1. Mitochondrial respiration atlas reveals differential changes in mitochondrial function across sex and age

    This article has 4 authors:
    1. Dylan C Sarver
    2. Muzna Saqib
    3. Fangluo Chen
    4. G William Wong
    This article has been curated by 1 group:
    • Curated by eLife

      eLife Assessment

      This important study provides a comprehensive assessment of mitochondrial function across age and sex in mice. The strength of evidence supporting this resource is compelling, given the exhaustive number of tissues profiled and in-depth analyses performed.

    Reviewed by eLife

    This article has 14 evaluationsAppears in 1 listLatest version Latest activity
  2. DNA O-MAP uncovers the molecular neighborhoods associated with specific genomic loci

    This article has 14 authors:
    1. Yuzhen Liu
    2. Christopher D McGann
    3. Mary Krebs
    4. Thomas A Perkins
    5. Rose Fields
    6. Conor K Camplisson
    7. David Z Nwizugbo
    8. Chris Hsu
    9. Shayan C Avanessian
    10. Ashley F Tsue
    11. Evan E Kania
    12. David M Shechner
    13. Brian J Beliveau
    14. Devin K Schweppe
    This article has been curated by 1 group:
    • Curated by eLife

      eLife Assessment

      This study presents a valuable new method for probing the DNA and proteins associated with targeted genomic elements in cells. The authors present solid evidence that the method can map DNA-DNA interactions for individual loci and can detect enriched proteins at repetitive DNA loci such as telomeres, but benchmarks of the method's resolution and specificity remain incomplete. The methodological details of this study will be of particular interest and utility to chromatin biologists.

    Reviewed by eLife

    This article has 5 evaluationsAppears in 1 listLatest version Latest activity
  3. PhysiMeSS - a new physiCell addon for extracellular matrix modelling

    This article has 4 authors:
    1. Vincent Noël
    2. Marco Ruscone
    3. Robyn Shuttleworth
    4. Cicely K. Macnamara
    This article has been curated by 1 group:
    • Curated by GigaByte

      Editors Assessment:

      PhysiCell is an open source multicellular systems simulator for studying many interacting cells in dynamic tissue microenvironments. As part of the PhysiCell ecosystem of tools and modules this paper presents a PhysiCell addon, PhysiMeSS (MicroEnvironment Structures Simulation) which allows the user to accurately represent the extracellular matrix (ECM) as a network of fibres. This can specify rod-shaped microenvironment elements such as the matrix fibres (e.g. collagen) of the ECM, allowing the PhysiCell user the ability to investigate physical interactions with cells and other fibres. Reviewers asked for additional clarification on a number of features. And the paper now clear future releases will provide full 3D compatibility and include working on fibrogenesis, i.e. the creation of new ECM fibres by cells.

      This evaluation refers to version 1 of the preprint

    Reviewed by GigaByte

    This article has 2 evaluationsAppears in 2 listsLatest version Latest activity
  4. Isobaric crosslinking mass spectrometry technology for studying conformational and structural changes in proteins and complexes

    This article has 2 authors:
    1. Jie Luo
    2. Jeff Ranish
    This article has been curated by 1 group:
    • Curated by eLife

      eLife Assessment

      This manuscript presents a valuable new quantitative crosslinking mass spectrometry approach using novel isobaric crosslinkers. The data are solid and the method has potential for a broad application in structural biology if more isobaric crosslinking channels are available and the quantitative information of the approach is exploited in more depth.

    Reviewed by eLife

    This article has 7 evaluationsAppears in 1 listLatest version Latest activity
  5. Diversity in Notch ligand-receptor signaling interactions

    This article has 3 authors:
    1. Rachael Kuintzle
    2. Leah A Santat
    3. Michael B Elowitz
    This article has been curated by 1 group:
    • Curated by eLife

      eLife Assessment

      This valuable study significantly enhances our understanding of how various ligands and receptors interact within the Notch signaling pathway. By developing novel cell-based assay systems, the authors systematically analyzed the effects of different ligand-receptor combinations on pathway activation. The convincing data reveal intriguing and unexpected differences and provide a foundation for interpreting Notch signalling in both normal and disease-related contexts.

    Reviewed by eLife

    This article has 8 evaluationsAppears in 1 listLatest version Latest activity
  6. Proteomic and functional comparison between human induced and embryonic stem cells

    This article has 15 authors:
    1. Alejandro J Brenes
    2. Eva Griesser
    3. Linda V Sinclair
    4. Lindsay Davidson
    5. Alan R Prescott
    6. Francois Singh
    7. Elizabeth KJ Hogg
    8. Carmen Espejo-Serrano
    9. Hao Jiang
    10. Harunori Yoshikawa
    11. Melpomeni Platani
    12. Jason R Swedlow
    13. Greg M Findlay
    14. Doreen A Cantrell
    15. Angus I Lamond
    This article has been curated by 1 group:
    • Curated by eLife

      eLife Assessment

      This study reports differences in proteomic profiles of embryonic versus induced pluripotent stem cells. This important finding cautions against the interchangeable use of both types of cells in biomedical research, although the mechanisms responsible for these differences remains unknown. The proteomic evidence is convincing, even though there is limited validation with other methods.

    Reviewed by eLife

    This article has 10 evaluationsAppears in 1 listLatest version Latest activity
  7. DGRPool, a web tool leveraging harmonized Drosophila Genetic Reference Panel phenotyping data for the study of complex traits

    This article has 6 authors:
    1. Vincent Gardeux
    2. Roel PJ Bevers
    3. Fabrice PA David
    4. Emily Rosschaert
    5. Romain Rochepeau
    6. Bart Deplancke
    This article has been curated by 1 group:
    • Curated by eLife

      eLife Assessment

      Genetic analysis of complex traits in Drosophila provides a resource for exploring the relationship between genetic and phenotypic variation. The web tool DGRPool presented in this paper makes data and results from the Drosophila Genetic Reference Panel accessible that will enable downstream analyses of genetic association. The findings of this paper are considered to be important, with practical implications beyond a single subfield, supported by convincing evidence using appropriate and validated methodology in line with current state of the art.

    Reviewed by eLife

    This article has 8 evaluationsAppears in 1 listLatest version Latest activity
  8. Genome-wide conditional degron libraries for functional genomics

    This article has 6 authors:
    1. Eduardo Gameiro
    2. Karla A. Juárez-Núñez
    3. Jia Jun Fung
    4. Susmitha Shankar
    5. Brian Luke
    6. Anton Khmelinskii

    Reviewed by Review Commons

    This article has 4 evaluationsAppears in 1 listLatest version Latest activity
  9. Unveiling Gene Perturbation Effects through Gene Regulatory Networks Inference from single-cell transcriptomic data

    This article has 7 authors:
    1. Clelia Corridori
    2. Merrit Romeike
    3. Giorgio Nicoletti
    4. Christa Buecker
    5. Samir Suweis
    6. Sandro Azaele
    7. Graziano Martello

    Reviewed by Review Commons

    This article has 4 evaluationsAppears in 1 listLatest version Latest activity
  10. Inference of gene regulatory networks for overcoming low performance in real-world data

    This article has 4 authors:
    1. Yusuke Hiki
    2. Yuta Tokuoka
    3. Takahiro G. Yamada
    4. Akira Funahashi

    Reviewed by Arcadia Science

    This article has 9 evaluationsAppears in 1 listLatest version Latest activity
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