Nature Protocols
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#1Tony P. Huang (Broad Institute)H-Index: 5
#2Gregory A. Newby (Broad Institute)H-Index: 17
Last. David R. Liu (Broad Institute)H-Index: 106
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#1Nikolay L Malinin (St. Jude Children's Research Hospital)H-Index: 1
#2GaHyun Lee (St. Jude Children's Research Hospital)H-Index: 2
Last. Shengdar Q. Tsai (St. Jude Children's Research Hospital)H-Index: 28
view all 13 authors...
Genome-wide unbiased identification of double-stranded breaks enabled by sequencing (GUIDE-seq) is a sensitive, unbiased, genome-wide method for defining the activity of genome-editing nucleases in living cells. GUIDE-seq is based on the principle of efficient integration of an end-protected double-stranded oligodeoxynucleotide tag into sites of nuclease-induced DNA double-stranded breaks, followed by amplification of tag-containing genomic DNA molecules and high-throughput sequencing. Here we d...
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#1Rozemarijn Kleinendorst (EBI: European Bioinformatics Institute)H-Index: 2
#2Guido Barzaghi (Heidelberg University)H-Index: 1
Last. Arnaud R Krebs (EBI: European Bioinformatics Institute)H-Index: 19
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Precise control of gene expression requires the coordinated action of multiple factors at cis-regulatory elements. We recently developed single-molecule footprinting to simultaneously resolve the occupancy of multiple proteins including transcription factors, RNA polymerase II and nucleosomes on single DNA molecules genome-wide. The technique combines the use of cytosine methyltransferases to footprint the genome with bisulfite sequencing to resolve transcription factor binding patterns at cis-r...
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#1Zongyang Du (NKU: Nankai University)H-Index: 1
#2Hong Su (NKU: Nankai University)H-Index: 2
Last. Jianyi Yang (SDU: Shandong University)
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The trRosetta (transform-restrained Rosetta) server is a web-based platform for fast and accurate protein structure prediction, powered by deep learning and Rosetta. With the input of a protein’s amino acid sequence, a deep neural network is first used to predict the inter-residue geometries, including distance and orientations. The predicted geometries are then transformed as restraints to guide the structure prediction on the basis of direct energy minimization, which is implemented under the ...
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#1Lika Drakhlis (MHH: Hannover Medical School)H-Index: 1
#2Santoshi Biswanath Devadas (MHH: Hannover Medical School)
Last. Robert Zweigerdt (MHH: Hannover Medical School)H-Index: 28
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Heart-forming organoids (HFOs) derived from human pluripotent stem cells (hPSCs) are a complex, highly structured in vitro model of early heart, foregut and vasculature development. The model represents a potent tool for various applications, including teratogenicity studies, gene function analysis and drug discovery. Here, we provide a detailed protocol describing how to form HFOs within 14 d. In an initial 4 d preculture period, hPSC aggregates are individually formed in a 96-well format and t...
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#1Anna Chiara Vicini (University of Oxford)H-Index: 3
#2Gabriele Pupo (University of Oxford)H-Index: 5
Last. Véronique Gouverneur (University of Oxford)H-Index: 61
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Fluorine is a key element present in ~35% of agrochemicals and 25% of marketed pharmaceutical drugs. The availability of reliable synthetic protocols to prepare catalysts that allow the efficient incorporation of fluorine in organic molecules is therefore essential for broad applicability. Herein, we report a protocol for the multigram synthesis of two representative enantiopure N-alkyl bis-urea organocatalysts derived from (S)-(–)-1,1′-binaphthyl-2,2′-diamine ((S)-BINAM). These tridentate hydro...
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#1Melissa S. Unger (Mannheim University of Applied Sciences)
#2Martina Blank (UFSC: Universidade Federal de Santa Catarina)H-Index: 12
Last. Carsten Hopf (Mannheim University of Applied Sciences)H-Index: 31
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Cell-based assays for compound screening and profiling are fundamentally important in life sciences, chemical biology and pharmaceutical research. Most cell assays measure the amount of a single reporter molecule or cellular endpoint, and require the use of fluorescence or other labeled materials. Consequently, there is high demand for label-free technologies that enable multiple biomolecules or endpoints to be measured simultaneously. Here, we describe how to develop, optimize and validate MALD...
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#1Amy C. Reichelt (UWO: Western University)H-Index: 22
#2Cecilia P Kramar (McGill University)
Last. Timothy J. Bussey (UWO: Western University)H-Index: 83
view all 8 authors...
Keeping similar memories distinct from one another is a critical cognitive process without which we would have difficulty functioning in everyday life. Memories are thought to be kept distinct through the computational mechanism of pattern separation, which reduces overlap between similar input patterns to amplify differences among stored representations. At the behavioral level, impaired pattern separation has been shown to contribute to memory deficits seen in neuropsychiatric and neurodegener...
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#1Shuxia Guo (IPHT: Leibniz Institute of Photonic Technology)H-Index: 1
#2Jürgen Popp (IPHT: Leibniz Institute of Photonic Technology)H-Index: 86
Last. Thomas Bocklitz (IPHT: Leibniz Institute of Photonic Technology)H-Index: 32
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Raman spectroscopy is increasingly being used in biology, forensics, diagnostics, pharmaceutics and food science applications. This growth is triggered not only by improvements in the computational and experimental setups but also by the development of chemometric techniques. Chemometric techniques are the analytical processes used to detect and extract information from subtle differences in Raman spectra obtained from related samples. This information could be used to find out, for example, whe...
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