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More articles from Resources

  • Mitochondrial phosphoproteomes are functionally specialized across tissues
    Open Access
    Mitochondrial phosphoproteomes are functionally specialized across tissues

    Fynn M Hansen, Laura S Kremer, Ozge Karayel, Isabell Bludau, Nils-Göran Larsson, Inge Kühl, Matthias Mann

    Fynn M Hansen ... Matthias Mann

    Published 20 November 2023

    This study explores tissue-specific mitochondrial proteomes and phosphoproteomes in unprecedented depth, offering valuable insights into mitochondrial organization and specialization.

  • Performance and robustness analysis reveals phenotypic trade-offs in yeast
    Open Access
    Performance and robustness analysis reveals phenotypic trade-offs in yeast

    Cecilia Trivellin, Peter Rugbjerg, Lisbeth Olsson

    Cecilia Trivellin ... Lisbeth Olsson

    Published 30 October 2023

    This study combines phenotypic data from yeast cultivations with quantification of robustness over a defined perturbation space, revealing trade-offs between performance and robustness.

  • MICA: a multi-omics method to predict gene regulatory networks in early human embryos
    Open Access
    MICA: a multi-omics method to predict gene regulatory networks in early human embryos

    Gregorio Alanis-Lobato, Thomas E Bartlett, Qiulin Huang, Claire S Simon, Afshan McCarthy, Kay Elder, Phil Snell, Leila Christie, Kathy K Niakan

    Gregorio Alanis-Lobato ... Kathy K Niakan

    Published 25 October 2023

    Our comparative analysis of gene regulatory network predictions defines a pipeline to infer transcription factor–target gene regulatory interactions in early human embryos. Mutual information refined by chromatin accessibility allowed us to construct the first network during early human development.

  • Identification of biomarkers, pathways, and therapeutic targets for EGFR–TKI resistance in NSCLC
    Open Access
    Identification of biomarkers, pathways, and therapeutic targets for EGFR–TKI resistance in NSCLC

    Leilei Zhu, Shanshan Gao, Xianya Zhao, Ying Wang

    Leilei Zhu ... Ying Wang

    Published 10 October 2023

    The exploration of the hub genes related to EGFR–TKI resistance in NSCLC through bioinformatics technologies can improve the understanding of the mechanisms of EGFR–TKI resistance and provide novel insights into therapeutics.

  • The highly improved genome of <em>Ixodes scapularis</em> with X and Y pseudochromosomes
    Open Access
    The highly improved genome of Ixodes scapularis with X and Y pseudochromosomes

    Andrew B Nuss, Johnathan S Lomas, Jeremiah B Reyes, Omar Garcia-Cruz, Wenlong Lei, Arvind Sharma, Michael N Pham, Saransh Beniwal, Mia L Swain, Molly McVicar, Isaac Amankona Hinne, Xingtan Zhang, Won C Yim, Monika Gulia-Nuss

    Andrew B Nuss ... Monika Gulia-Nuss

    Published 9 October 2023

    Ixodes scapularis Gulia-Nuss (IscGN) genome assembly and gene set were obtained using DNA from eggs and male and female adult ticks. By combining Hi-C, PacBio HiFi, and Illumina sequencing technologies, we assembled 13 pseudoautosomes and sex chromosomes: X and Y.

  • Dissecting morphogenetic apoptosis through a genetic screen in Drosophila
    Open Access
    Dissecting morphogenetic apoptosis through a genetic screen in Drosophila

    Audrey Barbaste, Sonia Schott, Corinne Benassayag, Magali Suzanne

    Audrey Barbaste ... Magali Suzanne

    Published 26 July 2023

    This genetic screen identifies elements of the “morphogenetic apoptosis pathway” potentially involved in the regulation, the orchestration or the impact of the apoptotic process on morphogenesis.

  • Comparative membrane proteomics reveals diverse cell regulators concentrated at the nuclear envelope
    Open Access
    Comparative membrane proteomics reveals diverse cell regulators concentrated at the nuclear envelope

    Li-Chun Cheng, Xi Zhang, Sabyasachi Baboo, Julie A Nguyen, Salvador Martinez-Bartolomé, Esther Loose, Jolene Diedrich, John R Yates, Larry Gerace

    Li-Chun Cheng ... Larry Gerace

    Published 11 July 2023

    A cohort of low-abundance transmembrane proteins concentrated at the nuclear envelope has been identified, predicting diverse new functions for this membrane system.

  • Predictive data-driven modeling of C-terminal tyrosine function in the EGFR signaling network
    Open Access
    Predictive data-driven modeling of C-terminal tyrosine function in the EGFR signaling network

    Jacqueline S Gerritsen, Joseph S Faraguna, Rudy Bonavia, Frank B Furnari, Forest M White

    Jacqueline S Gerritsen ... Forest M White

    Published 11 May 2023

    The site-specific function of EGFR’s C-terminal tyrosines is interrogated by phosphotyrosine phosphoproteomics to build a data-driven model that links cell response to signaling nodes and elucidates novel associations in the EGFR signaling network.

  • A practical comparison of the next-generation sequencing platform and assemblers using yeast genome
    Open Access
    A practical comparison of the next-generation sequencing platform and assemblers using yeast genome

    Min-Seung Jeon, Da Min Jeong, Huijeong Doh, Hyun Ah Kang, Hyungtaek Jung, Seong-il Eyun

    Min-Seung Jeon ... Seong-il Eyun

    Published 6 February 2023

    This research analyzes the general and optimal de novo yeast assembly pipeline using the repetitive yeast genome assembly by benchmarking four different sequencing platforms and seven assembly programs.

  • Disease- and sex-specific differences in patients with heart valve disease: a proteome study
    Open Access
    Disease- and sex-specific differences in patients with heart valve disease: a proteome study

    Sarah Nordmeyer, Milena Kraus, Matthias Ziehm, Marieluise Kirchner, Marie Schafstedde, Marcus Kelm, Sylvia Niquet, Mariet Mathew Stephen, Istvan Baczko, Christoph Knosalla, Matthieu-P Schapranow, Gunnar Dittmar, Michael Gotthardt, Martin Falcke, Vera Regitz-Zagrosek, Titus Kuehne, Philipp Mertins

    Sarah Nordmeyer ... Philipp Mertins

    Published 10 January 2023

    Proteomics provide novel insights into molecular mechanisms and cardiac remodeling in heart failure because of pressure overload in aortic valve stenosis and volume overload in mitral valve regurgitation.

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