Molecular systems biology

Keyphrases

Publications

volume 20, number 6, 2024

Aleš Holfeld, Dina Schuster, Fabian Sesterhenn, Alison K Gillingham, Patrick Stalder, Walther Haenseler, Inigo Barrio-Hernandez, Dhiman Ghosh, Jane Vowles, Sally A Cowley, Luise Nagel, Basavraj Khanppnavar, Tetiana Serdiuk, Pedro Beltrao, Volodymyr M Korkhov, Sean Munro, Roland Riek, Natalie de Souza, Paola Picotti
Systematic identification of structure-specific protein-protein interactions. Molecular systems biology 20 (6) (2024)
Francesco Gualdrini, Stefano Rizzieri, Sara Polletti, Francesco Pileri, Yinxiu Zhan, Alessandro Cuomo, Gioacchino Natoli
An integrative epigenome-based strategy for unbiased functional profiling of clinical kinase inhibitors. Molecular systems biology 20 (6) (2024)
Mathis Wolter, Erica T Grant, Marie Boudaud, Nicholas A Pudlo, Gabriel V Pereira, Kathryn A Eaton, Eric C Martens, Mahesh S Desai
Diet-driven differential response of Akkermansia muciniphila modulates pathogen susceptibility. Molecular systems biology 20 (6) (2024)

volume 20, number 7, 2024

Alexander F McDonnell, Marcin Plech, Benjamin J Livesey, Lukas Gerasimavicius, Liusaidh J Owen, Hildegard Nikki Hall, David R FitzPatrick, Joseph A Marsh, Grzegorz Kudla
Deep mutational scanning quantifies DNA binding and predicts clinical outcomes of PAX6 variants. Molecular systems biology 20 (7) (2024)
Alexander F McDonnell, Marcin Plech, Benjamin J Livesey, Lukas Gerasimavicius, Liusaidh J Owen, Hildegard Nikki Hall, David R FitzPatrick, Joseph A Marsh, Grzegorz Kudla
Deep mutational scanning quantifies DNA binding and predicts clinical outcomes of PAX6 variants. Molecular systems biology 20 (7) (2024)
Alexander F McDonnell, Marcin Plech, Benjamin J Livesey, Lukas Gerasimavicius, Liusaidh J Owen, Hildegard Nikki Hall, David R FitzPatrick, Joseph A Marsh, Grzegorz Kudla
Deep mutational scanning quantifies DNA binding and predicts clinical outcomes of PAX6 variants. Molecular systems biology 20 (7) (2024)
Alan F Rubin
A new way of looking at transcription factor assays. Molecular systems biology 20 (7) (2024)
Alexander F McDonnell, Marcin Plech, Benjamin J Livesey, Lukas Gerasimavicius, Liusaidh J Owen, Hildegard Nikki Hall, David R FitzPatrick, Joseph A Marsh, Grzegorz Kudla
Deep mutational scanning quantifies DNA binding and predicts clinical outcomes of PAX6 variants. Molecular systems biology 20 (7) (2024)
Mariia Bilous, Léonard Hérault, Aurélie A G Gabriel, Matei Teleman, David Gfeller
Building and analyzing metacells in single-cell genomics data. Molecular systems biology 20 (7) (2024)
Siling Hu, Yangying Liu, Qifan Zhang, Juan Bai, Chenhuan Xu
A continuum of zinc finger transcription factor retention on native chromatin underlies dynamic genome organization. Molecular systems biology 20 (7) (2024)
Jelena Ulicevic, Zhihao Shao, Olga Jasnovidova, Annkatrin Bressin, Martyna Gajos, Alex Hm Ng, Siddharth Annaldasula, David Meierhofer, George M Church, Volker Busskamp, Andreas Mayer
Uncovering the dynamics and consequences of RNA isoform changes during neuronal differentiation. Molecular systems biology 20 (7) (2024)
Alan F Rubin
A new way of looking at transcription factor assays. Molecular systems biology 20 (7) (2024)
Jelena Ulicevic, Zhihao Shao, Olga Jasnovidova, Annkatrin Bressin, Martyna Gajos, Alex Hm Ng, Siddharth Annaldasula, David Meierhofer, George M Church, Volker Busskamp, Andreas Mayer
Uncovering the dynamics and consequences of RNA isoform changes during neuronal differentiation. Molecular systems biology 20 (7) (2024)
Siling Hu, Yangying Liu, Qifan Zhang, Juan Bai, Chenhuan Xu
A continuum of zinc finger transcription factor retention on native chromatin underlies dynamic genome organization. Molecular systems biology 20 (7) (2024)
Jelena Ulicevic, Zhihao Shao, Olga Jasnovidova, Annkatrin Bressin, Martyna Gajos, Alex Hm Ng, Siddharth Annaldasula, David Meierhofer, George M Church, Volker Busskamp, Andreas Mayer
Uncovering the dynamics and consequences of RNA isoform changes during neuronal differentiation. Molecular systems biology 20 (7) (2024)
Alan F Rubin
A new way of looking at transcription factor assays. Molecular systems biology 20 (7) (2024)
Mariia Bilous, Léonard Hérault, Aurélie A G Gabriel, Matei Teleman, David Gfeller
Building and analyzing metacells in single-cell genomics data. Molecular systems biology 20 (7) (2024)
Siling Hu, Yangying Liu, Qifan Zhang, Juan Bai, Chenhuan Xu
A continuum of zinc finger transcription factor retention on native chromatin underlies dynamic genome organization. Molecular systems biology 20 (7) (2024)
Mariia Bilous, Léonard Hérault, Aurélie A G Gabriel, Matei Teleman, David Gfeller
Building and analyzing metacells in single-cell genomics data. Molecular systems biology 20 (7) (2024)
Alexander F McDonnell, Marcin Plech, Benjamin J Livesey, Lukas Gerasimavicius, Liusaidh J Owen, Hildegard Nikki Hall, David R FitzPatrick, Joseph A Marsh, Grzegorz Kudla
Deep mutational scanning quantifies DNA binding and predicts clinical outcomes of PAX6 variants. Molecular systems biology 20 (7) (2024)

volume 20, number 8, 2024

Sebastian Lobentanzer, Pablo Rodríguez-Mier, Stefan Bauer, Julio Saez-Rodriguez
Molecular causality in the advent of foundation models. Molecular systems biology 20 (8) (2024)
Claire Darnell McWhite, Wisath Sae-Lee, Yaning Yuan, Anna L Mallam, Nicolas A Gort-Freitas, Silvia Ramundo, Masayuki Onishi, Edward M Marcotte
Alternative proteoforms and proteoform-dependent assemblies in humans and plants. Molecular systems biology 20 (8) (2024)
Emrah Şimşek, Kyeri Kim, Jia Lu, Anita Silver, Nan Luo, Charlotte T Lee, Lingchong You
A 'rich-get-richer' mechanism drives patchy dynamics and resistance evolution in antibiotic-treated bacteria. Molecular systems biology 20 (8) (2024)
Kyle R Allison
Multicellular dynamics and wealth distribution in bacteria. Molecular systems biology 20 (8) (2024)
Kyle R Allison
Multicellular dynamics and wealth distribution in bacteria. Molecular systems biology 20 (8) (2024)
Kyle R Allison
Multicellular dynamics and wealth distribution in bacteria. Molecular systems biology 20 (8) (2024)
Denys Oliinyk, Andreas Will, Felix R Schneidmadel, Maximilian Böhme, Jenny Rinke, Andreas Hochhaus, Thomas Ernst, Nina Hahn, Christian Geis, Markus Lubeck, Oliver Raether, Sean J Humphrey, Florian Meier
µPhos: a scalable and sensitive platform for high-dimensional phosphoproteomics. Molecular systems biology 20 (8) (2024)
Claire Darnell McWhite, Wisath Sae-Lee, Yaning Yuan, Anna L Mallam, Nicolas A Gort-Freitas, Silvia Ramundo, Masayuki Onishi, Edward M Marcotte
Alternative proteoforms and proteoform-dependent assemblies in humans and plants. Molecular systems biology 20 (8) (2024)
Xiaofang Zhong, Qiongyu Li, Benjamin J Polacco, Trupti Patil, Aaron Marley, Helene Foussard, Prachi Khare, Rasika Vartak, Jiewei Xu, Jeffrey F DiBerto, Bryan L Roth, Manon Eckhardt, Mark Von Zastrow, Nevan J Krogan, Ruth Hüttenhain
A proximity proteomics pipeline with improved reproducibility and throughput. Molecular systems biology 20 (8) (2024)
Stefanie Luecke, Xiaolu Guo, Katherine M Sheu, Apeksha Singh, Sarina C Lowe, Minhao Han, Jessica Diaz, Francisco J P Lopes, Roy Wollman, Alexander Hoffmann
Dynamical and combinatorial coding by MAPK p38 and NFκB in the inflammatory response of macrophages. Molecular systems biology 20 (8) (2024)
Aleks Danov, Inbal Pollin, Eric Moon, Mengfei Ho, Brenda A Wilson, Philippos A Papathanos, Tommy Kaplan, Asaf Levy
Identification of novel toxins associated with the extracellular contractile injection system using machine learning. Molecular systems biology 20 (8) (2024)
Emrah Şimşek, Kyeri Kim, Jia Lu, Anita Silver, Nan Luo, Charlotte T Lee, Lingchong You
A 'rich-get-richer' mechanism drives patchy dynamics and resistance evolution in antibiotic-treated bacteria. Molecular systems biology 20 (8) (2024)
Xiaofang Zhong, Qiongyu Li, Benjamin J Polacco, Trupti Patil, Aaron Marley, Helene Foussard, Prachi Khare, Rasika Vartak, Jiewei Xu, Jeffrey F DiBerto, Bryan L Roth, Manon Eckhardt, Mark Von Zastrow, Nevan J Krogan, Ruth Hüttenhain
A proximity proteomics pipeline with improved reproducibility and throughput. Molecular systems biology 20 (8) (2024)
Emrah Şimşek, Kyeri Kim, Jia Lu, Anita Silver, Nan Luo, Charlotte T Lee, Lingchong You
A 'rich-get-richer' mechanism drives patchy dynamics and resistance evolution in antibiotic-treated bacteria. Molecular systems biology 20 (8) (2024)
Stefanie Luecke, Xiaolu Guo, Katherine M Sheu, Apeksha Singh, Sarina C Lowe, Minhao Han, Jessica Diaz, Francisco J P Lopes, Roy Wollman, Alexander Hoffmann
Dynamical and combinatorial coding by MAPK p38 and NFκB in the inflammatory response of macrophages. Molecular systems biology 20 (8) (2024)
Claire Darnell McWhite, Wisath Sae-Lee, Yaning Yuan, Anna L Mallam, Nicolas A Gort-Freitas, Silvia Ramundo, Masayuki Onishi, Edward M Marcotte
Alternative proteoforms and proteoform-dependent assemblies in humans and plants. Molecular systems biology 20 (8) (2024)
Sebastian Lobentanzer, Pablo Rodríguez-Mier, Stefan Bauer, Julio Saez-Rodriguez
Molecular causality in the advent of foundation models. Molecular systems biology 20 (8) (2024)
Xiaofang Zhong, Qiongyu Li, Benjamin J Polacco, Trupti Patil, Aaron Marley, Helene Foussard, Prachi Khare, Rasika Vartak, Jiewei Xu, Jeffrey F DiBerto, Bryan L Roth, Manon Eckhardt, Mark Von Zastrow, Nevan J Krogan, Ruth Hüttenhain
A proximity proteomics pipeline with improved reproducibility and throughput. Molecular systems biology 20 (8) (2024)
Stefanie Luecke, Xiaolu Guo, Katherine M Sheu, Apeksha Singh, Sarina C Lowe, Minhao Han, Jessica Diaz, Francisco J P Lopes, Roy Wollman, Alexander Hoffmann
Dynamical and combinatorial coding by MAPK p38 and NFκB in the inflammatory response of macrophages. Molecular systems biology 20 (8) (2024)
Denys Oliinyk, Andreas Will, Felix R Schneidmadel, Maximilian Böhme, Jenny Rinke, Andreas Hochhaus, Thomas Ernst, Nina Hahn, Christian Geis, Markus Lubeck, Oliver Raether, Sean J Humphrey, Florian Meier
µPhos: a scalable and sensitive platform for high-dimensional phosphoproteomics. Molecular systems biology 20 (8) (2024)
Aleks Danov, Inbal Pollin, Eric Moon, Mengfei Ho, Brenda A Wilson, Philippos A Papathanos, Tommy Kaplan, Asaf Levy
Identification of novel toxins associated with the extracellular contractile injection system using machine learning. Molecular systems biology 20 (8) (2024)
Stefanie Luecke, Xiaolu Guo, Katherine M Sheu, Apeksha Singh, Sarina C Lowe, Minhao Han, Jessica Diaz, Francisco J P Lopes, Roy Wollman, Alexander Hoffmann
Dynamical and combinatorial coding by MAPK p38 and NFκB in the inflammatory response of macrophages. Molecular systems biology 20 (8) (2024)
Denys Oliinyk, Andreas Will, Felix R Schneidmadel, Maximilian Böhme, Jenny Rinke, Andreas Hochhaus, Thomas Ernst, Nina Hahn, Christian Geis, Markus Lubeck, Oliver Raether, Sean J Humphrey, Florian Meier
µPhos: a scalable and sensitive platform for high-dimensional phosphoproteomics. Molecular systems biology 20 (8) (2024)
Sebastian Lobentanzer, Pablo Rodríguez-Mier, Stefan Bauer, Julio Saez-Rodriguez
Molecular causality in the advent of foundation models. Molecular systems biology 20 (8) (2024)
Aleks Danov, Inbal Pollin, Eric Moon, Mengfei Ho, Brenda A Wilson, Philippos A Papathanos, Tommy Kaplan, Asaf Levy
Identification of novel toxins associated with the extracellular contractile injection system using machine learning. Molecular systems biology 20 (8) (2024)

volume 20, number 9, 2024

Yanqing Huang, Avik Mukherjee, Severin Schink, Nina Catherine Benites, Markus Basan
Evolution and stability of complex microbial communities driven by trade-offs. Molecular systems biology 20 (9) (2024)
Aidan Flynn, Sebastian M Waszak, Joachim Weischenfeldt
Somatic CpG hypermutation is associated with mismatch repair deficiency in cancer. Molecular systems biology 20 (9) (2024)
Johanna Kliche, Leandro Simonetti, Izabella Krystkowiak, Hanna Kuss, Marcel Diallo, Emma Rask, Jakob Nilsson, Norman E Davey, Ylva Ivarsson
Proteome-scale characterisation of motif-based interactome rewiring by disease mutations. Molecular systems biology 20 (9) (2024)
Lutz Fischer, Juri Rappsilber
Rescuing error control in crosslinking mass spectrometry. Molecular systems biology 20 (9) (2024)
Madison T Wright, Bibek Timalsina, Valeria Garcia Lopez, Jake N Hermanson, Sarah Garcia, Lars Plate
Time-resolved interactome profiling deconvolutes secretory protein quality control dynamics. Molecular systems biology 20 (9) (2024)