Matches in SemOpenAlex for { <https://semopenalex.org/work/W2285285366> ?p ?o ?g. }
Showing items 1 to 82 of
82
with 100 items per page.
- W2285285366 abstract "The recent advances in DNA sequencing technology and their many potential applications to Biology and Medicine have rekindled enormous interest in several classical algorithmic problems at the core of Genomics and Computational Biology: primarily, the whole-genome sequence assembly problem (WGSA). Two decades back, in the context of the Human Genome Project, the problem had received unprecedented scientific prominence: its computational complexity and intractability were thought to have been well understood; various competitive heuristics, thoroughly explored and the necessary software, properly implemented and validated. However, several recent studies, focusing on the experimental validation of de novo assemblies, have highlighted several limitations of the current assemblers. Intrigued by these negative results, this dissertation reinvestigates the algorithmic techniques required to correctly and efficiently assemble genomes. Mired by its connection to a well-known NP -complete combinatorial optimization problem, historically, WGSA has been assumed to be amenable only to greedy and heuristic methods. By placing efficiency as their priority, these methods opted to rely on local searches, and are thus inherently approximate, ambiguous or error-prone. This dissertation presents a novel sequence assembler, SUTTA, that dispenses with the idea of limiting the solutions to just the approximated ones, and instead favors an approach that could potentially lead to an exhaustive (exponential-time) search of all possible layouts but tames the complexity through constrained search (Branch-and-Bound) and quick identification and pruning of implausible solutions. Complementary to this problem is the task of validating the generated assemblies. Unfortunately, no commonly accepted method exists yet and widely used metrics to compare the assembled sequences emphasize only size, poorly capturing quality and accuracy. This dissertation also addresses these concerns by developing a more comprehensive metric, the Feature-Response Curve, that, using ideas from classical ROC (receiver-operating characteristic) curve, more faithfully captures the trade-off between contiguity and quality. Finally, this dissertation demonstrates the advantages of a complete pipeline integrating base-calling (TotalReCaller) with assembly (SUTTA) in a Bayesian manner." @default.
- W2285285366 created "2016-06-24" @default.
- W2285285366 creator A5053379558 @default.
- W2285285366 creator A5081842800 @default.
- W2285285366 date "2011-01-01" @default.
- W2285285366 modified "2023-09-26" @default.
- W2285285366 title "Scoring-and-unfolding trimmed tree assembler: algorithms for assembling genome sequences accurately and efficiently" @default.
- W2285285366 hasPublicationYear "2011" @default.
- W2285285366 type Work @default.
- W2285285366 sameAs 2285285366 @default.
- W2285285366 citedByCount "2" @default.
- W2285285366 countsByYear W22852853662012 @default.
- W2285285366 crossrefType "journal-article" @default.
- W2285285366 hasAuthorship W2285285366A5053379558 @default.
- W2285285366 hasAuthorship W2285285366A5081842800 @default.
- W2285285366 hasConcept C108010975 @default.
- W2285285366 hasConcept C111919701 @default.
- W2285285366 hasConcept C113174947 @default.
- W2285285366 hasConcept C11413529 @default.
- W2285285366 hasConcept C127413603 @default.
- W2285285366 hasConcept C127705205 @default.
- W2285285366 hasConcept C134306372 @default.
- W2285285366 hasConcept C151730666 @default.
- W2285285366 hasConcept C154945302 @default.
- W2285285366 hasConcept C173801870 @default.
- W2285285366 hasConcept C201995342 @default.
- W2285285366 hasConcept C2778112365 @default.
- W2285285366 hasConcept C2779343474 @default.
- W2285285366 hasConcept C2780451532 @default.
- W2285285366 hasConcept C33923547 @default.
- W2285285366 hasConcept C41008148 @default.
- W2285285366 hasConcept C54355233 @default.
- W2285285366 hasConcept C6557445 @default.
- W2285285366 hasConcept C80444323 @default.
- W2285285366 hasConcept C86803240 @default.
- W2285285366 hasConceptScore W2285285366C108010975 @default.
- W2285285366 hasConceptScore W2285285366C111919701 @default.
- W2285285366 hasConceptScore W2285285366C113174947 @default.
- W2285285366 hasConceptScore W2285285366C11413529 @default.
- W2285285366 hasConceptScore W2285285366C127413603 @default.
- W2285285366 hasConceptScore W2285285366C127705205 @default.
- W2285285366 hasConceptScore W2285285366C134306372 @default.
- W2285285366 hasConceptScore W2285285366C151730666 @default.
- W2285285366 hasConceptScore W2285285366C154945302 @default.
- W2285285366 hasConceptScore W2285285366C173801870 @default.
- W2285285366 hasConceptScore W2285285366C201995342 @default.
- W2285285366 hasConceptScore W2285285366C2778112365 @default.
- W2285285366 hasConceptScore W2285285366C2779343474 @default.
- W2285285366 hasConceptScore W2285285366C2780451532 @default.
- W2285285366 hasConceptScore W2285285366C33923547 @default.
- W2285285366 hasConceptScore W2285285366C41008148 @default.
- W2285285366 hasConceptScore W2285285366C54355233 @default.
- W2285285366 hasConceptScore W2285285366C6557445 @default.
- W2285285366 hasConceptScore W2285285366C80444323 @default.
- W2285285366 hasConceptScore W2285285366C86803240 @default.
- W2285285366 hasLocation W22852853661 @default.
- W2285285366 hasOpenAccess W2285285366 @default.
- W2285285366 hasPrimaryLocation W22852853661 @default.
- W2285285366 hasRelatedWork W1582754268 @default.
- W2285285366 hasRelatedWork W2033558663 @default.
- W2285285366 hasRelatedWork W2040092713 @default.
- W2285285366 hasRelatedWork W2043186892 @default.
- W2285285366 hasRelatedWork W2068543706 @default.
- W2285285366 hasRelatedWork W2078331392 @default.
- W2285285366 hasRelatedWork W2093421535 @default.
- W2285285366 hasRelatedWork W2095622347 @default.
- W2285285366 hasRelatedWork W2112439337 @default.
- W2285285366 hasRelatedWork W2133531097 @default.
- W2285285366 hasRelatedWork W2159507326 @default.
- W2285285366 hasRelatedWork W2168038373 @default.
- W2285285366 hasRelatedWork W2171074043 @default.
- W2285285366 hasRelatedWork W2807853583 @default.
- W2285285366 hasRelatedWork W2967298165 @default.
- W2285285366 hasRelatedWork W2988523778 @default.
- W2285285366 hasRelatedWork W3164564480 @default.
- W2285285366 hasRelatedWork W392057909 @default.
- W2285285366 hasRelatedWork W2187601130 @default.
- W2285285366 hasRelatedWork W2542287170 @default.
- W2285285366 isParatext "false" @default.
- W2285285366 isRetracted "false" @default.
- W2285285366 magId "2285285366" @default.
- W2285285366 workType "article" @default.