DSKernel: AI and Strength Training

T ackling a problem by reducing it in smaller, more tractable parts, is the pathway that is followed to solve numerous, yet different, real-life problems. And divide-and-conquer can be rationally helpful to read through a genome's sequences of As, Ts, Cs, and Gs too. A method published in Genome Research facilitates reading genomes with partitioning. Sébastien Boisvert reports. Reading life Genomes contain the core code of life, or so we think. Recent technological advances are pushing for massively parallel acquisition of short digital sequences of DNA. However, these new sequencers -- machines that literally read DNA molecules -- can only decode about 30-150 digital letters at once of each DNA molecule among the many of them. Accordingly, algorithms implemented as computer programs make sense from these sequence reads by assembling them in longer sequences -- akin to solving puzzles. High-hanging fruit Whole-genome shotgun short read seq...

Programme d'études: http://capsuleweb.ulaval.ca/pls/etprod7/y_bwckprog.p_afficher_fiche?p_session=200909&p_code_prog=D-PEN&p_code_majr=PEN&p_code_camp= Session 1/11 -- Janvier 2010 à Avril 2010 PHS-8801 Activité de recherche - thèse 1 Session 2/11 -- Mai 2010 à Août 2010 PHS-8802 Activité de recherche - thèse 2 Session 3/11 -- Septembre 2010 à Décembre 2010 BIF-7900 Bio-informatique I A+ PHS-8803 Activité de recherche - thèse 3 Session 4/11 -- Janvier 2011 à Avril 2011 PHS-8000 Examen de doctorat (écrit: 1 mars 2011, oral: 1 avril 2011) PHS-8804 Activité de recherche - thèse 4 Session 5/11 -- Mai 2011 à Août 2011 PHS-8805 Activité de recherche - thèse 5 Session 6/11 -- Septembre 2011 à Décembre 2011 PHS-8001 Séminaire de doctorat PHS-8806 Activité de recherche - thèse 6 Session 7/11 -- Janvier 2012 à Avril 2012 BMO-7007 Analyse critique de publications PHS-8807 Activité de recherche - thèse 7 Sess...

Detailed Information Project Information Project Title:   Assembly of reads from a mix of high-throughput sequencing technologies Period:   from: 2010-09-01 to: 2013-08-31 Principal Investigator(s): BOISVERT, Sébastien Co-Investigators: Supervisors: CORBEIL, Jacques ; MARCHAND, Mario Previous Investigators/Supervisors: Institution: Université Laval Department: Program: Doctoral Award - Frederick Banting and Charles Best Canada Graduate Scholarships  Assigned PRC: DRA  Primary Institute: Genetics  Primary Theme: Biomedical  Keywords: BIOINFORMATICS, BIOSTATISTICS, BIOSTATISTIQUES, DE NOVO SEQUENCING, GENOME ASSEMBLY, GENOME VARIATION, GENOMICS, PROTEOMICS, AND BIOINFORMATICS, GÉNOMIQUE, PROTÉOMIQUE ET BIOINFORMATIQUE, MUTATION DISCOVERY, RESEQUENCING  Abstract: The treatment of diseases costs each Canadian a large amount of money. There is a genetic basis behind resistance to antibiotics and various ...

Detailed Information Project Information Project Title:   Kernel methods for the annotation of trypanosomatid genomes. Period:   from: 2009-09-01 to: 2010-08-31 Principal Investigator(s): BOISVERT, Sébastien Co-Investigators: Supervisors: CORBEIL, Jacques ; MARCHAND, Mario Previous Investigators/Supervisors: Institution: Centre hospitalier de l'Université Laval (Québec) Department: Molecular Medicine  Program: Frederick Banting and Charles Best Canada Graduate Scholarships - Master's Award  Assigned PRC: CGA  Primary Institute: Genetics  Primary Theme: Biomedical  Keywords: BIOINFORMATICS, COMPARATIVE GENETICS, GENETICS, GENOME ANNOTATION, GENOMICS, GENOMICS, PROTEOMICS, AND BIOINFORMATICS, GÉNOMIQUE, PROTÉOMIQUE ET BIOINFORMATIQUE, GÉNÉTIQUE, HIV, INFECTIEUSES ET PARASITAIRES, INFECTIOUS AND PARASITIC, INFECTIOUS MICROORGANISMS, KERNEL METHODS, LEISHMANIA, MACHINE LEARNING, TRYPANOSOMATIDS...

SHREC: a short-read error correction method Bioinformatics doi:10.1093/bioinformatics/btp379 (2009) In their paper, the authors stress on the importance of read correction in sequencing applications -- such as resequencing and de novo assembly. They mention that error correction techniques for Sanger reads are outdated, and that novelty is required. The authors say that assemblers are better when there're no errors -- that they work well with error-corrected reads. This is incorrect, as both the resequencing and de novo assembly applications, allow consensus calling. The authors write that the Euler assembly program is 'established', meanwhile, nobody uses it. Over the Sanger reign, only a very few software were introduced for error correction in reads. Accordingly, the authors only cite two such works. They compare SHREC with the error-correction component of EULER-SR and ALLPATHS -- two assemblers -- on simulated and real data. The paper is fun to read, and the desc...

Whole genome assembly from 454 sequencing output via modified DNA graph concept Computational Biology and Chemistry doi:10.1016/j.compbiolchem.2009.04.005 (2009) The human genome project was a scientific success which allowed bioinformatics to grow. During this project, only Sanger sequencing was in action. Recently, with pyrosequencing, however, new platforms are emerging, and they provide much more data at lower cost, in a few hours. This data storm has prompted the need for novel assembly algorithms. The authors provide a new computational framework for genome assembly -- SR-ASM (Short Reads ASseMbly). They utilize the 'recently available' Roche/454 technology, released in 2005. They evaluate their tool against Velvet and Newbler. Velvet is designed solely for Illumina (the authors say it runs on 454), whereas Newbler is sold along with the 454 sequencer from Roche. The authors say Newbler can not load fasta files, but it can. With this argument, they avoided the need...

The advent of computing in our world has made research endeavours easier. The whole field of bioinformatics is built on the mindset that once you have data, regardless of its quality, you can go on and publish the data-analysis recipe and associated observations. Why do computational biologists feel they have to tell everyone that their sequence contains specific sub-sequences? Even more alarming, unless you are publishing in a good journal -- like Nature -- a bioinformatic paper is very unlikely to undergo extensive copy-editing, and thus, will presumably be super-boring to read, unless you are an outstanding writer. Suppose that a person prepares bread with his own novel recipe (yeah, right -- a novel bread recipe). He mixes the ingredients rightly, then he put the mix in the oven, sets it up, waits, and gets his result. This result is void of any scientific value, just as most of the creepy crap published in the bioinformatics sphere is void of discoveries. One could tell that this ...