| Year |
Citation |
Score |
| 2024 |
Koutrouli M, Nastou K, Líndez PP, Bouwmeester R, Rasmussen S, Martens L, Jensen LJ. FAVA: High-quality functional association networks inferred from scRNA-seq and proteomics data. Bioinformatics (Oxford, England). PMID 38192003 DOI: 10.1093/bioinformatics/btae010 |
0.343 |
|
| 2023 |
Tantoso E, Eisenhaber B, Sinha S, Jensen LJ, Eisenhaber F. Did the early full genome sequencing of yeast boost gene function discovery? Biology Direct. 18: 46. PMID 37574542 DOI: 10.1186/s13062-023-00403-8 |
0.305 |
|
| 2023 |
Kelleher KJ, Sheils TK, Mathias SL, Yang JJ, Metzger VT, Siramshetty VB, Nguyen DT, Jensen LJ, Vidović D, Schürer SC, Holmes J, Sharma KR, Pillai A, Bologa CG, Edwards JS, et al. Pharos 2023: an integrated resource for the understudied human proteome. Nucleic Acids Research. 51: D1405-D1416. PMID 36624666 DOI: 10.1093/nar/gkac1033 |
0.309 |
|
| 2022 |
Doncheva NT, Morris JH, Holze H, Kirsch R, Nastou KC, Cuesta-Astroz Y, Rattei T, Szklarczyk D, von Mering C, Jensen LJ. Cytoscape stringApp 2.0: Analysis and Visualization of Heterogeneous Biological Networks. Journal of Proteome Research. PMID 36512705 DOI: 10.1021/acs.jproteome.2c00651 |
0.62 |
|
| 2022 |
Hernández-Plaza A, Szklarczyk D, Botas J, Cantalapiedra CP, Giner-Lamia J, Mende DR, Kirsch R, Rattei T, Letunic I, Jensen LJ, Bork P, von Mering C, Huerta-Cepas J. eggNOG 6.0: enabling comparative genomics across 12 535 organisms. Nucleic Acids Research. PMID 36399505 DOI: 10.1093/nar/gkac1022 |
0.824 |
|
| 2022 |
Szklarczyk D, Kirsch R, Koutrouli M, Nastou K, Mehryary F, Hachilif R, Gable AL, Fang T, Doncheva NT, Pyysalo S, Bork P, Jensen LJ, von Mering C. The STRING database in 2023: protein-protein association networks and functional enrichment analyses for any sequenced genome of interest. Nucleic Acids Research. PMID 36370105 DOI: 10.1093/nar/gkac1000 |
0.774 |
|
| 2021 |
Baltoumas FA, Zafeiropoulou S, Karatzas E, Paragkamian S, Thanati F, Iliopoulos I, Eliopoulos AG, Schneider R, Jensen LJ, Pafilis E, Pavlopoulos GA. OnTheFly: a text-mining web application for automated biomedical entity recognition, document annotation, network and functional enrichment analysis. Nar Genomics and Bioinformatics. 3: lqab090. PMID 34632381 DOI: 10.1093/nargab/lqab090 |
0.33 |
|
| 2021 |
Szklarczyk D, Gable AL, Nastou KC, Lyon D, Kirsch R, Pyysalo S, Doncheva NT, Legeay M, Fang T, Bork P, Jensen LJ, von Mering C. Correction to 'The STRING database in 2021: customizable protein-protein networks, and functional characterization of user-uploaded gene/measurement sets'. Nucleic Acids Research. PMID 34530444 DOI: 10.1093/nar/gkab835 |
0.731 |
|
| 2020 |
Szklarczyk D, Gable AL, Nastou KC, Lyon D, Kirsch R, Pyysalo S, Doncheva NT, Legeay M, Fang T, Bork P, Jensen LJ, von Mering C. The STRING database in 2021: customizable protein-protein networks, and functional characterization of user-uploaded gene/measurement sets. Nucleic Acids Research. PMID 33237311 DOI: 10.1093/nar/gkaa1074 |
0.776 |
|
| 2020 |
Sheils TK, Mathias SL, Kelleher KJ, Siramshetty VB, Nguyen DT, Bologa CG, Jensen LJ, Vidović D, Koleti A, Schürer SC, Waller A, Yang JJ, Holmes J, Bocci G, Southall N, et al. TCRD and Pharos 2021: mining the human proteome for disease biology. Nucleic Acids Research. PMID 33156327 DOI: 10.1093/nar/gkaa993 |
0.362 |
|
| 2020 |
Locard-Paulet M, Bouyssie D, Froment C, Burlet-Schiltz O, Jensen LJ. Comparing 22 popular phosphoproteomics pipelines for peptide identification and site localization. Journal of Proteome Research. PMID 31975593 DOI: 10.1021/Acs.Jproteome.9B00679 |
0.305 |
|
| 2019 |
Lundby A, Franciosa G, Emdal KB, Refsgaard JC, Gnosa SP, Bekker-Jensen DB, Secher A, Maurya SR, Paul I, Mendez BL, Kelstrup CD, Francavilla C, Kveiborg M, Montoya G, Jensen LJ, et al. Oncogenic Mutations Rewire Signaling Pathways by Switching Protein Recruitment to Phosphotyrosine Sites. Cell. 179: 543-560.e26. PMID 31585087 DOI: 10.1016/J.Cell.2019.09.008 |
0.313 |
|
| 2019 |
Tagore S, Gorohovski A, Jensen LJ, Frenkel-Morgenstern M. ProtFus: A Comprehensive Method Characterizing Protein-Protein Interactions of Fusion Proteins. Plos Computational Biology. 15: e1007239. PMID 31437145 DOI: 10.1371/journal.pcbi.1007239 |
0.337 |
|
| 2019 |
Hjaltelin JX, Izarzugaza JMG, Jensen LJ, Russo F, Westergaard D, Brunak S. Identification of hyper-rewired genomic stress non-oncogene addiction genes across 15 cancer types. Npj Systems Biology and Applications. 5: 27. PMID 31396397 DOI: 10.1038/s41540-019-0104-5 |
0.461 |
|
| 2019 |
Cook HV, Jensen LJ. A Guide to Dictionary-Based Text Mining. Methods in Molecular Biology (Clifton, N.J.). 1939: 73-89. PMID 30848457 DOI: 10.1007/978-1-4939-9089-4_5 |
0.335 |
|
| 2019 |
Cuesta-Astroz Y, Santos A, Oliveira G, Jensen LJ. Analysis of Predicted Host-Parasite Interactomes Reveals Commonalities and Specificities Related to Parasitic Lifestyle and Tissues Tropism. Frontiers in Immunology. 10: 212. PMID 30815000 DOI: 10.3389/Fimmu.2019.00212 |
0.349 |
|
| 2018 |
Szklarczyk D, Gable AL, Lyon D, Junge A, Wyder S, Huerta-Cepas J, Simonovic M, Doncheva NT, Morris JH, Bork P, Jensen LJ, von Mering C. STRING v11: protein-protein association networks with increased coverage, supporting functional discovery in genome-wide experimental datasets. Nucleic Acids Research. PMID 30476243 DOI: 10.1093/Nar/Gky1131 |
0.702 |
|
| 2018 |
Doncheva NT, Morris J, Gorodkin J, Jensen LJ. Cytoscape stringApp: Network analysis and visualization of proteomics data. Journal of Proteome Research. PMID 30450911 DOI: 10.1021/Acs.Jproteome.8B00702 |
0.391 |
|
| 2018 |
Cook HV, Jensen LJ. An Integrative Approach to Virus-Host Protein-Protein Interactions. Methods in Molecular Biology (Clifton, N.J.). 1819: 175-196. PMID 30421404 DOI: 10.1007/978-1-4939-8618-7_8 |
0.359 |
|
| 2018 |
Huerta-Cepas J, Szklarczyk D, Heller D, Hernández-Plaza A, Forslund SK, Cook H, Mende DR, Letunic I, Rattei T, Jensen LJ, von Mering C, Bork P. eggNOG 5.0: a hierarchical, functionally and phylogenetically annotated orthology resource based on 5090 organisms and 2502 viruses. Nucleic Acids Research. PMID 30418610 DOI: 10.1093/Nar/Gky1085 |
0.814 |
|
| 2018 |
Pan X, Jensen LJ, Gorodkin J. Inferring disease-associated long non-coding RNAs using genome-wide tissue expression profiles. Bioinformatics (Oxford, England). PMID 30295698 DOI: 10.1093/Bioinformatics/Bty859 |
0.318 |
|
| 2018 |
Sinha S, Eisenhaber B, Jensen LJ, Kalbuaji B, Eisenhaber F. Darkness in the Human Gene and Protein Function Space: Widely Modest or Absent Illumination by the Life Science Literature and the Trend for Fewer Protein Function Discoveries Since 2000. Proteomics. e1800093. PMID 30265449 DOI: 10.1002/Pmic.201800093 |
0.334 |
|
| 2018 |
Cook HV, Doncheva NT, Szklarczyk D, von Mering C, Jensen LJ. Viruses.STRING: A Virus-Host Protein-Protein Interaction Database. Viruses. 10. PMID 30249048 DOI: 10.3390/V10100519 |
0.628 |
|
| 2018 |
Oprea TI, Bologa CG, Brunak S, Campbell A, Gan GN, Gaulton A, Gomez SM, Guha R, Hersey A, Holmes J, Jadhav A, Jensen LJ, Johnson GL, Karlson A, Leach AR, et al. Unexplored therapeutic opportunities in the human genome. Nature Reviews. Drug Discovery. PMID 29567993 DOI: 10.1038/Nrd.2018.52 |
0.636 |
|
| 2018 |
Oprea TI, Bologa CG, Brunak S, Campbell A, Gan GN, Gaulton A, Gomez SM, Guha R, Hersey A, Holmes J, Jadhav A, Jensen LJ, Johnson GL, Karlson A, Leach AR, et al. Unexplored therapeutic opportunities in the human genome. Nature Reviews. Drug Discovery. PMID 29472638 DOI: 10.1038/Nrd.2018.14 |
0.724 |
|
| 2018 |
Westergaard D, Stærfeldt HH, Tønsberg C, Jensen LJ, Brunak S. A comprehensive and quantitative comparison of text-mining in 15 million full-text articles versus their corresponding abstracts. Plos Computational Biology. 14: e1005962. PMID 29447159 DOI: 10.1371/Journal.Pcbi.1005962 |
0.47 |
|
| 2017 |
Russo F, Di Bella S, Vannini F, Berti G, Scoyni F, Cook HV, Santos A, Nigita G, Bonnici V, Laganà A, Geraci F, Pulvirenti A, Giugno R, De Masi F, Belling K, ... Jensen LJ, et al. miRandola 2017: a curated knowledge base of non-invasive biomarkers. Nucleic Acids Research. PMID 29036351 DOI: 10.1093/Nar/Gkx854 |
0.501 |
|
| 2017 |
Mullari M, Lyon D, Jensen LJ, Nielsen ML. Specifying RNA-binding regions in proteins by peptide Cross-Linking and Affinity Purification. Journal of Proteome Research. PMID 28648085 DOI: 10.1021/Acs.Jproteome.7B00042 |
0.301 |
|
| 2017 |
Cannon DC, Yang JJ, Mathias SL, Ursu O, Mani S, Waller A, Schürer SC, Jensen LJ, Sklar LA, Bologa CG, Oprea TI. TIN-X: Target Importance and Novelty Explorer. Bioinformatics (Oxford, England). PMID 28398460 DOI: 10.1093/Bioinformatics/Btx200 |
0.319 |
|
| 2017 |
Francavilla C, Lupia M, Tsafou K, Villa A, Kowalczyk K, Rakownikow Jersie-Christensen R, Bertalot G, Confalonieri S, Brunak S, Jensen LJ, Cavallaro U, Olsen JV. Phosphoproteomics of Primary Cells Reveals Druggable Kinase Signatures in Ovarian Cancer. Cell Reports. 18: 3242-3256. PMID 28355574 DOI: 10.1016/J.Celrep.2017.03.015 |
0.457 |
|
| 2017 |
Hendriks IA, Lyon D, Young C, Jensen LJ, Vertegaal AC, Nielsen ML. Site-specific mapping of the human SUMO proteome reveals co-modification with phosphorylation. Nature Structural & Molecular Biology. PMID 28112733 DOI: 10.1038/Nsmb.3366 |
0.313 |
|
| 2017 |
Junge A, Refsgaard JC, Garde C, Pan X, Santos A, Alkan F, Anthon C, von Mering C, Workman CT, Jensen LJ, Gorodkin J. RAIN: RNA-protein Association and Interaction Networks. Database : the Journal of Biological Databases and Curation. 2017. PMID 28077569 DOI: 10.1093/database/baw167 |
0.64 |
|
| 2016 |
Szklarczyk D, Morris JH, Cook H, Kuhn M, Wyder S, Simonovic M, Santos A, Doncheva NT, Roth A, Bork P, Jensen LJ, von Mering C. The STRING database in 2017: quality-controlled protein-protein association networks, made broadly accessible. Nucleic Acids Research. PMID 27924014 DOI: 10.1093/Nar/Gkw937 |
0.822 |
|
| 2016 |
Nguyen DT, Mathias S, Bologa C, Brunak S, Fernandez N, Gaulton A, Hersey A, Holmes J, Jensen LJ, Karlsson A, Liu G, Ma'ayan A, Mandava G, Mani S, Mehta S, et al. Pharos: Collating protein information to shed light on the druggable genome. Nucleic Acids Research. PMID 27903890 DOI: 10.1093/Nar/Gkw1072 |
0.547 |
|
| 2016 |
Altenhoff AM, Boeckmann B, Capella-Gutierrez S, Dalquen DA, DeLuca T, Forslund K, Huerta-Cepas J, Linard B, Pereira C, Pryszcz LP, Schreiber F, da Silva AS, Szklarczyk D, Train CM, Bork P, ... ... Jensen LJ, et al. Standardized benchmarking in the quest for orthologs. Nature Methods. PMID 27043882 DOI: 10.1038/Nmeth.3830 |
0.706 |
|
| 2016 |
Pafilis E, Buttigieg PL, Ferrell B, Pereira E, Schnetzer J, Arvanitidis C, Jensen LJ. EXTRACT: interactive extraction of environment metadata and term suggestion for metagenomic sample annotation. Database : the Journal of Biological Databases and Curation. 2016. PMID 26896844 DOI: 10.1093/Database/Baw005 |
0.342 |
|
| 2015 |
Franceschini A, Lin J, von Mering C, Jensen LJ. SVD-Phy: Improved prediction of protein functional associations through singular value decomposition of phylogenetic profiles. Bioinformatics (Oxford, England). PMID 26614125 DOI: 10.1093/bioinformatics/btv696 |
0.585 |
|
| 2015 |
Szklarczyk D, Santos A, von Mering C, Jensen LJ, Bork P, Kuhn M. STITCH 5: augmenting protein-chemical interaction networks with tissue and affinity data. Nucleic Acids Research. PMID 26590256 DOI: 10.1093/Nar/Gkv1277 |
0.78 |
|
| 2015 |
Huerta-Cepas J, Szklarczyk D, Forslund K, Cook H, Heller D, Walter MC, Rattei T, Mende DR, Sunagawa S, Kuhn M, Jensen LJ, von Mering C, Bork P. eggNOG 4.5: a hierarchical orthology framework with improved functional annotations for eukaryotic, prokaryotic and viral sequences. Nucleic Acids Research. PMID 26582926 DOI: 10.1093/Nar/Gkv1248 |
0.827 |
|
| 2015 |
Kuhn M, Letunic I, Jensen LJ, Bork P. The SIDER database of drugs and side effects. Nucleic Acids Research. PMID 26481350 DOI: 10.1093/Nar/Gkv1075 |
0.753 |
|
| 2015 |
Warrer P, Jensen PB, Aagaard L, Jensen LJ, Brunak S, Krag MH, Rossing P, Almdal T, Andersen HU, Hansen EH. Identification of possible adverse drug reactions in clinical notes: The case of glucose-lowering medicines. Journal of Research in Pharmacy Practice. 4: 64-72. PMID 25984543 DOI: 10.4103/2279-042X.155753 |
0.408 |
|
| 2015 |
Szklarczyk D, Jensen LJ. Protein-protein interaction databases. Methods in Molecular Biology (Clifton, N.J.). 1278: 39-56. PMID 25859942 DOI: 10.1007/978-1-4939-2425-7_3 |
0.374 |
|
| 2015 |
Pletscher-Frankild S, Pallejà A, Tsafou K, Binder JX, Jensen LJ. DISEASES: text mining and data integration of disease-gene associations. Methods (San Diego, Calif.). 74: 83-9. PMID 25484339 DOI: 10.1016/J.Ymeth.2014.11.020 |
0.344 |
|
| 2015 |
Santos A, Wernersson R, Jensen LJ. Cyclebase 3.0: a multi-organism database on cell-cycle regulation and phenotypes. Nucleic Acids Research. 43: D1140-4. PMID 25378319 DOI: 10.1093/nar/gku1092 |
0.329 |
|
| 2015 |
Szklarczyk D, Franceschini A, Wyder S, Forslund K, Heller D, Huerta-Cepas J, Simonovic M, Roth A, Santos A, Tsafou KP, Kuhn M, Bork P, Jensen LJ, von Mering C. STRING v10: protein-protein interaction networks, integrated over the tree of life. Nucleic Acids Research. 43: D447-52. PMID 25352553 DOI: 10.1093/Nar/Gku1003 |
0.81 |
|
| 2014 |
Eriksson R, Aagaard L, Jensen LJ, Borisova L, Hørlück D, Brunak S, Hansen EH. Discrepancies in listed adverse drug reactions in pharmaceutical product information supplied by the regulatory authorities in Denmark and the USA. Pharmacology Research & Perspectives. 2: e00038. PMID 25505588 DOI: 10.1002/Prp2.38 |
0.429 |
|
| 2014 |
Jensen AB, Moseley PL, Oprea TI, Ellesøe SG, Eriksson R, Schmock H, Jensen PB, Jensen LJ, Brunak S. Temporal disease trajectories condensed from population-wide registry data covering 6.2 million patients. Nature Communications. 5: 4022. PMID 24959948 DOI: 10.1038/Ncomms5022 |
0.376 |
|
| 2014 |
Eriksson R, Werge T, Jensen LJ, Brunak S. Dose-specific adverse drug reaction identification in electronic patient records: temporal data mining in an inpatient psychiatric population. Drug Safety. 37: 237-47. PMID 24634163 DOI: 10.1007/S40264-014-0145-Z |
0.446 |
|
| 2014 |
Binder JX, Pletscher-Frankild S, Tsafou K, Stolte C, O'Donoghue SI, Schneider R, Jensen LJ. COMPARTMENTS: unification and visualization of protein subcellular localization evidence. Database : the Journal of Biological Databases and Curation. 2014: bau012. PMID 24573882 DOI: 10.1093/Database/Bau012 |
0.302 |
|
| 2014 |
Powell S, Forslund K, Szklarczyk D, Trachana K, Roth A, Huerta-Cepas J, Gabaldón T, Rattei T, Creevey C, Kuhn M, Jensen LJ, von Mering C, Bork P. eggNOG v4.0: nested orthology inference across 3686 organisms. Nucleic Acids Research. 42: D231-9. PMID 24297252 DOI: 10.1093/Nar/Gkt1253 |
0.808 |
|
| 2014 |
Kuhn M, Szklarczyk D, Pletscher-Frankild S, Blicher TH, von Mering C, Jensen LJ, Bork P. STITCH 4: integration of protein-chemical interactions with user data. Nucleic Acids Research. 42: D401-7. PMID 24293645 DOI: 10.1093/Nar/Gkt1207 |
0.783 |
|
| 2013 |
Blair DR, Lyttle CS, Mortensen JM, Bearden CF, Jensen AB, Khiabanian H, Melamed R, Rabadan R, Bernstam EV, Brunak S, Jensen LJ, Nicolae D, Shah NH, Grossman RL, Cox NJ, et al. A nondegenerate code of deleterious variants in Mendelian loci contributes to complex disease risk. Cell. 155: 70-80. PMID 24074861 DOI: 10.1016/J.Cell.2013.08.030 |
0.403 |
|
| 2013 |
Orlando L, Ginolhac A, Zhang G, Froese D, Albrechtsen A, Stiller M, Schubert M, Cappellini E, Petersen B, Moltke I, Johnson PL, Fumagalli M, Vilstrup JT, Raghavan M, Korneliussen T, ... ... Jensen LJ, et al. Recalibrating Equus evolution using the genome sequence of an early Middle Pleistocene horse. Nature. 499: 74-8. PMID 23803765 DOI: 10.1038/Nature12323 |
0.51 |
|
| 2013 |
Eriksson R, Jensen PB, Frankild S, Jensen LJ, Brunak S. Dictionary construction and identification of possible adverse drug events in Danish clinical narrative text. Journal of the American Medical Informatics Association : Jamia. 20: 947-53. PMID 23703825 DOI: 10.1136/Amiajnl-2013-001708 |
0.483 |
|
| 2013 |
Kuhn M, Al Banchaabouchi M, Campillos M, Jensen LJ, Gross C, Gavin AC, Bork P. Systematic identification of proteins that elicit drug side effects. Molecular Systems Biology. 9: 663. PMID 23632385 DOI: 10.1038/Msb.2013.10 |
0.806 |
|
| 2013 |
Jensen PB, Jensen LJ, Brunak S. Reply to 'Mining electronic health records: an additional perspective'. Nature Reviews. Genetics. 14: 75. PMID 23247438 DOI: 10.1038/Nrg3208-C2 |
0.338 |
|
| 2013 |
Franceschini A, Szklarczyk D, Frankild S, Kuhn M, Simonovic M, Roth A, Lin J, Minguez P, Bork P, von Mering C, Jensen LJ. STRING v9.1: protein-protein interaction networks, with increased coverage and integration. Nucleic Acids Research. 41: D808-15. PMID 23203871 DOI: 10.1093/Nar/Gks1094 |
0.812 |
|
| 2012 |
Jensen PB, Jensen LJ, Brunak S. Mining electronic health records: towards better research applications and clinical care. Nature Reviews. Genetics. 13: 395-405. PMID 22549152 DOI: 10.1038/Nrg3208 |
0.471 |
|
| 2012 |
Powell S, Szklarczyk D, Trachana K, Roth A, Kuhn M, Muller J, Arnold R, Rattei T, Letunic I, Doerks T, Jensen LJ, von Mering C, Bork P. eggNOG v3.0: orthologous groups covering 1133 organisms at 41 different taxonomic ranges. Nucleic Acids Research. 40: D284-9. PMID 22096231 DOI: 10.1093/Nar/Gkr1060 |
0.79 |
|
| 2012 |
Kuhn M, Szklarczyk D, Franceschini A, von Mering C, Jensen LJ, Bork P. STITCH 3: zooming in on protein-chemical interactions. Nucleic Acids Research. 40: D876-80. PMID 22075997 DOI: 10.1093/Nar/Gkr1011 |
0.771 |
|
| 2011 |
Roque FS, Jensen PB, Schmock H, Dalgaard M, Andreatta M, Hansen T, Søeby K, Bredkjær S, Juul A, Werge T, Jensen LJ, Brunak S. Using electronic patient records to discover disease correlations and stratify patient cohorts. Plos Computational Biology. 7: e1002141. PMID 21901084 DOI: 10.1371/Journal.Pcbi.1002141 |
0.404 |
|
| 2011 |
Raes J, Letunic I, Yamada T, Jensen LJ, Bork P. Toward molecular trait-based ecology through integration of biogeochemical, geographical and metagenomic data. Molecular Systems Biology. 7: 473. PMID 21407210 DOI: 10.1038/Msb.2011.6 |
0.784 |
|
| 2011 |
Danielsen JM, Sylvestersen KB, Bekker-Jensen S, Szklarczyk D, Poulsen JW, Horn H, Jensen LJ, Mailand N, Nielsen ML. Mass spectrometric analysis of lysine ubiquitylation reveals promiscuity at site level. Molecular & Cellular Proteomics : McP. 10: M110.003590. PMID 21139048 DOI: 10.1074/Mcp.M110.003590 |
0.327 |
|
| 2011 |
Dinkel H, Chica C, Via A, Gould CM, Jensen LJ, Gibson TJ, Diella F. Phospho.ELM: a database of phosphorylation sites--update 2011. Nucleic Acids Research. 39: D261-7. PMID 21062810 DOI: 10.1093/Nar/Gkq1104 |
0.371 |
|
| 2011 |
Szklarczyk D, Franceschini A, Kuhn M, Simonovic M, Roth A, Minguez P, Doerks T, Stark M, Muller J, Bork P, Jensen LJ, von Mering C. The STRING database in 2011: functional interaction networks of proteins, globally integrated and scored. Nucleic Acids Research. 39: D561-8. PMID 21045058 DOI: 10.1093/Nar/Gkq973 |
0.83 |
|
| 2010 |
Gallego O, Betts MJ, Gvozdenovic-Jeremic J, Maeda K, Matetzki C, Aguilar-Gurrieri C, Beltran-Alvarez P, Bonn S, Fernández-Tornero C, Jensen LJ, Kuhn M, Trott J, Rybin V, Müller CW, Bork P, et al. A systematic screen for protein-lipid interactions in Saccharomyces cerevisiae. Molecular Systems Biology. 6: 430. PMID 21119626 DOI: 10.1038/Msb.2010.87 |
0.687 |
|
| 2010 |
Iskar M, Campillos M, Kuhn M, Jensen LJ, van Noort V, Bork P. Drug-induced regulation of target expression. Plos Computational Biology. 6. PMID 20838579 DOI: 10.1371/Journal.Pcbi.1000925 |
0.773 |
|
| 2010 |
Jensen LJ, Bork P. Ontologies in quantitative biology: a basis for comparison, integration, and discovery. Plos Biology. 8: e1000374. PMID 20520843 DOI: 10.1371/Journal.Pbio.1000374 |
0.552 |
|
| 2010 |
Blicher T, Gupta R, Wesolowska A, Jensen LJ, Brunak S. Protein annotation in the era of personal genomics. Current Opinion in Structural Biology. 20: 335-41. PMID 20403684 DOI: 10.1016/J.Sbi.2010.03.008 |
0.531 |
|
| 2010 |
Granovskaia MV, Jensen LJ, Ritchie ME, Toedling J, Ning Y, Bork P, Huber W, Steinmetz LM. High-resolution transcription atlas of the mitotic cell cycle in budding yeast. Genome Biology. 11: R24. PMID 20193063 DOI: 10.1186/Gb-2010-11-3-R24 |
0.55 |
|
| 2010 |
Trachana K, Jensen LJ, Bork P. Evolution and regulation of cellular periodic processes: a role for paralogues. Embo Reports. 11: 233-8. PMID 20168326 DOI: 10.1038/Embor.2010.9 |
0.785 |
|
| 2010 |
Kuhn M, Campillos M, Letunic I, Jensen LJ, Bork P. A side effect resource to capture phenotypic effects of drugs. Molecular Systems Biology. 6: 343. PMID 20087340 DOI: 10.1038/Msb.2009.98 |
0.778 |
|
| 2010 |
Olsen JV, Vermeulen M, Santamaria A, Kumar C, Miller ML, Jensen LJ, Gnad F, Cox J, Jensen TS, Nigg EA, Brunak S, Mann M. Quantitative phosphoproteomics reveals widespread full phosphorylation site occupancy during mitosis. Science Signaling. 3: ra3. PMID 20068231 DOI: 10.1126/Scisignal.2000475 |
0.51 |
|
| 2010 |
Gauthier NP, Jensen LJ, Wernersson R, Brunak S, Jensen TS. Cyclebase.org: version 2.0, an updated comprehensive, multi-species repository of cell cycle experiments and derived analysis results. Nucleic Acids Research. 38: D699-702. PMID 19934261 DOI: 10.1093/Nar/Gkp1044 |
0.507 |
|
| 2010 |
Muller J, Szklarczyk D, Julien P, Letunic I, Roth A, Kuhn M, Powell S, von Mering C, Doerks T, Jensen LJ, Bork P. eggNOG v2.0: extending the evolutionary genealogy of genes with enhanced non-supervised orthologous groups, species and functional annotations. Nucleic Acids Research. 38: D190-5. PMID 19900971 DOI: 10.1093/Nar/Gkp951 |
0.822 |
|
| 2010 |
Kuhn M, Szklarczyk D, Franceschini A, Campillos M, von Mering C, Jensen LJ, Beyer A, Bork P. STITCH 2: an interaction network database for small molecules and proteins. Nucleic Acids Research. 38: D552-6. PMID 19897548 DOI: 10.1093/Nar/Gkp937 |
0.818 |
|
| 2010 |
Soldatos TG, O'Donoghue SI, Satagopam VP, Jensen LJ, Brown NP, Barbosa-Silva A, Schneider R. Martini: using literature keywords to compare gene sets. Nucleic Acids Research. 38: 26-38. PMID 19858102 DOI: 10.1093/Nar/Gkp876 |
0.525 |
|
| 2010 |
O'Donoghue SI, Horn H, Pafilis E, Haag S, Kuhn M, Satagopam VP, Schneider R, Jensen LJ. Reflect: A practical approach to web semantics Journal of Web Semantics. 8: 182-189. DOI: 10.1016/J.Websem.2010.03.003 |
0.467 |
|
| 2009 |
Pafilis E, O'Donoghue SI, Jensen LJ, Horn H, Kuhn M, Brown NP, Schneider R. Reflect: augmented browsing for the life scientist. Nature Biotechnology. 27: 508-10. PMID 19513049 DOI: 10.1038/Nbt0609-508 |
0.686 |
|
| 2009 |
Juncker AS, Jensen LJ, Pierleoni A, Bernsel A, Tress ML, Bork P, von Heijne G, Valencia A, Ouzounis CA, Casadio R, Brunak S. Sequence-based feature prediction and annotation of proteins. Genome Biology. 10: 206. PMID 19226438 DOI: 10.1186/Gb-2009-10-2-206 |
0.685 |
|
| 2009 |
Saunders N, Beltrão P, Jensen L, Jurczak D, Krause R, Kuhn M, Wu S. Microblogging the ISMB: a new approach to conference reporting. Plos Computational Biology. 5: e1000263. PMID 19180175 DOI: 10.1371/Journal.Pcbi.1000263 |
0.509 |
|
| 2009 |
Gianoulis TA, Raes J, Patel PV, Bjornson R, Korbel JO, Letunic I, Yamada T, Paccanaro A, Jensen LJ, Snyder M, Bork P, Gerstein MB. Quantifying environmental adaptation of metabolic pathways in metagenomics. Proceedings of the National Academy of Sciences of the United States of America. 106: 1374-9. PMID 19164758 DOI: 10.1073/Pnas.0808022106 |
0.782 |
|
| 2009 |
Jensen LJ, Kuhn M, Stark M, Chaffron S, Creevey C, Muller J, Doerks T, Julien P, Roth A, Simonovic M, Bork P, von Mering C. STRING 8--a global view on proteins and their functional interactions in 630 organisms. Nucleic Acids Research. 37: D412-6. PMID 18940858 DOI: 10.1093/Nar/Gkn760 |
0.828 |
|
| 2008 |
Jensen LJ, Bork P. Biochemistry. Not comparable, but complementary. Science (New York, N.Y.). 322: 56-7. PMID 18832636 DOI: 10.1126/Science.1164801 |
0.583 |
|
| 2008 |
Miller ML, Jensen LJ, Diella F, Jørgensen C, Tinti M, Li L, Hsiung M, Parker SA, Bordeaux J, Sicheritz-Ponten T, Olhovsky M, Pasculescu A, Alexander J, Knapp S, Blom N, et al. Linear motif atlas for phosphorylation-dependent signaling. Science Signaling. 1: ra2. PMID 18765831 DOI: 10.1126/Scisignal.1159433 |
0.65 |
|
| 2008 |
Campillos M, Kuhn M, Gavin AC, Jensen LJ, Bork P. Drug target identification using side-effect similarity. Science (New York, N.Y.). 321: 263-6. PMID 18621671 DOI: 10.1126/Science.1158140 |
0.78 |
|
| 2008 |
Jensen LJ, de Lichtenberg U, Jensen TS, Brunak S, Bork P. Circular reasoning rather than cyclic expression. Genome Biology. 9: 403. PMID 18598377 DOI: 10.1186/Gb-2008-9-6-403 |
0.614 |
|
| 2008 |
Harrington ED, Jensen LJ, Bork P. Predicting biological networks from genomic data. Febs Letters. 582: 1251-8. PMID 18294967 DOI: 10.1016/J.Febslet.2008.02.033 |
0.744 |
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| 2008 |
Kuhn M, Campillos M, González P, Jensen LJ, Bork P. Large-scale prediction of drug-target relationships. Febs Letters. 582: 1283-90. PMID 18291108 DOI: 10.1016/J.Febslet.2008.02.024 |
0.816 |
|
| 2008 |
Kuhn M, von Mering C, Campillos M, Jensen LJ, Bork P. STITCH: interaction networks of chemicals and proteins. Nucleic Acids Research. 36: D684-8. PMID 18084021 DOI: 10.1093/Nar/Gkm795 |
0.824 |
|
| 2008 |
Shah PK, Tripathi LP, Jensen LJ, Gahnim M, Mason C, Furlong EE, Rodrigues V, White KP, Bork P, Sowdhamini R. Enhanced function annotations for Drosophila serine proteases: a case study for systematic annotation of multi-member gene families. Gene. 407: 199-215. PMID 17996400 DOI: 10.1016/J.Gene.2007.10.012 |
0.709 |
|
| 2008 |
Linding R, Jensen LJ, Pasculescu A, Olhovsky M, Colwill K, Bork P, Yaffe MB, Pawson T. NetworKIN: a resource for exploring cellular phosphorylation networks. Nucleic Acids Research. 36: D695-9. PMID 17981841 DOI: 10.1093/Nar/Gkm902 |
0.557 |
|
| 2008 |
Günther S, Kuhn M, Dunkel M, Campillos M, Senger C, Petsalaki E, Ahmed J, Urdiales EG, Gewiess A, Jensen LJ, Schneider R, Skoblo R, Russell RB, Bourne PE, Bork P, et al. SuperTarget and Matador: resources for exploring drug-target relationships. Nucleic Acids Research. 36: D919-22. PMID 17942422 DOI: 10.1093/Nar/Gkm862 |
0.802 |
|
| 2008 |
Jensen LJ, Julien P, Kuhn M, von Mering C, Muller J, Doerks T, Bork P. eggNOG: automated construction and annotation of orthologous groups of genes. Nucleic Acids Research. 36: D250-4. PMID 17942413 DOI: 10.1093/Nar/Gkm796 |
0.818 |
|
| 2008 |
Gauthier NP, Larsen ME, Wernersson R, de Lichtenberg U, Jensen LJ, Brunak S, Jensen TS. Cyclebase.org--a comprehensive multi-organism online database of cell-cycle experiments. Nucleic Acids Research. 36: D854-9. PMID 17940094 DOI: 10.1093/Nar/Gkm729 |
0.566 |
|
| 2008 |
Yeats C, Orengo C, Veuthey AL, Boeckmann B, Jensen LJ, Valencia A, Rausell A, Bork P. Modern genome annotation: The BioSapiens network Modern Genome Annotation: the Biosapiens Network. 213-238. DOI: 10.1007/978-3-211-75123-7_11 |
0.553 |
|
| 2007 |
Harrington ED, Singh AH, Doerks T, Letunic I, von Mering C, Jensen LJ, Raes J, Bork P. Quantitative assessment of protein function prediction from metagenomics shotgun sequences. Proceedings of the National Academy of Sciences of the United States of America. 104: 13913-8. PMID 17717083 DOI: 10.1073/Pnas.0702636104 |
0.818 |
|
| 2007 |
de Lichtenberg U, Jensen TS, Brunak S, Bork P, Jensen LJ. Evolution of cell cycle control: same molecular machines, different regulation. Cell Cycle (Georgetown, Tex.). 6: 1819-25. PMID 17671420 DOI: 10.4161/Cc.6.15.4537 |
0.683 |
|
| 2007 |
Linding R, Jensen LJ, Ostheimer GJ, van Vugt MA, Jørgensen C, Miron IM, Diella F, Colwill K, Taylor L, Elder K, Metalnikov P, Nguyen V, Pasculescu A, Jin J, Park JG, et al. Systematic discovery of in vivo phosphorylation networks. Cell. 129: 1415-26. PMID 17570479 DOI: 10.1016/J.Cell.2007.05.052 |
0.576 |
|
| 2007 |
von Mering C, Hugenholtz P, Raes J, Tringe SG, Doerks T, Jensen LJ, Ward N, Bork P. Quantitative phylogenetic assessment of microbial communities in diverse environments. Science (New York, N.Y.). 315: 1126-30. PMID 17272687 DOI: 10.1126/Science.1133420 |
0.788 |
|
| 2007 |
Hooper SD, Boué S, Krause R, Jensen LJ, Mason CE, Ghanim M, White KP, Furlong EE, Bork P. Identification of tightly regulated groups of genes during Drosophila melanogaster embryogenesis. Molecular Systems Biology. 3: 72. PMID 17224916 DOI: 10.1038/Msb4100112 |
0.789 |
|
| 2007 |
von Mering C, Jensen LJ, Kuhn M, Chaffron S, Doerks T, Krüger B, Snel B, Bork P. STRING 7--recent developments in the integration and prediction of protein interactions. Nucleic Acids Research. 35: D358-62. PMID 17098935 DOI: 10.1093/Nar/Gkl825 |
0.835 |
|
| 2006 |
Perocchi F, Jensen LJ, Gagneur J, Ahting U, von Mering C, Bork P, Prokisch H, Steinmetz LM. Assessing systems properties of yeast mitochondria through an interaction map of the organelle. Plos Genetics. 2: e170. PMID 17054397 DOI: 10.1371/Journal.Pgen.0020170 |
0.717 |
|
| 2006 |
Jensen LJ, Jensen TS, de Lichtenberg U, Brunak S, Bork P. Co-evolution of transcriptional and post-translational cell-cycle regulation. Nature. 443: 594-7. PMID 17006448 DOI: 10.1038/Nature05186 |
0.685 |
|
| 2006 |
Sandmann T, Jensen LJ, Jakobsen JS, Karzynski MM, Eichenlaub MP, Bork P, Furlong EE. A temporal map of transcription factor activity: mef2 directly regulates target genes at all stages of muscle development. Developmental Cell. 10: 797-807. PMID 16740481 DOI: 10.1016/J.Devcel.2006.04.009 |
0.541 |
|
| 2006 |
Marguerat S, Jensen TS, de Lichtenberg U, Wilhelm BT, Jensen LJ, Bähler J. The more the merrier: comparative analysis of microarray studies on cell cycle-regulated genes in fission yeast. Yeast (Chichester, England). 23: 261-77. PMID 16544289 DOI: 10.1002/Yea.1351 |
0.384 |
|
| 2006 |
Campillos M, von Mering C, Jensen LJ, Bork P. Identification and analysis of evolutionarily cohesive functional modules in protein networks. Genome Research. 16: 374-82. PMID 16449501 DOI: 10.1101/Gr.4336406 |
0.819 |
|
| 2006 |
Gavin AC, Aloy P, Grandi P, Krause R, Boesche M, Marzioch M, Rau C, Jensen LJ, Bastuck S, Dümpelfeld B, Edelmann A, Heurtier MA, Hoffman V, Hoefert C, Klein K, et al. Proteome survey reveals modularity of the yeast cell machinery. Nature. 440: 631-6. PMID 16429126 DOI: 10.1038/Nature04532 |
0.817 |
|
| 2006 |
Jensen LJ, Saric J, Bork P. Literature mining for the biologist: from information retrieval to biological discovery. Nature Reviews. Genetics. 7: 119-29. PMID 16418747 DOI: 10.1038/Nrg1768 |
0.609 |
|
| 2006 |
Saric J, Jensen LJ, Ouzounova R, Rojas I, Bork P. Extraction of regulatory gene/protein networks from Medline. Bioinformatics (Oxford, England). 22: 645-50. PMID 16046493 DOI: 10.1093/Bioinformatics/Bti597 |
0.571 |
|
| 2005 |
Taxis C, Keller P, Kavagiou Z, Jensen LJ, Colombelli J, Bork P, Stelzer EH, Knop M. Spore number control and breeding in Saccharomyces cerevisiae: a key role for a self-organizing system. The Journal of Cell Biology. 171: 627-40. PMID 16286509 DOI: 10.1083/Jcb.200507168 |
0.529 |
|
| 2005 |
Shah PK, Jensen LJ, Boué S, Bork P. Extraction of transcript diversity from scientific literature. Plos Computational Biology. 1: e10. PMID 16103899 DOI: 10.1371/Journal.Pcbi.0010010 |
0.758 |
|
| 2005 |
Korbel JO, Doerks T, Jensen LJ, Perez-Iratxeta C, Kaczanowski S, Hooper SD, Andrade MA, Bork P. Systematic association of genes to phenotypes by genome and literature mining. Plos Biology. 3: e134. PMID 15799710 DOI: 10.1371/Journal.Pbio.0030134 |
0.8 |
|
| 2005 |
de Lichtenberg U, Jensen LJ, Brunak S, Bork P. Dynamic complex formation during the yeast cell cycle. Science (New York, N.Y.). 307: 724-7. PMID 15692050 DOI: 10.1126/Science.1105103 |
0.688 |
|
| 2005 |
von Mering C, Jensen LJ, Snel B, Hooper SD, Krupp M, Foglierini M, Jouffre N, Huynen MA, Bork P. STRING: known and predicted protein-protein associations, integrated and transferred across organisms. Nucleic Acids Research. 33: D433-7. PMID 15608232 DOI: 10.1093/Nar/Gki005 |
0.821 |
|
| 2005 |
de Lichtenberg U, Jensen LJ, Fausbøll A, Jensen TS, Bork P, Brunak S. Comparison of computational methods for the identification of cell cycle-regulated genes. Bioinformatics (Oxford, England). 21: 1164-71. PMID 15513999 DOI: 10.1093/Bioinformatics/Bti093 |
0.672 |
|
| 2004 |
Korbel JO, Jensen LJ, von Mering C, Bork P. Analysis of genomic context: prediction of functional associations from conserved bidirectionally transcribed gene pairs. Nature Biotechnology. 22: 911-7. PMID 15229555 DOI: 10.1038/Nbt988 |
0.79 |
|
| 2004 |
Jensen LJ, Lagarde J, von Mering C, Bork P. ArrayProspector: a web resource of functional associations inferred from microarray expression data. Nucleic Acids Research. 32: W445-8. PMID 15215427 DOI: 10.1093/Nar/Gkh407 |
0.728 |
|
| 2004 |
Bork P, Jensen LJ, von Mering C, Ramani AK, Lee I, Marcotte EM. Protein interaction networks from yeast to human. Current Opinion in Structural Biology. 14: 292-9. PMID 15193308 DOI: 10.1016/J.Sbi.2004.05.003 |
0.746 |
|
| 2004 |
Bendtsen JD, Jensen LJ, Blom N, Von Heijne G, Brunak S. Feature-based prediction of non-classical and leaderless protein secretion. Protein Engineering, Design & Selection : Peds. 17: 349-56. PMID 15115854 DOI: 10.1093/Protein/Gzh037 |
0.547 |
|
| 2004 |
Jensen LJ, Bork P. Quality analysis and integration of large-scale molecular data sets Drug Discovery Today: Targets. 3: 51-56. DOI: 10.1016/S1741-8372(04)02408-9 |
0.601 |
|
| 2003 |
Linding R, Jensen LJ, Diella F, Bork P, Gibson TJ, Russell RB. Protein disorder prediction: implications for structural proteomics. Structure (London, England : 1993). 11: 1453-9. PMID 14604535 DOI: 10.1016/J.Str.2003.10.002 |
0.635 |
|
| 2003 |
Jensen LJ, Ussery DW, Brunak S. Functionality of system components: conservation of protein function in protein feature space. Genome Research. 13: 2444-9. PMID 14559779 DOI: 10.1101/Gr.1190803 |
0.581 |
|
| 2003 |
de Lichtenberg U, Jensen TS, Jensen LJ, Brunak S. Protein feature based identification of cell cycle regulated proteins in yeast. Journal of Molecular Biology. 329: 663-74. PMID 12787668 DOI: 10.1016/S0022-2836(03)00490-X |
0.575 |
|
| 2003 |
Jensen LJ, Skovgaard M, Sicheritz-Pontén T, Jørgensen MK, Lundegaard C, Pedersen CC, Petersen N, Ussery D. Analysis of two large functionally uncharacterized regions in the Methanopyrus kandleri AV19 genome. Bmc Genomics. 4: 12. PMID 12697059 DOI: 10.1186/1471-2164-4-12 |
0.447 |
|
| 2003 |
Jensen LJ, Gupta R, Staerfeldt HH, Brunak S. Prediction of human protein function according to Gene Ontology categories. Bioinformatics (Oxford, England). 19: 635-42. PMID 12651722 DOI: 10.1093/Bioinformatics/Btg036 |
0.602 |
|
| 2002 |
Jensen LJ, Skovgaard M, Brunak S. Prediction of novel archaeal enzymes from sequence-derived features. Protein Science : a Publication of the Protein Society. 11: 2894-8. PMID 12441387 DOI: 10.1110/Ps.0225102 |
0.544 |
|
| 2002 |
Workman C, Jensen LJ, Jarmer H, Berka R, Gautier L, Nielser HB, Saxild HH, Nielsen C, Brunak S, Knudsen S. A new non-linear normalization method for reducing variability in DNA microarray experiments. Genome Biology. 3: research0048. PMID 12225587 DOI: 10.1186/Gb-2002-3-9-Research0048 |
0.479 |
|
| 2002 |
Jensen LJ, Gupta R, Blom N, Devos D, Tamames J, Kesmir C, Nielsen H, Staerfeldt HH, Rapacki K, Workman C, Andersen CA, Knudsen S, Krogh A, Valencia A, Brunak S. Prediction of human protein function from post-translational modifications and localization features. Journal of Molecular Biology. 319: 1257-65. PMID 12079362 DOI: 10.1016/S0022-2836(02)00379-0 |
0.573 |
|
| 2002 |
Gupta R, Jensen LJ, Brunak S. Orphan protein function and its relation to glycosylation. Ernst Schering Research Foundation Workshop. 276-94. PMID 12061006 |
0.48 |
|
| 2002 |
Skovgaard M, Jensen LJ, Friis C, Stærfeldt HH, Worning P, Brunak S, Ussery D. The Atlas visualization of genomewide information Methods in Microbiology. 33: 49-63. DOI: 10.1016/S0580-9517(02)33004-6 |
0.489 |
|
| 2001 |
Skovgaard M, Jensen LJ, Brunak S, Ussery D, Krogh A. On the total number of genes and their length distribution in complete microbial genomes. Trends in Genetics : Tig. 17: 425-8. PMID 11485798 DOI: 10.1016/S0168-9525(01)02372-1 |
0.57 |
|
| 2000 |
Jensen LJ, Knudsen S. Automatic discovery of regulatory patterns in promoter regions based on whole cell expression data and functional annotation. Bioinformatics (Oxford, England). 16: 326-33. PMID 10869030 DOI: 10.1093/Bioinformatics/16.4.326 |
0.421 |
|
| 2000 |
Pedersen AG, Jensen LJ, Brunak S, Staerfeldt HH, Ussery DW. A DNA structural atlas for Escherichia coli. Journal of Molecular Biology. 299: 907-30. PMID 10843847 DOI: 10.1006/Jmbi.2000.3787 |
0.508 |
|
| 2000 |
Worning P, Jensen LJ, Nelson KE, Brunak S, Ussery DW. Structural analysis of DNA sequence: evidence for lateral gene transfer in Thermotoga maritima. Nucleic Acids Research. 28: 706-9. PMID 10637321 DOI: 10.1093/Nar/28.3.706 |
0.474 |
|
| 1999 |
Jensen LJ, Friis C, Ussery DW. Three views of microbial genomes. Research in Microbiology. 150: 773-7. PMID 10673014 DOI: 10.1016/S0923-2508(99)00116-3 |
0.346 |
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