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HFSP: high speed homology-driven function annotation of proteins

Yannick Mahlich, Martin Steinegger, Burkhard Rost, Yana Bromberg
2018 Bioinformatics  
Results: Here we describe homology-derived functional similarity of proteins (HFSP), a novel computational method that uses results of a high-speed alignment algorithm, MMseqs2, to infer functional similarity  ...  Most of these methods employ homology-based inference, approximated via sequence alignments, to transfer functional annotations between proteins.  ...  Conflict of Interest: none declared.  ... 
doi:10.1093/bioinformatics/bty262 pmid:29950013 pmcid:PMC6022561 fatcat:i2qq3lpoajd4pchbdzgdvmaxte

Histone degradation in response to DNA damage enhances chromatin dynamics and recombination rates

Michael H Hauer, Andrew Seeber, Vijender Singh, Raphael Thierry, Ragna Sack, Assaf Amitai, Mariya Kryzhanovska, Jan Eglinger, David Holcman, Tom Owen-Hughes, Susan M Gasser
2017 Nature Structural & Molecular Biology  
image shows the experimental setup for high-speed imaging.  ...  A.A. and D.H. performed biophysical analysis of high-speed tracking data. R.T. 311 performed and maintained the coding for 3D SIM-data analysis.  ...  Figure 5 High-speed, live cell imaging reveals increase in chromatin movement and loss of constraining forces following DNA damage (a) High-speed (Δt=80 ms) imaging of the undamaged MET10 locus (as in  ... 
doi:10.1038/nsmb.3347 pmid:28067915 fatcat:3bvnimetqjhgvimy3ggmhpupgm

AnnoMiner: a new web-tool to integrate epigenetics, transcription factor occupancy, and transcriptomics data to predict transcriptional regulators [article]

Arno Meiler, Fabio Marchiano, Manuela Weitkunat, Frank Schnorrer, Bianca H Habermann
2021 bioRxiv   pre-print
AnnoMiners fourth function performs transcription factor or histone mark enrichment analysis for user-provided gene lists by utilizing hundreds of public, high-quality datasets from ENCODE for the model  ...  Third, AnnoMiner offers to explore the transcriptional deregulation of 10 genes nearby a user-provided peak.  ...  Gain-of-function of yorkie results in muscle fiber hyper-compaction and premature expression of sarcomeric protein components (47) .  ... 
doi:10.1101/2021.01.28.428613 fatcat:6somk63oibdtresrkrauaz2r4q

Detecting macroevolutionary genotype-phenotype associations using error-corrected rates of protein convergence [article]

Kenji Fukushima, David D. Pollock
2022 bioRxiv   pre-print
rate of protein evolution.  ...  in functionally important sites, providing hypotheses on undiscovered phenotypes.  ...  To infer the functional effect of convergent amino acid substitutions, we mapped the positions of substitutions onto known conformations of homologous proteins.  ... 
doi:10.1101/2022.04.06.487346 fatcat:6mx5bgebzzc6zapsjkkwehjb3e

Interactome of Two Diverse RNA Granules Links mRNA Localization to Translational Repression in Neurons

Renate Fritzsche, Daniela Karra, Keiryn L. Bennett, Foong yee Ang, Jacki E. Heraud-Farlow, Marco Tolino, Michael Doyle, Karl E. Bauer, Sabine Thomas, Melanie Planyavsky, Eric Arn, Anetta Bakosova (+9 others)
2013 Cell Reports  
Here, we identified a specific set of interactors for two RNA-binding proteins that are known components of neuronal RNA granules, Barentsz and Staufen2.  ...  Transport of RNAs to dendrites occurs in neuronal RNA granules, which allows local synthesis of specific proteins at active synapses on demand, thereby contributing to learning and memory.  ...  /2005), the ESF/Eurocores program RNA Quality (FWF I127-B12), an FWF grant (FWF P20583-B12), the SFB RNA-Seq (FWF F4314-B09), the Doktoratskolleg RNA Biology (FWF W1207-B09), a project grant from the HFSP  ... 
doi:10.1016/j.celrep.2013.11.023 pmid:24360960 fatcat:s43t3srorngp3fhe242behtj7e

The Hippo pathway controls myofibril assembly and muscle fiber growth by regulating sarcomeric gene expression [article]

Frank Schnorrer, Aynur Kaya-Çopur, Fabio Marchiano, Marco Y Hein, Daniel Alpern, Julie Russeil, Nuno Miguel Luis, Matthias Mann, Bart Deplancke, Bianca H Habermann
2020 biorxiv/medrxiv   pre-print
We find that regulated activity of core members of the Hippo pathway is required to support flight muscle growth.  ...  How muscle growth is coordinated with growth of the contractile apparatus is not understood.  ...  Acknowledgements 760 The authors are indebted to Reinhard Fässler for hosting part of this work in his  ... 
doi:10.1101/2020.10.08.330951 fatcat:7gnsugtpf5hudhrzprnbkqgkd4

Precise transcription timing by a second-messenger drives a bacterial G1/S cell cycle transition [article]

Andreas Kaczmarczyk, Antje M. Hempel, Christoph von Arx, Raphael Boehm, Badri N. Dubey, Jutta Nesper, Tilman Schirmer, Sebastian Hiller, Urs Jenal
2019 bioRxiv   pre-print
Activation of the ShkA-dependent genetic program also causes c-di-GMP to reach peak levels, which triggers S-phase entry and, in parallel, promotes proteolysis of ShkA and TacA.  ...  Bacteria adapt their growth rate to their metabolic status and environmental conditions by modulating the length of their quiescent G1 period.  ...  ACKNOWLEDGEMENTS 357 We thank Tim Sharpe (Biophysics Facility, Biozentrum, University of Basel), Alexander 358 Schmidt (Proteomics Core Facility, Biozentrum, University of Basel), Janine Bögli and  ... 
doi:10.1101/675330 fatcat:lex325ztyfa7ler2hg6xvzodvy

XXI International Symposium on Glycoconjugates

2011 Glycoconjugate Journal  
Work in his laboratory focuses on the structure, biosynthesis, and function of proteoglycans, including structural studies of heparan sulphate by mass spectrometry, application of genome-wide methods to  ...  of Uppsala.  ...  We also examine the elongation of chondroitin by chondroitin polymerase, by singlemolecule force spectroscopy and high-speed AFM.  ... 
doi:10.1007/s10719-011-9334-5 pmid:21695399 fatcat:m5gds7jlzrdzlm2v65mbhsx3oq

Abstracts from the Thirty-second Annual Meeting of the Association for Chemoreception Sciences

2010 Chemical Senses  
Acknowledgements: Northwestern University FSM in-house funds 378 Influence of sinunasal diseases on olfactory function and quality of life Franziska Krone 1 , Ilona Croy 1 , Jü rgen Pade 2 , Angelika Pade  ...  of the McCusker et al  ...  This special feature of hTAS2Rs must ultimately be a function of the architecture of agonist binding pockets.By mutagenesis experiments, functional expression studies, and homology modeling we investigated  ... 
doi:10.1093/chemse/bjq071 fatcat:bhlqdbsexfb5na6oqr4v5dsaoq

Hand2 delineates mesothelium progenitors and is reactivated in mesothelioma [article]

Karin D. Prummel, Helena L. Crowell, Susan Nieuwenhuize, Eline C. Brombacher, Stephan Daetwyler, Charlotte Soneson, Jelena Kresoja-Rakic, Manuel Ronner, Agnese Kocere, Alexander Ernst, Zahra Labbaf, David E. Clouthier (+10 others)
2020 bioRxiv   pre-print
Functionally, hand2 mutants fail to close the ventral mesothelium due to perturbed migration of mesothelium progenitors.  ...  the re-initiation of a developmental transcriptional program in mesothelioma.  ...  (E) Immunoreactivity of HAND2 protein in HAND2-high human mesothelioma.  ... 
doi:10.1101/2020.11.11.355693 fatcat:6ga42zmwbnajha67ilex4xfc3y

Twentieth Annual Meeting of the Association for Chemoreception Sciences

1998 Chemical Senses  
Specifically, the angle between a horizontal line parallel to the floor of the wind tunnel and the antennae decreases as a function of increasing wind speed.  ...  These proteins may have key roles in determining the apparently high degree of specificity exhibited toward these signaling molecules.  ...  Two of seven peaks found to be unique to rutting males were tentatively identified by mass spectra analysis and are most likely homologs of tetrahydro-6-methyl pyranone, and 2-nonen-4-one.  ... 
doi:10.1093/chemse/23.5.545 fatcat:v2hv5w77onan7f6cs3tclcwmly

30th Annual Computational Neuroscience Meeting: CNS*2021–Meeting Abstracts

2021 Journal of Computational Neuroscience  
Currently, most functional models of neural activity are based on firing rates, while the most relevant signals for inter-neuron communication are spikes.  ...  One of the goals of neuroscience is to understand the computational principles that describe the formation of behaviorally relevant signals in the brain, as well as how these computations are realized  ...  Acknowledgments Vetenskapsrådet 2018-05,360; SNIC resources at PDC Centre for High Performance Computing, KTH Royal Institute of Technology; Swedish e-Science Research Centre (SeRC).  ... 
doi:10.1007/s10827-021-00801-9 pmid:34931275 pmcid:PMC8687879 fatcat:evpmmfpaivgpxdqpive5xdgmwu

Extraction of spatio-temporal primitives of emotional body expressions

Lars Omlor, Martin A. Giese
2007 Neurocomputing  
We are currently using AnimatLab to study the neural control of locomotion and the escape behavior of crayfish. High-speed video will be used to record the escape movements in 3D.  ...  In particular, the model incorporates the finding that there is a difference between the speed of familiarity and recollection, and that the two processes are functionally independent.  ... 
doi:10.1016/j.neucom.2006.10.100 fatcat:esivhljzsbcihdl5qbp756josu

Chromatin Dynamics In Homology Directed Repair

Anais Thiziri Cheblal
We thank all members of the Gasser laboratory for valuable discussions and technical support, and S.M.G. thanks the HFSP, SNSF and the Novartis Research Foundation for support.  ...  Sketch of the experimental set-up for high-speed time-lapse imaging of a GFP-tagged chromosomal locus near an inducible DSB (see STAR Methods).  ...  A) Experimental set-up for high-speed imaging of an undamaged MET10 locus through LacI-GFP after galacatose-induction of HO endonuclease, which creates a single DSB at the MAT locus.  ... 
doi:10.5451/unibas-ep84486 fatcat:cqyglohrajb55iumqkuw2jmh24

Mining real-world networks in systems biology and economics

Vuk Janjic, Natasa Przulj, European Research Council
molecular interaction data and use it to construct the first unified model of the cell's functional organisation and cross-communication lines.  ...  We perform three lines of experimental work: 1) the macro-scale study, where we model the yeast and human interactomes and show that their interactome data are growing in structurally and functionally  ...  A large-scale evaluation of computational protein function prediction. Nat. Methods, 10(3):221–227, 2013. 282 Loewenstein, Y. et al. Protein function annotation by homology-based inference.  ... 
doi:10.25560/29869 fatcat:uc76i4xp7ncxzgx5ngixhl3d34
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