List of works by Ioannis Xenarios

A 2D/3D image analysis system to track fluorescently labeled structures in rod-shaped cells: application to measure spindle pole asymmetry during mitosis

scientific article

A Chemical Proteomics Approach to Phosphatidylinositol 3-Kinase Signaling in Macrophages

article by Christian Pasquali et al published 7 July 2007 in Molecular & Cellular Proteomics

A Clb/Cdk1-mediated regulation of Fkh2 synchronizes CLB expression in the budding yeast cell cycle

scientific article

A method for the generation of standardized qualitative dynamical systems of regulatory networks

scientific article published on 16 March 2006

A multi-omics digital research object for the genetics of sleep regulation

scientific article published on 31 October 2019

A qualitative continuous model of cellular auxin and brassinosteroid signaling and their crosstalk

scientific article

A robust second-generation genome-wide test for fetal aneuploidy based on shotgun sequencing cell-free DNA in maternal blood

article by N. Guex et al published 3 May 2013 in Prenatal Diagnosis

A systems genetics resource and analysis of sleep regulation in the mouse

article

Activities at the Universal Protein Resource (UniProt)

scientific article (publication date: 2014)

An Extended, Boolean Model of the Septation Initiation Network in S.Pombe Provides Insights into Its Regulation.

scientific article published on 5 August 2015

An enhanced workflow for variant interpretation in UniProtKB/Swiss-Prot improves consistency and reuse in ClinVar

article

An integrated ontology resource to explore and study host-virus relationships

scientific article

Analysis of S. pombe SIN protein association to the SPB reveals two genetically separable states of the SIN.

scientific article published on 12 December 2014

Analysis of stop-gain and frameshift variants in human innate immunity genes

scientific article

Analysis of stop-gain and frameshift variants in human innate immunity genes

article

Analysis of the dynamic co-expression network of heart regeneration in the zebrafish.

scientific article

Angiogenic activity of breast cancer patients' monocytes reverted by combined use of systems modeling and experimental approaches

scientific article

Animal toxins: How is complexity represented in databases?

scientific article

Application of text-mining for updating protein post-translational modification annotation in UniProtKB

scientific article

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

scientific article

Automated quantitative histology reveals vascular morphodynamics during Arabidopsis hypocotyl secondary growth

scientific article published on 11 February 2014

Bacterial Virus Ontology; Coordinating across Databases.

scientific article

Biocurators and biocuration: surveying the 21st century challenges

scientific article

Boolean regulatory network reconstruction using literature based knowledge with a genetic algorithm optimization method

scientific article

Broadening the horizon--level 2.5 of the HUPO-PSI format for molecular interactions

scientific article

CDK9 regulates AR promoter selectivity and cell growth through serine 81 phosphorylation

scientific article

Cell-free DNA testing of an extended range of chromosomal anomalies: clinical experience with 6,388 consecutive cases

scientific article published on 30 June 2016

Characterization and mutagenesis of Chinese hamster ovary cells endogenous retroviruses to inactivate viral particle release

scientific article published on 12 November 2019

Characterization of the human ABCG1 gene: liver X receptor activates an internal promoter that produces a novel transcript encoding an alternative form of the protein

scientific article

Clade-level Spatial Modelling of HPAI H5N1 Dynamics in the Mekong Region Reveals New Patterns and Associations with Agro-Ecological Factors

scientific article published on 25 July 2016

Comparative transcriptome profiling of the injured zebrafish and mouse hearts identifies miRNA-dependent repair pathways

scientific article published on 7 February 2016

Comparison of strategies to detect epistasis from eQTL data

scientific article

Complement facilitates early prion pathogenesis

scientific article published in April 2001

Conceptual framework and pilot study to benchmark phylogenomic databases based on reference gene trees

scientific article

Consent insufficient for data release-Response

scientific article published on 01 May 2019

Contribution of exome sequencing to the identification of genes involved in the response to clopidogrel in cardiovascular patients

scientific article published on 20 February 2020

Control of Cognate Sense mRNA Translation by cis-Natural Antisense RNAs

article

Cooperative development of logical modelling standards and tools with CoLoMoTo

scientific article published on 25 January 2015

Cooperative development of logical modelling standards and tools with CoLoMoTo

article

DIP, the Database of Interacting Proteins: a research tool for studying cellular networks of protein interactions

scientific article

Database resources for the tuberculosis community

scientific article published on 17 January 2013

Deciphering the Dynamic Transcriptional and Post-transcriptional Networks of Macrophages in the Healthy Heart and after Myocardial Injury

scientific article published on 01 April 2018

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

scientific article published on 28 March 2013

Describing biological protein interactions in terms of protein states and state transitions: the LiveDIP database

scientific article

Detection and identification of plasma proteins that bind GlialCAM using ProteinChip arrays, SELDI-TOF MS, and nano-LC MS/MS.

scientific article

Differential reactivity of TCR Vbeta10 alleles to a mouse mammary tumor virus superantigen

scientific article published in October 1998

Differentially phased leaf growth and movements in Arabidopsis depend on coordinated circadian and light regulation

scientific article published on 3 October 2014

Drug Design Workshop: A Web-Based Educational Tool To Introduce Computer-Aided Drug Design to the General Public

article by Antoine Daina et al published 27 February 2017 in Journal of Chemical Education

DynaStI: A Dynamic Retention Time Database for Steroidomics.

scientific article published on 30 April 2019

Dynamic simulation of regulatory networks using SQUAD

scientific article

ENFIN--A European network for integrative systems biology

scientific article

Efficient computation of minimal perturbation sets in gene regulatory networks

scientific article

Enhanced metabolite annotation via dynamic retention time prediction: Steroidogenesis alterations as a case study

scientific article

Enzyme annotation in UniProtKB using Rhea

scientific article published on 01 March 2020

Erratum: Corrigendum: Protein interaction data curation: the International Molecular Exchange (IMEx) consortium

article

Estimating the Contribution of Proteasomal Spliced Peptides to the HLA-I Ligandome

scientific article published on 31 August 2018

EuroDia: a beta-cell gene expression resource

scientific article (publication date: 12 October 2010)

Evolution of the ferric reductase domain (FRD) superfamily: modularity, functional diversification, and signature motifs

scientific article

Evolutionary trajectories of primate genes involved in HIV pathogenesis.

scientific article published on 2 September 2009

ExPASy: SIB bioinformatics resource portal

scientific article published on 31 May 2012

Exome sequencing identifies recurrent somatic MAP2K1 and MAP2K2 mutations in melanoma.

scientific article

Expert curation for building network-based dynamical models: a case study on atherosclerotic plaque formation.

scientific article

Expert curation in UniProtKB: a case study on dealing with conflicting and erroneous data

scientific article

Extensive remodeling of DC function by rapid maturation-induced transcriptional silencing

scientific article

FastEpistasis: a high performance computing solution for quantitative trait epistasis

scientific article

Fifteen years SIB Swiss Institute of Bioinformatics: life science databases, tools and support

scientific article

Fisetin protects against cardiac cell death through reduction of ROS production and caspases activity

scientific article published on 19 February 2020

Functional and Evolutionary Analysis of the CASPARIAN STRIP MEMBRANE DOMAIN PROTEIN Family

scientific article published on 11 June 2014

Gene Ontology annotations and resources

scientific article

Gene expression across mammalian organ development

scientific article published on 26 June 2019

Generation of Molecular Models and Pathways

Genetic variations and diseases in UniProtKB/Swiss-Prot: the ins and outs of expert manual curation

scientific article published on 24 June 2014

Genome-wide analysis of SREBP1 activity around the clock reveals its combined dependency on nutrient and circadian signals

scientific article

Genome-wide identification of microRNAs regulating the human prion protein

scientific article published on 21 December 2018

Genome-wide profiling of the cardiac transcriptome after myocardial infarction identifies novel heart-specific long non-coding RNAs

scientific article

Global mapping of highly pathogenic avian influenza H5N1 and H5Nx clade 2.3.4.4 viruses with spatial cross-validation

scientific article

Guidelines for reporting the use of mass spectrometry in proteomics.

scientific article

HAMAP as SPARQL rules-A portable annotation pipeline for genomes and proteomes

scientific article published on 01 February 2020

HAMAP in 2013, new developments in the protein family classification and annotation system

scientific article

HAMAP in 2015: updates to the protein family classification and annotation system

scientific article

HENA, heterogeneous network-based data set for Alzheimer's disease

scientific article published on 14 August 2019

Hard-wired heterogeneity in blood stem cells revealed using a dynamic regulatory network model

scientific article published on July 2013

Human ERK1 Induces Filamentous Growth and Cell Wall Remodeling Pathways inSaccharomyces cerevisiae

scientific article published in Journal of Biological Chemistry

IL-4 Rapidly Produced by Vβ4 Vα8 CD4+ T Cells Instructs Th2 Development and Susceptibility to Leishmania major in BALB/c Mice

article

Identification of a RAI1-associated disease network through integration of exome sequencing, transcriptomics, and 3D genomics.

scientific article

Identification of a novel PPARβ/δ/miR-21-3p axis in UV-induced skin inflammation.

scientific article published on June 2016

Identifying biological mechanisms for favorable cancer prognosis using non-hypothesis-driven iterative survival analysis

scientific article

Implicit methods for qualitative modeling of gene regulatory networks

scientific article

Improving HIV proteome annotation: new features of BioAfrica HIV Proteomics Resource

scientific article published on 17 April 2016

Improving the quality and workflow of bacterial genome sequencing and analysis: paving the way for a Switzerland-wide molecular epidemiological surveillance platform

scientific article published on 15 December 2018

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

scientific article published on 01 April 2020

Integrated proteogenomic deep sequencing and analytics accurately identify non-canonical peptides in tumor immunopeptidomes

scientific article published on 10 March 2020

Integrative knowledge management to enhance pharmaceutical R&D

scientific article

InterPro in 2017-beyond protein family and domain annotations

scientific article

Interplays between mouse mammary tumor virus and the cellular and humoral immune response.

scientific article

KIAA1109 Variants Are Associated with a Severe Disorder of Brain Development and Arthrogryposis ⬇️

scientific article published on 27 December 2017

Laser capture microdissection of human pancreatic islets reveals novel eQTLs associated with type 2 diabetes

Local auxin production underlies a spatially restricted neighbor-detection response in Arabidopsis

scientific article

Localizing proteins in the cell from their phylogenetic profiles.

scientific article

Low Rate of Somatic Mutations in a Long-Lived Oak Tree

Low number of fixed somatic mutations in a long-lived oak tree.

scientific article published on 4 December 2017

MAR-Mediated transgene integration into permissive chromatin and increased expression by recombination pathway engineering

scientific article published on 29 August 2016

MIMAS 3.0 is a Multiomics Information Management and Annotation System

scientific article

Measuring the diurnal pattern of leaf hyponasty and growth in Arabidopsis - a novel phenotyping approach using laser scanning

scientific article published on 01 November 2012

Microarray analysis of isolated human islet transcriptome in type 2 diabetes and the role of the ubiquitin-proteasome system in pancreatic beta cell dysfunction

scientific article published on 12 December 2012

Microarray deacetylation maps determine genome-wide functions for yeast histone deacetylases

scientific article

Modeling of multiple valued gene regulatory networks.

scientific article published in January 2007

Modeling stochasticity and robustness in gene regulatory networks

scientific article published in June 2009

Molecular docking of competitive phosphodiesterase inhibitors

scientific article published in January 2002

Molecular phenotyping of multiple mouse strains under metabolic challenge uncovers a role for Elovl2 in glucose-induced insulin secretion

scientific article published on 26 January 2017

MorphoGraphX: A platform for quantifying morphogenesis in 4D

scientific article published on 6 May 2015

MsViz: A Graphical Software Tool for In-Depth Manual Validation and Quantitation of Post-translational Modifications

scientific article published on 21 June 2017

Multiple imputations applied to the DREAM3 phosphoproteomics challenge: a winning strategy

scientific article

Mutations inLONP1, a mitochondrial matrix protease, cause CODAS syndrome

scientific article published on 21 March 2015

Navigating in vitro bioactivity data by investigating available resources using model compounds

scientific article published on 29 April 2019

Neighbor Detection Induces Organ-Specific Transcriptomes, Revealing Patterns Underlying Hypocotyl-Specific Growth.

scientific article

Network-guided analysis of genes with altered somatic copy number and gene expression reveals pathways commonly perturbed in metastatic melanoma

scientific article

Neutrophils and Snail Orchestrate the Establishment of a Pro-tumor Microenvironment in Lung Cancer.

scientific article published in December 2017

New and continuing developments at PROSITE.

scientific article

New genome assembly of the barn owl (Tyto alba alba)

scientific article published on 19 February 2020

New molecular insights into modulation of platelet reactivity in aspirin-treated patients using a network-based approach

scientific article

Ongoing and future developments at the Universal Protein Resource

scientific article

OpenFluDB, a database for human and animal influenza virus

scientific article

PamgeneAnalyzeR: open and reproducible pipeline for kinase profiling

scientific article published on 10 January 2020

Personalized cancer vaccine effectively mobilizes antitumor T cell immunity in ovarian cancer.

scientific article published in April 2018

Phytochrome interacting factors 4 and 5 control seedling growth in changing light conditions by directly controlling auxin signaling.

scientific article published on 22 June 2012

Plant species distributions along environmental gradients: do belowground interactions with fungi matter?

scientific article published on 10 December 2013

Plasma Dihydroceramides Are Diabetes Susceptibility Biomarker Candidates in Mice and Humans

scientific article published in February 2017

Predicting combinations of immunomodulators to enhance dendritic cell-based vaccination based on a hybrid experimental and computational platform

scientific article published on 08 August 2020

Pressing needs of biomedical text mining in biocuration and beyond: opportunities and challenges

scientific article

Probabilistic base calling of Solexa sequencing data

scientific article

Protein function in the post-genomic era.

scientific article

Protein interaction data curation: the International Molecular Exchange (IMEx) consortium

scientific article

Protein interaction databases

scientific article

Protein interactions: two methods for assessment of the reliability of high throughput observations

scientific article

ProteomeXchange provides globally coordinated proteomics data submission and dissemination

scientific article (publication date: March 2014)

Proteomic analysis of the mouse liver mitochondrial inner membrane

scientific journal article

Qualitative modeling identifies IL-11 as a novel regulator in maintaining self-renewal in human pluripotent stem cells

scientific article published on 28 October 2013

Quest for Orthologs Entails Quest for Tree of Life: In Search of the Gene Stream

scientific article published in July 2015

R-Coffee: a web server for accurately aligning noncoding RNA sequences

scientific article

Reconciliation of metabolites and biochemical reactions for metabolic networks

scientific article

Reorganizing the protein space at the Universal Protein Resource (UniProt)

scientific article (publication date: 2012)

Rhea--a manually curated resource of biochemical reactions

scientific article published on December 2011

SBML qualitative models: a model representation format and infrastructure to foster interactions between qualitative modelling formalisms and tools

scientific article

Scaling up data curation using deep learning: An application to literature triage in genomic variation resources

scientific article published on 13 August 2018

Sensitive and frequent identification of high avidity neo-epitope specific CD8 + T cells in immunotherapy-naive ovarian cancer.

scientific article published on 15 March 2018

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

scientific article published on 21 April 2020

Sleep-wake-driven and circadian contributions to daily rhythms in gene expression and chromatin accessibility in the murine cortex

scientific article published on 27 November 2019

Social networks help to infer causality in the tumor microenvironment

scientific article

SourceData - a semantic platform for curating and searching figures

SourceData: a semantic platform for curating and searching figures

scientific article published in October 2017

Standardized benchmarking in the quest for orthologs

scientific article (publication date: 4 April 2016)

Strengths and Weaknesses of Selected Modeling Methods Used in Systems Biology

Substantial deletion overlap among divergent Arabidopsis genomes revealed by intersection of short reads and tiling arrays

scientific article

Synchronous versus asynchronous modeling of gene regulatory networks

scientific article published on 9 July 2008

Systems biology of the IMIDIA biobank from organ donors and pancreatectomised patients defines a novel transcriptomic signature of islets from individuals with type 2 diabetes

scientific article published on 28 November 2017

Systems biology to battle vascular disease

scientific article published on 03 February 2010

T-Coffee: a web server for the multiple sequence alignment of protein and RNA sequences using structural information and homology extension

scientific article

TBC1D7 mutations are associated with intellectual disability, macrocrania, patellar dislocation, and celiac disease

scientific article published on April 2014

TIE-2 and VEGFR kinase activities drive immunosuppressive function of TIE-2-expressing monocytes in human breast tumors

scientific article published on 6 May 2013

TIE-2 expressing monocytes in human cancers.

scientific article

TIE-2-expressing monocytes are lymphangiogenic and associate specifically with lymphatics of human breast cancer

scientific article published on 20 August 2015

TRAL: tandem repeat annotation library

scientific article published on 18 May 2015

Taxon sampling unequally affects individual nodes in a phylogenetic tree: consequences for model gene tree construction in SwissTree

article

The EMPRES-i genetic module: a novel tool linking epidemiological outbreak information and genetic characteristics of influenza viruses

scientific article published on 06 March 2014

The HUPO PSI's molecular interaction format--a community standard for the representation of protein interaction data

scientific article (publication date: February 2004)

The InterPro protein families database: the classification resource after 15 years

scientific article

The Microbe browser for comparative genomics

scientific article published on 30 April 2009

The SwissLipids knowledgebase for lipid biology

scientific article published on 5 May 2015

The UniProt-GO Annotation database in 2011.

scientific article published on 28 November 2011

The UniProtKB/Swiss-Prot Tox-Prot program: A central hub of integrated venom protein data

scientific article

The direct effects of tacrolimus and cyclosporin A on isolated human islets: A functional, survival and gene expression study.

scientific article published on September 2009

The genome of the fire ant Solenopsis invicta

scientific article

The ins and outs of eukaryotic viruses: Knowledge base and ontology of a viral infection

scientific article

The minimum information required for reporting a molecular interaction experiment (MIMIx).

scientific article published on August 2007

The mzTab data exchange format: communicating mass-spectrometry-based proteomics and metabolomics experimental results to a wider audience

scientific article

Three-dimensional chromatin interactions remain stable upon CAG/CTG repeat expansion

scientific article published on 03 July 2020

Three-dimensional cluster analysis identifies interfaces and functional residue clusters in proteins

scientific article published in April 2001

Toward a rational design of combination therapy in cancer

scientific article published on 7 July 2015

Toward interoperable bioscience data

scientific article (publication date: 27 January 2012)

Toward unrestricted use of public genomic data:

scientific article

Transcriptional response to cardiac injury in the zebrafish: systematic identification of genes with highly concordant activity across in vivo models.

scientific article

Type I interferons protect T cells against NK cell attack mediated by the activating receptor NCR1.

scientific article published on 5 June 2014

UniPathway: a resource for the exploration and annotation of metabolic pathways

scientific article published on 18 November 2011

UniProtKB/Swiss-Prot, the Manually Annotated Section of the UniProt KnowledgeBase: How to Use the Entry View

scientific article published in January 2016

Updates in Rhea - an expert curated resource of biochemical reactions

scientific article

Updates in Rhea - an expert curated resource of biochemical reactions

scientific article published on 15 December 2016

Updates in Rhea--a manually curated resource of biochemical reactions

scientific article

Updates in Rhea: SPARQLing biochemical reaction data

scientific article

ViralZone: a knowledge resource to understand virus diversity

scientific article

ViralZone: recent updates to the virus knowledge resource

scientific article

Virosaurus A Reference to Explore and Capture Virus Genetic Diversity

scientific article published on 01 November 2020

Visualization and quality assessment of de novo genome assemblies

scientific article published on 12 October 2011

West syndrome caused by homozygous variant in the evolutionary conserved gene encoding the mitochondrial elongation factor GUF1

scientific article published on 21 October 2015

pfsearchV3: a code acceleration and heuristic to search PROSITE profiles

scientific article published on 16 March 2013

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