Training on test proteins improves fitness, structure, and function prediction

Authors: Bushuiev, Anton, Bushuiev, Roman, Zadorozhny, Nikola, Samusevich, Raman, Stärk, Hannes, Sedlar, Jiri, Pluskal, Tomáš, Sivic, Josef

Subject Terms: Computer Science - Machine Learning, Quantitative Biology - Biomolecules

Access URL: http://arxiv.org/abs/2411.02109

MassSpecGym: A benchmark for the discovery and identification of molecules

Authors: Bushuiev, Roman, Bushuiev, Anton, de Jonge, Niek F., Young, Adamo, Kretschmer, Fleming, Samusevich, Raman, Heirman, Janne, Wang, Fei, Zhang, Luke, Dührkop, Kai, Ludwig, Marcus, Haupt, Nils A., Kalia, Apurva, Brungs, Corinna, Schmid, Robin, Greiner, Russell, Wang, Bo, Wishart, David S., Liu, Li-Ping, Rousu, Juho, Bittremieux, Wout, Rost, Hannes, Mak, Tytus D., Hassoun, Soha, Huber, Florian, van der Hooft, Justin J. J., Stravs, Michael A., Böcker, Sebastian, Sivic, Josef, Pluskal, Tomáš

Subject Terms: Quantitative Biology - Quantitative Methods, Computer Science - Machine Learning

Access URL: http://arxiv.org/abs/2410.23326

Revealing data leakage in protein interaction benchmarks

Authors: Bushuiev, Anton, Bushuiev, Roman, Sedlar, Jiri, Pluskal, Tomas, Damborsky, Jiri, Mazurenko, Stanislav, Sivic, Josef

Subject Terms: Computer Science - Machine Learning

Access URL: http://arxiv.org/abs/2404.10457

Learning to design protein-protein interactions with enhanced generalization

Authors: Bushuiev, Anton, Bushuiev, Roman, Kouba, Petr, Filkin, Anatolii, Gabrielova, Marketa, Gabriel, Michal, Sedlar, Jiri, Pluskal, Tomas, Damborsky, Jiri, Mazurenko, Stanislav, Sivic, Josef

Subject Terms: Computer Science - Machine Learning

Access URL: http://arxiv.org/abs/2310.18515

Opportunities of hidden hydropower technologies towards the energy transition

Authors: Karapici, Valbona ^a, Trojer, Alex ^b, Lazarevikj, Marija ^c, Pluskal, Tomáš ^d, Chernobrova, Anna ^e, Nezirić, Emir ^f, Zuecco, Giulia ^{g, h}, Alerci, Aldo Leonardo ⁱ, Seydoux, Martin ⁱ, Doujak, Eduard ^{j, ⁎}, Rudolf, Pavel ^k

Source: In Energy Reports December 2024 12:5633-5647

Software and Computational Tools for LC-MS-Based Epilipidomics: Challenges and Solutions

Authors: Damiani, Tito, Bonciarelli, Stefano, Thallinger, Gerhard G., Koehler, Nikolai, Krettler, Christoph A., Salihoğlu, Arif K., Korf, Ansgar, Pauling, Josch K., Pluskal, Tomáš, Ni, Zhixu

Source: Analytical chemistry. 95(1):287-303

Availability: http://explore.bl.uk/primo_library/libweb/action/display.do?tabs=detailsTab&gathStatTab=true&ct=display&fn=search&doc=ETOCRN631552259&indx=1&recIds=ETOCRN631552259

Computational metabolomics reveals overlooked chemodiversity of alkaloid scaffolds in Piper fimbriulatum.

Authors: Damiani, Tito, Smith, Joshua, Hebra, Téo, Perković, Milana, Čičak, Marijo, Kadlecová, Alžběta, Rybka, Vlastimil, Dračínský, Martin, Pluskal, Tomáš

Source: Plant Journal; Mar2025, Vol. 121 Issue 5, p1-14, 14p

Subject Terms: ALKALOIDS, PIPERACEAE, CHEMICAL ecology, METABOLOMICS, CHEMICAL species, PLANT metabolites, TANDEM mass spectrometry

Statistical analysis of feature-based molecular networking results from non-targeted metabolomics data

Authors: Pakkir Shah, Abzer K., Walter, Axel, Ottosson, Filip, Russo, Francesco, Navarro-Diaz, Marcelo, Boldt, Judith, Kalinski, Jarmo-Charles J., Kontou, Eftychia Eva, Elofson, James, Polyzois, Alexandros, González-Marín, Carolina, Farrell, Shane, Aggerbeck, Marie R., Pruksatrakul, Thapanee, Chan, Nathan, Wang, Yunshu, Pöchhacker, Magdalena, Brungs, Corinna, Cámara, Beatriz, Caraballo-Rodríguez, Andrés Mauricio, Cumsille, Andres, de Oliveira, Fernanda, Dührkop, Kai, El Abiead, Yasin, Geibel, Christian, Graves, Lana G., Hansen, Martin, Heuckeroth, Steffen, Knoblauch, Simon, Kostenko, Anastasiia, Kuijpers, Mirte C. M., Mildau, Kevin, Papadopoulos Lambidis, Stilianos, Portal Gomes, Paulo Wender, Schramm, Tilman, Steuer-Lodd, Karoline, Stincone, Paolo, Tayyab, Sibgha, Vitale, Giovanni Andrea, Wagner, Berenike C., Xing, Shipei, Yazzie, Marquis T., Zuffa, Simone, de Kruijff, Martinus, Beemelmanns, Christine, Link, Hannes, Mayer, Christoph, van der Hooft, Justin J. J., Damiani, Tito, Pluskal, Tomáš, Dorrestein, Pieter, Stanstrup, Jan, Schmid, Robin, Wang, Mingxun, Aron, Allegra, Ernst, Madeleine, Petras, Daniel

Source: Nature Protocols; January 2025, Vol. 20 Issue: 1 p92-162, 71p

PBS3 and EPS1 Complete Salicylic Acid Biosynthesis from Isochorismate in Arabidopsis

Authors: Torrens-Spence, Michael P., Bobokalonova, Anastassia, Carballo, Valentina, Glinkerman, Christopher M., Pluskal, Tomáš, Shen, Amber, Weng, Jing-Ke

Source: In Molecular Plant 2 December 2019 12(12):1577-1586

Independent evolution of rosmarinic acid biosynthesis in two sister families under the Lamiids clade of flowering plants

Alternate Title: Evolution of rosmarinic acid biosynthesis (English)

Authors: Levsh, Olesya, Pluskal, Tomáš, Carballo, Valentina, Mitchell, Andrew J., Weng, Jing-Ke

Source: In Journal of Biological Chemistry 18 October 2019 294(42):15193-15205

The Reference Genome Sequence of Scutellaria baicalensis Provides Insights into the Evolution of Wogonin Biosynthesis

Authors: Zhao, Qing, Yang, Jun, Cui, Meng-Ying, Liu, Jie, Fang, Yumin, Yan, Mengxiao, Qiu, Wenqing, Shang, Huiwen, Xu, Zhicheng, Yidiresi, Reheman, Weng, Jing-Ke, Pluskal, Tomáš, Vigouroux, Marielle, Steuernagel, Burkhard, Wei, Yukun, Yang, Lei, Hu, Yonghong, Chen, Xiao-Ya, Martin, Cathie

Source: In Molecular Plant 1 July 2019 12(7):935-950

Metabolomics Data Preprocessing Using ADAP and MZmine 2

Authors: Du, Xiuxia, Smirnov, Aleksandr, Pluskal, Tomáš, Jia, Wei, Sumner, Susan

Source: Methods in molecular biology. 2104:25-48

Availability: http://explore.bl.uk/primo_library/libweb/action/display.do?tabs=detailsTab&gathStatTab=true&ct=display&fn=search&doc=ETOCRN622757587&indx=1&recIds=ETOCRN622757587

Reproducible mass spectrometry data processing and compound annotation in MZmine 3.

Authors: Heuckeroth, Steffen, Damiani, Tito, Smirnov, Aleksandr, Mokshyna, Olena, Brungs, Corinna, Korf, Ansgar, Smith, Joshua David, Stincone, Paolo, Dreolin, Nicola, Nothias, Louis-Félix, Hyötyläinen, Tuulia, Orešič, Matej, Karst, Uwe, Dorrestein, Pieter C., Petras, Daniel, Du, Xiuxia, van der Hooft, Justin J. J., Schmid, Robin, Pluskal, Tomáš

Source: Nature Protocols; Sep2024, Vol. 19 Issue 9, p2597-2641, 45p

Contribution of Untargeted Metabolomics for Future Assessment of Biotech Crops

Authors: Christ, Bastien, Pluskal, Tomáš, Aubry, Sylvain, Weng, Jing-Ke

Source: In Trends in Plant Science December 2018 23(12):1047-1056

Complete Pathway Elucidation and Heterologous Reconstitution of Rhodiola Salidroside Biosynthesis

Authors: Torrens-Spence, Michael P., Pluskal, Tomáš, Li, Fu-Shuang, Carballo, Valentina, Weng, Jing-Ke

Source: In Molecular Plant 8 January 2018 11(1):205-217

The biosynthetic origin of psychoactive kavalactones in kava

Authors: Pluskal, Tomáš, Torrens-Spence, Michael P., Fallon, Timothy R., De Abreu, Andrea, Shi, Cindy H., Weng, Jing-Ke

Source: Nature plants. 5(8):867-878

Availability: http://explore.bl.uk/primo_library/libweb/action/display.do?tabs=detailsTab&gathStatTab=true&ct=display&fn=search&doc=ETOCvdc_100131039590.0x000001&indx=1&recIds=ETOCvdc_100131039590.0x000001

Monoamine Biosynthesis via a Noncanonical Calcium-Activatable Aromatic Amino Acid Decarboxylase in Psilocybin Mushroom

Authors: Torrens-Spence, Michael Patrick, Liu, Chun-Ting, Pluskal, Tomáš, Chung, Yin Kwan, Weng, Jing-Ke

Source: ACS chemical biology. 13(12):3343-3353

Availability: http://explore.bl.uk/primo_library/libweb/action/display.do?tabs=detailsTab&gathStatTab=true&ct=display&fn=search&doc=ETOCRN618513190&indx=1&recIds=ETOCRN618513190

A Transcript-Specific eIF3 Complex Mediates Global Translational Control of Energy Metabolism

Authors: Shah, Meera, Su, Dan, Scheliga, Judith S., Pluskal, Tomáš, Boronat, Susanna, Motamedchaboki, Khatereh, Campos, Alexandre Rosa, Qi, Feng, Hidalgo, Elena, Yanagida, Mitsuhiro, Wolf, Dieter A.

Source: In Cell Reports 16 August 2016 16(7):1891-1902

POMBOX: A Fission Yeast Cloning Toolkit for Molecular and Synthetic Biology.

Authors: Hebra, Téo, Smrčková, Helena, Elkatmis, Büsra, Převorovský, Martin, Pluskal, Tomáš

Source: ACS Synthetic Biology; 2/16/2024, Vol. 13 Issue 2, p558-567, 10p

A Red Algal Bourbonane Sesquiterpene Synthase Defined by Microgram-Scale NMR-Coupled Crystalline Sponge X-ray Diffraction Analysis

Authors: Kersten, Roland D., Lee, Shoukou, Fujita, Daishi, Pluskal, Tomáš, Kram, Susan, Smith, Jennifer E., Iwai, Takahiro, Noel, Joseph P., Fujita, Makoto, Weng, Jing-Ke

Source: Journal of the American Chemical Society. 139(46):16838-16844

Availability: http://explore.bl.uk/primo_library/libweb/action/display.do?tabs=detailsTab&gathStatTab=true&ct=display&fn=search&doc=ETOCRN613864440&indx=1&recIds=ETOCRN613864440