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bio:start [23/05/2018 alle 11:25 (17 mesi fa)]
Nadia Pisanti
bio:start [07/05/2019 alle 09:54 (6 mesi fa)]
Nadia Pisanti
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 +====== BIOINFORMATICS ======
  
 Lecturer: **Nadia Pisanti** Lecturer: **Nadia Pisanti**
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 === NEWS === === NEWS ===
  
-[May 10thThe seminar'​s schedule is published in this site.+[April 30thPlease be aware that there will be no class on Monday, May 27th due to University cancelling all lectures on that day to allow students to go home and vote for EU elections.
  
-[May 3rdThe lecture of Monday ​May 7th will not take place due to the Director'​s decision to grant students the time to for an assembly.+[April 15thAs communicated in the class, on Monday ​April 29th we will lecture 4 academic hours starting at 14:00 to catch up the classes that were canceled last week.
  
-[April ​17thThe lecture ​of Monday ​April 30th will not take place.+[April ​1st *not a joke*I recall that next week there will be no classes as comunicated at the beginning ​of the course. See you on April 15th.
  
-[March ​13thThe assignment of papers for the final exam will take place during the lectures of Monday April 16th and Tuesday April 17th.+[March ​26thPapers have been assigned! __The student Antonio Nuzzo is asked to send an email to prof.Pisanti__ (his email bounced).
  
-[March ​8thOn Tuesday March 20th there will be no class due to other professional engagement ​of the teacher.+[March ​12thThe assignment ​of papers for the seminar will take place on Monday March 25th.
  
-[February 27th] On Monday ​March 5th there will be no classes due to the University'​s ​decision ​to stop teaching activities to support participation ​to political elections.+[March 5th] From now on, in absence of news, lectures ​will be on Monday'​s ​from 14:00 to 15:30 and on Tuesday'​s from 9:15 to 10:45. Always in room L1.
  
-[February ​19thThe lectures schedule is: Monday ​from 14 to 15:30 in classroom L1, and Tuesday from 9:15 to 10:45 in classrom ​L1.+[February ​27thNext week we will have classes on Monday ​both at 14:00 and at 16:00, and both in room L1.
  
-[February ​18th] 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. 
 + 
 +[February 12th] This page has been created!
  
 === LEARNING GOALS === === LEARNING GOALS ===
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 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. 
- 
-The list of papers suggested for this year are here: {{:​bio:​PAPERI-BI-2018.zip|}}. 
  
 Students presentations usually take place all together somewhen at the end of the course. Exceptions are possible upon request for specific needs. Once the course is over, students can undergo the examination anytime during the academic year by agreeing an appointment:​ please, send an email to the teacher. Students presentations usually take place all together somewhen at the end of the course. Exceptions are possible upon request for specific needs. Once the course is over, students can undergo the examination anytime during the academic year by agreeing an appointment:​ please, send an email to the teacher.
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 === SEMINARS SCHEDULE === === SEMINARS SCHEDULE ===
  
-- Monday ​May 21st, from 14 to 15:30, room L1:\\ +**MONDAY ​May 20th** 
-# MICHAL PUNCOCHAR ​Fixed-Parameter Tractable Sampling for RNA Design with Multiple Target Structures\\ +Marco CardiaMALVAgenotyping by Mapping-free ALlele detection of known VAriants.\\ 
-# IVAN GRUJIC - Designing RNA Secondary Structures is Hard\\ +Luca CorbucciHaplotype-aware graph indexes.\\ 
-# FEDERICO LAZZARI - Reverse de BruijnUtilizing Reverse Peptide Synthesis to Cover All Amino Acid k-mers\\ +Nicolas ManiniEfficient computation of Sequence ​Mappability.\\ 
-# NICOLA FERRONE - Modeling Biological Problems in Computer ScienceA Case Study in Genome Assembly\\ +Andre' SantosGenMap: Fast and Exact Computation ​of Genome Mappability.\\
- +
-- Tuesday May 22nd, from 9:15 to 11, room L1:\\ +
-# RUGGIERO DI BENEDETTO - Longest substring palindrome after edit\\ +
-# GIULIA PUNZI - Nearest constrained circular words\\ +
-# SILVIA STRANIERI - Order-Preserving Pattern Matching Indeterminate Strings\\ +
-# FRANCESCO LANDOLFI - Algorithmic Framework for Approximate Matching Under Bounded Edits with Applications to Sequence ​Analysis\\ +
- +
-- Wednesday May 23rd, from 16:00 to 17:45, Sala Seminari Ovest:\\ +
-# AYTAN YAGUBLU - AllSome Sequence Bloom Trees\\ +
-# FRANCESCA NARETTO - MantisFast, Small, ​and Exact Large-Scale Sequence-Search Index\\ +
-# MADDALENA AMENDOLA - DISCOSNP++: de novo detection ​of small variant from raw unassembled read set(s)\\ +
- +
-- Thursday May 24th, from 16:00 to 17:45, Sala Seminari Ovest:\\ +
-# DAVIDE RUCCI - Dynamic Programming on DAGs: Co-Linear Chaining Extended\\ +
-# GIANMARCO RICCIARELLI - Circular Networks from Distorted Metrics\\ +
-# ANTONIO SISBARRA - Algorithms for Computing the Family-Free Genomic Similarity under DCJ \\ +
-# LEONARDO CARIAGGI - GTED: Graph Traversal Edit Distance\\+
  
-- Monday ​May 28st, from 14 to 15:30, room L1:\\ +**TUESDAY ​May 21st** 
-# GEMMA MARTINI - Assembly of Long Error-Prone Reads and Repeat Classification\\ +Shadi ShajariSimulating the DNA String Graph in Succint Space.\\ 
-# MICHELE MICCINESI - Optimal Omnitig Listing for Safe and Complete Contig Assembly\\ +Antonio Nuzzo: Indexing de Bruijn Graphs with minimizers.\\ 
-# VLAD PANDELEA - Full-length ​de novo viral quasispecies assembly through variation graph construction\\ +Riccardo Manetti: An Efficient, Scalable ​and Exact representation of High-Dimensional Color Information via de Bruijn Graph Search.\\ 
-# CARMINE CASERIO - De novo assembly ​of viral quasispecies using overlap graphs\\ +Pouria Faraji: Parallel decompression ​of gzip-compressed files and random access ​to DNA sequences.\\
-# FRANCESCO CARIAGGI ​A graph-based approach ​to diploid genome assembly\\+
  
-- Tuesday ​May 29th, from 9:15 to 11, room L1:\\ +**TUESDAY ​May 28th** 
-# GASPARE FERRARO - TwoPaCo: an efficient algorithm ​to build the compacted de Bruijn graph from many complete genomes\\ +Tabriz HajiyevFaster queries for longest substring palindrome after block edit.\\ 
-# SIMONE SCHIRINZI ​Faster Online Elastic Degenerate String Matching\\ +Newsha OzgoliSafe and Complete algorithms for dynamin programming problems, with an application ​to RNA folding.\\ 
-# JOHANNES BUSCH Efficient Algorithms to Discover Alterations ​with Complementary Functional Association in Cancer\\ +Federico Finocchio: CONSENT ​Scalable Self-Correction of long reads with multiple sequence alignment.\\ 
-# GIULIANO CORNACCHIA ​Long Reads Enable Accurate Estimates Of Complexity Of Metagenomes\\+Paolo Contenti: Efficient Construction of a Complete Index for Pan-Genomics Read Alignments.
  
-- Dates to be defined during or after summer exams session:\\ 
-# JAVAD KHALILI - Designing small universal k-mer hitting sets for improved analysis of high-throughput sequencing\\ 
-# LAPO TOLONI - Analysis of genomic rearrangements by using the Burrows-Wheeler transform of short-read data\\ 
-# SARA VITELLARO - A safe and complete algorithm for metagenomic assembly\\ 
  
 === "​REGISTRO DELLE LEZIONI"​ === === "​REGISTRO DELLE LEZIONI"​ ===
  
-     * [[http://​unimap.unipi.it/​registri/​dettregistriNEW.php?​re=2090749::::&​ri=80312|REGISTRO DELLE LEZIONI]]+     * [[https://​unimap.unipi.it/​registri/​dettregistriNEW.php?​re=3290064::::&​ri=80312|REGISTRO DELLE LEZIONI]]
bio/start.txt · Ultima modifica: 07/05/2019 alle 09:55 (6 mesi fa) da Nadia Pisanti