1. A single-cell atlas of the miracidium larva of the human blood fluke Schistosoma mansoni : cell types, developmental pathways and tissue architecture

    This article has 10 authors:
    1. Teresa Attenborough
    2. Kate A. Rawlinson
    3. Carmen L. Diaz Soria
    4. Kirsty Ambridge
    5. Geetha Sankaranarayanan
    6. Jennie Graham
    7. James A. Cotton
    8. Stephen R. Doyle
    9. Gabriel Rinaldi
    10. Matthew Berriman
    This article has been curated by 1 group:
    • Curated by eLife

      eLife assessment

      This is a valuable study in which the authors provide an expression profile of the human blood fluke, Schistosoma mansoni. A strength of this solid study is in its inclusion of in situ hybridisation to validate the predictions of the transcript analysis.

    Reviewed by eLife

    This article has 7 evaluationsAppears in 1 listLatest version Latest activity
  2. Genome-wide mapping of native co-localized G4s and R-loops in living cells

    This article has 8 authors:
    1. Ting Liu
    2. Xing Shen
    3. Yijia Ren
    4. Hongyu Lu
    5. Yu Liu
    6. Chong Chen
    7. Lin Yu
    8. Zhihong Xue
    This article has been curated by 1 group:
    • Curated by eLife

      eLife assessment

      This useful study describes an antibody-free method to map G-quadruplexes (G4s) in vertebrate cells. While the method might have potential, the current analysis is primarily descriptive and does not add substantial new insights beyond existing data (e.g., PMID:34792172). While the datasets provided might constitute a good starting point for future functional studies, additional data and analyses would be needed to fully support the major conclusions and, at the same time, clarify the advantage of this method over other methods. Specifically, the strength of the evidence for DHX9 interfering with the ability of mESCs to differentiate by regulating directly the stability of either G4s or R-loops is still incomplete.

    Reviewed by eLife

    This article has 5 evaluationsAppears in 1 listLatest version Latest activity
  3. Beyond A and B Compartments: how major nuclear locales define nuclear genome organization and function

    This article has 13 authors:
    1. Omid Gholamalamdari
    2. Tom van Schaik
    3. Yuchuan Wang
    4. Pradeep Kumar
    5. Liguo Zhang
    6. Yang Zhang
    7. Gabriela A. Hernandez Gonzalez
    8. Athanasios E. Vouzas
    9. Peiyao A. Zhao
    10. David M. Gilbert
    11. Jian Ma
    12. Bas van Steensel
    13. Andrew S. Belmont
    This article has been curated by 1 group:
    • Curated by eLife

      eLife assessment

      This is a valuable manuscript that successfully integrates several datasets to determine genome interactions with several nuclear bodies. The integrative datasets are a major strength of the manuscript. The evidence supporting the central claims is varied in its strength ranging from solid to incomplete. Orthogonal evidence validating the novel methodologies with alternative approaches would better support the central claims. We encourage the authors to consider a revised manuscript which addresses these points.

    Reviewed by eLife

    This article has 4 evaluationsAppears in 1 listLatest version Latest activity
  4. Tradeoffs in Modeling Context Dependency in Complex Trait Genetics

    This article has 4 authors:
    1. Eric Weine
    2. Samuel Pattillo Smith
    3. Rebecca Kathryn Knowlton
    4. Arbel Harpak
    This article has been curated by 1 group:
    • Curated by eLife

      eLife assessment

      The study presents a framework viewing gene-by-environment (GxE) effect estimation as a bias-variance tradeoff problem. The authors convincingly show that greater statistical power can be achieved in detecting GxE if an underlying model of polygenic GxE is assumed. This polygenic amplification model is a truly novel view with fundamental promise for the detection of GxE in genomic datasets. That said, at present the polygenic architecture investigation presented in the manuscript is somewhat limited to specific models and may not adequately build over the bias-variance tradeoff part of the manuscript. If the authors can show in their simulations that they can in principle detect more complex scenarios of amplification, then the strength of the paper would be enhanced.

    Reviewed by eLife

    This article has 4 evaluationsAppears in 1 listLatest version Latest activity
  5. Increased inflammatory signature in myeloid cells of non-small cell lung cancer patients with high clonal hematopoiesis burden

    This article has 7 authors:
    1. Hyungtai Sim
    2. Hyun Jung Park
    3. Geun-Ho Park
    4. Yeon Jeong Kim
    5. Woong-Yang Park
    6. Se-Hoon Lee
    7. Murim Choi
    This article has been curated by 1 group:
    • Curated by eLife

      eLife assessment

      This valuable article represents a significant body of work that addresses some novel aspects of the biology of lung cancer influence of CHIP and its impacts on responses to therapy. While a high clonal hematopoiesis burden was previously linked with an inflammatory phenotype in other disease settings, the authors demonstrate with solid evidence that this is also true for lung cancer.

    Reviewed by eLife

    This article has 3 evaluationsAppears in 1 listLatest version Latest activity
  6. Recurrent loss of crossover interference punctuates the recombination landscape across yeast species

    This article has 9 authors:
    1. Abhishek Dutta
    2. Fabien Dutreux
    3. Marion Garin
    4. Claudia Caradec
    5. Anne Friedrich
    6. Gauthier Brach
    7. Pia Thiele
    8. Bertrand Llorente
    9. Joseph Schacherer

    Reviewed by Review Commons

    This article has 4 evaluationsAppears in 1 listLatest version Latest activity
  7. Multicellular, IVT-derived, unmodified human transcriptome for nanopore-direct RNA analysis

    This article has 7 authors:
    1. Caroline A. McCormick
    2. Stuart Akeson
    3. Sepideh Tavakoli
    4. Dylan Bloch
    5. Isabel N. Klink
    6. Miten Jain
    7. Sara H. Rouhanifard
    This article has been curated by 1 group:
    • Curated by GigaByte

      Editors Assessment:

      Oxford nanopore direct RNA sequencing (DRS) is a relatively new sequencing technology enabling measurements of RNA modifications. In vitro transcription (IVT)-based negative controls (i.e. modification-free transcripts) are a practical and targeted control for this direct sequencing, providing a baseline measurement for canonical nucleotides within a matched and biologically-derived sequence context. This work presents exactly this type of a long-read, multicellular, poly-A RNA-based, IVT-derived, unmodified transcriptome dataset. Review flagging more statistical analyses needed be performed for the data quality, and this was provided. The resulting data providing a resource to the direct RNA analysis community, helping reduce the need for expensive IVT library preparation and sequencing for human samples. And also serving as a framework for RNA modification analysis in other organisms.

      This evaluation refers to version 1 and 2 of the preprint

    Reviewed by GigaByte

    This article has 2 evaluationsAppears in 2 listsLatest version Latest activity
  8. Enhancer-driven cell type comparison reveals similarities between the mammalian and bird pallium

    This article has 16 authors:
    1. Nikolai Hecker
    2. Niklas Kempynck
    3. David Mauduit
    4. Darina Abaffyová
    5. Roel Vandepoel
    6. Sam Dieltiens
    7. Ioannis Sarropoulos
    8. Carmen Bravo González-Blas
    9. Elke Leysen
    10. Rani Moors
    11. Gert Hulselmans
    12. Lynette Lim
    13. Joris De Wit
    14. Valerie Christiaens
    15. Suresh Poovathingal
    16. Stein Aerts

    Reviewed by preLights

    This article has 1 evaluationAppears in 1 listLatest version Latest activity
  9. SERBP1 interacts with PARP1 and is present in PARylation-dependent protein complexes regulating splicing, cell division, and ribosome biogenesis

    This article has 19 authors:
    1. Kira Breunig
    2. Xiufen Lei
    3. Mauro Montalbano
    4. Gabriela D. A. Guardia
    5. Shiva Ostadrahimi
    6. Victoria Alers
    7. Adam Kosti
    8. Jennifer Chiou
    9. Nicole Klein
    10. Corina Vinarov
    11. Lily Wang
    12. Mujia Li
    13. Weidan Song
    14. W. Lee Kraus
    15. David S. Libich
    16. Stefano Tiziani
    17. Susan T. Weintraub
    18. Pedro A. F. Galante
    19. Luiz O. F. Penalva
    This article has been curated by 1 group:
    • Curated by eLife

      eLife assessment

      This study reports valuable insights into the interactome of the RNA-binding protein SERBP1 and possible links through PARylation to a diverse set of processes including splicing, cell division, and ribosome biogenesis. The diversity of processes SERBP1 may regulate means this work would be of very broad interest to the cell biology community. However, whereas the proteomics data are solid, the functional connection to downstream processes and the link to Alzheimer's disease are still incomplete, as they rely on a very limited set of experiments and patient samples.

    Reviewed by eLife

    This article has 4 evaluationsAppears in 1 listLatest version Latest activity
  10. Exploring polymorphic interspecies structural variants in Eucalyptus: Unravelling Their Role in Reproductive Isolation and Adaptive Divergence

    This article has 7 authors:
    1. Scott Ferguson
    2. Ashley Jones
    3. Kevin Murray
    4. Rose L. Andrew
    5. Helen Bothwell
    6. Benjamin Schwessinger
    7. Justin Borevitz

    Reviewed by GigaScience

    This article has 2 evaluationsAppears in 1 listLatest version Latest activity