Henning Hermjakob

Henning Hermjakob's AcademicInfluence.com Rankings

Henning Hermjakob

Engineering

#5472

World Rank

#6731

Historical Rank

Applied Physics

#1588

World Rank

#1620

Historical Rank

engineering Degrees

Henning Hermjakob

Biology

#10256

World Rank

#13567

Historical Rank

Bioinformatics

#120

World Rank

#122

Historical Rank

biology Degrees

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Engineering
Biology

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Henning Hermjakob's Published Works

Number of citations in a given year to any of this author's works

Total number of citations to an author for the works they published in a given year. This highlights publication of the most important work(s) by the author

Published Works

Initial sequencing and analysis of the human genome. (2001) (15222)
The Reactome pathway knowledgebase (2013) (3833)
2016 update of the PRIDE database and its related tools (2016) (2753)
ProteomeXchange provides globally co-ordinated proteomics data submission and dissemination (2014) (2398)
The Reactome pathway Knowledgebase (2015) (1905)
The Proteomics Identifications (PRIDE) database and associated tools: status in 2013 (2012) (1847)
On the frequency of protein glycosylation, as deduced from analysis of the SWISS-PROT database. (1999) (1681)
Databases on transcriptional regulation: TRANSFAC, TRRD and COMPEL (1998) (1574)
The MIntAct project—IntAct as a common curation platform for 11 molecular interaction databases (2013) (1505)
The Reactome Pathway Knowledgebase (2017) (1475)
Reactome: a database of reactions, pathways and biological processes (2010) (1462)
The minimum information about a genome sequence (MIGS) specification (2008) (1344)
The IntAct molecular interaction database in 2012 (2011) (1259)
The InterPro database, an integrated documentation resource for protein families, domains and functional sites (2001) (1061)
Reactome knowledgebase of human biological pathways and processes (2008) (981)
IntAct: an open source molecular interaction database (2004) (967)
IntAct—open source resource for molecular interaction data (2006) (832)
2016 update of the PRIDE database and its related tools (2015) (826)
Reactome pathway analysis: a high-performance in-memory approach (2017) (791)
Overview of the HUPO Plasma Proteome Project: Results from the pilot phase with 35 collaborating laboratories and multiple analytical groups, generating a core dataset of 3020 proteins and a publicly‐available database (2005) (766)
A common open representation of mass spectrometry data and its application to proteomics research (2004) (764)
The minimum information about a proteomics experiment (MIAPE) (2007) (704)
The ProteomeXchange consortium in 2017: supporting the cultural change in proteomics public data deposition (2016) (693)
The HUPO PSI's Molecular Interaction format—a community standard for the representation of protein interaction data (2004) (672)
iProX: an integrated proteome resource (2018) (648)
mzML—a Community Standard for Mass Spectrometry Data* (2010) (565)
The reactome pathway knowledgebase (2019) (555)
PRIDE: The proteomics identifications database (2005) (547)
Promoting coherent minimum reporting guidelines for biological and biomedical investigations: the MIBBI project (2008) (543)
The IntAct molecular interaction database in 2010 (2009) (533)
Reactome graph database: Efficient access to complex pathway data (2018) (487)
Protein interaction data curation: the International Molecular Exchange (IMEx) consortium (2012) (477)
The ProteomeXchange consortium in 2020: enabling ‘big data’ approaches in proteomics (2019) (449)
Disrupted in Schizophrenia 1 Interactome: evidence for the close connectivity of risk genes and a potential synaptic basis for schizophrenia (2007) (433)
Toward interoperable bioscience data (2012) (388)
InterPro: An Integrated Documentation Resource for Protein Families, Domains and Functional Sites (2002) (376)
The reactome pathway knowledgebase 2022 (2021) (335)
Open Targets: a platform for therapeutic target identification and validation (2016) (321)
Clinical proteomics: A need to define the field and to begin to set adequate standards (2007) (303)
Annotating Cancer Variants and Anti-Cancer Therapeutics in Reactome (2012) (296)
PSICQUIC and PSISCORE: accessing and scoring molecular interactions (2011) (284)
BioModels: ten-year anniversary (2014) (280)
Broadening the horizon – level 2.5 of the HUPO-PSI format for molecular interactions (2007) (280)
PRIDE: a public repository of protein and peptide identifications for the proteomics community (2005) (279)
The minimum information required for reporting a molecular interaction experiment (MIMIx) (2007) (279)
The Proteomics Identifications database: 2010 update (2009) (255)
ProteomeBinders: planning a European resource of affinity reagents for analysis of the human proteome (2007) (241)
A guide to the Proteomics Identifications Database proteomics data repository (2009) (237)
The Ontology Lookup Service, a lightweight cross-platform tool for controlled vocabulary queries (2006) (229)
The implications of alternative splicing in the ENCODE protein complement (2007) (227)
MEMOTE for standardized genome-scale metabolic model testing (2020) (214)
The Proteomics Standards Initiative (2003) (201)
The mzIdentML Data Standard for Mass Spectrometry-Based Proteomics Results (2012) (182)
Reactome enhanced pathway visualization (2017) (179)
Path2Models: large-scale generation of computational models from biochemical pathway maps (2013) (167)
BioModels—15 years of sharing computational models in life science (2019) (167)
Calling on a million minds for community annotation in WikiProteins (2008) (163)
InterPro--an integrated documentation resource for protein families, domains and functional sites. (2000) (157)
Making proteomics data accessible and reusable: Current state of proteomics databases and repositories (2015) (151)
Capturing variation impact on molecular interactions in the IMEx Consortium mutations data set (2019) (148)
The Protein Identifier Cross-Referencing (PICR) service: reconciling protein identifiers across multiple source databases (2007) (146)
Human Proteome Project Mass Spectrometry Data Interpretation Guidelines 2.1. (2016) (144)
PRIDE: new developments and new datasets (2007) (139)
SBML Level 3: an extensible format for the exchange and reuse of biological models (2020) (137)
A comparison of signal sequence prediction methods using a test set of signal peptides (2000) (137)
Analyzing protein-protein interaction networks. (2012) (136)
The Ontology Lookup Service: bigger and better (2010) (125)
PRIDE Inspector Toolsuite: Moving Toward a Universal Visualization Tool for Proteomics Data Standard Formats and Quality Assessment of ProteomeXchange Datasets* (2015) (121)
PRIDE Inspector: a tool to visualize and validate MS proteomics data (2011) (120)
Recognizing millions of consistently unidentified spectra across hundreds of shotgun proteomics datasets (2016) (119)
The PRoteomics IDEntification (PRIDE) Converter 2 Framework: An Improved Suite of Tools to Facilitate Data Submission to the PRIDE Database and the ProteomeXchange Consortium* (2012) (116)
Discovering and linking public omics data sets using the Omics Discovery Index (2017) (115)
BioJS: an open source JavaScript framework for biological data visualization (2013) (113)
Integrating biological data – the Distributed Annotation System (2008) (113)
Identifiers for the 21st century: How to design, provision, and reuse persistent identifiers to maximize utility and impact of life science data (2017) (110)
The Functional Genomics Experiment model (FuGE): an extensible framework for standards in functional genomics (2007) (110)
The mzTab Data Exchange Format: Communicating Mass-spectrometry-based Proteomics and Metabolomics Experimental Results to a Wider Audience* (2014) (108)
PhaSepDB: a database of liquid–liquid phase separation related proteins (2019) (107)
COVID-19 Disease Map, building a computational repository of SARS-CoV-2 virus-host interaction mechanisms (2020) (107)
Erratum: Initial sequencing and analysis of the human genome: International Human Genome Sequencing Consortium (Nature (2001) 409 (860-921)) (2001) (106)
Reactome pathway analysis to enrich biological discovery in proteomics data sets (2011) (98)
Common interchange standards for proteomics data: Public availability of tools and schema. Report on the Proteomic Standards Initiative Workshop, 2nd Annual HUPO Congress, Montreal, Canada, 8–11th October 2003 (2004) (96)
Recommendations for Mass Spectrometry Data Quality Metrics for Open Access Data (Corollary to the Amsterdam Principles)* (2011) (93)
The Ontology Lookup Service: more data and better tools for controlled vocabulary queries (2008) (90)
A new reference implementation of the PSICQUIC web service (2013) (88)
The complex portal - an encyclopaedia of macromolecular complexes (2014) (87)
The Proteomics Identifications Database (PRIDE) and the ProteomExchange Consortium: making proteomics data accessible (2006) (85)
Minimum information about a bioactive entity (MIABE) (2011) (84)
Reactome diagram viewer: data structures and strategies to boost performance (2017) (83)
Open source libraries and frameworks for mass spectrometry based proteomics: A developer's perspective☆ (2014) (80)
A Reagent Resource to Identify Proteins and Peptides of Interest for the Cancer Community (2006) (76)
Proteomics Standards Initiative: Fifteen Years of Progress and Future Work (2017) (76)
The HUPO proteomics standards initiative- mass spectrometry controlled vocabulary (2013) (75)
LipidHome: A Database of Theoretical Lipids Optimized for High Throughput Mass Spectrometry Lipidomics (2013) (73)
Recommendations from the 2008 International Summit on Proteomics Data Release and Sharing Policy: the Amsterdam principles. (2009) (73)
Complex Portal 2018: extended content and enhanced visualization tools for macromolecular complexes (2018) (70)
BioModels: expanding horizons to include more modelling approaches and formats (2017) (70)
R spider: a network-based analysis of gene lists by combining signaling and metabolic pathways from Reactome and KEGG databases (2010) (70)
The work of the Human Proteome Organisation's Proteomics Standards Initiative (HUPO PSI). (2006) (70)
Wikidata as a knowledge graph for the life sciences (2020) (70)
Submit Your Interaction Data the IMEx Way (2007) (70)
Hydra: a scalable proteomic search engine which utilizes the Hadoop distributed computing framework (2012) (66)
PRIDE Cluster: building a consensus of proteomics data (2013) (62)
Memote: A community driven effort towards a standardized genome-scale metabolic model test suite (2018) (61)
Organelle proteomics experimental designs and analysis (2010) (59)
Characterization, design, and function of the mitochondrial proteome: from organs to organisms. (2014) (58)
Recurated protein interaction datasets (2009) (58)
The HUPO Proteomics Standards Initiative – Overcoming the Fragmentation of Proteomics Data (2006) (57)
Data management and preliminary data analysis in the pilot phase of the HUPO Plasma Proteome Project (2005) (57)
The PSI semantic validator: A framework to check MIAPE compliance of proteomics data (2009) (56)
Integrated omics dissection of proteome dynamics during cardiac remodeling (2018) (56)
ReactomeGSA - Efficient Multi-Omics Comparative Pathway Analysis (2020) (55)
Five years of progress in the Standardization of Proteomics Data 4th Annual Spring Workshop of the HUPO‐Proteomics Standards Initiative April 23–25, 2007 Ecole Nationale Supérieure (ENS), Lyon, France (2007) (55)
Integration of Cardiac Proteome Biology and Medicine by a Specialized Knowledgebase (2013) (54)
Development of data representation standards by the human proteome organization proteomics standards initiative (2015) (54)
Harnessing the heart of big data. (2015) (54)
Reproducibility in systems biology modelling (2020) (53)
A critical appraisal of techniques, software packages, and standards for quantitative proteomic analysis. (2012) (53)
Quantifying the impact of public omics data (2018) (52)
Do we want our data raw? Including binary mass spectrometry data in public proteomics data repositories (2005) (52)
Uniform resolution of compact identifiers for biomedical data (2017) (51)
How to submit MS proteomics data to ProteomeXchange via the PRIDE database (2014) (51)
Merging and scoring molecular interactions utilising existing community standards: tools, use-cases and a case study (2015) (51)
Minimum information about a protein affinity reagent (MIAPAR) (2010) (50)
The HUPO proteomics standards initiative - easing communication and minimizing data loss in a changing world (2007) (48)
A domain level interaction network of amyloid precursor protein and Aβ of Alzheimer's disease (2010) (48)
Accurate estimation of isoelectric point of protein and peptide based on amino acid sequences (2015) (48)
VARSPLIC: alternatively-spliced protein sequences derived from SWISS-PROT and TrEMBL (2000) (48)
The PSI formal document process and its implementation on the PSI website (2007) (47)
qcML: An Exchange Format for Quality Control Metrics from Mass Spectrometry Experiments* (2014) (45)
Controlled vocabularies and ontologies in proteomics: Overview, principles and practice☆ (2014) (45)
In-depth analysis of protein inference algorithms using multiple search engines and well-defined metrics. (2017) (45)
Proteomics data validation: why all must provide data. (2007) (44)
InteroPORC: automated inference of highly conserved protein interaction networks (2008) (44)
A Community Standard Format for the Representation of Protein Affinity Reagents* (2009) (42)
Analyzing large-scale proteomics projects with latent semantic indexing. (2008) (41)
ReactomeGSA - Efficient Multi-Omics Comparative Pathway Analysis (2020) (41)
Encompassing new use cases - level 3.0 of the HUPO-PSI format for molecular interactions (2018) (40)
The evolution of standards and data management practices in systems biology (2015) (39)
A data citation roadmap for scholarly data repositories (2019) (38)
PRIDE: Quality control in a proteomics data repository (2012) (38)
Understudied proteins: opportunities and challenges for functional proteomics (2022) (38)
Open source libraries and frameworks for biological data visualisation: A guide for developers (2015) (37)
Mapping Plant Interactomes Using Literature Curated and Predicted Protein–Protein Interaction Data Sets[W] (2010) (37)
A visual review of the interactome of LRRK2: Using deep-curated molecular interaction data to represent biology (2015) (36)
The Reactome BioMart (2011) (35)
Dasty2, an Ajax protein DAS client (2008) (35)
Dasty and UniProt DAS: a perfect pair for protein feature visualization (2005) (35)
Recommendations for mass spectrometry data quality metrics for open access data (corollary to the Amsterdam principles) (2012) (35)
jmzIdentML API: A Java interface to the mzIdentML standard for peptide and protein identification data (2012) (34)
ms-data-core-api: an open-source, metadata-oriented library for computational proteomics (2015) (33)
Current status of proteomic standards development (2004) (33)
jmzReader: A Java parser library to process and visualize multiple text and XML-based mass spectrometry data formats (2012) (33)
Further Steps in Standardisation Report of the Second Annual Proteomics Standards Initiative Spring Workshop (Siena, Italy 17–20th April 2005) (2005) (33)
Advances in the development of common interchange standards for proteomic data (2004) (33)
MINT and IntAct contribute to the Second BioCreative challenge: serving the text-mining community with high quality molecular interaction data (2008) (33)
Annotating the Human Proteome (2005) (32)
A public repository for mass spectrometry imaging data (2014) (32)
A toolkit for the mzIdentML standard: the ProteoIDViewer, the mzidLibrary and the mzidValidator (2013) (32)
The HUPO Proteomics Standards Initiative Meeting: Towards Common Standards for Exchanging Proteomics Data (2003) (32)
Tools (Viewer, Library and Validator) that Facilitate Use of the Peptide and Protein Identification Standard Format, Termed mzIdentML* (2013) (31)
Towards a unified open access dataset of molecular interactions (2020) (31)
Further steps towards data standardisation: The Proteomic Standards Initiative HUPO 3rd annual congress, Beijing 25–27th October, 2004 (2005) (31)
Consequences of the discontinuation of the International Protein Index (IPI) database and its substitution by the UniProtKB “complete proteome” sets (2011) (31)
Testing and Validation of Computational Methods for Mass Spectrometry. (2016) (31)
Meeting Report from the Second “Minimum Information for Biological and Biomedical Investigations” (MIBBI) workshop (2010) (31)
The Protein Feature Ontology: a tool for the unification of protein feature annotations (2008) (29)
The Use of Common Ontologies and Controlled Vocabularies to Enable Data Exchange and Deposition for Complex Proteomic Experiments (2004) (29)
Corrigendum: Protein interaction data curation: the International Molecular Exchange (IMEx) consortium (2012) (28)
An informatic pipeline for the data capture and submission of quantitative proteomic data using iTRAQTM (2007) (28)
BioJS: an open source standard for biological visualisation – its status in 2014 (2014) (27)
Improvements in the protein identifier cross-reference service (2012) (27)
The role SWISS-PROT and TrEMBL play in the genome research environment. (2000) (27)
Swissknife - 'lazy parsing' of SWISS-PROT entries (1999) (26)
Published and Perished? The Influence of the Searched Protein Database on the Long-Term Storage of Proteomics Data* (2011) (26)
The IntAct database: efficient access to fine-grained molecular interaction data (2021) (25)
HENA, heterogeneous network-based data set for Alzheimer’s disease (2019) (25)
Further advances in the development of a data interchange standard for proteomics data (2003) (25)
COVID19 Disease Map, a computational knowledge repository of virus–host interaction mechanisms (2021) (24)
Autumn 2005 Workshop of the Human Proteome Organisation Proteomics Standards Initiative (HUPO‐PSI) Geneva, September, 4–6, 2005 (2006) (24)
The Gel Electrophoresis Markup Language (GelML) from the Proteomics Standards Initiative (2010) (24)
Pathway Analysis (2020) (22)
A reference set of curated biomedical data and metadata from clinical case reports (2018) (22)
Human Proteome Organization Proteomics Standards Initiative: data standardization, a view on developments and policy. (2007) (22)
ISPIDER Central: an integrated database web-server for proteomics (2008) (21)
CausalTAB: the PSI-MITAB 2.8 updated format for signalling data representation and dissemination (2019) (21)
Dasty3, a WEB framework for DAS (2011) (21)
The systematic annotation of the three main GPCR families in Reactome (2010) (21)
Computational proteomics pitfalls and challenges: HavanaBioinfo 2012 workshop report. (2013) (21)
Biomedical Informatics on the Cloud: A Treasure Hunt for Advancing Cardiovascular Medicine. (2018) (20)
The IMEx Coronavirus interactome: an evolving map of Coronaviridae-Host molecular interactions (2020) (20)
Introducing the PRIDE Archive RESTful web services (2015) (20)
Analysis of the experimental detection of central nervous system‐related genes in human brain and cerebrospinal fluid datasets (2008) (20)
Progress in Establishing Common Standards for Exchanging Proteomics Data: The Second Meeting of the HUPO Proteomics Standards Initiative (2003) (19)
Identifying novel biomarkers through data mining—A realistic scenario? (2015) (19)
Implementing Data Standards: A report on the HUPOPSI Workshop September 2009, Toronto, Canada (2010) (19)
Recommendations for mass spectrometry data quality metrics for open access data (corollary to the Amsterdam Principles). (2012) (19)
The EBI enzyme portal (2012) (18)
The first 10 years of the international coordination network for standards in systems and synthetic biology (COMBINE) (2020) (18)
Ten Years of Standardizing Proteomic Data: A Report on the HUPO‐PSI Spring Workshop (2012) (17)
jmzTab: A Java interface to the mzTab data standard (2014) (17)
TOWARDS COORDINATED INTERNATIONAL SUPPORT OF CORE DATA RESOURCES FOR THE LIFE SCIENCES (2017) (16)
Integr8: Enhanced Inter-Operability of European Molecular Biology Databases (2003) (15)
Expression Data Analysis with Reactome (2015) (15)
Second Proteomics Standards Initiative Spring Workshop (2005) (15)
An open invitation to the Understudied Proteins Initiative (2022) (15)
Entering the Implementation Era A report on the HUPO‐PSI Fall workshop 25–27 September 2006, Washington DC, USA (2007) (15)
Proteomic Data Exchange and Storage (2007) (15)
BioModels linked dataset (2014) (14)
Preparing to Work with Big Data in Proteomics – A Report on the HUPO‐PSI Spring Workshop (2013) (14)
From Peptidome to PRIDE: Public proteomics data migration at a large scale (2013) (14)
The Minimum Information about a Molecular Interaction CAusal STatement (MI2CAST) (2020) (14)
Charting online OMICS resources: A navigational chart for clinical researchers (2009) (13)
Tackling Quantitation: A Report on the Annual Spring Workshop of the HUPO‐PSI 28–30 March 2010, Seoul, South Korea (2010) (13)
A data citation roadmap for scholarly data repositories (2016) (13)
Proteome Data Integration: Characteristics and Challenges (2005) (12)
SPARQL-enabled identifier conversion with Identifiers.org (2015) (12)
Annual Spring Meeting of the Proteomics Standards Initiative (2009) (12)
IntAct App: a Cytoscape application for molecular interaction network visualization and analysis (2021) (12)
Proteomic data exchange and storage: the need for common standards and public repositories. (2007) (12)
Omics Discovery Index - Discovering and Linking Public ‘Omics’ Datasets (2016) (12)
iProX in 2021: connecting proteomics data sharing with big data (2021) (12)
Annual Spring Meeting of the Proteomics Standards Initiative 23–25 April 2008, Toledo, Spain (2008) (11)
COVID-19 Disease Map, a computational knowledge repository of SARS-CoV-2 virus-host interaction mechanisms (2020) (11)
Interleukins and their signaling pathways in the Reactome biological pathway database (2018) (11)
Data standards and controlled vocabularies for proteomics. (2008) (11)
Capturing cooperative interactions with the PSI-MI format (2013) (11)
Towards the Collaborative Curation of the Registry underlying identifiers.org (2013) (11)
Gene regulation knowledge commons: community action takes care of DNA binding transcription factors (2016) (11)
Corrigendum: ProteomeBinders: planning a European resource of affinity reagents for analysis of the human proteome (2007) (11)
The IMEx coronavirus interactome: an evolving map of Coronaviridae–host molecular interactions (2020) (11)
Critical amino acid residues in proteins: a BioMart integration of Reactome protein annotations with PRIDE mass spectrometry data and COSMIC somatic mutations (2011) (10)
Shared resources, shared costs—leveraging biocuration resources (2015) (10)
HI-bone: a scoring system for identifying phenylisothiocyanate-derivatized peptides based on precursor mass and high intensity fragment ions. (2013) (10)
Proteomics and Beyond A report on the 3rd Annual Spring Workshop of the HUPO‐PSI 21–23 April 2006, San Francisco, CA, USA (2006) (10)
Complex Portal 2022: new curation frontiers (2021) (10)
A reference set of curated biomedical data and metadata from clinical case reports. (2018) (9)
ComplexViewer: visualization of curated macromolecular complexes (2017) (9)
The HUPO initiative on Model Organism Proteomes, iMOP (2012) (9)
From Proteomics Data Representation to Public Data Flow: A Report on the HUPO‐PSI Workshop September 2011, Geneva, Switzerland (2012) (9)
Reactome and ORCID—fine-grained credit attribution for community curation (2019) (9)
Data standardization by the HUPO-PSI: how has the community benefitted? (2011) (9)
Rintact: enabling computational analysis of molecular interaction data from the IntAct repository (2008) (9)
Enabling BioSharing – a report on the Annual Spring Workshop of the HUPO‐PSI April 11–13, 2011, EMBL‐Heidelberg, Germany (2011) (8)
ENFIN--A European network for integrative systems biology. (2009) (8)
The European Bioinformatics Institute (EMBL-EBI) in 2021 (2021) (8)
Second Joint HUPO Publication and Proteomics Standards Initiative Workshop (2009) (8)
COVID‐19 Disease Map, a computational knowledge repository of virus‐host interaction mechanisms (2021) (8)
Human Proteome Organisation Proteomics Standards Initiative Pre‐Congress Initiative (2005) (7)
Protein-protein interactions: analysis and prediction (2009) (7)
Meeting New Challenges: The 2014 HUPO‐PSI/COSMOS Workshop (2014) (7)
Network expansion of genetic associations defines a pleiotropy map of human cell biology (2021) (7)
Author Correction: COVID-19 Disease Map, building a computational repository of SARS-CoV-2 virus-host interaction mechanisms (2020) (7)
easyDAS: Automatic creation of DAS servers (2011) (7)
DAS Writeback: A Collaborative Annotation System (2011) (6)
The HUPO Brain Proteome Project Jamboree: Centralised summary of the pilot studies (2006) (6)
6th HUPO Annual World Congress – Proteomics Standards Initiative Workshop 6–10 October 2007, Seoul, Korea (2008) (6)
OntoDas – a tool for facilitating the construction of complex queries to the Gene Ontology (2008) (5)
Recommendations for mass spectrometry data quality metrics for open access data (corollary to the Amsterdam principles) (2011) (5)
Standardising Proteomics Data - the work of the HUPO Proteomics Standards Initiative (2008) (5)
HUPO 2011: The New Cardiovascular Initiative ‐ Integrating Proteomics and Cardiovascular Biology in Health and Disease (2012) (5)
The Publication and Database Deposition of Molecular Interaction Data (2010) (5)
iAnn: an event sharing platform for the life sciences (2013) (5)
BioModels Parameters: a treasure trove of parameter values from published systems biology models (2020) (5)
InteroPORC: an automated tool to predict highly conserved protein interaction networks (2008) (4)
Identifiers.org: Compact Identifier services in the cloud (2020) (4)
Proteomics and data standardisation (2004) (4)
TEMBLOR – Perspectives of EBI Database Services (2002) (4)
MyDas, an Extensible Java DAS Server (2012) (4)
MIACA – Minimum Information About a Cellular Assay: Standardized description of cell-based functional assay projects (2013) (4)
Path4Drug: Data Science Workflow for Identification of Tissue-Specific Biological Pathways Modulated by Toxic Drugs (2021) (4)
CausalTab: PSI-MITAB 2.8 updated format for signaling data representation and dissemination (2018) (3)
Deep learning embedder method and tool for spectral similarity search. (2020) (3)
Analysing the Yeast Complexome - The Complex Portal rising to the challenge (2020) (3)
SPTR: A comprehensive, non redundant and up-to-date view of the protein sequence world (1998) (3)
Equipping Physiologists with an Informatics Tool Chest: Toward an Integerated Mitochondrial Phenome. (2017) (3)
Capturing variation impact on molecular interactions in the IMEx Consortium mutations data set (2018) (3)
ENFIN - An Integrative Structure for Systems Biology (2008) (3)
PathwayMatcher: proteoform-centric network construction enables fine-granularity multiomics pathway mapping (2019) (3)
Using Reactome to build an autophagy mechanism knowledgebase (2020) (3)
Organizational principles of the Reactome human BioPAX model using graph theory methods (2016) (2)
Preparing molecular interaction data for publication. (2011) (2)
10 Simple rules for design, provision, and reuse of identifiers for web-based life science data (2015) (2)
Complex Portal - A Unifying Protein Complex Database (2017) (2)
Publisher Correction: MEMOTE for standardized genome-scale metabolic model testing (2020) (2)
Addressing barriers in comprehensiveness, accessibility, reusability, interoperability and reproducibility of computational models in systems biology (2022) (2)
Proteomics Data Visualisation (2015) (2)
RIFLE: Rapid Identification of Microorganisms by Fragment Length Evaluation (1997) (2)
Publisher Correction: Capturing variation impact on molecular interactions in the IMEx Consortium mutations data set (2019) (2)
Original article The Reactome BioMart (2011) (2)
10 Simple rules for design, provision, and reuse of persistent identifiers for life science data (2015) (2)
Meeting Review: Progress in Establishing Common Standards for Exchanging Proteomics Data: the second meeting of the HUPO Proteomics Standards (2003) (2)
Delivering 'Cool URIs' That Do Not Change (2012) (2)
Proteomics' framework for success? (2007) (2)
Ten Simple Rules for Sharing Experimental and Clinical Data with the Modeling Community (2021) (1)
Wikidata as a FAIR knowledge graph for the life sciences (2019) (1)
New open drug activity data at EBI (2009) (1)
The BioJS: an open source standard for biological visualisation (2014) (1)
Identifiers.org Compact Identifier services (2018) (1)
The omics discovery REST interface (2020) (1)
Proteomics Standards Initiative at Twenty Years: Current Activities and Future Work (2023) (1)
Ten Simple Rules for FAIR Sharing of Experimental and Clinical Data with the Modeling Community (2021) (1)
Hydra: a scalable proteomic search engine which utilizes the Hadoop distributed computing framework (2012) (1)
An Application of Latent Topic Document Analysis to Large-Scale Proteomics Databases (2007) (1)
Abstract P327: COPa Library: A Proteomic Knowledge Base for Cardiovascular Biology and Medicine (2011) (1)
Feature Propagation - Semi Automatic transfer of position dependent SWISS-PROT annotation (1999) (1)
The ESF Programme on Functional Genomics Workshop on ‘Data Integration in Functional Genomics: Application to Biological Pathways’ (2004) (1)
PRIDE: The proteomics identifications database (vol. 5, Issue 13, pp. 3537‐3545) (1)
HENA, heterogeneous network-based data set for Alzheimer’s disease (2019) (1)
Data standardization and the HUPO proteomics standards initiative (2005) (1)
Databases and ontologies Dasty 2 , an Ajax protein DAS client (2008) (1)
Identifiers for the 21 st century : How to design , provision , and reuse identifiers to maximize data utility and impact (2016) (1)
KNIME workflow for retrieving causal drug and protein interactions, building networks, and performing topological enrichment analysis demonstrated by a DILI case study (2022) (1)
Pride Wizard: generation of standards compliant quantitative proteomics data (2007) (1)
Development and Implementation of the PSI MI Standard for Molecular Interaction (2006) (1)
A pipeline for identifying endogenous neuropeptides from spectral archives (2018) (0)
Session II : Network inference in diseases-Part I (2019) (0)
Proteomic Data Standardization, Deposition and Exchange (2006) (0)
PathwayMatcher: multi-omics pathway mapping and proteoform network generation (2018) (0)
A decoupled, modular and scriptable architecture for tools to curate data platforms (2020) (0)
Author response: Wikidata as a knowledge graph for the life sciences (2020) (0)
Exploring Leishmania-Host Interaction with Reactome, a Database of Biological Pathways and Processes (2021) (0)
COVID-19 Disease Map, building a computational repository of SARS-CoV-2 virus-host interaction mechanisms (2020) (0)
Infrastructure for distributed protein annotation (2008) (0)
A domain level interaction network of amyloid precursor protein and Aβ of Alzheimer's disease (2010) (0)
Systems Biology in ELIXIR: modelling in the spotlight (2022) (0)
Session 19: Plasma Proteomics I (2004) (0)
Reactome pathway analysis: a high-performance in-memory approach (2017) (0)
The Proteomics Identifications database (PRIDE), its associated tools and the ProteomeXchange consortium (2010) (0)
Publisher Correction: Capturing variation impact on molecular interactions in the IMEx Consortium mutations data set (2019) (0)
Inference and validation of Synechocystis protein interaction network using orthology (2007) (0)
Sequence analysis Accurate estimation of isoelectric point of protein and peptide based on amino acid sequences (2016) (0)
BIOINFORMATICS APPLICATIONS NOTE Databases and ontologies Dasty3, a WEB framework for DAS (2011) (0)
Towards a New Curation Environment for the TrEMBL Database (2001) (0)
and the mzidValidator (2013) (0)
In-depth Analysis of Protein Inference Algorithms using a Workflow Framework and Well-Defined Metrics (2017) (0)
ISBE - draft proposal on connections (2014) (0)
Reactome: new services and widgets to ease third-party integration (2016) (0)
Final Recommendations for a Data and Model Management Framework. Data and Model Stewardship for the ISBE Infrastructure. (2015) (0)
Reactome - Pathway Context and Visualisation for Omics Data (2019) (0)
Present and future of proteomics data curation at the PRIDE database (2009) (0)
Quality control and standarization efforts at the proteomics identification (PRIDE) database (2011) (0)
Inference of Synechocystis protein interaction network (2008) (0)
EBI Proteomics Services (2008) (0)
Identifiers.org: services towards interoperability (2016) (0)
The Apoptosis Gene Ontology project and the IntAct-Apoptosis dataset: updating the conceptual representation of apoptosis (2013) (0)
The Complex Portal – annotating protein complexes made easy (2016) (0)
The ESF Programme on Functional Genomics workshop on ‘Data Integration in Functional Genomics: Application to Biological Pathways’: Conference Editorials (2004) (0)
The HUPO Proteomics Standards Initiative (PSI): Helping to develop the proteomics field (2014) (0)
Analysing latent topics in large-scale proteomics (2007) (0)
PRIDE Inspector Toolsuite: Moving towards a quality assessment tool for proteomics data standards and ProteomeXchange repositories (2016) (0)
Shouldn't enantiomeric purity be included in the 'minimum information about a bioactive entity? Response from the MIABE group (2012) (0)
Pathway Analysis Tool Suite (2014) (0)
High‐throughput proteomics and bioinformatics: joined at the hip (2010) (0)
Integrated omics dissection of proteome dynamics during cardiac remodeling (2018) (0)
Innate Immune Signaling Pathways in Reactome (2010) (0)
Reactome: A curated knowledgebase of biomolecular pathways (2016) (0)
Call for Papers – Dataset Briefs (2006) (0)
Publisher Correction: MEMOTE for standardized genome-scale metabolic model testing (2020) (0)
Yeast Complexome – The Complex Portal rising to the challenge (2019) (0)
The cardiovascular gene annotation initiative: Impact on data analysis (2015) (0)
The Reactome reloaded (2010) (0)
Analysing the yeast complexome—the Complex Portal rising to the challenge (2021) (0)
Implementing Recommendations for ISBE Asset Stewardship (2015) (0)
p rotein interaction data curation: the i nternational m olecular exchange (ime x) consortium (2012) (0)
PathwayMatcher: proteoform-centric network construction enables fine-granularity multi-omics pathway mapping (2018) (0)
Deliverable 4.7 Using the PID Graph: Community Workflows and Discoverability Services (2020) (0)
Do networks help in making sense of the omics data deluge ? (2015) (0)
Databases Dasty2, an Ajax protein DAS client (2008) (0)
BioJS 2.0: an open source standard for biological visualization (2015) (0)
Protein interaction databases (2005) (0)
Using the Reactome Database (2023) (0)
Author Correction: COVID-19 Disease Map, building a computational repository of SARS-CoV-2 virus-host interaction mechanisms (2020) (0)
Encompassing new use cases - level 3.0 of the HUPO-PSI format for molecular interactions (2018) (0)
The cardiovascular gene annotation initiative: current and future aims (2014) (0)
Databases and ontologies SPARQL-enabled identifier conversion with Identifiers . org (2015) (0)
EnVision – Leveraging community standards for set-oriented data analysis (2010) (0)
How to organise and run an ISBE modelling service (2015) (0)
Phoenix Enhancer: an online service/tool for proteomics data mining using clustered spectra (2019) (0)
Innate Immune Signaling Pathways in Reactome (94.13) (2010) (0)
Databases and ontologies Reactome enhanced pathway visualisation (2017) (0)
MEMOTE for standardized genome-scale metabolic model testing (2020) (0)
Phoenix Enhancer: proteomics data mining using clustered spectra (2019) (0)
BioModels Database: a public repository for sharing models of biological processes (2014) (0)
Autophagy Targeted Curation (2019) (0)

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Zhejiang University
Bielefeld University

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