Lars Juhl Jensen

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• 2024

  A quantitative and site-specific atlas of the citrullinome reveals widespread existence of citrullination and insights into PADI4 substrates

  Rebak, A. S., Hendriks, I. A., Elsborg, J. D., Buch-Larsen, S. C., Nielsen, C. H., Terslev, L., Kirsch, R., Damgaard, D., Doncheva, N. T., Lennartsson, C., Rykær, M., Jensen, L. J., Christophorou, M. A. & Nielsen, M. L., 2024, In: Nature Structural and Molecular Biology. 31, 6, p. 977–995 34 p.

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• CoNECo: a Corpus for Named Entity recognition and normalization of protein Complexes

  Nastou, K., Koutrouli, M., Pyysalo, S. & Jensen, L. J., 2024, In: Bioinformatics Advances. 4, 1, 7 p., vbae116.

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• ECCB2024: The 23rd European Conference on Computational Biology

  Kukkonen-Macchi, A., Hautaniemi, S., Heil, K. F., Heinäniemi, M., Jensen, L. J., Junttila, S., Käll, L., Laiho, A., Maccallum, P., Nykter, M., Persson, B., Suomi, T., Van Den Bossche, T., Nyrönen, T. H. & Elo, L. L., 2024, In: Bioinformatics (Oxford, England). 40, Supplement 2, p. ii1-ii3 4 p.

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• FAVA: High-quality functional association networks inferred from scRNA-seq and proteomics data

  Koutrouli, M., Nastou, K., Piera Líndez, P., Bouwmeester, R., Rasmussen, S., Martens, L. & Jensen, L. J., 2024, In: Bioinformatics. 40, 2, 11 p., btae010.

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• Impact of acute alcohol consumption on circulating microbiome in asymptomatic alcohol-related liver disease

  Israelsen, M., Alvarez-Silva, C., Madsen, B. S., Hansen, C. D., Torp, N. C., Johansen, S., Hansen, J. K., Prier Lindvig, K., Insonere, J., Riviere, V., Juel, H. B., Brejnrod, A., Jensen, L. J., Thiele, M., Lelouvier, B., Hansen, T., Arumugam, M. & Krag, A., 2024, In: Gut. 73, 6, p. 1041-1044 gutjnl-2023-330360.

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  5 Citations (Scopus)

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• Improving dictionary-based named entity recognition with deep learning

  Nastou, K., Koutrouli, M., Pyysalo, S. & Jensen, L. J., 2024, In: Bioinformatics. 40, p. ii45-ii52 8 p.

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  1 Citation (Scopus)

• Imputation of label-free quantitative mass spectrometry-based proteomics data using self-supervised deep learning

  Webel, H., Niu, L., Nielsen, A. B., Locard-Paulet, M., Mann, M., Jensen, L. J. & Rasmussen, S., 2024, In: Nature Communications. 15, 15 p., 5405.

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  2 Citations (Scopus)

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• Lifestyle factors in the biomedical literature: an ontology and comprehensive resources for named entity recognition

  Nourani, E., Koutrouli, M., Xie, Y., Vagiaki, D., Pyysalo, S., Nastou, K., Brunak, S. & Jensen, L. J., 2024, In: Bioinformatics. 40, 11, 8 p., btae613.

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  1 Citation (Scopus)

• Opportunities and barriers in omics-based biomarker discovery for steatotic liver diseases

  Thiele, M., Villesen, I. F., Niu, L., Johansen, S., Sulek, K., Nishijima, S., Espen, L. V., Keller, M., Israelsen, M., Suvitaival, T., Zawadzki, A. D., Juel, H. B., Brol, M. J., Stinson, S. E., Huang, Y., Silva, M. C. A., Kuhn, M., Anastasiadou, E., Leeming, D. J., Karsdal, M. & 12 others, Matthijnssens, J., Arumugam, M., Dalgaard, L. T., Legido-Quigley, C., Mann, M., Trebicka, J., Bork, P., Jensen, L. J., Hansen, T., Krag, A., MicrobLiver Consortium & GALAXY Consortium, 2024, In: Journal of Hepatology. 81, 2, p. 345-359

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• Overview of the Knowledge Management Center for Illuminating the Druggable Genome

  Oprea, T. I., Bologa, C., Holmes, J., Mathias, S., Metzger, V. T., Waller, A., Yang, J. J., Leach, A. R., Jensen, L. J., Kelleher, K. J., Sheils, T. K., Mathé, E., Avram, S. & Edwards, J. S., 2024, In: Drug Discovery Today. 29, 3, 8 p., 103882.

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• RegulaTome: a corpus of typed, directed, and signed relations between biomedical entities in the scientific literature

  Nastou, K., Mehryary, F., Ohta, T., Luoma, J., Pyysalo, S. & Jensen, L. J., 2024, In: Database. 2024, 7 p., baae095.

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  2 Citations (Scopus)

• Streamlined analysis of drug targets by proteome integral solubility alteration indicates organ-specific engagement

  Batth, T. S., Locard-Paulet, M., Doncheva, N. T., Lopez Mendez, B., Jensen, L. J. & Olsen, J. V., 2024, In: Nature Communications. 15, 1, 17 p., 8923.

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  1 Citation (Scopus)

• STRING-ing together protein complexes: corpus and methods for extracting physical protein interactions from the biomedical literature

  Mehryary, F., Nastou, K., Ohta, T., Jensen, L. J. & Pyysalo, S., 2024, In: Bioinformatics. 40, 9, 10 p., btae552.

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  2 Citations (Scopus)

• TIN-X version 3: update with expanded dataset and modernized architecture for enhanced illumination of understudied targets

  Metzger, V. T., Cannon, D. C., Yang, J. J., Mathias, S. L., Bologa, C. G., Waller, A., Schürer, S. C., Vidović, D., Kelleher, K. J., Sheils, T. K., Jensen, L. J., Lambert, C. G., Oprea, T. I. & Edwards, J. S., 2024, In: PeerJ. 12, 15 p., e17470.

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• 2023

  About the dark corners in the gene function space of Escherichia coli remaining without illumination by scientific literature

  Tantoso, E., Eisenhaber, B., Sinha, S., Jensen, L. J. & Eisenhaber, F., 2023, In: Biology Direct. 18, 17 p., 7.

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  6 Citations (Scopus)

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• Arena3D^web: interactive 3D visualization of multilayered networks supporting multiple directional information channels, clustering analysis and application integration

  Kokoli, M., Karatzas, E., Baltoumas, F. A., Schneider, R., Pafilis, E., Paragkamian, S., Doncheva, N. T., Jensen, L. J. & Pavlopoulos, G. A., 2023, In: NAR Genomics and Bioinformatics. 5, 2, 8 p., lqad053.

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  5 Citations (Scopus)

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• Cross-species high-resolution transcriptome profiling suggests biomarkers and therapeutic targets for ulcerative colitis

  Yarani, R., Palasca, O., Doncheva, N. T., Anthon, C., Pilecki, B., Svane, C. A. S., Mirza, A. H., Litman, T., Holmskov, U., Bang-Berthelsen, C. H., Vilien, M., Jensen, L. J., Gorodkin, J. & Pociot, F., 2023, In: Frontiers in Molecular Biosciences. 9, 1081176.

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• Did the early full genome sequencing of yeast boost gene function discovery?

  Tantoso, E., Eisenhaber, B., Sinha, S., Jensen, L. J. & Eisenhaber, F., 2023, In: Biology Direct. 18, 11 p., 46.

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• Differential Expression of the β3 Subunit of Voltage-Gated Ca²⁺ Channel in Mesial Temporal Lobe Epilepsy

  Kjær, C., Palasca, O., Barzaghi, G., Bak, L. K., Durhuus, R. K. J., Jakobsen, E., Pedersen, L., Bartels, E. D., Woldbye, D. P. D., Pinborg, L. H. & Jensen, L. J., 2023, In: Molecular Neurobiology. 60, p. 5755–5769

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• eggNOG 6.0: enabling comparative genomics across 12 535 organisms

  Hernández-Plaza, A., Szklarczyk, D., Botas, J., Cantalapiedra, C. P., Giner-Lamia, J., Mende, D. R., Kirsch, R., Rattei, T., Letunic, I., Jensen, L. J., Bork, P., von Mering, C. & Huerta-Cepas, J., 2023, In: Nucleic Acids Research. 51, D1, p. D389-D394 6 p.

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• Hunting for the elusive target antigen in gestational alloimmune liver disease (GALD)

  Rieneck, K., Rasmussen, K. K., Schoof, E. M., Clausen, F. B., Holze, H., Bergholt, T., Jørgensen, M. H., Christensen, V. B., Almaas, R., Jordal, P. L., Locard-Paulet, M., Runager, K., Nielsen, L. K., Schlotmann, B. C., Weischenfeldt, J. L., Jensen, L. J. & Dziegiel, M. H., 2023, In: PLoS ONE. 18, 10, 25 p., e0286432.

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• Loss of N-terminal acetyltransferase A activity induces thermally unstable ribosomal proteins and increases their turnover in Saccharomyces cerevisiae

  Guzman, U. H., Aksnes, H., Ree, R., Krogh, N., Jakobsson, M. E., Jensen, L. J., Arnesen, T. & Olsen, J. V., 2023, In: Nature Communications. 14, 4517.

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  8 Citations (Scopus)

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• Metastatic Infiltration of Nervous Tissue and Periosteal Nerve Sprouting in Multiple Myeloma-Induced Bone Pain in Mice and Human

  Diaz-delCastillo, M., Palasca, O., Nemler, T. T., Thygesen, D. M., Chávez-Saldaña, N. A., Vázquez-Mora, J. A., Ponce Gomez, L. Y., Jensen, L. J., Evans, H., Andrews, R. E., Mandal, A., Neves, D., Mehlen, P., Caruso, J. P., Dougherty, P. M., Price, T. J., Chantry, A., Lawson, M. A., Andersen, T. L., Jimenez-Andrade, J. M. & 1 others, Heegaard, A-M., 2023, In: The Journal of Neuroscience. 43, 29, p. 5414-5430

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  3 Citations (Scopus)

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• Pancreatic cancer symptom trajectories from Danish registry data and free text in electronic health records

  Hjaltelin, J. X., Novitski, S. I., Jørgensen, I. F., Siggaard, T., Vulpius, S. A., Westergaard, D., Johansen, J. S., Chen, I. M., Juhl Jensen, L. & Brunak, S., 2023, In: eLife. 12, 15 p., e84919.

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  3 Citations (Scopus)

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• Pharos 2023: an integrated resource for the understudied human proteome

  Kelleher, K. J., Sheils, T. K., Mathias, S. L., Yang, J. J., Metzger, V. T., Siramshetty, V. B., Nguyen, D-T., Jensen, L. J., Vidovic, D., Schurer, S. C., Holmes, J., Sharma, K. R., Pillai, A., Bologa, C. G., Edwards, J. S., Mathe, E. A. & Oprea, T., 2023, In: Nucleic Acids Research. 51, D1, p. D1405-D1416 12 p., gkac1033.

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  33 Citations (Scopus)

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• Recent advances in kinase signaling network profiling by mass spectrometry

  Franciosa, G., Locard-Paulet, M., Jensen, L. J. & Olsen, J. V., 2023, In: Current Opinion in Chemical Biology. 73, 11 p., 102260.

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  7 Citations (Scopus)

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• S1000: a better taxonomic name corpus for biomedical information extraction

  Luoma, J., Nastou, K., Ohta, T., Toivonen, H., Pafilis, E., Jensen, L. J. & Pyysalo, S., 2023, In: Bioinformatics. 39, 6, 8 p., btad369.

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  8 Citations (Scopus)

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• The STRING database in 2023: protein-protein association networks and functional enrichment analyses for any sequenced genome of interest

  Szklarczyk, D., Kirsch, R., Koutrouli, M., Nastou, K., Mehryary, F., Hachilif, R., Gable, A. L., Fang, T., Doncheva, N. T., Pyysalo, S., Bork, P., Jensen, L. J. & von Mering, C., 2023, In: Nucleic Acids Research. 51, D1, p. D638-D646 9 p.

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• 2022

  A knowledge graph to interpret clinical proteomics data

  Santos, A., Colaço, A. R., Nielsen, A. B., Niu, L., Strauss, M., Geyer, P. E., Coscia, F., Albrechtsen, N. J. W., Mundt, F., Jensen, L. J. & Mann, M., 2022, In: Nature Biotechnology. 40, p. 692–702

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  132 Citations (Scopus)

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• A time-resolved multi-omics atlas of Acanthamoeba castellanii encystment

  Bernard, C., Locard-Paulet, M., Noël, C., Duchateau, M., Giai Gianetto, Q., Moumen, B., Rattei, T., Hechard, Y., Jensen, L. J., Matondo, M. & Samba-Louaka, A., 2022, In: Nature Communications. 13, 1, 14 p., 4104.

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  17 Citations (Scopus)

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• A Workflow of Integrated Resources to Catalyze Network Pharmacology Driven COVID-19 Research

  Zahoránszky-Kőhalmi, G., Siramshetty, V. B., Kumar, P., Gurumurthy, M., Grillo, B., Mathew, B., Metaxatos, D., Backus, M., Mierzwa, T., Simon, R., Grishagin, I., Brovold, L., Mathé, E. A., Hall, M. D., Michael, S. G., Godfrey, A. G., Mestres, J., Jensen, L. J. & Oprea, T. I., 2022, In: Journal of Chemical Information and Modeling. 62, 3, p. 718-729

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• Cytoscape stringApp 2.0: Analysis and Visualization of Heterogeneous Biological Networks

  Doncheva, N. T., Morris, J. H., Holze, H., Kirsch, R., Nastou, K. C., Cuesta-Astroz, Y., Rattei, T., Szklarczyk, D., Von Mering, C. & Jensen, L. J., 2022, In: Journal of Proteome Research. 22, 2, p. 637-646

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  39 Citations (Scopus)

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• Differentially Expressed miRNAs in Ulcerative Colitis and Crohn's Disease

  Yarani, R., Shojaeian, A., Palasca, O., Doncheva, N. T., Jensen, L. J., Gorodkin, J. & Pociot, F., 2022, In: Frontiers in Immunology. 13, 21 p., 865777.

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  25 Citations (Scopus)

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• Diseases 2.0: a weekly updated database of disease-gene associations from text mining and data integration

  Grissa, D., Junge, A., Oprea, T. I. & Jensen, L. J., 2022, In: Database : the journal of biological databases and curation. 2022, 2022, 8 p.

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  37 Citations (Scopus)

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• Identifying the genes impacted by cell proliferation in proteomics and transcriptomics studies

  Locard-Paulet, M., Palasca, O. & Jensen, L. J., 2022, In: PLOS Computational Biology. 18, 10, 20 p., e1010604.

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  11 Citations (Scopus)

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• Light-induced asymmetries in embryonic retinal gene expression are mediated by the vascular system and extracellular matrix

  Versace, E., Sgadò, P., George, J., Loveland, J. L., Ward, J., Thorpe, P., Jensen, L. J., Spencer, K. A., Paracchini, S. & Vallortigara, G., 2022, In: Scientific Reports. 12, 1, 12 p., 12086.

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  4 Citations (Scopus)

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• Myeloma-induced bone pain: lessons learnt from a localized, immunocompetent mouse model

  Diaz-delCastillo, M., Nemler, T., Thygesen, D. M., Chavez-Saldana, N. A., Vazquez-Mora, J. A., Palasca, O., Juhl, L., Evans, H., Andrews, R. E., Mandal, A., Chantry, A. D., Lawson, M. A., Andersen, T., Jimenez-Andrade, J. M. & Heegaard, A-M., 2022, In: Clinical Lymphoma, Myeloma & Leukemia. 22, Suppl., p. S108-S108 P-133.

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• Phosphorylation of SHP2 at Tyr62 enables acquired resistance to SHP2 allosteric inhibitors in FLT3-ITD-driven AML

  Pfeiffer, A., Franciosa, G., Locard-Paulet, M., Piga, I., Reckzeh, K., Vemulapalli, V., Blacklow, S. C., Theilgaard-Mönch, K., Jensen, L. J. & Olsen, J. V., 2022, In: Cancer Research. 82, 11, p. 2141-2155 15 p.

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• PREGO: A Literature and Data-Mining Resource to Associate Microorganisms, Biological Processes, and Environment Types

  Zafeiropoulos, H., Paragkamian, S., Ninidakis, S., Pavlopoulos, G. A., Jensen, L. J. & Pafilis, E., 2022, In: Microorganisms. 10, 2, 22 p., 293.

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• The impact of PrsA over-expression on the Bacillus subtilis transcriptome during fed-batch fermentation of alpha-amylase production

  Geissler, A. S., Poulsen, L. D., Doncheva, N. T., Anthon, C., Seemann, S. E., González-Tortuero, E., Breüner, A., Jensen, L. J., Hjort, C., Vinther, J. & Gorodkin, J., 2022, In: Frontiers in Microbiology. 13, 17 p., 909493.

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• U-CIE [/juː ‘siː/]: Color encoding of high-dimensional data

  Koutrouli, M., Morris, J. H. & Jensen, L. J., 2022, In: Protein Science. 31, 9, 8 p., e4388.

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• 2021

  Homology-directed repair protects the replicating genome from metabolic assaults

  Somyajit, K., Spies, J., Coscia, F., Kirik, U., Rask, M-B., Lee, J-H., Neelsen, K. J., Mund, A., Jensen, L. J., Paull, T. T., Mann, M. & Lukas, J., 2021, In: Developmental Cell. 56, 4, p. 461-477.e7

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• Human pathways in animal models: possibilities and limitations

  Doncheva, N. T., Palasca, O., Yarani, R., Litman, T., Anthon, C., Groenen, M. A. M., Stadler, P. F., Pociot, F., Jensen, L. J. & Gorodkin, J., 2021, In: Nucleic Acids Research. 49, 4, p. 1859-1871 13 p.

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• Improved metagenome binning and assembly using deep variational autoencoders

  Nissen, J. N., Johansen, J., Allesoe, R. L., Sonderby, C. K., Armenteros, J. J. A., Gronbech, C. H., Jensen, L. J., Nielsen, H. B., Petersen, T. N., Winther, O. & Rasmussen, S., 2021, In: Nature Biotechnology. 39, p. 555-560

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  228 Citations (Scopus)

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• OnTheFly2.0: a text-mining web application for automated biomedical entity recognition, document annotation, network and functional enrichment analysis

  Baltoumas, F. A., Zafeiropoulou, S., Karatzas, E., Paragkamian, S., Thanati, F., Iliopoulos, I., Eliopoulos, A. G., Schneider, R., Jensen, L. J., Pafilis, E. & Pavlopoulos, G. A., 2021, In: NAR Genomics and Bioinformatics. 3, 4, 10 p., lqab090.

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• Quantitative proteome comparison of human hearts with those of model organisms

  Linscheid, N., Santos, A., Poulsen, P. C., Mills, R. W., Calloe, K., Leurs, U., Ye, J. Z., Stolte, C., Thomsen, M. B., Bentzen, B. H., Lundegaard, P. R., Olesen, M. S., Jensen, L. J., Olsen, J. V. & Lundby, A., 2021, In: PLOS Biology. 19, 4, 22 p., e3001144.

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• TCRD and Pharos 2021: mining the human proteome for disease biology

  Sheils, T. K., Mathias, S. L., Kelleher, K. J., Siramshetty, V. B., Nguyen, D. T., Bologa, C. G., Jensen, L. J., Vidović, D., Koleti, A., Schürer, S. C., Waller, A., Yang, J. J., Holmes, J., Bocci, G., Southall, N., Dharkar, P., Mathé, E., Simeonov, A. & Oprea, T. I., 2021, In: Nucleic Acids Research. 49, D1, p. D1334-D1346 13 p.

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  93 Citations (Scopus)

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• The STRING database in 2021: customizable protein-protein networks, and functional characterization of user-uploaded gene/measurement sets

  Szklarczyk, D., Gable, A. L., Nastou, K. C., Lyon, D., Kirsch, R., Pyysalo, S., Doncheva, N. T., Legeay, M., Fang, T., Bork, P., Jensen, L. J. & von Mering, C., 2021, In: Nucleic Acids Symposium Series. 49, D1, p. D605-D612 8 p.

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• TIGA: target illumination GWAS analytics

  Yang, J. J., Grissa, D., Lambert, C. G., Bologa, C. G., Mathias, S. L., Waller, A., Wild, D. J., Jensen, L. J. & Oprea, T. I., 2021, In: Bioinformatics. 37, 21, p. 3865-3873

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  8 Citations (Scopus)

• Yield and Integrity of RNA from Brain Samples are Largely Unaffected by Pre-analytical Procedures

  Jensen, P. S. H., Johansen, M., Bak, L. K., Jensen, L. J. & Kjær, C., 2021, In: Neurochemical Research. 46, p. 447-454

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  4 Citations (Scopus)