Indexing highly repetitive string collections, part II: Compressed indexes
G Navarro - ACM Computing Surveys (CSUR), 2021 - dl.acm.org
Two decades ago, a breakthrough in indexing string collections made it possible to
represent them within their compressed space while at the same time offering indexed …
represent them within their compressed space while at the same time offering indexed …
Use and misuse of the gene ontology annotations
Abstract The Gene Ontology (GO) project is a collaboration among model organism
databases to describe gene products from all organisms using a consistent and computable …
databases to describe gene products from all organisms using a consistent and computable …
Ultrafast Sample placement on Existing tRees (UShER) enables real-time phylogenetics for the SARS-CoV-2 pandemic
As the SARS-CoV-2 virus spreads through human populations, the unprecedented
accumulation of viral genome sequences is ushering in a new era of 'genomic contact …
accumulation of viral genome sequences is ushering in a new era of 'genomic contact …
Space-efficient preprocessing schemes for range minimum queries on static arrays
J Fischer, V Heun - SIAM Journal on Computing, 2011 - SIAM
Given a static array of n totally ordered objects, the range minimum query problem is to build
a data structure that allows us to answer efficiently subsequent on-line queries of the form …
a data structure that allows us to answer efficiently subsequent on-line queries of the form …
Efficient algorithms for the reconciliation problem with gene duplication, horizontal transfer and loss
Motivation: Gene family evolution is driven by evolutionary events such as speciation, gene
duplication, horizontal gene transfer and gene loss, and inferring these events in the …
duplication, horizontal gene transfer and gene loss, and inferring these events in the …
Simultaneous identification of duplications and lateral gene transfers
A Tofigh, M Hallett, J Lagergren - IEEE/ACM transactions on …, 2010 - ieeexplore.ieee.org
The incongruency between a gene tree and a corresponding species tree can be attributed
to evolutionary events such as gene duplication and gene loss. This paper describes a …
to evolutionary events such as gene duplication and gene loss. This paper describes a …
Theoretical and practical improvements on the RMQ-problem, with applications to LCA and LCE
J Fischer, V Heun - Annual Symposium on Combinatorial Pattern Matching, 2006 - Springer
Abstract The Range-Minimum-Query-Problem is to preprocess an array such that the
position of the minimum element between two specified indices can be obtained efficiently …
position of the minimum element between two specified indices can be obtained efficiently …
Using hierarchical skills for optimized task assignment in knowledge-intensive crowdsourcing
P Mavridis, D Gross-Amblard, Z Miklós - Proceedings of the 25th …, 2016 - dl.acm.org
Besides the simple human intelligence tasks such as image labeling, crowdsourcing
platforms propose more and more tasks that require very specific skills, especially in …
platforms propose more and more tasks that require very specific skills, especially in …
[图书][B] Sequential and Parallel Algorithms and Data Structures
viii Preface reason for this change is that sequential processors have ceased to get
proportional performance improvements from increased circuit complexity. Although the …
proportional performance improvements from increased circuit complexity. Although the …
A fully dynamic reachability algorithm for directed graphs with an almost linear update time
We obtain a new fully dynamic algorithm for the reachability problem in directed graphs. Our
algorithm has an amortized update time of O (m+ n log n) and a worst-case query time of O …
algorithm has an amortized update time of O (m+ n log n) and a worst-case query time of O …