Functional Analysis of MS-Based Proteomics Data: From Protein Groups to Networks

Authors: Locard-Paulet, Marie ^{1, 2, 3, ∗, ‡}, Doncheva, Nadezhda T. ^{1, ‡}, Morris, John H. ⁴, Jensen, Lars Juhl ^{1, ∗}

Source: In Molecular & Cellular Proteomics December 2024 23(12)

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

Authors: Hansen, Torben, Mann, Matthias, Matthijnssens, Jelle, Krag, Aleksander, Bork, Peer, Arumugam, Manimozhiyan, Trebicka, Jonel, Karsdal, Morten, Anastasiadou, Ema, Israelsen, Hans, Melberg, Hans Olav, Legido-Quigley, Cristina, Thiele, Maja, Villesen, Ida Falk, Niu, Lili, Johansen, Stine, Sulek, Karolina, Nishijima, Suguru, Espen, Lore Van, Keller, Marisa, Israelsen, Mads, Suvitaival, Tommi, Zawadzki, Andressa de, Juel, Helene Bæk, Brol, Maximilian Joseph, Stinson, Sara Elizabeth, Huang, Yun, Silva, Maria Camilla Alvarez, Kuhn, Michael, Leeming, Diana Julie, Dalgaard, Louise Torp, Jensen, Lars Juhl

Source: In Journal of Hepatology August 2024 81(2):345-359

Overview of the Knowledge Management Center for Illuminating the Druggable Genome

Authors: Oprea, Tudor I., Bologa, Cristian, Holmes, Jayme, Mathias, Stephen, Metzger, Vincent T., Waller, Anna, Yang, Jeremy J., Leach, Andrew R., Jensen, Lars Juhl, Kelleher, Keith J., Sheils, Timothy K., Mathé, Ewy, Avram, Sorin, Edwards, Jeremy S.

Source: In Drug Discovery Today March 2024 29(3)

OnTheFly 2.0: A tool for automatic annotation of files and biological information extraction

Authors: Pafilis, Evangelos, Pavlopoulos, Georgios A., Satagopam, Venkata P., Papanikolaou, Nikolas, Horn, Heiko, Arvanitidis, Christos, Jensen, Lars Juhl, Schneider, Reinhard, Iliopoulos, Ioannis

Source: 13th IEEE International Conference on BioInformatics and BioEngineering Bioinformatics and Bioengineering (BIBE), 2013 IEEE 13th International Conference on. :1-4 Nov, 2013

Relation: 2013 IEEE 13th International Conference on Bioinformatics and Bioengineering (BIBE)

Homology-directed repair protects the replicating genome from metabolic assaults

Authors: Somyajit, Kumar, Spies, Julian, Coscia, Fabian, Kirik, Ufuk, Rask, Maj-Britt, Lee, Ji-Hoon, Neelsen, Kai John, Mund, Andreas, Jensen, Lars Juhl, Paull, Tanya T., Mann, Matthias, Lukas, Jiri

Source: In Developmental Cell 22 February 2021 56(4):461-477

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

Authors: Nourani, Esmaeil^1,2, Koutrouli, Mikaela¹, Xie, Yijia¹, Vagiaki, Danai¹, Pyysalo, Sampo³, Nastou, Katerina¹, katerina.nastou@cpr.ku.dk, Brunak, Søren¹, katerina.nastou@cpr.ku.dk, Jensen, Lars Juhl¹, katerina.nastou@cpr.ku.dk

Source: Bioinformatics; Nov2024, Vol. 40 Issue 11, p1-8, 8p

Graph databases in systems biology: a systematic review.

Authors: Mazein, Ilya¹, ilya.mazein@uni-greifswald.de, Rougny, Adrien², Mazein, Alexander², Henkel, Ron¹, Gütebier, Lea¹, Michaelis, Lea¹, Ostaszewski, Marek², Schneider, Reinhard², Satagopam, Venkata², Jensen, Lars Juhl³, Waltemath, Dagmar¹, Wodke, Judith A H¹, Balaur, Irina², ilya.mazein@uni-greifswald.de

Source: Briefings in Bioinformatics; Nov2024, Vol. 25 Issue 6, p1-12, 12p

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

Authors: Batth, Tanveer Singh, Locard-Paulet, Marie, Doncheva, Nadezhda T., Lopez Mendez, Blanca, Jensen, Lars Juhl, Olsen, Jesper Velgaard

Source: Nature Communications; 10/17/2024, Vol. 15 Issue 1, p1-17, 17p

Subject Terms: DRUG target, SMALL molecules, DRUG repositioning, DRUG design, ENZYME inhibitors

CoCoScore: context-aware co-occurrence scoring for text mining applications using distant supervision

Authors: Junge, Alexander, Jensen, Lars Juhl

Source: Bioinformatics. 36(1):264-271

Availability: http://explore.bl.uk/primo_library/libweb/action/display.do?tabs=detailsTab&gathStatTab=true&ct=display&fn=search&doc=ETOCvdc_100097105648.0x000001&indx=1&recIds=ETOCvdc_100097105648.0x000001

Improving dictionary-based named entity recognition with deep learning.

Authors: Nastou, Katerina¹, Koutrouli, Mikaela¹, Pyysalo, Sampo², Jensen, Lars Juhl¹, lars.juhl.jensen@cpr.ku.dk

Source: Bioinformatics; 2024 Supplement, Vol. 40, pii45-ii52, 8p

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

Authors: Mehryary, Farrokh¹, Nastou, Katerina², Ohta, Tomoko³, Jensen, Lars Juhl², sampo.pyysalo@utu.fi, Pyysalo, Sampo¹, sampo.pyysalo@utu.fi

Source: Bioinformatics; Sep2024, Vol. 40 Issue 9, p1-10, 10p

Spore Number Control and Breeding in Soccharomyces cerevisioe: A Key Role for a Self-Organizing System

Authors: Taxis, Christof, Keller, Philipp, Kavagiou, Zaharoula, Jensen, Lars Juhl, Colombelli, Julien, Bork, Peer, Knop, Michael

Source: The Journal of Cell Biology, 2005 Nov . 171(4), 627-640.

Access URL: https://www.jstor.org/stable/3658470

Dynamic Complex Formation during the Yeast Cell Cycle

Authors: de Lichtenberg, Ulrik, Jensen, Lars Juhl, Brunak, Søren, Bork, Peer

Source: Science, 2005 Feb 01. 307(5710), 724-727.

Access URL: https://www.jstor.org/stable/3840272

A Guide to Dictionary-Based Text Mining

Authors: Cook, Helen V., Jensen, Lars Juhl

Source: Methods in molecular biology. 1939:73-90

Availability: http://explore.bl.uk/primo_library/libweb/action/display.do?tabs=detailsTab&gathStatTab=true&ct=display&fn=search&doc=ETOCRN619452007&indx=1&recIds=ETOCRN619452007

U‐CIE [/juː 'siː/]: Color encoding of high‐dimensional data

Authors: Koutrouli, Mikaela, Morris, John H., Jensen, Lars Juhl

Source: Protein science. 31(9)

Availability: http://explore.bl.uk/primo_library/libweb/action/display.do?tabs=detailsTab&gathStatTab=true&ct=display&fn=search&doc=ETOCvdc_100160079578.0x000001&indx=1&recIds=ETOCvdc_100160079578.0x000001

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

Authors: Webel, Henry, Niu, Lili, Nielsen, Annelaura Bach, Locard-Paulet, Marie, Mann, Matthias, Jensen, Lars Juhl, Rasmussen, Simon

Source: Nature Communications; 6/26/2024, Vol. 15 Issue 1, p1-15, 15p

Subject Terms: DEEP learning, MACHINE learning, PROTEOMICS, MASS spectrometry, MISSING data (Statistics), BLOOD plasma

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

Authors: Metzger, Vincent T., Cannon, Daniel C., Yang, Jeremy J., Mathias, Stephen L., Bologa, Cristian G., Waller, Anna, Schürer, Stephan C., Vidović, Dušica, Kelleher, Keith J., Sheils, Timothy K., Jensen, Lars Juhl, Lambert, Christophe G., Oprea, Tudor I., Edwards, Jeremy S.

Source: PeerJ; Jun2024, p1-15, 15p

Subject Terms: NATURAL language processing, TEXT mining, DRUG target, DISEASE nomenclature, DATABASES

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

Authors: Israelsen, Mads, Alvarez-Silva, Camila, Madsen, Bjørn Stæhr, Hansen, Camilla Dalby, Torp, Nikolaj Christian, Johansen, Stine, Hansen, Johanne Kragh, Lindvig, Katrine Prier, Insonere, Jeanlouis, Riviere, Virginie, Bæk Juel, Helene, Brejnrod, Asker, Jensen, Lars Juhl, Thiele, Maja, Lelouvier, Benjamin, Hansen, Torben, Arumugam, Manimozhiyan, Krag, Aleksander

Source: Gut; Jun2024, Vol. 73 Issue 6, p1041-1044, 12p

Subject Terms: LIVER diseases, ALCOHOL-induced disorders, ALCOHOL drinking, MARIJUANA, MEDICAL sciences, HEPATIC fibrosis

An Integrative Approach to Virus—Host Protein—Protein Interactions

Authors: Cook, Helen V., Jensen, Lars Juhl

Source: Methods in molecular biology. 1819:175-196

Availability: http://explore.bl.uk/primo_library/libweb/action/display.do?tabs=detailsTab&gathStatTab=true&ct=display&fn=search&doc=ETOCRN618276465&indx=1&recIds=ETOCRN618276465

ECCB2024: The 23rd European Conference on Computational Biology.

Authors: Kukkonen-Macchi, Anu¹, anukuk@utu.fi, Hautaniemi, Sampsa², Heil, Katharina F³, Heinäniemi, Merja⁴, Jensen, Lars Juhl⁵, Junttila, Sini¹, Käll, Lukas⁶, Laiho, Asta¹, Maccallum, Peter³, Nykter, Matti⁷, Persson, Bengt⁸, Suomi, Tomi¹, Bossche, Tim Van Den^9,10, Nyrönen, Tommi H^11,12, Elo, Laura L^1,13, anukuk@utu.fi

Source: Bioinformatics; 2024 Supplement, Vol. 40, pii1-ii3, 3p