Democratising Knowledge Representation with BioCypher

Authors: Lobentanzer, Sebastian, Aloy, Patrick, Baumbach, Jan, Bohar, Balazs, Charoentong, Pornpimol, Danhauser, Katharina, Doğan, Tunca, Dreo, Johann, Dunham, Ian, Fernandez-Torras, Adrià, Gyori, Benjamin M., Hartung, Michael, Hoyt, Charles Tapley, Klein, Christoph, Korcsmaros, Tamas, Maier, Andreas, Mann, Matthias, Ochoa, David, Pareja-Lorente, Elena, Popp, Ferdinand, Preusse, Martin, Probul, Niklas, Schwikowski, Benno, Sen, Bünyamin, Strauss, Maximilian T., Turei, Denes, Ulusoy, Erva, Wodke, Judith Andrea Heidrun, Saez-Rodriguez, Julio

Subject Terms: Quantitative Biology - Molecular Networks

Access URL: http://arxiv.org/abs/2212.13543

Spatial characterization and stratification of colorectal adenomas by deep visual proteomics

Authors: Kabatnik, Sonja ¹, Post, Frederik ¹, Drici, Lylia ¹, Bartels, Annette Snejbjerg ², Strauss, Maximilian T. ¹, Zheng, Xiang ¹, Madsen, Gunvor I. ³, Mund, Andreas ¹, Rosenberger, Florian A. ⁴, Moreira, José ^{2, ∗}, Mann, Matthias ^{1, 4, 5, ∗∗}

Source: In iScience 20 September 2024 27(9)

Transparent Exploration of Machine Learning for Biomarker Discovery from Proteomics and Omics Data

Authors: Torun, Furkan M., Winter, Sebastian Virreira, Doll, Sophia, Riese, Felix M., Vorobyev, Artem, Mueller-Reif, Johannes B., Geyer, Philipp E., Strauss, Maximilian T.

Source: Journal of proteome research. 22(2):359-367

Availability: http://explore.bl.uk/primo_library/libweb/action/display.do?tabs=detailsTab&gathStatTab=true&ct=display&fn=search&doc=ETOCRN631750022&indx=1&recIds=ETOCRN631750022

AlphaMap: an open-source Python package for the visual annotation of proteomics data with sequence-specific knowledge

Authors: Voytik, Eugenia, Bludau, Isabell, Willems, Sander, Hansen, Fynn M, Brunner, Andreas-David, Strauss, Maximilian T, Mann, Matthias

Source: Bioinformatics. 38(3):849-852

Availability: http://explore.bl.uk/primo_library/libweb/action/display.do?tabs=detailsTab&gathStatTab=true&ct=display&fn=search&doc=ETOCvdc_100139037421.0x000001&indx=1&recIds=ETOCvdc_100139037421.0x000001

Artificial intelligence for proteomics and biomarker discovery

Authors: Mann, Matthias, Kumar, Chanchal, Zeng, Wen-Feng, Strauss, Maximilian T.

Source: In Cell Systems 18 August 2021 12(8):759-770

AlphaTims: Indexing Trapped Ion Mobility Spectrometry–TOF Data for Fast and Easy Accession and Visualization

Authors: Willems, Sander, Voytik, Eugenia, Skowronek, Patricia, Strauss, Maximilian T., Mann, Matthias

Source: In Molecular & Cellular Proteomics 2021 20

Spatial proteomics identifies JAKi as treatment for a lethal skin disease.

Authors: Nordmann, Thierry M., Anderton, Holly, Hasegawa, Akito, Schweizer, Lisa, Zhang, Peng, Stadler, Pia-Charlotte, Sinha, Ankit, Metousis, Andreas, Rosenberger, Florian A., Zwiebel, Maximilian, Satoh, Takashi K., Anzengruber, Florian, Strauss, Maximilian T., Tanzer, Maria C., Saito, Yuki, Gong, Ting, Thielert, Marvin, Kimura, Haruna, Silke, Natasha, Rodriguez, Edwin H.

Source: Nature; Nov2024, Vol. 635 Issue 8040, p1001-1009, 9p

Molecular mechanism to recruit galectin-3 into multivesicular bodies for polarized exosomal secretion

Authors: Bänfer, Sebastian, Schneider, Dominik, Dewes, Jenny, Strauss, Maximilian T., Freibert, Sven-A., Heimerl, Thomas, Maier, Uwe G., Elsässer, Hans-Peter, Jungmann, Ralf, Jacob, Ralf

Source: Proceedings of the National Academy of Sciences of the United States of America, 2018 May 01. 115(19), E4396-E4405.

Access URL: https://www.jstor.org/stable/26509609

Direct Visualization of Single Nuclear Pore Complex Proteins Using Genetically‐Encoded Probes for DNA‐PAINT

Authors: Schlichthaerle, Thomas, Strauss, Maximilian T., Schueder, Florian, Auer, Alexander, Nijmeijer, Bianca, Kueblbeck, Moritz, Jimenez Sabinina, Vilma, Thevathasan, Jervis V., Ries, Jonas, Ellenberg, Jan, Jungmann, Ralf

Source: Angewandte Chemie international edition. 58(37):13004-13008

Availability: http://explore.bl.uk/primo_library/libweb/action/display.do?tabs=detailsTab&gathStatTab=true&ct=display&fn=search&doc=ETOCvdc_100135379246.0x000001&indx=1&recIds=ETOCvdc_100135379246.0x000001

Single Particle Tracking and Super-Resolution Imaging of Membrane-Assisted Stop-and-Go Diffusion and Lattice Assembly of DNA Origami

Authors: Kempter, Susanne, Khmelinskaia, Alena, Strauss, Maximilian T., Schwille, Petra, Jungmann, Ralf, Liedl, Tim, Bae, Wooli

Source: ACS nano. 13(2):996-1002

Availability: http://explore.bl.uk/primo_library/libweb/action/display.do?tabs=detailsTab&gathStatTab=true&ct=display&fn=search&doc=ETOCRN619444782&indx=1&recIds=ETOCRN619444782

Correlating DNA-PAINT and single-molecule FRET for multiplexed super-resolution imaging
Single Molecule Spectroscopy and Superresolution Imaging XIII

Authors: Deussner-Helfmann, Nina S., Auer, Alexander, Strauss, Maximilian T., Donlin-Asp, Paul, Malkusch, Sebastian, Dietz, Marina S., Barth, Hans-Dieter, Schuman, Erin, Jungmann, Ralf, Heilemann, Mike

Source: Proceedings of SPIE, the International Society for Optical Engineering. 11246:112460L-112460L-7

Availability: http://explore.bl.uk/primo_library/libweb/action/display.do?tabs=detailsTab&gathStatTab=true&ct=display&fn=search&doc=ETOCCN900017340&indx=1&recIds=ETOCCN900017340

DNA nanotechnology and fluorescence applications

Authors: Schlichthaerle, Thomas, Strauss, Maximilian T, Schueder, Florian, Woehrstein, Johannes B, Jungmann, Ralf

Source: In Current Opinion in Biotechnology June 2016 39:41-47

AlphaPept: a modern and open framework for MS-based proteomics.

Authors: Strauss, Maximilian T., Bludau, Isabell, Zeng, Wen-Feng, Voytik, Eugenia, Ammar, Constantin, Schessner, Julia P., Ilango, Rajesh, Gill, Michelle, Meier, Florian, Willems, Sander, Mann, Matthias

Source: Nature Communications; 3/9/2024, Vol. 15 Issue 1, p1-16, 16p

Subject Terms: PYTHON programming language, PROTEOMICS, COMPUTER science, PEPTIDES, LIBRARY users, MASS spectrometry

Urinary proteome profiling for stratifying patients with familial Parkinson's disease

Authors: Virreira Winter, Sebastian, Karayel, Ozge, Strauss, Maximilian T, Padmanabhan, Shalini, Surface, Matthew, Merchant, Kalpana, Alcalay, Roy N, Mann, Matthias

Source: EMBO molecular medicine. 13(3)

Availability: http://explore.bl.uk/primo_library/libweb/action/display.do?tabs=detailsTab&gathStatTab=true&ct=display&fn=search&doc=ETOCvdc_100131430318.0x000001&indx=1&recIds=ETOCvdc_100131430318.0x000001

High‐resolution serum proteome trajectories in COVID‐19 reveal patient‐specific seroconversion

Authors: Geyer, Philipp E, Arend, Florian M, Doll, Sophia, Louiset, Marie‐Luise, Virreira Winter, Sebastian, Müller‐Reif, Johannes B, Torun, Furkan M, Weigand, Michael, Eichhorn, Peter, Bruegel, Mathias, Strauss, Maximilian T, Holdt, Lesca M, Mann, Matthias, Teupser, Daniel

Source: EMBO molecular medicine. 13(8)

Availability: http://explore.bl.uk/primo_library/libweb/action/display.do?tabs=detailsTab&gathStatTab=true&ct=display&fn=search&doc=ETOCvdc_100125714302.0x000001&indx=1&recIds=ETOCvdc_100125714302.0x000001

The social and structural architecture of the yeast protein interactome.

Authors: Michaelis, André C., Brunner, Andreas-David, Zwiebel, Maximilian, Meier, Florian, Strauss, Maximilian T., Bludau, Isabell, Mann, Matthias

Source: Nature; Dec2023, Vol. 624 Issue 7990, p192-200, 9p

The structural context of posttranslational modifications at a proteome-wide scale.

Authors: Bludau, Isabell¹, Willems, Sander¹, Zeng, Wen-Feng¹, Strauss, Maximilian T.², Hansen, Fynn M.¹, Tanzer, Maria C.¹, Karayel, Ozge¹, Schulman, Brenda A.³, Mann, Matthias^1,2, mmann@biochem.mpg.de

Source: PLoS Biology; 5/16/2022, Vol. 20 Issue 5, p1-23, 23p, 5 Graphs

Proteome profiling in cerebrospinal fluid reveals novel biomarkers of Alzheimer's disease

Authors: Bader, Jakob M, Geyer, Philipp E, Müller, Johannes B, Strauss, Maximilian T, Koch, Manja, Leypoldt, Frank, Koertvelyessy, Peter, Bittner, Daniel, Schipke, Carola G, Incesoy, Enise I, Peters, Oliver, Deigendesch, Nikolaus, Simons, Mikael, Jensen, Majken K, Zetterberg, Henrik, Mann, Matthias

Source: Molecular systems biology. 16(6)

Availability: http://explore.bl.uk/primo_library/libweb/action/display.do?tabs=detailsTab&gathStatTab=true&ct=display&fn=search&doc=ETOCvdc_100129470745.0x000001&indx=1&recIds=ETOCvdc_100129470745.0x000001

Complex multicomponent patterns rendered on a 3D DNA-barrel pegboard

Authors: Wickham, Shelley F. J., Auer, Alexander, Min, Jianghong, Ponnuswamy, Nandhini, Woehrstein, Johannes B., Schueder, Florian, Strauss, Maximilian T., Schnitzbauer, Jörg, Nathwani, Bhavik, Zhao, Zhao, Perrault, Steven D., Hahn, Jaeseung, Lee, Seungwoo, Bastings, Maartje M., Helmig, Sarah W., Kodal, Anne Louise, Yin, Peng, Jungmann, Ralf, Shih, William M.

Source: Nature communications. 11(1)

Availability: http://explore.bl.uk/primo_library/libweb/action/display.do?tabs=detailsTab&gathStatTab=true&ct=display&fn=search&doc=ETOCvdc_100186943956.0x000001&indx=1&recIds=ETOCvdc_100186943956.0x000001

AlphaPeptStats: an open-source Python package for automated and scalable statistical analysis of mass spectrometry-based proteomics.

Authors: Krismer, Elena¹, Bludau, Isabell², Strauss, Maximilian T¹, mmann@biochem.mpg.de, Mann, Matthias^1,2, mmann@biochem.mpg.de

Source: Bioinformatics; Aug2023, Vol. 39 Issue 8, p1-4, 4p