Bioinformatics
Algorithms and statistical models on biological sequences and data: sequence alignment, genome assembly, motifs, RNA secondary structure, clustering and network reconstruction.
- Sequence alignment
- ARACNE gene network reconstruction
- ChromHMM chromatin-state model
- De Bruijn graph genome assembly
- GPS model of ChIP-seq binding events
- Lander–Waterman coverage model
- Nussinov algorithm for RNA secondary structure
- McCaskill partition function for RNA folding
- Omnitigs and safe walks in genome assembly
- Optimal leaf ordering of dendrograms
- Position weight matrices
- Profile scores for amino acid substitutions
- Zuker's minimum free energy algorithm
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