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Bioinformatics - 6 CFU - a.a. 2016-2017





General Information
Bioinformatics page on DISIM Web Site

Office hours:
Friday 10:00 - 11:30 a.m. - email for appointment
office: Building A. Turing, second Floor
email address: antinisca.dimarco@univaq.it


Exam: homeworks; project and its discussion.


Syllabus
  • Biological definitions and concepts (DNA, RNA, microRNA, Central dogma, mutations,)
  • Main biological on-line DB. Data extraction from such systems.
  • Alignment algorithms and substitution matrix. Suffix Tree.
  • Phylogenetic analysis. Algorithms to build Phylogenetic trees. Test and accuracy.
  • Computation models for biological systems modeling. Petri Nets and Hidden Markov Model
  • Technologies and languages: Python, Bio-Python e NEO4J

Reference Tests:
  • An introduction to bioinformtics algorithms. N.C. Jones and P.A. Pevzner. (Capitoli 3,6,9)
  • Scientific papers, slides and other material

Communications
  • If not done, send me an email with name and course (e.g., master in Computer Science, etc)
  • the lesson of today, March 30th is canceled. See you tomorrow


Slides and teaching material
  • [March 2nd 2017] - Introduction to the course and to Bioinformatics. Cell Structure and Functions [slides]
  • [March 3rd 2017] - Central Dogma. On-line DB.[slides]
  • [March 9h 2017] - On-line DB: NCBI and flat-file format.[slides]
  • [March 10h 2017] - Single Alignement, Substitution Matrix, PAM.[slides]
  • [March 16h 2017] - BLOSUM, score schema for gap,exahustive and heuristic algoritm, first homework.[slides]
  • [March 17h 2017] - FASTA, Dynamic Programming [slides]
  • [March 24h 2017] - BLAST [slides]
  • [March 25h 2017] - Multiple Alignment, CLUSTAL [slides]
  • [March 31h 2017] - Edit Distance[slides]
  • [April 07h 2017] - Phylogenetic Analysis[slides]
  • [April 20th 2017] - Second Homework assignment: assay on one of the presented algorithm or a report on the allignment of two proteins with 4 configuration using FASTA. Send an email to communicate the type of homework to develop and to have details on the second type. Deadline on 15th of May.
  • [April 27th-28th 2017] - Neo4J DB, Cypher query language [slides]
  • [May 4th 2017] - Project Presentation [pdf], [slide], [MirNA-HCC], [article], [Report].
  • [May 5th 2017] - EduDay
  • [May 11th 2017] - Introduction to Python [links]
  • [May 12th 2017] - Laboratory: DIANA DB, Cypher Queries, Excercise.
  • [May 18th, 25th and June 8th 2017] - Introduction to Petri Net and modeling exercises. [paper]. Pathways modeling using Petri Nets[slides].
  • [May 19th, 26th and June 1sr and 9th 2017] - Project reviews and implementation. Documentation: [slides on visualization frameworks].