Benchmarking of alignment-free sequence comparison methods
Background Alignment-free (AF) sequence comparison is attracting persistent interest driven
by data-intensive applications. Hence, many AF procedures have been proposed in recent …
by data-intensive applications. Hence, many AF procedures have been proposed in recent …
[HTML][HTML] The SeqAn C++ template library for efficient sequence analysis: A resource for programmers
Background The use of novel algorithmic techniques is pivotal to many important problems
in life science. For example the sequencing of the human genome (Venter et al., 2001) …
in life science. For example the sequencing of the human genome (Venter et al., 2001) …
MetaProb: accurate metagenomic reads binning based on probabilistic sequence signatures
Motivation Sequencing technologies allow the sequencing of microbial communities directly
from the environment without prior culturing. Taxonomic analysis of microbial communities, a …
from the environment without prior culturing. Taxonomic analysis of microbial communities, a …
K2mem: discovering discriminative k-mers from sequencing data for metagenomic reads classification
D Storato, M Comin - IEEE/ACM Transactions on Computational …, 2021 - ieeexplore.ieee.org
The major problem when analyzing a metagenomic sample is to taxonomically annotate its
reads to identify the species they contain. Most of the methods currently available focus on …
reads to identify the species they contain. Most of the methods currently available focus on …
Exploiting regulatory heterogeneity to systematically identify enhancers with high accuracy
H Arbel, S Basu, WW Fisher, AS Hammonds… - Proceedings of the …, 2019 - pnas.org
Identifying functional enhancer elements in metazoan systems is a major challenge. Large-
scale validation of enhancers predicted by ENCODE reveal false-positive rates of at least …
scale validation of enhancers predicted by ENCODE reveal false-positive rates of at least …
MetaCon: unsupervised clustering of metagenomic contigs with probabilistic k-mers statistics and coverage
Motivation Sequencing technologies allow the sequencing of microbial communities directly
from the environment without prior culturing. Because assembly typically produces only …
from the environment without prior culturing. Because assembly typically produces only …
Fast and sensitive classification of short metagenomic reads with skraken
The major problem when analyzing a metagenomic sample is to taxonomically annotate its
reads in order to identify the species and their relative abundances. Many tools have been …
reads in order to identify the species and their relative abundances. Many tools have been …
A framework for space-efficient variable-order Markov models
Motivation Markov models with contexts of variable length are widely used in bioinformatics
for representing sets of sequences with similar biological properties. When models contain …
for representing sets of sequences with similar biological properties. When models contain …
Improving metagenomic classification using discriminative k-mers from sequencing data
D Storato, M Comin - … 16th International Symposium, ISBRA 2020, Moscow …, 2020 - Springer
The major problem when analyzing a metagenomic sample is to taxonomically annotate its
reads to identify the species they contain. Most of the methods currently available focus on …
reads to identify the species they contain. Most of the methods currently available focus on …
Data-driven smart bike-sharing system by implementing machine learning algorithms
This paper aims to solve a real-life problem: the bike-sharing management system arises the
requirement of offering the customers the accessibility of the bikes in different bike-stations …
requirement of offering the customers the accessibility of the bikes in different bike-stations …