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bio:start [27/02/2019 alle 11:13 (5 anni fa)]
Nadia Pisanti 		bio:start [07/07/2021 alle 07:30 (3 anni fa)] (versione attuale)
Nadia Pisanti [BIOINFORMATICS]
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 +====== BIOINFORMATICS 2020 ======
  
-Lecturer: **Nadia Pisanti**+Lecturer: Prof. **Nadia Pisanti**
  
 === NEWS === === NEWS ===
  
-[February 27th] Next week we will have classes on Monday both at 14:00 and at 16:00, and both in room L1.+[February 8th] This page has been created!
  
-[February 12th] The classes of April 8th and April 9th will not take place: we will have to find two slots to catch them up.+===== CLASSES IN COVID-19 TIMES ===== 
 + 
 +**Regular live classes are suspended from March 5th, 2020** \\ 
 +Classes will thus take place [[https://meet.google.com/lookup/d2ubhrxcxh | here]] 
 + 
 +Prof. Pisanti makes office hours on skype or meet upon appointment arranged by mail.\\
  
-[February 12th] This page has been created! 
  
 === LEARNING GOALS === === LEARNING GOALS ===
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 //Sequences Alignments//: Dynamic Programming methods for local, global, and semi-local alignments. Computing the Longest Common Subsequences. Multiple Alignments.\\  //Sequences Alignments//: Dynamic Programming methods for local, global, and semi-local alignments. Computing the Longest Common Subsequences. Multiple Alignments.\\ 
 //Pattern Matching//: Exact Pattern Matching: algorithms (Knuth-)Morris-Pratt, Boyer-Moore, Karp-Rabin with preprocessing of the pattern. Algorithm with preprocessing of the text: use of indexes. //Pattern Matching//: Exact Pattern Matching: algorithms (Knuth-)Morris-Pratt, Boyer-Moore, Karp-Rabin with preprocessing of the pattern. Algorithm with preprocessing of the text: use of indexes.
-//Motifs Extraction//: KMR Algorithm for the extracion of exact motifs and its modifications for the inference of approximate motifs.\\ +//Motifs Extraction//: KMR Algorithm for the extraction of exact motifs and its modifications for the inference of approximate motifs.\\ 
 //Finding Repetitions//: Algorithms for the inference of long approximate repetitions. Filters for preprocessing. \\  //Finding Repetitions//: Algorithms for the inference of long approximate repetitions. Filters for preprocessing. \\ 
 //Fragment Assembly//: Genomes sequencing: some history, scientific opportunities, and practical problems. Some possible approaches for the problem of assembling sequenced fragments. Link with the "Shortest common superstring" problem, the Greedy solution. Data structures for representing and searching sequencing data.\\  //Fragment Assembly//: Genomes sequencing: some history, scientific opportunities, and practical problems. Some possible approaches for the problem of assembling sequenced fragments. Link with the "Shortest common superstring" problem, the Greedy solution. Data structures for representing and searching sequencing data.\\ 
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 === STUDY MATERIAL === === STUDY MATERIAL ===
  
-SUFFIX TREE {{:magistraleinformatica:alg2:tre.pdf|}} \\  +SEQUENCES ALIGNMENTS {{:bio:allineamenti.pdf| Alignments}}\\  
-PATTERN MATCHING {{:biotecnologie:informatica:patternmatching1.pdf}} e {{:biotecnologie:informatica:patternmatching2.pdf}} \\ +PATTERN MATCHING {{:biotecnologie:informatica:patternmatching1.pdf | ExactPatternMatching}} e {{:biotecnologie:informatica:patternmatching2.pdf | KnuthMorrisPratt&BoyerMoore}} {{:bio:kr87.pdf| KarpRabin87}} \\ 
-FRAGMENT ASSEMBLY {{:bio:fragmentassembly.pdf|}}\\  +SUFFIX TREE {{:magistraleinformatica:alg2:tre.pdf| SuffixTrees }} \\  
-SEQUENCES ALIGNMENTS {{:bio:allineamenti.pdf|}}\\  +EXACT MOTIFS EXTRACTION  {{:bio:KarpMillerRosenberg.pdf| KarpMillerRosenberg}} \\ 
-FINDING REPETITIONS: FILTERING {{:bio:amb.pdf|}}\\  +APPROXIMATE MOTIFS EXTRACTION {{:bio:kmrc.pdf| KMRC}} {{:bio:Speller.pdf| Speller}} {{:bio:structured_motifs.pdf| StructuredMotifs}} \\ 
-NEW GENERATION SEQUENCING {{:bio:illumina-assembly.pdf|}}\\  +FINDING REPETITIONS: FILTERING {{:bio:amb.pdf| TUIUIU}}\\  
-OVERVIEW OF SEQUENCING TECNOLOGIES {{:bio:en104-pisanti.pdf}}\\ +FRAGMENT ASSEMBLY {{:bio:fragmentassembly.pdf| FragmentAssembly}}\\  
-BUBBLES IN DE BRUIJN GRAPHS (slides) {{bio:Seminar-Bubbles.pdf}}\\+NEW GENERATION SEQUENCING {{:bio:illumina-assembly.pdf| NewGenerationSequencing}}\\  
 +OVERVIEW OF SEQUENCING TECNOLOGIES {{:bio:en104-pisanti.pdf | SequencingTechnologies}}\\ 
 +HAPLOTYPE ASSEMBLY {{:bio:jcbwhatshap.pdf | WhatsHap }}\\ 
 +BUBBLES IN DE BRUIJN GRAPHS (slides) {{bio:Seminar-Bubbles.pdf | Bubbles }}\\
  
 == EXAM ASSIGNMENT == == EXAM ASSIGNMENT ==
  
-Each student is assigned a paper that is a very recent scientific work on topics related to those of the course (tipically it is a paper accepted for publication in the proceedings of an international conference that is going to be held in a few weeks/months). The paper is part of a pool of possible papers selected by the lecturer. The paper assignment follows a brief description of all papers in the pool made by the lecturer, and a bidding phase of the students over such papers. +Each student will have to undergo an oral exam over the topics of the classes. 
 +Moreover, each student is assigned a paper that is a very recent scientific work on topics related to those of the course (tipically it is a paper accepted for publication in the proceedings of an international conference that is going to be held in a few weeks/months). The paper is part of a pool of possible papers selected by the lecturer. The paper assignment follows a brief description of all papers in the pool made by the lecturer, and a bidding phase of the students over such papers. 
 Once the student has his/her paper assigned, the task is to prepare and make a presentation of that work that: Once the student has his/her paper assigned, the task is to prepare and make a presentation of that work that:
 (1) describes the results presented in that paper, (2) is suited for the actual audience (that will be the course class) as for comprehension opportunity, (3) sticks to the allowed time slot.  (1) describes the results presented in that paper, (2) is suited for the actual audience (that will be the course class) as for comprehension opportunity, (3) sticks to the allowed time slot. 
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 === SEMINARS SCHEDULE === === SEMINARS SCHEDULE ===
  
-TBD+TBA
  
 === "REGISTRO DELLE LEZIONI" === === "REGISTRO DELLE LEZIONI" ===
  
-     * [[https://unimap.unipi.it/registri/dettregistriNEW.php?re=3290064::::&ri=80312|REGISTRO DELLE LEZIONI]]+[[https://unimap.unipi.it/registri/dettregistriNEW.php?re=3314294::::&ri=80312|REGISTRO DELLE LEZIONI]] 
 + 
 +===== WHITEBOARDS AND RECORDING OF LECTURES and MATERIAL ===== 
 +^ Lecture Date ^ Topic ^ Material ^   
 +| dd/mm/aaaa | bla bla | links and files |  
bio/start.1551266001.txt.gz · Ultima modifica: 27/02/2019 alle 11:13 (5 anni fa) da Nadia Pisanti

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