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Bioinformatics - 6 CFU - a.a. 2017-2018





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
  • Applications: the HCC and Melanoma Cancer

Reference Tests:
  • Slides and some provided chapters
  • Scientific papers, slides and other material

Communications
  • Send me an email with name and course (e.g., master in Computer Science, etc)
  • Please send me email with groups partecipants and paper to present. The presentation will be on April 23 at 16:30 (room A1.3) and April 26 at 16:30 (room A1.6). Please and me also your preference. All students are invited to partecipate to the presentations.


Slides and teaching material
  • [March 1st 2018] - Introduction to the course and to Bioinformatics. Cell Structure and Functions [slides]
  • [March 2nd 2018] - MicroRNA. On-line DB.[slides]
  • [March 8h 2018] - Mutations. Single Alignment. [slides]
  • [March 09h 2018] - Petri nets for modelling and analysing Trophic networks [slides]
  • [March 15h 2018] - Lesson Cancelled
  • [March 16h 2018] - Substitution Matrix, PAM, BLOSUM, score schema for gap, exahustive and heuristic algoritm. [Slides publiced on march 8th]
  • [March 22h 2018] - NGS Technologies. [Slides]
  • [March 23h 2018] - Markov Model and Markov Decision Model [slides]
  • [April 5th 2018] - Paper assignment - Homework/presentation due the April 26th 2018 [archive]. - FASTA, Dynamic Programming [slides]
  • [April 12h and 13th 2018] - Lessons Cancelled
  • [April 26th 2018] - BLAST [slide].
  • [April 26h 2018] - 16:30-20:00 Paper Presentation
  • [April 27th 2018] - Multiple Alignment, CLUSTAL [slide].
  • [May 3th 2018] - Seminar [slide to appear].
  • [May 4th 2018] - Projects Presentation [slide].
  • [May 10th 2018] - Projects Presentation [slide].
  • [May 10th 2018 - afternoon] - Paper presentation.
  • [May 11th 2018] - Phylogenetic Analysis, Phylogenetic Tree, [slide].
  • [May 17th, May 24th and June 1st 2018] Project discussion and progress, technical aspects and biological requiremets.
  • [May 17th afternoon, May 25th, May 31 2018] Petri Net, notations, modeling of systems and pathways. [paper] [paper].