Ioannis Xenarios

According to our database1, Ioannis Xenarios authored at least 62 papers between 2000 and 2022.

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Bibliography

2022
Towards mouse genetic-specific RNA-sequencing read mapping.
PLoS Comput. Biol., September, 2022

XSI - a genotype compression tool for compressive genomics in large biobanks.
Bioinform., 2022

2021
Setting the basis of best practices and standards for curation and annotation of logical models in biology - highlights of the [BC]2 2019 CoLoMoTo/SysMod Workshop.
Briefings Bioinform., 2021

2020
Enzyme annotation in UniProtKB using Rhea.
Bioinform., 2020

Incorporating heterogeneous sampling probabilities in continuous phylogeographic inference - Application to H5N1 spread in the Mekong region.
Bioinform., 2020

PamgeneAnalyzeR: open and reproducible pipeline for kinase profiling.
Bioinform., 2020

2019
Updates in Rhea: SPARQLing biochemical reaction data.
Nucleic Acids Res., 2019

An enhanced workflow for variant interpretation in UniProtKB/Swiss-Prot improves consistency and reuse in ClinVar.
Database J. Biol. Databases Curation, 2019

2018
Scaling up data curation using deep learning: An application to literature triage in genomic variation resources.
PLoS Comput. Biol., 2018

Expert curation for building network-based dynamical models: a case study on atherosclerotic plaque formation.
Database J. Biol. Databases Curation, 2018

Towards in the Field Fast Pathogens Detection Using FPGAs.
Proceedings of the 28th International Conference on Field Programmable Logic and Applications, 2018

2017
Updates in Rhea - an expert curated resource of biochemical reactions.
Nucleic Acids Res., 2017

InterPro in 2017 - beyond protein family and domain annotations.
Nucleic Acids Res., 2017

HumaReC project: digital New Testament and continuous data publishing.
Proceedings of the 12th Annual International Conference of the Alliance of Digital Humanities Organizations, 2017

2016
Boolean regulatory network reconstruction using literature based knowledge with a genetic algorithm optimization method.
BMC Bioinform., 2016

Pressing needs of biomedical text mining in biocuration and beyond: opportunities and challenges.
Database J. Biol. Databases Curation, 2016

Improving HIV proteome annotation: new features of BioAfrica HIV Proteomics Resource.
Database J. Biol. Databases Curation, 2016

2015
Angiogenic Activity of Breast Cancer Patients' Monocytes Reverted by Combined Use of Systems Modeling and Experimental Approaches.
PLoS Comput. Biol., 2015

HAMAP in 2015: updates to the protein family classification and annotation system.
Nucleic Acids Res., 2015

Updates in Rhea - a manually curated resource of biochemical reactions.
Nucleic Acids Res., 2015

The InterPro protein families database: the classification resource after 15 years.
Nucleic Acids Res., 2015

TRAL: tandem repeat annotation library.
Bioinform., 2015

Cooperative development of logical modelling standards and tools with CoLoMoTo.
Bioinform., 2015

The SwissLipids knowledgebase for lipid biology.
Bioinform., 2015

2014
Analysis of Stop-Gain and Frameshift Variants in Human Innate Immunity Genes.
PLoS Comput. Biol., 2014

Fifteen years SIB Swiss Institute of Bioinformatics: life science databases, tools and support.
Nucleic Acids Res., 2014

The EMPRES-i genetic module: a novel tool linking epidemiological outbreak information and genetic characteristics of influenza viruses.
Database J. Biol. Databases Curation, 2014

Reconciliation of metabolites and biochemical reactions for metabolic networks.
Briefings Bioinform., 2014

2013
New and continuing developments at PROSITE.
Nucleic Acids Res., 2013

HAMAP in 2013, new developments in the protein family classification and annotation system.
Nucleic Acids Res., 2013

ViralZone: recent updates to the virus knowledge resource.
Nucleic Acids Res., 2013

SBML qualitative models: a model representation format and infrastructure to foster interactions between qualitative modelling formalisms and tools.
BMC Syst. Biol., 2013

Application of text-mining for updating protein post-translational modification annotation in UniProtKB.
BMC Bioinform., 2013

pfsearchV3: a code acceleration and heuristic to search PROSITE profiles.
Bioinform., 2013

Density-based hierarchical clustering of pyro-sequences on a large scale - the case of fungal ITS1.
Bioinform., 2013

Hard-wired heterogeneity in blood stem cells revealed using a dynamic regulatory network model.
Bioinform., 2013

2012
UniPathway: a resource for the exploration and annotation of metabolic pathways.
Nucleic Acids Res., 2012

The UniProt-GO Annotation database in 2011.
Nucleic Acids Res., 2012

ExPASy: SIB bioinformatics resource portal.
Nucleic Acids Res., 2012

Rhea - a manually curated resource of biochemical reactions.
Nucleic Acids Res., 2012

Biocurators and Biocuration: surveying the 21st century challenges.
Database J. Biol. Databases Curation, 2012

2011
T-Coffee: a web server for the multiple sequence alignment of protein and RNA sequences using structural information and homology extension.
Nucleic Acids Res., 2011

ViralZone: a knowledge resource to understand virus diversity.
Nucleic Acids Res., 2011

A qualitative continuous model of cellular auxin and brassinosteroid signaling and their crosstalk.
Bioinform., 2011

Visualization and quality assessment of <i>de novo</i> genome assemblies.
Bioinform., 2011

Conceptual framework and pilot study to benchmark phylogenomic databases based on reference gene trees.
Briefings Bioinform., 2011

2010
FastEpistasis: a high performance computing solution for quantitative trait epistasis.
Bioinform., 2010

OpenFluDB, a database for human and animal influenza virus.
Database J. Biol. Databases Curation, 2010

EuroDia: a beta-cell gene expression resource.
Database J. Biol. Databases Curation, 2010

2009
The Microbe browser for comparative genomics.
Nucleic Acids Res., 2009

MIMAS 3.0 is a Multiomics Information Management and Annotation System.
BMC Bioinform., 2009

AssociationViewer: a scalable and integrated software tool for visualization of large-scale variation data in genomic context.
Bioinform., 2009

Modeling stochasticity and robustness in gene regulatory networks.
Bioinform., 2009

2008
R-Coffee: a web server for accurately aligning noncoding RNA sequences.
Nucleic Acids Res., 2008

Probabilistic base calling of Solexa sequencing data.
BMC Bioinform., 2008

Synchronous versus asynchronous modeling of gene regulatory networks.
Bioinform., 2008

2007
Dynamic simulation of regulatory networks using SQUAD.
BMC Bioinform., 2007

An Efficient Method for Dynamic Analysis of Gene Regulatory Networks and <i>in silico</i> Gene Perturbation Experiments.
Proceedings of the Research in Computational Molecular Biology, 2007

2002
DIP, the Database of Interacting Proteins: a research tool for studying cellular networks of protein interactions.
Nucleic Acids Res., 2002

2001
DIP: The Database of Interacting Proteins: 2001 update.
Nucleic Acids Res., 2001

Mining literature for protein-protein interactions.
Bioinform., 2001

2000
DIP: the Database of Interacting Proteins.
Nucleic Acids Res., 2000


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