1. Switching of RNA splicing regulators in immature neuroblasts during adult neurogenesis

    This article has 13 authors:
    1. Corentin Bernou
    2. Marc-André Mouthon
    3. Mathieu Daynac
    4. Thierry Kortulewski
    5. Benjamin Demaille
    6. Vilma Barroca
    7. Sebastien Couillard-Despres
    8. Nathalie Dechamps
    9. Véronique Ménard
    10. Léa Bellenger
    11. Christophe Antoniewski
    12. Alexandra Déborah Chicheportiche
    13. François Dominique Boussin
    This article has been curated by 1 group:
    • Curated by eLife

      eLife assessment

      This useful manuscript presents an intriguing potential refinement of models for adult SVZ neurogenesis, and highlights the role of RNA splicing at specific stages in the lineage. Unfortunately, the evidence does not fully support the claims, leaving it currently incomplete. The proposed role of RNA splicing in neuronal differentiation, though interesting, remains unexplored and would benefit significantly from targeted gene manipulation studies.

    Reviewed by eLife

    This article has 7 evaluationsAppears in 1 listLatest version Latest activity
  2. NERD-seq: a novel approach of Nanopore direct RNA sequencing that expands representation of non-coding RNAs

    This article has 10 authors:
    1. Luke Saville
    2. Li Wu
    3. Jemaneh Habtewold
    4. Yubo Cheng
    5. Babita Gollen
    6. Liam Mitchell
    7. Matthew Stuart-Edwards
    8. Travis Haight
    9. Majid Mohajerani
    10. Athanasios Zovoilis

    Reviewed by Review Commons

    This article has 3 evaluationsAppears in 1 listLatest version Latest activity
  3. Meta-Research: Understudied genes are lost in a leaky pipeline between genome-wide assays and reporting of results

    This article has 4 authors:
    1. Reese Richardson
    2. Heliodoro Tejedor Navarro
    3. Luis A Nunes Amaral
    4. Thomas Stoeger
    This article has been curated by 1 group:
    • Curated by eLife

      eLife assessment

      This study investigated the factors related to understudied genes in biomedical research. It showed that understudied genes are largely abandoned at the writing stage, and it identified a number of biological and experimental factors that influence which genes are selected for investigation. The study is an important contribution to this branch of meta-research, and the evidence in support of the findings is solid.

    Reviewed by eLife

    This article has 10 evaluationsAppears in 1 listLatest version Latest activity
  4. Structural variation discovery in wheat using PacBio high‐fidelity sequencing

    This article has 15 authors:
    1. Zhiliang Zhang
    2. Jijin Zhang
    3. Lipeng Kang
    4. Xuebing Qiu
    5. Song Xu
    6. Jun Xu
    7. Yafei Guo
    8. Zelin Niu
    9. Beirui Niu
    10. Aoyue Bi
    11. Xuebo Zhao
    12. Daxing Xu
    13. Jing Wang
    14. Changbin Yin
    15. Fei Lu

    Reviewed by PREreview

    This article has 1 evaluationAppears in 1 listLatest version Latest activity
  5. Single-cell ‘omic profiles of human aortic endothelial cells in vitro and human atherosclerotic lesions ex vivo reveal heterogeneity of endothelial subtype and response to activating perturbations

    This article has 9 authors:
    1. Maria L Adelus
    2. Jiacheng Ding
    3. Binh T Tran
    4. Austin C Conklin
    5. Anna K Golebiewski
    6. Lindsey K Stolze
    7. Michael B Whalen
    8. Darren A Cusanovich
    9. Casey E Romanoski
    This article has been curated by 1 group:
    • Curated by eLife

      eLife assessment

      This is a fundamental resource of snRNA-seq and and chromatin accessibility data from human aortic endothelial cells (ECs), treated with relevant perturbations such as IL1b, TGFB2, or si-EGR. The authors show that ECs can be categorized by distinct subpopulations of differing plasticity. The support for the existence of these subpopulations is compelling, supported also by three publicly available scRNA-seq datasets, and differential enrichment of coronary artery disease associated SNPs in open chromatin in these subpopulations.

    Reviewed by eLife

    This article has 6 evaluationsAppears in 1 listLatest version Latest activity
  6. Near chromosome-level and highly repetitive genome assembly of the snake pipefish Entelurus aequoreus (Syngnathiformes: Syngnathidae)

    This article has 20 authors:
    1. Magnus Wolf
    2. Bruno Lopes da Silva Ferrette
    3. Raphael T. F. Coimbra
    4. Menno de Jong
    5. Marcel Nebenfuehr
    6. David Prochotta
    7. Yannis Schöneberg
    8. Konstantin Zapf
    9. Jessica Rosenbaum
    10. Hannah A. Mc Intyre
    11. Julia Maier
    12. Clara C.S. de Souza
    13. Lucas M. Gehlhaar
    14. Melina J. Werner
    15. Henrik Oechler
    16. Marie Wittekind
    17. Moritz Sonnewald
    18. Maria A. Nilsson
    19. Axel Janke
    20. Sven Winter
    This article has been curated by 1 group:
    • Curated by GigaByte

      Editors Assessment:

      The snake pipefish, Entelurus aequoreus, is a species of fish that dwells in open seagrass habitats in the northern Atlantic. As a pipefish, it is a member of the Syngnathidae family of fish which also includes seahorses and seadragons. In recent years it has expanded its population size and range into arctic waters. To better understand these demographic changes genomic data is useful, and to address this a high-quality reference genome has been produced. Building on a previous short-read reference, a near chromosome-scale genome assembly for the snake pipefish was assembled using PacBio CLR and Hi-C reads. After revisions the authors provided more details on the assembly metrics, the final assembly has a length of 1.6 Gbp, with scaffold and contig N50s of 62.3 Mbp and 45.0 Mbp respectively. Demographic inference analysis of the snake pipefish genome using this data enables tracing of population changes over the past 1 million years, and this reference will allow further analyses and studies relating these to changes in climate.

      **This evaluation refers to version 1 of the preprint

    Reviewed by GigaByte

    This article has 2 evaluationsAppears in 1 listLatest version Latest activity
  7. A metagenomics pipeline reveals insertion sequence-driven evolution of the microbiota

    This article has 3 authors:
    1. Joshua M. Kirsch
    2. Andrew J. Hryckowian
    3. Breck A. Duerkop

    Reviewed by Arcadia Science

    This article has 27 evaluationsAppears in 1 listLatest version Latest activity
  8. The genomic landscape of transposable elements in yeast hybrids is shaped by structural variation and genotype-specific modulation of transposition rate

    This article has 4 authors:
    1. Mathieu Hénault
    2. Souhir Marsit
    3. Guillaume Charron
    4. Christian R Landry
    This article has been curated by 1 group:
    • Curated by eLife

      eLife assessment

      This valuable study advances our understanding of the forces that shape the genomic landscape of transposable elements. By exploiting both long-read sequencing of mutation accumulation lines and in vivo transposition assays, the authors offer compelling evidence that structural variation rather than transposition largely shapes transposable element copy number evolution in budding yeast. The work will be of interest to the transposable element and genome evolution communities.

    Reviewed by eLife

    This article has 8 evaluationsAppears in 1 listLatest version Latest activity
  9. Architecture and evolutionary conservation of Xenopus tropicalis osteoblast-specific regulatory regions shed light on bone diseases and early skeletal evolution

    This article has 6 authors:
    1. Héctor Castillo
    2. Francisco Godoy
    3. Clément Gilbert
    4. Felipe Aguilera
    5. Salvatore Spicuglia
    6. Sylvain Marcellini

    Reviewed by Review Commons

    This article has 4 evaluationsAppears in 1 listLatest version Latest activity
  10. DNA methylation-environment interactions in the human genome

    This article has 5 authors:
    1. Rachel A Johnston
    2. Katherine A Aracena
    3. Luis B Barreiro
    4. Amanda J Lea
    5. Jenny Tung
    This article has been curated by 1 group:
    • Curated by eLife

      eLife assessment

      This important paper uses a genome-wide, massively parallel reporter assay to determine how CpG methylation affects regulatory sequences that control the expression of human genes. The authors provide compelling evidence that methylation not only influences baseline activity of regulatory sequences but also the magnitude of acute responses to environmental stimuli. The findings are of broad interest, and the extensive data set will likely become a key resource for the community.

    Reviewed by eLife

    This article has 7 evaluationsAppears in 1 listLatest version Latest activity
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