DR. A.P.J.

ABDUL KALAM TECHNICAL UNIVERSITY,

UTTAR PRADESH, LUCKNOW

EVALUATION SCHEME & SYLLABUS

FOR
B.TECH. HONORS DEGREE
IN

Computational Biology and Bioinformatics

Eligible Branches: BIOTECHNOLOGY

As per NEP 2020

[Effective from the Session: 2023-24]

Curriculum & Evaluation Scheme BT (B.TECH. HONORS DEGREE)

HONORS DEGREE in Computational Biology and Bioinformatics
Eligible Branches: BIOTECHNOLOGY
EVALUATION SCHEME
(Effective from the Session: 2023-24)

Examination

Examination
Theory End

Practical
Sessional

Semester

Semester
Practical
Semester

Theory Sessional

End

Credits
Sl. No.

Periods

Total
Subject (TS)
Subject
Codes

L T P CT TA CT+TA PS TE PE
BIOLOGICAL
1 IV HTCB401 3 1 0 30 20 50 100 150 4
DATA MINING
MACHINE
2 V HTCB501 LEARNING IN 3 1 0 30 20 50 100 150 4
BIOINFORMATICS
MEDICAL
3 VI HTCB601 3 1 0 30 20 50 100 150 4
INFORMATICS
*NGS
HTCB701 TECHNOLOGY &
DATA ANALYSIS
*BIOINFORMATIC
S : ALGORITHMS
AND
HTCB702 APPLICATIONS
4 VII 3 1 0 30 20 50 100 150 4
(NPTEL)
https://nptel.ac.in/cou
rses/102106065
*STRUCTURAL
BIOLOGY (NPTEL)
HTCB703 https://nptel.ac.in/cou
rses/102107086
*AI IN DRUG
HTCB801
DISCOVERY
*COMPUTATIONA
L CHEMISTRY
AND CLASSICAL
MOLECULAR
HTCB802
DYNAMICS(NPTEL
5 VIII ) 3 1 0 30 20 50 100 150 4
https://nptel.ac.in/cou
rses/104101095
*COMPUTATIONA
L SYSTEMS
HTCB803 BIOLOGY (NPTEL)
https://nptel.ac.in/cou
rses/102106068
Total 750 20

* Elective subject: Chose any one at serial no 4 and anyone at serial no 5.

 Syllabus
HTCB401 BIOLOGICAL DATA MINING

Course Description
Outcome At the end of the course, the student will be able to
CO1 Study about construction of data warehouse, multidimensional data modeling, OLAP &
OLTP technologies.
CO2 Understand concepts of data mining and KDD process and various mining tasks.
CO3 Apply mining association rules in large databases.
CO4 Understand and apply classification & prediction methods.

CO5 Understand and apply clustering methods.

Detailed Syllabus (Theory)
Unit No. Topics CO No. of
No. proposed
lectures
I Data Warehousing: Components of Data warehousing; Need, 1 8
Building and Interpretation of data warehouse, Data Mart, Multi
Dimensional Data Model and related schemas, Data warehouse and
OLAP technology, Online Analytical Processing (OLAP) - OLAP Vs
OLTP, different OLAP operations.

II Data Mining: Basic concept, Data Collection, Types of data, KDD 2 8

process, Data preprocessing, Outlier detection, Data integration, Data
transformation, Data reduction, Data generation, Data summarization,
Data presentation, Data Mining functionalities, Classification and
architecture of data mining systems, Data Mining query language,
Data mining task primitives, Integration of a data mining system with
a data warehouse.

III Mining Association Rules in large databases: Association rule 3 8

mining, Mining methods, Mining Multi Level Association Rule
Mining, Multi Dimensional Association Rule, Mining Correlation
analysis, Constraint based association mining, multidimensional
association rules from relational DBS and DWS, Correlation analysis,
Constraint based association mining, Mining frequent patterns,
Mining various kinds of association rules.

IV Classification and Prediction: Classification methods: Decision tree 4 8

induction, Artificial neural network, Baye’s Theorem, Bayesian
classification and Bayesian Belief Network, Support vector machines,
rule based classification, association based classification. Prediction:
Linear & Non Linear Regression, Issues Regarding Classification and
Prediction.
 V Clustering: Cluster analysis, Types of clustering, partitioning method, 5 8
hierarchical method, k means method, self optimization method,
density based methods, grid based methods, text mining, web mining,
temporal and spatial data mining.

Text Books:
1. Data Mining Concepts & Techniques by Jiawei Han & Micheline Kamber; Harcourt India Pvt Ltd.
2. Data warehousing by S . Anahory and D.Murray, Pearson Education, ASIA.
3. Data Mining Techniques by A.K. Pujari , University Press.
Reference Books:
1. Building Data Ware House by W.H.Inmon, John Wiley & Sons.
2. Data Ware Housing with oracle by SimaYazdanri&Shirky S. Wong.
3. Data Mining, Practical Machine Cearing tools & techniques with Java by I.H. Whiffen.
HTCB501 MACHINE LEARNING IN BIOINFORMATICS

Course Description
Outcome At the end of the course, the student will be able to
CO1 Understand various protein structure prediction methods, next generation sequencing, microarray
data analysis and relation methods to understand the application of machine learning methods.
CO2 Understand different types of machine learning methods and their utility in bioinformatics.
CO3 Apply basic concepts of molecular modelling and simulation.
CO4 Explore concepts behind document data management, document clustering and natural language
processing.
CO5 Implement different methods of drug designing and use of various machine learning tools.
Detailed Syllabus (Theory)
Unit No. Topics CO No. of
No. proposed
lectures
I Protein Structure prediction (Secondary and Tertiary), Genomic sequence 1 8
annotation, Protein function prediction, Next generation sequencing,
Gene expression analysis, Microarray data analysis, Data mining,
Biological network identification and gene regulation.
II Machine learning – concepts of supervised and unsupervised learning, 2 8
Classification: Decision tree induction, Artificial Neural Networks,
Hidden Markov Models, Genetic Algorithms, Support vector machines;
Clustering: Hierarchical and K-mean; The relation between statistics and
machine learning; Evaluation and validation methods.
III Molecular Modeling, Basic concept of Force field; Simulation: concepts 3 8
and computer simulation techniques, types of computer simulation
(Continuous, Discrete-event and Hybrid simulation).
IV Overview of key techniques for the management of large document 4 8
collections and the biological literature: Document clustering,
Information retrieval system; Natural Language Processing: Introduction,
Major areas of NLP, Natural language information extraction.
V Computer aided drug designing – concepts, major steps in Drug 5 8
Designing, Ligand and Structure based drug designing, Lipinski’s rule of
five, Protein ligand docking, QSAR Modeling, Pharmacodynamics,
Pharmacokinetics & Pharmacogenomics.
Text Books:
1. Arthur M.Lesk, Introduction to bioinformatics, Oxford University Press.
2. S.C. Rastogi & others, Bioinformatics- Concepts, Skills, and Applications, CBS Publishing.
3. R. Durbin, S. Eddy, A. Krogh, and G. Mitchison, Biological Sequence Analysis:Probabilistic Models of Proteins and
Nucleic Acids. Cambridge University Press
4. P Baldiand S Brunak, BIOINFORMATICS: The Machine Learning Approach
Reference Books:
1. Olson et al., 2018. Data-driven advice for applying machine learning to bioinformatics problems
2. Stephen Misner& Stephen Kraeetz; Bioinformatics- Methods and protocols, Humana press.
3.Andreas D Baxevanis& B F Francis, Bioinformatics- A practical guide to analysis of Genes & Proteins, John Wiley.
HTCB601 MEDICAL INFORMATICS

Course Description
Outcome At the end of the course, the student will be able to
CO1 Understand the concepts of medical informatics.
CO2 Understand various methods under artificial intelligence and expert systems.
CO3 Apply the structuring of hospital management using information systems.
CO4 Explore of computer based medical techniques.

CO5 Implement communication-based systems.

Detailed Syllabus (Theory)
Unit No. Topics CO No. of
No. proposed
lectures
I Introduction: Introduction to medical informatics, Information system 1 8
and management of Hospital, their requirements and related functional
areas, integrated hospital information systems, health information
system and disaster management plan.
II Knowledge Based And Expert Systems: Study various methods under 2 8
Artificial intelligence and expert systems with their applications in this
field, managing computer based patient records, studying computer
assisted medical education.
III Modules: Structuring Hospital Management using Information systems 3 8
and functions, computer assisted patient education and computer
assisted patient surgery.

IV Assisted Medical Techniques: Concept, Instrument and process of 4 8

three-dimensional imaging with its limitations, virtual endoscopy
methods and its limitations, applications, merits and demerits and other
surgical techniques.

V Communications Based Systems: Need, Use and methods, 5 8

Telemedicines, Internet telemedicines, Telesurgery, Applications.

Text Books:
1. Mohan Bansal, Medical Informatics- a primer, Tata McGraw-Hill.
2. De Dombal. F. T., Medical Informatics: The Essentials, Butterworth- Heinemann.

Reference Books:
1. Charles P. Friedman, Jeremy C. (EDT) Wyatt, Evaluation Methods in Medical Informatics- Springer Verlag
2.Hsinnchun Chen, Medical Informatics: Knowledge Management And Data Mining in Biomedicine, Springer.
HTCB701 NGS TECHNOLOGY AND DATA ANALYSIS
Course Description
Outcome At the end of the course, the student will be able to
CO1 Understand basic concepts of DNA sequencing and NGS technology.
CO2 Understand the methods of DNA sequencing and NGS technology.
CO3 Explain the process of RNA sequencing.
CO4 Understand concepts of ChiPSeq.

CO5 Analyze differentially expressed data and NGS applications.

Detailed Syllabus (Theory)
Unit No. Topics CO No. of
No. proposed
lectures
I Introduction: High throughput sequencing, Basic concept and 1 8
applications of NGS technology, Various methods NGS technology,
Recent advancements using NGS technology, Data types, Data
formats ,Data processing, Data analysis, Data evaluation, Data
visualization. Genome sequencing and Protein sequencing. Genetic
variations and genetics of complex disease. Non-synonymous and
Synonymous variants, Regulatory variants and Statistical methods on
rare variants.
II DNA Sequencing : Whole genome sequencing, Sanger sequencing, 2 8
Maxam Gilbert sequencing, Target sequencing, Pool sequencing,
Sequencing mappability, Refined alignment, Base quality
recalibration ,Variants identification for Diploid genome, Next
generation sequencing technologies (Illumina (Solexa), Ion Torrent,
Roche 454, SOLiD and Pac Bio) Short read assembly, alignment and
applications; gene expression analysis.

III RNA Sequencing: Biological theories on RNA seq experiments, Case 3 8

studies for experimental consideration, Scientific advancements
using RNA seq, Differential expression analysis, Alternative
splicing, Transcript variation, Allele-specific expression ,RNA
editing and smRNA.

IV ChiPSeq: Biological theories on ChIPseq analysis, Case studies for 4 8

experimental considerations, DNA fragment evaluation, Peak
identification, Two condition comparison, Saturation analysis, Motif
finding and related theories, DNA methylation, Case studies for
statistical considerations, Related Bioinformatics tools, Histone
modification and Hidden Markov model annotating histone marks.

V Analysis: Using RNA seq, Data to Detect Differentially Expressed 5 8

Genes, Differential Expression Analysis of Complex RNA seq
Experiments Using edger, Design of RNA Sequencing Experiments,
small RNA sequencing. Functional PCA differential expression
testing using RNA seq data. Statistical Analysis study of Rare
Variants. NGS applications in Agri-Biotech, health care,
metagenomics, GWAS and basic sciences.
Text Books:
1. Somnath Datta,Nettleton Dan (Eds.)Statistical Analysis of Next Generation Sequencing Data.
2. Stuart M. Brown. Next-Generation DNA Sequencing Informatics.

Reference Books:
1. Ali Masoudi-Nejad, Zahra Narimani, NazaninHosseinkhan. Next Generation Sequencing and Sequence
Assembly.
2. Methodologies and Algorithms (SpringerBriefs in Systems Biology), ISBN-10: 1461477255, Springer.
HTCB801 AI IN DRUG DISCOVERY
Course Description
Outcome At the end of the course, the student will be able to
CO1 Understand AI Fundamentals in Drug Discovery
CO2 Analyze Biological Data for Drug Target Identification
CO3 Implement Predictive Models for Drug Activity
CO4 Integrate Data Sources for Comprehensive Drug Discovery

CO5 Explain Ethical and Regulatory Considerations in AI for Drug Discovery

Detailed Syllabus (Theory)
Unit No. Topics CO No. of
No. proposed
lectures
I Overview of Drug Discovery: Drug development process, Importance 1 8
of target identification and validation; Fundamentals of Artificial
Intelligence: Introduction to AI and Machine Learning, Supervised
and Unsupervised Learning, Deep Learning and Neural Networks;
Applications of AI in Drug Discovery: Target identification using AI,
Predictive modelling in drug discovery, High-throughput screening
and virtual screening.
II Basics of Molecular Biology: DNA, RNA, and protein structures, 2 8
Cellular processes and pathways; Bioinformatics Tools in Drug
Discovery: Sequence analysis, Structure prediction, Data mining for
drug targets.

III Computational Chemistry Techniques: Molecular dynamics 3 8

simulations, Quantum mechanics in drug design; Chemo-informatics
Approaches: Chemical databases and their use, Ligand-based and
structure-based drug design.

IV Feature Engineering and Data Preprocessing: Handling biological and 4 8

chemical data, Feature selection and extraction; Predictive Modelling:
Regression and classification models, Model evaluation and
validation; Deep Learning in Drug Discovery: Convolutional Neural
Networks (CNNs) for molecular structures, Recurrent Neural
Networks (RNNs) for biological sequences.
V Successful Case Studies: Examples of drugs developed using AI, 5 8
Impact on pharmaceutical industry; Ethical and Regulatory
Considerations: Ethical issues in AI-based drug discovery, Regulatory
challenges and guidelines; Future Trends and Emerging
Technologies: Role of AI in personalized medicine, Integration of
multi-omics data in drug discovery.
Text Books:
1. Artificial Intelligence in Drug Discovery by Martin F. O'Donnell.
2. Computational Drug Discovery and Design by Tudor I. Oprea.
3. Artificial Intelligence for Drug Discovery by Mark Johnson.
4. Machine Learning in Drug Discovery and Development by Richard S. Segall.
Reference Books:
1.Bioinformatics for Beginners: Genes, Genomes, Molecular Evolution, Databases and Analytical Tools by
SupratimChoudhuri.
2.Artificial Intelligence in Drug Discovery by Patrick Walters.
3.Computational Drug Discovery and Design" by D. C. Young.