Computational Molecular Biology and Bioinformatics - Fall 2025

MTech (CS) : 2nd Year, 1st Semester

GENERAL INFORMATION

LECTURE DETAILS

Topic Lecture Date Lecture Topics Notes Resources
0 1-2 22-07-2025 A Little Bit of Biology Slides [PDF] [R1, R2, R5, R6]
I 3-4 25-07-2025 Alignment of Sequences Slides [PDF] [R1, R2, R3, R4]
... 5-6 29-07-2025 ... ...
II 7-8 01-08-2025 X-Mapper Slides [PDF] Gaston et al., Genome Biology, 26:15, 2025 [Link]
... 9-10 08-08-2025 ... ...
III 11-12 12-08-2025 MetaGraph Slides [PDF] Karasikov et al., Nature, In press, 2025 [Link]
IV 13-14 22-08-2025 DLVPM Slides [PDF] Ing et al., Nature Machine Intelligence, 7:1053-1075, 2025 [Link]
... 15-16 26-08-2025 ... ...
V 17-18 29-08-2025 CORNETO Slides [PDF] Rodriguez-Mier et al., Nature Machine Intelligence, 7:1168-1186, 2025 [Link]
VI 19-20 02-09-2025 PDGrapher Slides [PDF] Gonzalez et al., Nature Biomedical Engineering, In press, 2025 [Link]
... 21-22 05-09-2025 ... ...
Mid-semester examination break (08-09-2025 to 12-09-2025) Mid Semester Paper, Answer Keys
VII 23-24 26-09-2025 Kolmogorov-Arnold GNNs Slides [PDF] Li et al., Nature Machine Intelligence, 7:1346-1354, 2025 [Link]
... 25-26 07-10-2025 ... ...
VIII 27-28 10-10-2025 cpDistiller Slides [PDF] Yan et al., Nature Communications, 16:6886, 2025 [Link]
IX 29-30 14-10-2025 EvoGradient Slides [PDF] Wang et al., Nature Microbiology, 10:332-347, 2025 [Link]
X 31-32 21-10-2025 Evo 2 Slides [PDF] Brixi et al., bioRxiv, 2025.02.18.638918, 2025 [Link]
... 33-34 24-10-2025 ... ...
XI 35-36 28-10-2025 iKraph Slides [PDF] Zhang et al., Nature Machine Intelligence, 7:602-614, 2025 [Link]
XII 37-38 31-10-2025 SWING Slides [PDF] Siwek et al., Nature Methods, 22:1707-1719, 2025 [Link]
XIII 39-40 04-11-2025 MetaSUB Slides [PDF] Danko et al., Cell, 184(13):3376-3393, 2021 [Link]
XIV 41-42 07-11-2025 Virtual Lab Slides [PDF] Swanson et al., Nature, 646:716-723, 2025 [Link]


COURSE PLAN

No dues

ASSIGNMENTS

Set Due Date Solutions
Assignment 1 01-09-2025 Answer Keys
Assignment 2 01-10-2025 Answer Keys
Assignment 3 01-11-2025 Answer Keys


PROJECTS

Set Due Date Allotment
Projects 15-12-2025 Details


OTHERS

Topic Details
Attendance Link
Mid-semester Marks Link


REFERENCES

  1. C. Setubal and J. Meidanis: Introduction to Computational Molecular Biology, PWS Publishing Company, Boston, 1997.
  2. P. A. Pevzner: Computational Molecular Biology � An Algorithmic Approach, MIT Press, 2000.
  3. R. Durbin, S. R. Eddy, A. Krogh and G. Mitchison: Biological Sequence Analysis - Probabilistic Models of Proteins and Nucleic Acids, Cambridge University Press, 1998.
  4. D. Gusfield: Algorithms on Strings, Trees, and Sequences, Cambridge University Press, USA, 1997.
  5. H. Lodish, A. Berk, S. L. Zipursky, P. Matsudaira, D. Baltimore and J. Darnell: Molecular Cell Biology, W. H. Freeman, USA, 2000.
  6. C. -I. Branden, J. Tooze: Introduction to Protein Structure, Garland Publishing, 1998.
  7. A. Kowald, C.hristoph Wierling, E. Klipp, and W. Liebermeister: Systems Biology, Wiley-VCH, 2016.
  8. B. O. Palsson: Systems Biology : Constraint based Reconstruction and Analysis, Cambridge University Press, 2015.