Breast, lung, upper GI, colorectal, ovarian, prostate and skin cancers
Clinical trial issues in oncology
Unit- II: Oncogenomics (9L)

Basic Cancer Genetics
Protooncogene and Viral Oncogene, Tumor Suppressor Genes
Genome-wide Search for Mutations in Human Cancers
Expression Profiling and Model System of Cancer
Identification and validation of oncogenes
Molecularly Targeted Drugs
Comparative Oncogenomics, and functional genomics
Development, Progression, Conceptual & Clinical implications of melanoma
Unit- II: Current Cancer Targets (9L)

Implications for viral therapy of cancer
Toxicokinetics, Nanomedicines
Molecular Approaches to Cancer, Molecular Profiling in Cancer
Hereditary Cancers and Model Systems
Review of Basic Cancer Genetics and Molecularly Targeted Drugs
Array based genomic hybridization
NCI-60 and Tissue Analysis in Cancer
Proteomics and Model Systems in Cancer
Current Cancer Drug Targets
Genetic Engineering – A New Era for Cancer Immunotherapy
Epigenomics
Unit- III: Monitor signaling activity in cells (9L)

Basics of Signaling Pathways
Signaling by Nuclear Receptors
G-Protein Coupled Signal Transmission Pathways
Secondary Messengers
Serine Threonine Protein Kinases and Protein phosphatase
Tyrosine Specific Protein Kinases
Signal Transmission via Ras Proteins
Unit- III: Signaling Pathways (9L)
IntraCellular Signal Transduction
MAP Kinase Pathways
Membrane Receptors with Associated Tyrosine Kinase activity
Malfunctioning of Signaling Pathways and Tumorigenesis
Ion Channels and Signal Transduction
Biomarkers
Stem Cell & Development
Toxicology & Drug ADME
Text Book
Oncogenomics: Molecular Approaches to Cancer, Charles Brenner and David Duggan, ISBN:
978-0-471-22592-8, John Wiley & Sons India Pte. Ltd.
Biomarkers, Virendra Gomase and Shruti Gomase, VDM Verlag Dr. Müller, Germany,
ISBN:978-3639170306, (2010).
Transcriptomics: Expression Pattern Analysis, Virendra Gomase and Somnath Tagore, VDM
Verlag Dr. Müller, Germany, ISBN:978-3639214864, (2009).
ISBN:978-3639249958, (2010).
Molecular Genetics Of Cancer, C.B. Powar, ISBN-81-7866-680-4, Himalaya Publication House
Structure and Function in Cell Signalling, John Nelson, ISBN: 978-0-470-02551-2, John Wiley
& Sons India Pte. Ltd.
Cell Signalling, C.B. Powar, ISBN-81-8318-365-4, Himalaya Publication House
Cell Signalling, John Hancock, ISBN : 0199264678, I.K. International Publishing House Pvt. Ltd
The Biochemistry of Cell Signaling, Ernst J.M. Helmreich, ISBN:9780195673845, Oxford
University Press
Molecular And Cellular Physiology Of Neurons, Fain Gordon L., ISBN :81-203-2734-9,
Prentice-Hall of India
Cancer Bioinformatics: From Therapy Design to Treatment, Sylvia Nagl, ISBN: 978-0-470-
Lung Cancer, Sujal Desai, ISBN: 9780521872027, Cambridge University Press India Private
Limited
IPR and Industrial Psychology
Course Objectives: To enable the students to gain knowledge about IPR and Industrial Psychology.
Unit- I: Intellectual Property Protection (9L)

Overview of Intellectual Property Law
The Use of Intellectual Property in Business
How to Read and Obtain Information from a Modern Patent
Introduction to Patents
Patentable Subject Matter and Utility
Novelty of the Invention
Requirement of Non-Obviousness for Patentability
The Patenting Process
Claims, Patent Application and Prosecution
Unit- II: Patentability and Inventions (9L)

Protection of Computer-Related Inventions
Patentability of Biotechnology Inventions
Business Method Protection
Foreign Patent Protection
Enforcement of the Patent Right
Ownership and Transfer of Patent Rights
The Engineer and Scientist as Expert Witness; and Ethics
Copyrights as a Vehicle for Technology Protection
Mask Work Protection
Trade Secrets, Trademarks
Unit- III: The Practice of Industrial-Organizational Psychology (9L)

Principles, Practices, and Problems
Techniques, Tools, and Tactics
The Development of Human Resources
Employee Selection Principles and Techniques
Psychological Testing
Performance Appraisal
Raining and Development
Unit- IV: Organizational Psychology (9L)

Research Methods
Attraction and socialization
Productive behaviour or organisation
Job satisfaction and organisational commitment
Counterproductive behaviour in organizations
Occupational Stress
Theories of motivation
Engineering Psychology
Consumer Psychology
Unit- V: Psychology and Leadership Traits (9L)

Leadership and Influence processes
Group behaviour
Organisational Culture
Interpersonal Skills - Delegation, Humour,
Trust, Expectations, Value, Status and Compatibility
Positive Thinking - Attitudes and Beliefs
Positive Thinking Martin Seligman’s Theory of Learned Helplessness
Positive Thinking- Martin Seligman’s Theory of Learned Optimism
Psychology and Leadership Traits
Text Book
High Performance Leadership, Dr. G. Vijayaragavan, ISBN-978-81-8318-901-9, Himalaya
Publication House
Intellectual Property Law for Engineers and Scientists, Howard B. Rockman, ISBN: 978-0-471-
Organisational Psychology, Steve M. Jex, ISBN:9812532307, John Wiley & Sons India Pte. Ltd.
Industrial and Organizational Psychology: Linking Theory with Practice, Cary L. Cooper, ISBN:
978-0-631-20992-8, John Wiley & Sons India Pte. Ltd.
Business Ethics, C.S.V. Murthy, ISBN-81-8318-148-1, Himalaya Publication House
Business Law For Management, P. Saravanavel & S. Sumathi, ISBN-81-8318-069-8, Himalaya
Publication House
Managing Intellectual Property, Vinod V. Sople, ISBN :81-203-3061-7, Prentice-Hall of India
Psychology, Baron Robert A., ISBN :978-81-203-2335-3, Prentice-Hall of India
Organizational Behavior 1: Essential Theories Of Motivation And Leadership, Miner John B.,
ISBN :81-203-2951-1, Prentice-Hall of India
Project
Course Objectives: Project carried out for the partial fulfillment of the M.Sc.Bioinformatics.
Total Credits: 8
Area for the projects
Sequence Analysis
Evolution and Phylogeny
Genomic
Proteomics
Metabolomics: NMR base genetic diversity
Immunogenomics: recent discoveries
Machine intelligence
Phosphoproteomics
Immunoinformatics and its role in microbes and vaccines
Cellunomics: the interaction analysis of cells
Phylogenomics: evolution and genomics intersection
microRNA: human disease and development
Interactomics: Chemical interaction analysis
Pathogenomics
RNomics: functional RNA analysis
Immunoproteomics
Phospho-onco-proteomics
Nutrigenomics
Fluxomics
Glycomics
Lipidomics
Vaccinomics
Transgenomics
Oncogenomics
Pharmacogenomics
Proteomics: Technologies for Protein Analysis
Microarray: An Approach for Current Drug Targets
Epigenomics
Transcriptomics
Toxicogenomics
Kinomics
Physiomics
Cytomics
Metabolomics
Metabolic Pathways
Networks and Systems Biology
Structural Bio-informatics
Neuro-informatics Bio-Ontologies
Biomedical Text Mining
Biological Data Modeling and Integration
LIMS, SIMS and Other Tools to Support Experimental Biology
Applications of Bio-informatics to Biomedicine
Agriculture and Drug Discovery
Information Technology
Computer application in Bioinformatics, Pharmacoinformatics
Databases and Software tools for analysis
Life Sciences Application
Drug Design and Discovery
Computational Neurosciences
Medical Informatics
New Trends in Computer Technology
Plant Genomics
Course Objectives: To enable the students to gain knowledge about Plant Genomics
Total Credits: 2
List of Experiments:
Plant Genome organization and evolution
Plant Functional genomics
Plant Transgenomics approach
Plant Metabolomics
Plant Comparative genomics
Molecular modeling & Docking
Plant Micro array data analysis
Plant Primer design
Phylogenetic analysis
Molecular Evolution
Metabolic pathways analysis
Text Books:
Plant Biotechnology: Green Revolution, Virendra Gomase and Anant Sherkhane, VDM Verlag
Dr. Müller, Germany, ISBN:978-3-639-03208-6, (2010).
Encyclopedia of Agricultural Sciences (5 Vol. Set), Virendra Gomase, Shruti Gomase, Serial
Publication, India, ISBN:978-8-183-87339-0, (2010).
ISBN:978-3639249958, (2010).
Plant Genomics: Methods and Protocols (Methods in Molecular Biology), Daryl J. Somers, Peter
Langridge, J.P. Gustafson, Humana Press; 1 edition, ISBN-13: 978-1588299970, (2009).
Principles and Practices of Plant Genomics, Volume 3: Advanced Genomics, Chittaranjan Kole,
Albert G. Abbott, Science Publishers; 1 edition, ISBN-13: 978-1578086832, (2010).
Plant Stress Biology: From Genomics to Systems Biology, Heribert Hirt, Wiley-VCH, ISBN-13:
978-3527322909, (2009).
Genetics and Genomics of Soybean (Plant Genetics and Genomics: Crops and Models), Gary
Stacey, B. Goldberg, Springer; 1 edition, ISBN-13: 978-0387722986, (2008).
Plant Pathogenic Bacteria: Genomics and Molecular Biology, Robert W. Jackson, Caister
Academic Press; illustrated edition edition, ISBN-13: 978-1904455370, (2009).
Metabolomics and Metabolic Engineering
Course Objectives: To enable the students to gain knowledge about Metabolomics and
Metabolic Engineering
Total Credits: 2
List of Experiments:
Metabolic engineering
Comprehensive models cellular reactions
Metabolic flux analysis and its applications
Metabolome and its study
Applications of metabolomics
Molecular Evolution
Metabolic pathways analysis
System Biology approach
Network Engineering
Metabolic pathway and disease interaction
Supervised and unsupervised approach
Machine learning techniques
Cluster analysis for pathways
Textbooks:
ISBN:978-3-639-24991-0, (2010).
Metabolomics- The Frontier of Systems Biology, M. Tomita, T. Nishioka, Springer Publications,
(2003).
Metabolic Engineering- Principles and Methodologies, Gregory N. Stephanopoulos, Academic
press, First Edition, (1998).
An Introduction to Metabolic and Cellular Engineering, S. Cortassa, World scientific public
company Ltd., (2002).
Metabolomics: Methods And Protocols, Wolfram Weckwerth, Humana Press, (2007).

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Swami Ramanand Teerth Marathwada

Syllabus For the

Academic Year 2010-11

Eligibility and Fees

Master Degree would be of 112 Credits each

Internal Exam External Exam

Break up internal exam marks for Theory

Theory Test-1 Theory Test-2 Home Assignments Total Marks

15 marks 15 marks 20 marks 50 Marks = 2 Credits

Practical Course = 50 Marks

Internal Exam External Exam

Break up internal exam marks for Practical

Practical Test-1 Practical Test-2 Total Marks

10 marks 15 marks 25 Marks = 1 Credit

Internal Exam External Exam

Break up internal exam marks for Project

BIM-101 (T) Genetics and Molecular 2 2 4

BIM-102 (T) Bioinformatics 2 2 4

BIM-105 (T) Linux 2 2 4

BIM-102 (P) Bioinformatics 1 1 2

BIM-105 (P) Linux 1 1 2

Total Credits in I Semester = 28

BIM-201 (T) Advanced Molecular Biology 2 2 4

BIM-202 (T) Computational Biology 2 2 4

BIM-203 (P) Immunoinformatics 1 1 2

BIM-206 (P) Numerical Methods and 1 1 2

Total Credits in II Semester = 28

BIM-301 (T) Computer Aided Drug Design 2 2 4

BIM-303 (T) Microbial Genomics 2 2 4

BIM-301 (P) Computer Aided Drug design 1 1 2

BIM-303 (P) Microbial Genomics 1 1 2

Total Credits in III Semester = 28

BIM-401 (T) Plant Genomics 2 2 4

BIM-403 (T) Oncogenomics and Cell 2 2 4

BIM-404 (T) IPR and Industrial Psychology 2 2 4

BIM-401 (P) Plant Genomics 1 1 2

Total Credits in IV Semester = 28

Syllabus For the

Total: 45L Total Credits: 4

Unit -I: Structure of Nucleic Acid (9L)

Unit -II: DNA Replication and Mutation (9L)

Unit -III: Gene Expression and Regulation (9L)

Unit -IV: Mendelian Genetics (9L)

Unit -V: Crossing Over and Linkage (9L)

Total: 45L Total Credits: 4

Unit -I: Biological Database Design and Management (9L)

Unit -II: Genomics Database (9L)

Unit -III: Biological Databanks (9L)

Unit -IV: Bioinformatics database & repositories (9L)

Unit -V: Genome Analysis (9L)

Total: 45L Total Credits: 4

Unit -I: Introduction (9L)

Unit -II: Statistical Sampling (9L)

Unit -III: Statistical Analysis (9L)

Unit -IV: Experimental design and trials (9L)

Unit -V: Bioassays-calculations (9L)

Total: 45L Total Credits: 4

Unit -I: Basic concepts (9L)

Unit -II: Relational model, languages & systems (9L)

Unit -III: Data Structure (9L)

Unit -IV: Relational data base design (9L)

Unit -V: Concurrency control & recovery techniques (9L)

Total: 45L Total Credits: 4