Publications

Helga Haberfehlner, Shankara S van de Ven, Sven A van der Burg, Florian Huber, Sonja Georgievska, Ignazio Aleo, Jaap Harlaar, Laura Bonouvrié, Marjolein Margaretha van der Krogt, Annemieke I Buizer (2023). Towards automated video-based assessment of dystonia in dyskinetic cerebral palsy: a novel approach using markerless motion tracking and machine learning. Frontiers in Robotics and AI.

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Niek F de Jonge, Joris JR Louwen, Elena Chekmeneva, Stephane Camuzeaux, Femke J Vermeir, Robert S Jansen, Florian Huber, Justin JJ Van Der Hooft (2023). MS2Query: reliable and scalable MS2 mass spectra-based analogue search. Nature Communications.

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David Elser, Florian Huber, Emmanuel Gaquerel (2023). Mass2SMILES: deep learning based fast prediction of structures and functional groups directly from high-resolution MS/MS spectra.. bioRxiv.

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Michael W Mullowney, Katherine R Duncan, Somayah S Elsayed, Neha Garg, Justin JJ Van Der Hooft, Nathaniel I Martin, David Meijer, Barbara R Terlouw, Friederike Biermann, Kai Blin, others (2023). Artificial intelligence for natural product drug discovery. Nature Reviews Drug Discovery.

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A Gaudry, F Huber, J Flückiger, L Quirós, A Rutz, M Kaiser, A Grondin, L Marcourt, E Ferreira Queiroz, JL Wolfender, others (2022). Short Lecture “Mass spectrometry-based sample vectorization for exploration of large chemodiverse datasets and efficient identification of new antiparasitic compounds”. Planta Medica.

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Arnaud Gaudry, Florian Huber, Louis-Félix Nothias, Sylvian Cretton, Marcel Kaiser, Jean-Luc Wolfender, Pierre-Marie Allard (2022). MEMO: mass spectrometry-based sample vectorization to explore chemodiverse datasets. Frontiers in Bioinformatics.

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Niek F de Jonge, Kevin Mildau, David Meijer, Joris JR Louwen, Christoph Bueschl, Florian Huber, Justin JJ Van Der Hooft (2022). Good practices and recommendations for using and benchmarking computational metabolomics metabolite annotation tools. Metabolomics.

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Wout Bittremieux, Robin Schmid, Florian Huber, Justin JJ Van Der Hooft, Mingxun Wang, Pieter C Dorrestein (2022). Comparison of cosine, modified cosine, and neutral loss based spectrum alignment for discovery of structurally related molecules. Journal of the American Society for Mass Spectrometry.

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Florian Huber, Lars Ridder, Stefan Verhoeven, Jurriaan H Spaaks, Faruk Diblen, Simon Rogers, Justin JJ Van Der Hooft (2021). Spec2Vec: Improved mass spectral similarity scoring through learning of structural relationships. PLoS computational biology.

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Florian Huber, Sven van der Burg, Justin JJ Van Der Hooft, Lars Ridder (2021). MS2DeepScore: a novel deep learning similarity measure to compare tandem mass spectra. Journal of cheminformatics.

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Maurits Kok, Florian Huber, Svenja-Marei Kalisch, Marileen Dogterom (2021). EB3-informed dynamics of the microtubule stabilizing cap during stalled growth. bioRxiv.

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Ian Walsh, Dmytro Fishman, Dario Garcia-Gasulla, Tiina Titma, Gianluca Pollastri, Jennifer Harrow, Fotis E Psomopoulos, Silvio CE Tosatto (2021). DOME: recommendations for supervised machine learning validation in biology. Nature methods.

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Mehdi A Beniddir, Kyo Bin Kang, Grégory Genta-Jouve, Florian Huber, Simon Rogers, Justin JJ Van Der Hooft (2021). Advances in decomposing complex metabolite mixtures using substructure-and network-based computational metabolomics approaches. Natural product reports.

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Michelle A Schorn, Stefan Verhoeven, Lars Ridder, Florian Huber, Deepa D Acharya, Alexander A Aksenov, Gajender Aleti, Jamshid Amiri Moghaddam, Allegra T Aron, Saefuddin Aziz, others (2021). A community resource for paired genomic and metabolomic data mining. Nature Chemical Biology.

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D Van Kuppevelt, C Meijer, F Huber, A van der Ploeg, S Georgievska, Vincent T van Hees (2020). Mcfly: Automated deep learning on time series. SoftwareX.

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Florian Huber, Stefan Verhoeven, Christiaan Meijer, Hanno Spreeuw, Efraı́n Manuel Villanueva Castilla, Cunliang Geng, Justin JJ Van Der Hooft, Simon Rogers, Adam Belloum, Faruk Diblen, others (2020). matchms - processing and similarity evaluation of mass spectrometry data. Journal of Open Source Software.

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Stefano Siccardi, Andrew Adamatzky, Jack Tuszy\ʼnski, Florian Huber, Jörg Schnauß (2020). Actin networks voltage circuits. Physical Review E.

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Jairo H Migueles, Alex V Rowlands, Florian Huber, Séverine Sabia, Vincent T van Hees (2019). GGIR: a research community--driven open source R package for generating physical activity and sleep outcomes from multi-day raw accelerometer data. Journal for the Measurement of Physical Behaviour.

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Gábor Kismihók, Fran Cardells, Pınar Burcu Güner, Frauke Kersten, Mattias Björnmalm, Karen Stroobants, Stefan T Mol, Florian Huber, Joachim Seipelt, Warren Winfried Kretzschmar, others (2019). Declaration on sustainable researcher careers. Zenodo.

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Andrew Adamatzky, Florian Huber, Jörg Schnauß (2019). Computing on actin bundles network. Scientific reports.

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Andrew Adamatzky, Jörg Schnauß, Florian Huber (2019). Actin droplet machine. Royal Society Open Science.

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Florian Huber, Dan Strehle, Jörg Schnauß, Josef Käs (2015). Formation of regularly spaced networks as a general feature of actin bundle condensation by entropic forces. New Journal of Physics.

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Florian Huber, Adeline Boire, Magdalena Preciado López, Gijsje H Koenderink (2015). Cytoskeletal crosstalk: when three different personalities team up. Current opinion in cell biology.

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Magdalena Preciado López, Florian Huber, Ilya Grigoriev, Michel O Steinmetz, Anna Akhmanova, Gijsje H Koenderink, Marileen Dogterom (2014). Actin--microtubule coordination at growing microtubule ends. Nature communications.

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Florian Huber, Jörg Schnauß, Susanne Rönicke, Philipp Rauch, Karla Müller, Claus Fütterer, Josef Käs (2013). Emergent complexity of the cytoskeleton: from single filaments to tissue. Advances in physics.

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Josef A Käs, Florian Huber, Dan Strehle (2012). Counterion-Induced Formation of Regular Actin Bundle Networks. Biophysical Journal.

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Florian Huber, Dan Strehle, Josef Käs (2012). Counterion-induced formation of regular actin bundle networks. Soft Matter.

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Florian Huber, Josef Käs (2011). Self-regulative organization of the cytoskeleton. Cytoskeleton.

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Björn Stuhrmann, Florian Huber, Josef Käs (2011). Robust organizational principles of protrusive biopolymer networks in migrating living cells. PloS one.

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Florian Huber (2011). Emergent structure formation of the actin cytoskeleton.

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David Smith, Brian Gentry, Björn Stuhrmann, Florian Huber, Dan Strehle, Claudia Brunner, Daniel Koch, Matthias Steinbeck, Timo Betz, Josef A Käs (2009). The cytoskeleton: An active polymer-based scaffold. Biophysical Reviews and Letters.

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Florian Huber, Josef Käs, Björn Stuhrmann (2008). Growing actin networks form lamellipodium and lamellum by self-assembly. Biophysical Journal.

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