Syllabus

Topics, readings, interactive tools and archived syllabi for DH607, Introduction to computational multi-omics at IIT Bombay.
ImportantTentative

The week-by-week schedule lives on the home page and is tentative until the term begins. Past editions are archived as taught: Autumn 2025 and Autumn 2024, both with links to the in-class recordings.

IITB’s academic calendar is here and holiday calendar is here.

Playlists of in-class recordings: Autumn 2026, Autumn 2025, and Autumn 2024.

Lecture material

Lecture 01 — Introduction to the course (Tue, Jul 28)

Slides | Video

Papers to read

  1. All biology is computational biology — Markowetz, PLOS Biology (2017)
  2. The baby whose life was saved by the first personalized CRISPR therapy — Nature (2025)
  3. Sickle cell disease — Kato et al., Nature Reviews Disease Primers (2018)
  4. A unified model of human hemoglobin switching through single-cell genome editing — Nature Communications (2021)
  5. Gene therapy: Erasing sickle-cell disease — Nature (2017)
  6. World’s first personalized CRISPR therapy given to baby with genetic disease — Nature (2025)
  7. Hope, despair and CRISPR — the race to save one woman’s life — Nature (2024)
  8. DNA sequencing at 40: past, present and future — Shendure et al., Nature (2017)
  9. Indexing compressed text — Ferragina and Manzini, Journal of the ACM (2005)
  10. Advancing RNA-Seq analysis — Haas and Zody, Nature Biotechnology (2010)
  11. Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2 — Love et al., Genome Biology (2014)
  12. A transcriptomic and epigenomic cell atlas of the mouse primary motor cortex — Yao et al., Nature (2021)
  13. Decoding heterogeneous single-cell perturbation responses — Nature Cell Biology (2025)
  14. Integrative single-cell analysis — Stuart and Satija, Nature Reviews Genetics (2019)
  15. How quickly are you ageing? What molecular ‘clocks’ can tell you about your health — Nature (2025)
  16. Epigenetic ageing clocks: statistical methods and emerging computational challenges — Nature Reviews Genetics (2024)
  17. Exploring tissue architecture using spatial transcriptomics — Rao et al., Nature (2021)
  18. An introduction to spatial transcriptomics for biomedical research — Genome Medicine (2022)
  19. Hotspot identifies informative gene modules across modalities of single-cell genomics — DeTomaso and Yosef, Cell Systems (2021)
  20. Genome-wide association studies — Uffelmann et al., Nature Reviews Methods Primers (2021)
  21. 10 Years of GWAS Discovery: Biology, Function, and Translation — Visscher et al., American Journal of Human Genetics (2017)
  22. Single nucleotide polymorphism arrays: a decade of biological, computational and technological advances — LaFramboise, Nucleic Acids Research (2009)
  23. Genetic evidence for recent population mixture in India — Moorjani et al., American Journal of Human Genetics (2013)
  24. 50,000 years of evolutionary history of India: insights from ~2,700 whole genome sequences — Kerdoncuff et al. (2023)
  25. Deep Learning Sequence Models for Transcriptional Regulation — Sokolova et al., Annual Review of Genomics and Human Genetics (2024)

Lecture 02A: A short introduction to molecular biology (Thu, Jul 30)

Slides | Video

Reading material

  1. Genomes, Brown (NCBI Bookshelf)
  2. National Human Genome Research Institute
  3. Sanger sequencing at the JNCI, Kuska (1998)
  4. DNA sequencing methods, Yadav (2007)
  5. Sequencing overview in GigaScience, Brien (2022)
  6. Sequencing technologies, Cristescu (2019)
  7. DNA data storage, Goldman et al. (2016)
  8. Molecular Biology of the Cell, Alberts et al.
  9. Molecular Biology of the Cell (1965 edition)
  10. On Protein Synthesis, Francis Crick (1958)
  11. Central Dogma of Molecular Biology, Francis Crick (1970)
  12. Does the central dogma still stand?, Koonin (2012)
  13. 60 years ago, Francis Crick changed the logic of biology, Cobb (2017)
  14. What Mad Pursuit, Francis Crick (1990)
  15. Composition of the desoxypentose nucleic acids, Chargaff et al. (1951)
  16. Molecular configuration in sodium thymonucleate, Franklin and Gosling (1953)
  17. The story behind Photograph 51, King’s College London
  18. Rosalind Franklin and DNA, Lucas (2008)
  19. Molecular Biology of the Gene, Watson et al.
  20. Never a Dull Enzyme, Kornberg (1989)
  21. Transitions and transversions, Manduz, CC BY-SA 4.0
  22. Positional cloning, Collins (1994)
  23. Genomes 5, Brown (Routledge)
  24. DNA methylation and psychiatric disorders, Suzuki et al. (2005)
  25. Complementary structure of DNA, Crick et al., PNAS (1957)
  26. The Molecular Biology of the Cell (Cell review)
  27. The DNA structure (Watson and Crick manuscript), Wellcome Collection
  28. FASTA format, Wikipedia

Hands on: R/RStudio basics (Thu, Aug 6)

R/RStudio installation instructions | R basics .qmd | Colab notebook

Lecture 03C: Sequences: Global Alignment (Thu, Aug 13)

Slides | Video

Papers to read

  1. A general method applicable to the search for similarities in the amino acid sequence of two proteins, Needleman and Wunsch, Journal of Molecular Biology (1970)
  2. Identification of common molecular subsequences, Smith and Waterman, Journal of Molecular Biology (1981)

Lecture 04A: Sequences: Local Alignment and Database Search (Mon, Aug 17)

Slides | Video

Readings

  1. Karlin-Altschul statistics

Sequencing 3.0 (Tue, Aug 18 / Thu, Aug 20)

Slides | Hands on

FASTQ file | Commands

Lecture (Mon, Sep 7)

Slides

Third Gen Sequencing (Mon, Aug 24)

Slides

DNA-seq Hands On (Thu, Aug 27)

Colab notebook

DNA mapping algorithms II (Mon, Aug 31)

Slides

Introduction to RNA sequencing (Tue, Sep 1)

Slides

Suggested readings

  1. Molecular Biology for Computer Scientists by Lawerence Hunter
  2. Genomes by TA Brown
  3. Computational Genome Analysis by Richard C. Deonier , Michael S. Waterman , and Simon Tavaré
  4. Bioinformatics Algorithms by Phillip Compeau and Pavel A. Pevzner
  5. Modern Statistics for Modern Biology by Susan Holmes and Wolfgang Huber
  6. Data Analysis for the Life Sciences by Rafael A Irizarry and Michael I Love