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Systems & Computational Biology

  • Metabolome-based prediction of yield heterosis contributes to the breeding of elite rice
    Open Access
    Metabolome-based prediction of yield heterosis contributes to the breeding of elite rice

    Zhiwu Dan, Yunping Chen, Weibo Zhao, Qiong Wang, Wenchao Huang

    Zhiwu Dan ... Wenchao Huang

    Published 13 December 2019

    Metabolite profiles obtained from parental seedlings can predict yield heterosis of rice hybrids with correctly dissected population structure across different growth conditions.

  • A comprehensive resource for retrieving, visualizing, and integrating functional genomics data
    Open Access
    A comprehensive resource for retrieving, visualizing, and integrating functional genomics data

    Matthias Blum, Pierre-Etienne Cholley, Valeriya Malysheva, Samuel Nicaise, Julien Moehlin, Hinrich Gronemeyer, Marco Antonio Mendoza-Parra

    Matthias Blum ... Marco Antonio Mendoza-Parra

    Published 9 December 2019

    This study presents qcGenomics, a user-friendly online resource for ultrafast retrieval, visualization, and comparative analysis of tens of thousands of genomics datasets to gain new functional insight from global or focused multi-dimensional data integration.

  • Phenotypic proteomic profiling identifies a landscape of targets for circadian clock–modulating compounds
    Open Access
    Phenotypic proteomic profiling identifies a landscape of targets for circadian clock–modulating compounds

    Sandipan Ray, Radoslaw Lach, Kate J Heesom, Utham K Valekunja, Vesela Encheva, Ambrosius P Snijders, Akhilesh B Reddy

    Sandipan Ray ... Akhilesh B Reddy

    Published 2 December 2019

    This study provides comprehensive insights into the mechanism of action and cellular effects of circadian period–modulating compounds, which is critical for clearly defining molecular targets to modulate daily rhythms for therapeutic benefit.

  • ADAPTABLE: a comprehensive web platform of antimicrobial peptides tailored to the user’s research
    Open Access
    ADAPTABLE: a comprehensive web platform of antimicrobial peptides tailored to the user’s research

    Francisco Ramos-Martín, Thibault Annaval, Sébastien Buchoux, Catherine Sarazin, Nicola D’Amelio

    Francisco Ramos-Martín ... Nicola D’Amelio

    Published 18 November 2019

    ADAPTABLE is a webserver and database of antimicrobial peptides that uses sequence and property alignment to highlight their mode of action against the threat of resistance in medicine and agriculture.

  • TRAIL-induced variation of cell signaling states provides nonheritable resistance to apoptosis
    Open Access
    TRAIL-induced variation of cell signaling states provides nonheritable resistance to apoptosis

    Reema Baskar, Harris G Fienberg, Zumana Khair, Patricia Favaro, Sam Kimmey, Douglas R Green, Garry P Nolan, Sylvia Plevritis, Sean C Bendall

    Reema Baskar ... Sean C Bendall

    Published 8 November 2019

    This work summarizes cellular apoptotic and signaling response to TRAIL across 10 cell lines and for the first time links signaling diversity to nongenetic resistance. This high-dimensional, single-cell approach toward TRAIL resistance sets a standard in studying nongenetic resistance.

  • Sufficiency analysis of estrogen responsive enhancers using synthetic activators
    Open Access
    Sufficiency analysis of estrogen responsive enhancers using synthetic activators

    Matthew Ginley-Hidinger, Julia B Carleton, Adriana C Rodriguez, Kristofer C Berrett, Jason Gertz

    Matthew Ginley-Hidinger ... Jason Gertz

    Published 30 September 2019

    Enhancers bound by synthetic activators can recreate a transcriptional response to estrogen, drive different levels of gene expression, and work independently to regulate transcription.

  • Detecting sequence signals in targeting peptides using deep learning
    Open Access
    Detecting sequence signals in targeting peptides using deep learning

    Jose Juan Almagro Armenteros, Marco Salvatore, Olof Emanuelsson, Ole Winther, Gunnar von Heijne, Arne Elofsson, Henrik Nielsen

    Jose Juan Almagro Armenteros ... Henrik Nielsen

    Published 30 September 2019

    During the development of TargetP 2.0, a state-of-the-art method to predict targeting signal, we find a previously overlooked biological signal for subcellular targeting using the output from a deep learning method.

  • Endogenous RNAi pathway evolutionarily shapes the destiny of the antisense lncRNAs transcriptome
    Open Access
    Endogenous RNAi pathway evolutionarily shapes the destiny of the antisense lncRNAs transcriptome

    Ugo Szachnowski, Sara Andus, Dominika Foretek, Antonin Morillon, Maxime Wery

    Ugo Szachnowski ... Maxime Wery

    Published 28 August 2019

    A genome-wide comparative analysis of “cryptic” aslncRNAs decay in RNAi-capable and RNAi-deficient budding yeasts suggests an evolutionary contribution of RNAi in shaping the aslncRNAs transcriptome.

  • Reconstructing B-cell receptor sequences from short-read single-cell RNA sequencing with BRAPeS
    Open Access
    Reconstructing B-cell receptor sequences from short-read single-cell RNA sequencing with BRAPeS

    Shaked Afik, Gabriel Raulet, Nir Yosef

    Shaked Afik ... Nir Yosef

    Published 26 August 2019

    BRAPeS is a software for B-cell receptor reconstruction in single cells from very short (25–30 bp) read lengths, which achieves similar success rates and accuracy as applying other methods on long reads.

  • KAP1 is an antiparallel dimer with a functional asymmetry
    Open Access
    KAP1 is an antiparallel dimer with a functional asymmetry

    Giulia Fonti, Maria J Marcaida, Louise C Bryan, Sylvain Träger, Alexandra S Kalantzi, Pierre-Yves JL Helleboid, Davide Demurtas, Mark D Tully, Sergei Grudinin, Didier Trono, Beat Fierz, Matteo Dal Peraro

    Giulia Fonti ... Matteo Dal Peraro

    Published 19 August 2019

    This study reveals the architecture of human KAP1 by integrating molecular modeling with small-angle X-ray scattering and single-molecule experiments. KAP1 dimers feature a structural asymmetry at the C-terminal domains that has functional implications for recruitment of HP1.

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  • Synthetic Biology (2)
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