Appendix C — Textbooks and general resources

C.1 Textbooks

No single textbook is required. These cover most of the material, but none is fully up to date.

  • Zvelebil and Baum (2008) — Understanding Bioinformatics. Broad coverage, recommended in the exam description.
  • Pevsner (2015) — Bioinformatics and Functional Genomics. Broad coverage; the basis of the 2021 exam variant.
  • Jones and Pevzner (2004) — An Introduction to Bioinformatics Algorithms. Algorithms: alignment, suffix trees, assembly, phylogeny, motifs.
  • Compeau and Pevzner (2018) — Bioinformatics Algorithms: An Active Learning Approach. With free online lectures.
  • Durbin et al. (1998) — Biological Sequence Analysis. The classic on probabilistic models and HMMs.
  • Felsenstein (2004) — Inferring Phylogenies.
  • Burkowski (2008) — Structural Bioinformatics: An Algorithmic Approach. Structure, dynamic programming, RNA secondary structure, superposition, machine learning.
  • Gagniuc (2021) — Algorithms in Bioinformatics: Theory and Implementation. Alignment, motifs, Markov chains.
  • Hastie et al. (2009) — The Elements of Statistical Learning.

C.2 Keeping up to date

  • Proceedings of the most recent ISMB and ECCB conferences (published as supplements of Bioinformatics).
  • The annual Nucleic Acids Research Database and Web Server issues.
  • Seminars and dissertations at DBB and SciLifeLab.

C.3 Collections of papers

C.3.1 Classical papers in bioinformatics

These papers were read in the PhD course Classical papers in bioinformatics (SciLifeLab, Arne Elofsson and Måns Magnusson). Each made a fundamental contribution or changed how the field thinks. For each paper, ask: what was new about it, how did it change the field, and what has happened in the field since?

Protein structure and folding

  • Levinthal (1966) — molecular model building by computer; the origin of Levinthal’s paradox (Section 9.5).
  • Chou and Fasman (1974a); Chou and Fasman (1974b) — the Chou–Fasman secondary-structure propensities and prediction method (Section 9.8).
  • Chothia et al. (1977) — how α-helices and β-sheets pack against each other.
  • McCammon et al. (1977) — the first molecular dynamics simulation of a protein (Section 9.11).
  • Dalal et al. (1997) — “protein alchemy”: changing a β-sheet protein into an α-helical one by changing half of its sequence.
  • Bradley et al. (2005) — Rosetta reaches high-resolution de novo structure prediction for small proteins (Section 9.8).
  • Meng et al. (1992) — automated docking with grid-based energy evaluation (DOCK).

Membrane and signal-peptide prediction

  • Heijne (1986) — weight-matrix prediction of signal-peptide cleavage sites.
  • Nielsen et al. (1997) — SignalP: neural networks for signal peptides (Section 10.5).
  • Heijne (1992) — hydrophobicity analysis and the positive-inside rule (Section 9.10).
  • Krogh et al. (2001) — TMHMM: a hidden Markov model for transmembrane topology (Section 1.6.4).

Phylogeny

  • Fitch (1971) — parsimony: minimum change on a given tree (Section 4.3).
  • Felsenstein (1981) — maximum-likelihood trees from DNA sequences (Section 4.2).
  • Huelsenbeck et al. (2001) — Bayesian inference of phylogeny (Section 4.3).

Sequencing

  • Sanger et al. (1977) — DNA sequencing with chain-terminating inhibitors (Section 5.2).
  • Li and Durbin (2009) — BWA: short-read alignment with the Burrows–Wheeler transform (Section 1.4).