Lectures' topics

 

September 25th, 2024

 

Introduction to Pattern Discovery for Life Sciences.

Big Data: Astronomical or Genomical?

Recall of some fundamentals in Biology: proteins.

September 26th, 2024

 

Recall of some fundamentals in Biology.

Nucleic acids. Replication, protein synthesis. The Central Dogma of Molecular Biology. Reading Frames. Junk DNA.

Introduction to Alignment. Homology and similarity.

October 03rd, 2024

 

Exercises on protein synthesis.

Pairwise alignment. Naive algorithm and a very simple way of computing the score.

Pairwise Alignment - gaps allowed: score computation.

October 9th, 2024

 

Different criteria for evaluating pairings either in the nucleotidic case or in the protein case.

Dynamic Programming algorithms for alignment: Needleman & Wunsch Algorithm.

October 10th, 2024

 

Global alignment through Needleman & Wunsch Algorithm.

October 16th, 2024

 

Needleman & Wunsch Algorithm: coding.

October 17th, 2024

 

Needleman & Wunsch Algorithm: coding.

Smith & Waterman Algorithm.

October 23rd, 2024

 

Needleman & Wunsch and Smith & Waterman Algorithms : coding.

October 24th, 2024

 

A general method applicable to the search for similarities in the amino acid sequence of two proteins, by Needleman and Wunsch

October 30th, 2024

 

Edit distance and Edit Graphs.

Heuristic algorithms. The filtering technique and Fasta.

October 31st, 2024

 

Blast.

Pairwise Alignment biological applications.

Exercises on FastA and Blast.

November 13th, 2024

 

Multiple Sequence Alignment. Algorithms based on Dynamic Programming and their running time. Less expensive alternatives in terms of running time.

November 14th, 2024

 

Greedy and progressive approach. Clustalw. Multiple alignment scoring.

Molecular Evolution. Distance estimation between sequences.

November 20th, 2024

 

Molecular clock hypothesis. Phylogenetic trees. Analysis on the paper "The number of Evolutionary trees" by Joseph Felsenstein.

UPGMA.

November 21st, 2024

 

Neighbor Joining.

Character state-based optimization trees: maximum parsimony, maximum likelihood. Phylogenetic analysis applications.

November 26th, 2024

 

Biological Databases and their characteristics. Primary Databases. Pubmed, OMIM. Protein Databases.

November 27th, 2024

 

Exercises on Biological Databases.

November 28th, 2024

 

Consensus, pattern.

December 3rd, 2024

 

Profile, site, signature, motif, fingerprint. Prosite: sintax and some examples. NAR Database Issue.

Introduction to the CG-Island Problem. Fair-Bet Casino problem.

December 5th, 2024

 

HMM and Decoding problem. Viterbi Algorithm. Forward-backward problem. Profiles Hmm. HMM Parameter Estimation.