A. Niknejad

发表

High‐performance peptide identification by tandem mass spectrometry allows reliable automatic data processing in proteomics

A. Masselot, J. Colinge, L. Bougueleret, 2004, Proteomics.

Experiments in searching small proteins in unannotated large eukaryotic genomes.

J. Colinge, L. Bougueleret, Isabelle Cusin, 2005, Journal of proteome research.

In vitro and in silico processes to identify differentially expressed proteins

Patricia Rodriguez-Tomé, Eduardo Gonzalez-Couto, Catherine Jeandenans, 2004, Proteomics.

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

I. Xenarios, A. Niknejad, A. Chasapi, 2015, PLoS ONE.

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

N. Guex, A. Reymond, C. Shaw, 2016, Genome Medicine.

Updates in Rhea – an expert curated resource of biochemical reactions

Anne Morgat, Elisabeth Coudert, Kristian B. Axelsen, 2017, Nucleic Acids Res..

The Bgee suite: integrated curated expression atlas and comparative transcriptomics in animals

M. Robinson‐Rechavi, A. Niknejad, K. Sanjeev, 2020, Nucleic acids research.

Uncovering hidden duplicated content in public transcriptomics data

Anne Niknejad, Frederic B. Bastian, Marc Robinson-Rechavi, 2013, Database J. Biol. Databases Curation.

The Minimum Information about a Molecular Interaction CAusal STatement (MI2CAST)

Charles Tapley Hoyt, C. Mungall, P. Thomas, 2020, Bioinform..

Creation and unification of development and life stage ontologies for animals

C. Mungall, D. Osumi-Sutherland, A. Niknejad, 2022, 2206.12231.

Databases and ontologies The SwissLipids knowledgebase for lipid biology

I. Xenarios, A. Bridge, L. Bougueleret, 2015 .

The Bgee suite: integrated curated expression atlas and comparative transcriptomics in animals

Sébastien Moretti, Philippe Moret, Anne Niknejad, 2020, bioRxiv.

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

N. Guex, A. Reymond, C. Shaw, 2016, Genome Medicine.

Unification of multi-species vertebrate anatomy ontologies for comparative biology in Uberon

Judith A. Blake, Chris Mungall, Melissa Haendel, 2014, Journal of Biomedical Semantics.

Generation of Molecular Models and Pathways

Alan Bridge, Ioannis Xenarios, Julien Dorier, 2018 .

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

Ioannis Xenarios, Martin Ebeling, Julien Dorier, 2016, BMC Bioinformatics.

The Confidence Information Ontology: a step towards a standard for asserting confidence in annotations

Marcus C. Chibucos, Michelle G. Giglio, Sandra E. Orchard, 2015, Database J. Biol. Databases Curation.

The SIB Swiss Institute of Bioinformatics’ resources: focus on curated databases

Oliver Horlacher, Damian Szklarczyk, Christian von Mering, 2015, Nucleic Acids Res..

The SwissLipids knowledgebase for lipid biology

Alan Bridge, Lydie Bougueleret, Ioannis Xenarios, 2015, Bioinform..

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

Alan Bridge, Ioannis Xenarios, Julien Dorier, 2018, Database J. Biol. Databases Curation.

Updates in Rhea: SPARQLing biochemical reaction data

Anne Morgat, Elisabeth Coudert, Kristian B. Axelsen, 2018, Nucleic Acids Res..

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

Brian J. Stevenson, I. Xenarios, Y. Daali, 2020, Journal of thrombosis and haemostasis : JTH.

Identification of biomarkers for glycaemic deterioration in type 2 diabetes

L. Groop, V. Gudnason, T. Suvitaival, 2023, Nature communications.

Novel biomarkers for glycaemic deterioration in type 2 diabetes: an IMI RHAPSODY study

L. Groop, V. Gudnason, T. Suvitaival, 2021, medRxiv.

vHOG, a multispecies vertebrate ontology of homologous organs groups

Anne Niknejad, Frederic B. Bastian, Marc Robinson-Rechavi, 2012, Bioinform..

Updates in Rhea—a manually curated resource of biochemical reactions

Christoph Steinbeck, Anne Morgat, Elisabeth Coudert, 2014, Nucleic Acids Res..

Bgee: a database for the study of gene expression evolution

A. Niknejad, K. Sanjeev, Y. Jarosz, 2010 .

Updates in Rhea – an expert curated resource of biochemical reactions

Anne Morgat, Elisabeth Coudert, Kristian B. Axelsen, 2016, Nucleic Acids Res..

The SIB Swiss Institute of Bioinformatics’ resources: focus on curated databases

Joshua L. Payne, Christian J. A. Sigrist, Brian J. Stevenson, 2015, Nucleic Acids Res..