Eric Rivals

Latest

• Translational control of cell plasticity drives 5-FU tolerance
• Counting overlapping pairs of strings
• Incremental algorithms for computing the set of period sets
• Mass Spectrometry-Based Pipeline for Identifying RNA Modifications Involved in a Functional Process: Application to Cancer Cell Adaptation
• EPIK: Precise and scalable evolutionary placement with informative k-mers
• Physical modeling of ribosomes along messenger RNA: Estimating kinetic parameters from ribosome profiling experiments using a ballistic model
• Computing Phylo-$k$-Mers
• Periodicity of Degenerate Strings
• dipwmsearch: a Python package for searching di-PWM motifs
• Convergence of the Number of Period Sets in Strings
• FT-GPI, a highly sensitive and accurate predictor of GPI-anchored proteins, reveals the composition and evolution of the GPI proteome in Plasmodium species
• Alteration of ribosome function upon 5-fluorouracil treatment favors cancer cell drug-tolerance
• Physical modeling of ribosomes along messenger RNA: estimating kinetic parameters from ribosome profiling experiments using a ballistic model
• The multifaceted functions of the Fat mass and Obesity-associated protein (FTO) in normal and cancer cells
• FTO-mediated cytoplasmic m6Am demethylation adjusts stem-like properties in colorectal cancer cell
• Rapid screening and detection of inter-type viral recombinants using phylo-k-mers
• Efficient Construction of Hierarchical Overlap Graphs
• PEWO: a collection of workflows to benchmark phylogenetic placement
• Greedy-reduction from Shortest Linear Superstring to Shortest Circular Superstring
• Hierarchical Overlap Graph
• AQUAPONY: visualization and interpretation of phylogeographic information on phylogenetic trees
• Linking indexing data structures to de Bruijn graphs: Construction and update
• Linking BWT and XBW via Aho-Corasick Automaton: Applications to Run-Length Encoding
• Fast and Accurate Genome-Scale Identification of DNA-Binding Sites
• Practical lower and upper bounds for the Shortest Linear Superstring
• Superstrings with multiplicities
• Functional analysis of Plasmodium falciparum subpopulations associated with artemisinin resistance in Cambodia
• Ribo-seq enlightens codon usage bias
• De novo assembly of viral quasispecies using overlap graphs
• Full Compressed Affix Tree Representations
• Population genomics of picophytoplankton unveils novel chromosome hypervariability
• Rearrangement Scenarios Guided by Chromatin Structure
• The power of greedy algorithms for approximating Max-ATSP, Cyclic Cover, and superstrings
• Accurate self-correction of errors in long reads using de Bruijn graphs
• Read mapping on de Bruijn graphs
• A linear time algorithm for Shortest Cyclic Cover of Strings
• Shortest DNA Cyclic Cover in Compressed Space
• Colib’read on galaxy: a tools suite dedicated to biological information extraction from raw NGS reads
• Superstring Graph: A New Approach for Genome Assembly
• Construction of a de Bruijn Graph for Assembly from a Truncated Suffix Tree
• The ancient Yakuts: a population genetic enigma
• YOC, A new strategy for pairwise alignment of collinear genomes
• Reverse engineering of compact suffix trees and links: A novel algorithm
• LoRDEC: accurate and efficient long read error correction
• An improved genome of the model marine alga Ostreococcus tauri unfolds by assessing Illumina de novo assemblies
• Approximation of Greedy Algorithms for Max-ATSP, Maximal Compression, Maximal Cycle Cover, and Shortest Cyclic Cover of Strings
• Diversity of Prdm9 Zinc Finger Array in Wild Mice Unravels New Facets of the Evolutionary Turnover of this Coding Minisatellite
• From Indexing Data Structures to de Bruijn Graphs
• Combining DGE and RNA-sequencing data to identify new polyA+ non-coding transcripts in the human genome
• CRAC: an integrated approach to the analysis of RNA-seq reads
• Scalable and Versatile k-mer Indexing for High-Throughput Sequencing Data
• Approximate Common Intervals in Multiple Genome Comparison
• Novel Definition and Algorithm for Chaining Fragments with Proportional Overlaps
• Evolutionary process of a tetranucleotide microsatellite locus in Acipenseriforms
• An alternative approach to multiple genome comparison
• Genome-scale analysis of metazoan replication origins reveals their organization in specific but flexible sites defined by conserved features
• Querying large read collections in main memory: a versatile data structure
• Novel definition and algorithm for chaining fragments with proportional overlaps
• Sequence analysis of two alleles reveals that intra-and intergenic recombination played a role in the evolution of the radish fertility restorer (Rfo)
• MPSCAN: Fast Localisation of Multiple Reads in Genomes
• Using reads to annotate the genome: influence of length, background distribution, and sequence errors on prediction capacity
• Hardness of optimal spaced seed design
• Detection of Recombination in Variable Number Tandem Repeat Sequences
• Transcriptome annotation using tandem SAGE tags
• Detecting microsatellites within genomes: significant variation among algorithms
• Longest common subsequence problem for unoriented and cyclic strings
• Species-wide distribution of highly polymorphic minisatellite markers suggests past and present genetic exchanges among house mouse subspecies
• Formation of the Arabidopsis Pentatricopeptide Repeat Family
• Tiling an Interval of the Discrete Line
• Hardness results for the center and median string problems under the weighted and unweighted edit distances
• Hardness of Optimal Spaced Seed Design
• A survey on algorithmic aspects of tandem repeats evolution
• Combinatorics of periods in strings
• Comparison of Minisatellites
• Complexities of the Centre and Median String Problems
• On the Distribution of the Number of Missing Words in Random Texts
• Comparison of minisatellites
• Combinatorics of Periods in Strings
• GeneNest: automated generation and visualization of gene indices
• Exact and Efficient Computation of the Expected Number of Missing and Common Words in Random Texts
• q-gram based database searching using a suffix array (QUASAR)
• Location of repetitive regions in sequences by optimizing a compression method
• Computational approaches to identify leucine zippers
• Optimal representation in average using Kolmogorov complexity
• The Transformation Distance: A Dissimilarity Measure Based on Movements of Segments
• Compression and genetic sequence analysis