Hermjakob, Henning

Initial sequencing and analysis of the human genome

International Human Genome Sequencing Consortium, Whitehead Institute for Biomedical Research, C. F. G. R., Lander, E. S., Linton, L. M., Birren, B., Nusbaum, C., Zody, M. C., Baldwin, J., Devon, K., Dewar, K., et al. (2001) · Nature

Genomics and Phylogenetic StudiesGenetic Associations and Epidemiology

Cited by 24,216

The Reactome pathway Knowledgebase

Fabregat, A., Sidiropoulos, K., Garapati, P., Gillespie, M., Hausmann, K., Haw, R., Jassal, B., Jupe, S., Korninger, F., McKay, S., et al. (2016) · Nucleic Acids Research

Bioinformatics and Genomic NetworksBiomedical Text Mining and Ontologies

Cited by 5,605

The Proteomics Identifications (PRIDE) database and associated tools: status in 2013

Vizcaíno, J. A., Côté, R. G., Csordas, A., Dianes, J. A., Fabregat, A., Foster, J. M., Griss, J., Alpi, E., Birim, M., Contell, J., et al. (2012) · Nucleic Acids Research

Advanced Proteomics Techniques and ApplicationsBioinformatics and Genomic Networks

Cited by 1,918

The Reactome pathway knowledgebase

Croft, D., Mundo, A. F., Haw, R., Milacic, M., Weiser, J., Wu, G., Caudy, M., Garapati, P., Gillespie, M., Kamdar, M. R., et al. (2014) · Nucleic Acids Research

Bioinformatics and Genomic NetworksBiomedical Text Mining and Ontologies

Cited by 1,889

Reactome: a database of reactions, pathways and biological processes

Croft, D., O'Kelly, G., Wu, G., Haw, R., Gillespie, M., Matthews, L., Caudy, M., Garapati, P., Gopinath, G., Jassal, B., et al. (2011) · Nucleic Acids Research

Bioinformatics and Genomic NetworksBiomedical Text Mining and Ontologies

Cited by 1,751

Reactome knowledgebase of human biological pathways and processes

Matthews, L., Gopinath, G., Gillespie, M., Caudy, M., Croft, D., de Bono, B., Garapati, P., Hemish, J., Hermjakob, H., Jassal, B., et al. (2009) · Nucleic Acids Research

Bioinformatics and Genomic NetworksBiomedical Text Mining and Ontologies

Cited by 873

The HUPO PSI's Molecular Interaction format—a community standard for the representation of protein interaction data

Hermjakob, H., Montecchi-Palazzi, L., Bader, G., Wojcik, J., Salwinski, L., Ceol, A., Moore, S., Orchard, S., Sarkans, U., von Mering, C., et al. (2004) · Nature Biotechnology

Bioinformatics and Genomic NetworksAdvanced Proteomics Techniques and Applications

Cited by 630

The IntAct molecular interaction database in 2010

Aranda, B., Achuthan, P., Alam-Faruque, Y., Armean, I., Bridge, A., Derow, C., Feuermann, M., Ghanbarian, A. T., Kerrien, S., Khadake, J., et al. (2010) · Nucleic Acids Research

Bioinformatics and Genomic NetworksBiomedical Text Mining and Ontologies

Cited by 620

PRIDE: The proteomics identifications database

Martens, L., Hermjakob, H., Jones, P., Adamski, M., Taylor, C., States, D., Gevaert, K., Vandekerckhove, J., & Apweiler, R. (2005) · PROTEOMICS

Advanced Proteomics Techniques and ApplicationsResearch Data Management Practices

Cited by 594

Promoting coherent minimum reporting guidelines for biological and biomedical investigations: the MIBBI project

Taylor, C. F., Field, D., Sansone, S.-A., Aerts, J., Apweiler, R., Ashburner, M., Ball, C. A., Binz, P.-A., Bogue, M., Booth, T., et al. (2008) · Nature Biotechnology

Research Data Management PracticesScientific Computing and Data Management

Cited by 558

MEMOTE for standardized genome-scale metabolic model testing

Lieven, C., Beber, M. E., Olivier, B. G., Bergmann, F. T., Ataman, M., Babaei, P., Bartell, J. A., Blank, L. M., Chauhan, S., Correia, K., et al. (2020) · Nature Biotechnology

Microbial Metabolic Engineering and BioproductionGene Regulatory Network Analysis

Cited by 509

Toward interoperable bioscience data

Sansone, S.-A., Rocca-Serra, P., Field, D., Maguire, E., Taylor, C., Hofmann, O., Fang, H., Neumann, S., Tong, W., Amaral-Zettler, L., et al. (2012) · Nature Genetics

Research Data Management PracticesScientific Computing and Data Management

Cited by 475

Disrupted in Schizophrenia 1 Interactome: evidence for the close connectivity of risk genes and a potential synaptic basis for schizophrenia

Camargo, L. M., Collura, V, Rain, J.-C., Mizuguchi, K., Hermjakob, H., Kerrien, S., Bonnert, T. P., Whiting, P. J., & Brandon, N. J. (2007) · Molecular Psychiatry

Schizophrenia research and treatmentBioinformatics and Genomic Networks

Cited by 405

The IntAct database: efficient access to fine-grained molecular interaction data

del Toro, N., Shrivastava, A., Ragueneau, E., Meldal, B., Combe, C., Barrera, E., Perfetto, L., How, K., Ratan, P., Shirodkar, G., et al. (2022) · Nucleic Acids Research

Bioinformatics and Genomic NetworksBiomedical Text Mining and Ontologies

Cited by 405

BioModels—15 years of sharing computational models in life science

Malik-Sheriff, R. S., Glont, M., Nguyen, T. V. N., Tiwari, K., Roberts, M. G., Xavier, A., Vu, M. T., Men, J., Maire, M., Kananathan, S., et al. (2019) · Nucleic Acids Research

Scientific Computing and Data ManagementGene Regulatory Network Analysis

Cited by 361

BioModels: ten-year anniversary

Chelliah, V., Juty, N., Ajmera, I., Ali, R., Dumousseau, M., Glont, M., Hucka, M., Jalowicki, G., Keating, S., Knight-Schrijver, V., et al. (2015) · Nucleic Acids Research

Gene Regulatory Network AnalysisBioinformatics and Genomic Networks

Cited by 281

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

Kerrien, S., Orchard, S., Montecchi-Palazzi, L., Aranda, B., Quinn, A. F., Vinod, N., Bader, G. D., Xenarios, I., Wojcik, J., Sherman, D., et al. (2007) · BMC Biology

Bioinformatics and Genomic NetworksAdvanced Proteomics Techniques and Applications

Cited by 266

Reproducibility in systems biology modelling

Tiwari, K., Kananathan, S., Roberts, M. G., Meyer, J. P., Sharif Shohan, M. U., Xavier, A., Maire, M., Zyoud, A., Men, J., Ng, S., et al. (2020) · bioRxiv (Cold Spring Harbor Laboratory)

Scientific Computing and Data ManagementGene Regulatory Network Analysis

Cited by 131

Reproducibility in systems biology modelling

Tiwari, K., Kananathan, S., Roberts, M. G., Meyer, J. P., Sharif Shohan, M. U., Xavier, A., Maire, M., Zyoud, A., Men, J., Ng, S., et al. (2021) · Molecular Systems Biology

Scientific Computing and Data ManagementGene Regulatory Network Analysis

Cited by 131

Reactome pathway analysis to enrich biological discovery in proteomics data sets

Haw, R., Hermjakob, H., D'Eustachio, P., & Stein, L. (2011) · PROTEOMICS

Bioinformatics and Genomic NetworksAdvanced Proteomics Techniques and Applications

Cited by 117

Integrating biological data – the Distributed Annotation System

Jenkinson, A. M., Albrecht, M., Birney, E., Blankenburg, H., Down, T., Finn, R. D., Hermjakob, H., Hubbard, T. J., Jimenez, R. C., Jones, P., et al. (2008) · BMC Bioinformatics

Genomics and Phylogenetic StudiesScientific Computing and Data Management

Cited by 100

BioModels: expanding horizons to include more modelling approaches and formats

Glont, M., Nguyen, T. V. N., Graesslin, M., Hälke, R., Ali, R., Schramm, J., Wimalaratne, S. M., Kothamachu, V. B., Rodriguez, N., Swat, M. J., et al. (2018) · Nucleic Acids Research

Gene Regulatory Network AnalysisScientific Computing and Data Management

Cited by 89

The evolution of standards and data management practices in systems biology

Stanford, N. J., Wolstencroft, K., Golebiewski, M., Kania, R., Juty, N., Tomlinson, C., Owen, S., Butcher, S., Hermjakob, H., Le Novère, N., et al. (2015) · Molecular Systems Biology

Scientific Computing and Data ManagementResearch Data Management Practices

Cited by 38

AI-readiness Criteria for Biomedical Data

Clark, T., Caufield, H., Parker, J. A., Al Manir, S., Amorim, E., Eddy, J., Gim, N., Gow, B., Goar, W., Hansen, J. N., et al. (2024) · bioRxiv (Cold Spring Harbor Laboratory)

Research Data Management PracticesArtificial Intelligence in Healthcare and Education

Cited by 32