TY - JOUR A1 - Siccardi, Stefano A1 - Adamatzky, Andrew A1 - Tuszyński, Jack A1 - Huber, Florian A1 - Schnauß, Jörg T1 - Actin networks voltage circuits JF - Physical Review E Y1 - 2020 U6 - https://doi.org/10.1103/PhysRevE.101.052314 SN - 2470-0053 VL - 101 IS - 5-1 PB - American Physical Society (APS) ER - TY - JOUR A1 - Smith, David A1 - Gentry, Brian A1 - Stuhrmann, Björn A1 - Huber, Florian A1 - Strehle, D. A.N. A1 - Brunner, Claudia A1 - Koch, Daniel A1 - Steinbeck, Matthias A1 - Betz, Timo A1 - Käs, Josef A. T1 - The cytoskeleton: An active polymer-based scaffold JF - Biophysical Reviews and Letters Y1 - 2009 U6 - https://doi.org/10.1142/S1793048009000983 SN - 1793-7035 VL - 04 SP - 179 EP - 208 ER - TY - JOUR A1 - Stuhrmann, Björn A1 - Huber, Florian A1 - Käs, Josef T1 - Robust organizational principles of protrusive biopolymer networks in migrating living cells JF - Plos One N2 - Cell migration is associated with the dynamic protrusion of a thin actin-based cytoskeletal extension at the cell front, which has been shown to consist of two different substructures, the leading lamellipodium and the subsequent lamellum. While the formation of the lamellipodium is increasingly well understood, organizational principles underlying the emergence of the lamellum are just beginning to be unraveled. We report here on a 1D mathematical model which describes the reaction-diffusion processes of a polarized actin network in steady state, and reproduces essential characteristics of the lamellipodium-lamellum system. We observe a steep gradient in filament lengths at the protruding edge, a local depolymerization maximum a few microns behind the edge, as well as a differential dominance of the network destabilizer ADF/cofilin and the stabilizer tropomyosin. We identify simple and robust organizational principles giving rise to the derived network characteristics, uncoupled from the specifics of any molecular implementation, and thus plausibly valid across cell types. An analysis of network length dependence on physico-chemical system parameters implies that to limit array treadmilling to cellular dimensions, network growth has to be truncated by mechanisms other than aging-induced depolymerization, e.g., by myosin-associated network dissociation at the transition to the cell body. Our work contributes to the analytical understanding of the cytoskeletal extension's bisection into lamellipodium and lamellum and sheds light on how cells organize their molecular machinery to achieve motility. KW - DOAJ Y1 - 2011 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:hbz:due62-opus-34901 SN - 1932-6203 N1 - Funding: This work has been supported by the Leipzig Graduate College ‘‘GK 1097 InterNeuro - Interdisciplinary Approaches in Cellular Neuroscience’’ (http:// www.uni-leipzig.de/˜ineuro/) and the Graduate School ‘‘Leipzig School of Natural Sciences - Building with Molecules and Nano-objects (BuildMoNa)’’ (http://www. buildmona.de/). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. VL - 6 IS - 1 PB - Public Library of Science (PLoS) ER - TY - JOUR A1 - Adamatzky, Andrew A1 - Huber, Florian A1 - Schnauß, Jörg T1 - Computing on actin bundles network JF - Scientific Reports N2 - Actin filaments are conductive to ionic currents, mechanical and voltage solitons. These travelling localisations can be utilised to generate computing circuits from actin networks. The propagation of localisations on a single actin filament is experimentally unfeasible to control. Therefore, we consider excitation waves propagating on bundles of actin filaments. In computational experiments with a two-dimensional slice of an actin bundle network we show that by using an arbitrary arrangement of electrodes, it is possible to implement two-inputs-one-output circuits. Y1 - 2019 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:hbz:due62-opus-34665 UR - http://www.ncbi.nlm.nih.gov/pubmed/31685834 SN - 2045-2322 VL - 9 IS - 1 PB - Springer Nature ER - TY - JOUR A1 - Adamatzky, Andrew A1 - Schnauß, Jörg A1 - Huber, Florian T1 - Actin droplet machine JF - Royal Society Open Science N2 - The actin droplet machine is a computer model of a three-dimensional network of actin bundles developed in a droplet of a physiological solution, which implements mappings of sets of binary strings. The actin bundle network is conductive to travelling excitations, i.e. impulses. The machine is interfaced with an arbitrary selected set of k electrodes through which stimuli, binary strings of length k represented by impulses generated on the electrodes, are applied and responses are recorded. The responses are recorded in a form of impulses and then converted to binary strings. The machine's state is a binary string of length k: if there is an impulse recorded on the ith electrode, there is a '1' in the ith position of the string, and '0' otherwise. We present a design of the machine and analyse its state transition graphs. We envisage that actin droplet machines could form an elementary processor of future massive parallel computers made from biopolymers. Y1 - 2019 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:hbz:due62-opus-34675 UR - http://www.ncbi.nlm.nih.gov/pubmed/31903204 SN - 2054-5703 N1 - A.A. was partially supported by EPSRC grant no. EP/P016677/1. The authors declare that they have no competing interests. VL - 6 IS - 12 PB - Royal Soc. Publ. ER - TY - JOUR A1 - Huber, Florian A1 - Ridder, Lars A1 - Verhoeven, Stefan A1 - Spaaks, Jurriaan H. A1 - Diblen, Faruk A1 - Rogers, Simon A1 - van der Hooft, Justin J. J. T1 - Spec2Vec: Improved mass spectral similarity scoring through learning of structural relationships JF - PLOS Computational Biology N2 - Spectral similarity is used as a proxy for structural similarity in many tandem mass spectrometry (MS/MS) based metabolomics analyses such as library matching and molecular networking. Although weaknesses in the relationship between spectral similarity scores and the true structural similarities have been described, little development of alternative scores has been undertaken. Here, we introduce Spec2Vec, a novel spectral similarity score inspired by a natural language processing algorithm-Word2Vec. Spec2Vec learns fragmental relationships within a large set of spectral data to derive abstract spectral embeddings that can be used to assess spectral similarities. Using data derived from GNPS MS/MS libraries including spectra for nearly 13,000 unique molecules, we show how Spec2Vec scores correlate better with structural similarity than cosine-based scores. We demonstrate the advantages of Spec2Vec in library matching and molecular networking. Spec2Vec is computationally more scalable allowing structural analogue searches in large databases within seconds. Y1 - 2021 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:hbz:due62-opus-34687 UR - http://www.ncbi.nlm.nih.gov/pubmed/33591968 SN - 1553-7358 N1 - Data Availability Statement: The pre-processed, cleaned dataset with all positive ionization mode spectra can be downloaded from https://doi.org/10.5281/zenodo.3978118, the original raw data can be accessed from https://doi.org/10.5281/zenodo.3979010. Funding: J.J.J.v.d.H. acknowledges funding from an ASDI eScience grant, ASDI.2017.030, from the Netherlands eScience Center—NLeSC, www.esciencecenter.nl, The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. VL - 17 IS - 2 PB - Cold Spring Harbor Laboratory ER - TY - JOUR A1 - Mullowney, Michael W. A1 - Duncan, Katherine R. A1 - Elsayed, Somayah S. A1 - Garg, Neha A1 - van der Hooft, Justin J. J. A1 - Martin, Nathaniel I. A1 - Meijer, David A1 - Terlouw, Barbara R. A1 - Biermann, Friederike A1 - Blin, Kai A1 - Durairaj, Janani A1 - Gorostiola González, Marina A1 - Helfrich, Eric J. N. A1 - Huber, Florian A1 - Leopold-Messer, Stefan A1 - Rajan, Kohulan A1 - de Rond, Tristan A1 - van Santen, Jeffrey A. A1 - Sorokina, Maria A1 - Balunas, Marcy J. A1 - Beniddir, Mehdi A. A1 - van Bergeijk, Doris A. A1 - Carroll, Laura M. A1 - Clark, Chase M. A1 - Clevert, Djork-Arné A1 - Dejong, Chris A. A1 - Du, Chao A1 - Ferrinho, Scarlet A1 - Grisoni, Francesca A1 - Hofstetter, Albert A1 - Jespers, Willem A1 - Kalinina, Olga V. A1 - Kautsar, Satria A. A1 - Kim, Hyunwoo A1 - Leao, Tiago F. A1 - Masschelein, Joleen A1 - Rees, Evan R. A1 - Reher, Raphael A1 - Reker, Daniel A1 - Schwaller, Philippe A1 - Segler, Marwin A1 - Skinnider, Michael A. A1 - Walker, Allison S. A1 - Willighagen, Egon L. A1 - Zdrazil, Barbara A1 - Ziemert, Nadine A1 - Goss, Rebecca J. M. A1 - Guyomard, Pierre A1 - Volkamer, Andrea A1 - Gerwick, William H. A1 - Kim, Hyun Uk A1 - Müller, Rolf A1 - van Wezel, Gilles P. A1 - van Westen, Gerard J. P. A1 - Hirsch, Anna K. H. A1 - Linington, Roger G. A1 - Robinson, Serina L. A1 - Medema, Marnix H. T1 - Artificial intelligence for natural product drug discovery JF - Nature Reviews Drug Discovery KW - Maschinelles Lernen KW - Arzneimittelforschung KW - Deep learning KW - Omics-Technologie Y1 - 2023 U6 - https://doi.org/10.1038/s41573-023-00774-7 SN - 1474-1776 VL - 22 IS - 11 SP - 895 EP - 916 PB - Springer Nature ER - TY - CHAP A1 - Gaudry, Arnaud A1 - Huber, Florian A1 - Flückiger, Julien A1 - Quirós, L A1 - Rutz, Adriano A1 - Kaiser, M A1 - Grondin, A A1 - Marcourt, Laurence A1 - Ferreira Queiroz, E A1 - Wolfender, Jean-Luc A1 - Allard, Pierre-Marie T1 - Short Lecture “Mass spectrometry-based sample vectorization for exploration of large chemodiverse datasets and efficient identification of new antiparasitic compounds” T2 - Planta Medica KW - Massenspektrometrie KW - Naturstoffchemie KW - Antiparasitäres Mittel KW - Arzneimittelforschung Y1 - 2022 U6 - https://doi.org/10.1055/s-0042-1758983 SN - 1439-0221 VL - 88 IS - 15 PB - Thieme ER - TY - CHAP A1 - Adamatzky, Andrew A1 - Huber, Florian A1 - Schnauß, Jörg ED - Adamatzky, Andrew T1 - Computing on Actin Bundles Network T2 - Actin Computation: Unlocking the Potential of Actin Filaments for Revolutionary Computing System KW - Actin-Filament KW - Informationsverarbeitung KW - Bioinformatik Y1 - 2024 SN - 9789811285066 U6 - https://doi.org/10.1142/9789811285073_0013 SN - 2737-520X VL - Wspc Book Series in Unconventional Computing, Vol. 3 SP - 245 EP - 261 PB - WORLD SCIENTIFIC ER - TY - CHAP A1 - Siccardi, Stefano A1 - Adamatzky, Andrew A1 - Tuszyński, Jack A1 - Huber, Florian A1 - Schnauß, Jörg ED - Adamatzky, Andrew T1 - Actin Networks Voltage Circuits T2 - Actin Computation: Unlocking the Potential of Actin Filaments for Revolutionary Computing Systems KW - Actin-Filament KW - Informationsverarbeitung KW - Bioinformatik Y1 - 2024 SN - 9789811285066 U6 - https://doi.org/10.1142/9789811285073_0006 SN - 2737-520X VL - Wspc Book Series in Unconventional Computing, Vol. 3 SP - 123 EP - 143 PB - WORLD SCIENTIFIC ER - TY - CHAP A1 - Adamatzky, Andrew A1 - Huber, Florian A1 - Schnauß, Jörg ED - Adamatzky, Andrew T1 - Actin Droplet Machine T2 - Actin Computation: Unlocking the Potential of Actin Filaments for Revolutionary Computing Systems Y1 - 2024 SN - 9789811285066 U6 - https://doi.org/10.1142/9789811285073_0014 SN - 2737-520X VL - Wspc Book Series in Unconventional Computing, Vol. 3 SP - 263 EP - 284 PB - WORLD SCIENTIFIC ER - TY - BOOK A1 - Huber, Florian T1 - Hands-on Introduction to Data Science with Python N2 - In today’s world, data is generated at an unprecedented pace, and our ability to harness it is changing the way we live, work, and even think. Data science, the interdisciplinary field that blends statistics, computer science, and domain-specific knowledge, empowers us to extract insights from this vast ocean of data. As data science becomes increasingly essential across various industries and sectors, there is a growing need for skilled professionals who can make sense of data and transform it into actionable information. This book is designed to give you a very broad and at the same time a very practical hands-on tour through the full spectrum of data science approaches KW - Data Science KW - Python (Programmiersprache) KW - Lehrmittel Y1 - 2024 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:hbz:due62-opus-49548 N1 - The DOI represents all versions, and will always resolve to the latest one. The online version of this book can be found here: https://florian-huber.github.io/data_science_course/book/intro.html All materials and source code to render the book can be found on GitHub: https://github.com/florian-huber/data_science_course PB - Zenodo ET - v0.21 ER - TY - JOUR A1 - Haberfehlner, Helga A1 - van de Ven, Shankara S. A1 - van der Burg, Sven A. A1 - Huber, Florian A1 - Georgievska, Sonja A1 - Aleo, Ignazio A1 - Harlaar, Jaap A1 - Bonouvrié, Laura A. A1 - van der Krogt, Marjolein M. A1 - Buizer, Annemieke I. T1 - Towards automated video-based assessment of dystonia in dyskinetic cerebral palsy: A novel approach using markerless motion tracking and machine learning JF - Frontiers in Robotics and AI Y1 - 2023 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:hbz:due62-opus-40592 SN - 2296-9144 VL - 10 PB - Frontiers ER - TY - JOUR A1 - Bittremieux, Wout A1 - Schmid, Robin A1 - Huber, Florian A1 - van der Hooft, Justin J. J. A1 - Wang, Mingxun A1 - Dorrestein, Pieter C. T1 - Comparison of Cosine, Modified Cosine, and Neutral Loss Based Spectrum Alignment For Discovery of Structurally Related Molecules JF - Journal of the American Society for Mass Spectrometry KW - Modification KW - Precursors KW - Mass spectrometry KW - Anatomy KW - Peptides and proteins Y1 - 2022 U6 - https://doi.org/10.1021/jasms.2c00153 SN - 1044-0305 N1 - Eingereichte Version ist online verfügbar (Open Access Grün) https://doi.org/10.1101/2022.06.01.494370 unter CC BY 4.0 VL - 33 IS - 9 SP - 1733 EP - 1744 PB - American Chemical Society (ACS) ER -