Practical guidelines for the comprehensive analysis of ChIP-seq data

T Bailey, P Krajewski, I Ladunga… - PLoS computational …, 2013 - journals.plos.org
Mapping the chromosomal locations of transcription factors, nucleosomes, histone
modifications, chromatin remodeling enzymes, chaperones, and polymerases is one of the …

A review of ensemble methods for de novo motif discovery in ChIP-Seq data

A Lihu, Ş Holban - Briefings in bioinformatics, 2015 - academic.oup.com
De novo motif discovery is a difficult computational task. Historically, dedicated algorithms
always reported a high percentage of false positives. Their performance did not improve …

Detecting and refining overlapping regions in complex networks with three-way decisions

H Yu, P Jiao, Y Yao, G Wang - Information Sciences, 2016 - Elsevier
The identification of communities is crucial to an understanding of the structural and
functional properties of a complex network. Many methods and algorithms have been …

MoTeX-II: structured MoTif eXtraction from large-scale datasets

SP Pissis - BMC bioinformatics, 2014 - Springer
Background Identifying repeated factors that occur in a string of letters or common factors
that occur in a set of strings represents an important task in computer science and biology …

Fast motif discovery in short sequences

H Liu, F Han, H Zhou, X Yan… - 2016 IEEE 32nd …, 2016 - ieeexplore.ieee.org
Motif discovery in sequence data is fundamental to many biological problems such as
antibody biomarker identification. Recent advances in instrumental techniques make it …

Clustering hypergraphs via the MapEquation

M Swan, J Zhan - IEEE Access, 2021 - ieeexplore.ieee.org
A hypergraph is a generalization of a graph in that the restriction of pairwise affinity scores is
lifted in favor of affinity scores that can be evaluated between an arbitrary number of inputs …

Computational discovery and modeling of novel gene expression rules encoded in the mRNA

S Bahiri-Elitzur, T Tuller - Biochemical Society Transactions, 2020 - portlandpress.com
The transcript is populated with numerous overlapping codes that regulate all steps of gene
expression. Deciphering these codes is very challenging due to the large number of …

A Comparative Analysis Between -Mers and Community Detection-Based Features for the Task of Protein Classification

K Tangirala, N Herndon… - IEEE transactions on …, 2016 - ieeexplore.ieee.org
Machine learning algorithms are widely used to annotate biological sequences. Low-
dimensional informative feature vectors can be crucial for the performance of the algorithms …

Community detection-based feature construction for protein sequence classification

K Tangirala, N Herndon, D Caragea - … , ISBRA 2015 Norfolk, USA, June 7 …, 2015 - Springer
Abstract Machine learning algorithms are widely used to annotate biological sequences.
Low-dimensional informative feature vectors can be crucial for the performance of the …

Extraction et analyse de connaissances à partir du Web

Y Slimani - 2018 - dspace.univ-setif.dz
La fouille du Web est l'application de la fouille de données Web. Le but de la fouille de
l'usage du Web est de comprendre le comportement des utilisateurs des sites Web à travers …