eLife

Latest preprint reviews

1. Generative modeling for RNA splicing predictions and design

   This article has 10 authors:

   1. Di Wu
   2. Natalie Maus
   3. Anupama Jha
   4. Kevin Yang
   5. Benjamin D Wales-McGrath
   6. San Jewell
   7. Anna Tangiyan
   8. Peter Choi
   9. Jacob R Gardner
   10. Yoseph Barash

   This article has been curated by 1 group:

   • Curated by eLife

     eLife Assessment

     TrASPr is an important contribution that leverages transformer models focused on regulatory regions to enhance predictions of tissue-specific splicing events. The evidence supporting the authors' claims is convincing, with rigorous analyses demonstrating improved performance relative to existing models, although some aspects of the evaluation would benefit from further clarification. This work will be of particular interest to researchers in computational genomics and RNA biology, as it offers both a refined predictive model and a new tool to designing RNA sequences for targeted splicing outcomes.

   Reviewed by eLife

2. The ALS-associated co-chaperone DNAJC7 mediates neuroprotection against proteotoxic stress by modulating HSF1 activity

   This article has 5 authors:

   1. Andrew C Fleming
   2. Nalini R Rao
   3. Matthew Wright
   4. Jeffrey N Savas
   5. Evangelos Kiskinis

   This article has been curated by 1 group:

   • Curated by eLife

     eLife Assessment

     Fleming et al sought to better understand DNAJC7's function in motor neurons as mutations in this gene have been associated with amyotrophic lateral sclerosis (ALS). Using iPSC-derived motor neurons, interactome, and transcriptomic data, they provide solid evidence that loss-of-function mutations in DNAJC7 disrupt RNA binding proteins and resistance to proteasomal stress. These important findings advance our understanding of DNAJC7 in motor neurons while providing clues to how its loss may be causal for ALS; nonetheless, the experiments were performed with a single iPSC line, while at least 3 are deemed to be required to validate the results. Furthermore, the mechanistic evidence is still incomplete with respect to how DNAJC7 mutations lead to HSF1 impaired activity, and whether it is direct or not.

   Reviewed by eLife

3. Pu.1/Spi1 dosage controls the turnover and maintenance of microglia in zebrafish and mammals

   This article has 8 authors:

   1. Yi Wu
   2. Weilin Guo
   3. Haoyue Kuang
   4. Xiaohai Wu
   5. Yuexin Wang
   6. Shizheng Zhao
   7. Zilong Wen
   8. Tao Yu

   This article has been curated by 1 group:

   • Curated by eLife

     eLife Assessment

     This study presents valuable findings on the control of survival and maintenance of a specific set of brain resident immune cells. The authors generate a new animal model to enable sophisticated analysis of cell function in vivo. The sophisticated knock-in/knock-out alleles are compelling, although the work would ultimately be strengthened with further mechanistic analyses.

   Reviewed by eLife

4. Distributed encoding of hippocampal information in mossy cells

   This article has 3 authors:

   1. Ayako Ouchi
   2. Taro Toyoizumi
   3. Yuji Ikegaya

   This article has been curated by 1 group:

   • Curated by eLife

     eLife assessment

     Using intracellular in vitro and in vivo recordings and a deep learning approach, this study shows that mouse dentate gyrus mossy cells (MCs) and CA3 pyramidal cells process information from an important electrophysiological hall mark of hippocampus, sharp wave-ripples (SWRs). The innovative use of deep learning to predict SWR waveforms from MC membrane potentials represents an interesting methodological advance. While the key findings are potentially fundamental, some of the evidence is currently incomplete and should be revised to better support the findings.

   Reviewed by eLife

5. Identification and comparison of orthologous cell types from primate embryoid bodies shows limits of marker gene transferability

   This article has 10 authors:

   1. Jessica Jocher
   2. Philipp Janssen
   3. Beate Vieth
   4. Fiona C Edenhofer
   5. Tamina Dietl
   6. Anita Térmeg
   7. Paulina Spurk
   8. Johanna Geuder
   9. Wolfgang Enard
   10. Ines Hellmann

   This article has been curated by 1 group:

   • Curated by eLife

     eLife Assessment

     The authors have generated important resources such as a reference dataset of early primate development by utilizing single-cell transcriptomic technology together with induced pluripotent stem cells (iPSCs) from four primate species: humans, orangutans, cynomolgus macaques, and rhesus macaques. By analyzing marker gene expression and cell types across species during undirected differentiation of iPSCs, the authors provide solid evidence that the transferability of marker genes decreases as the evolutionary distance between species increases. This work demonstrates the extended usage of iPSCs for broader fields, which will benefit several scientific communities including anthropology, comparative biology, and evolutionary biology.

   Reviewed by eLife

6. MerQuaCo: a computational tool for quality control in image-based spatial transcriptomics

   This article has 41 authors:

   1. Naomi Martin
   2. Paul Olsen
   3. Jacob Quon
   4. Jazmin Campos
   5. Nasmil Valera Cuevas
   6. Josh Nagra
   7. Marshall VanNess
   8. Zoe Maltzer
   9. Emily C Gelfand
   10. Alana Oyama
   11. Amanda Gary
   12. Yimin Wang
   13. Angela Alaya
   14. Augustin Ruiz
   15. Cade Reynoldson
   16. Cameron Bielstein
   17. Christina Alice Pom
   18. Cindy Huang
   19. Cliff Slaughterbeck
   20. Elizabeth Liang
   21. Jason Alexander
   22. Jeanelle Ariza
   23. Jocelin Malone
   24. Jose Melchor
   25. Kaity Colbert
   26. Krissy Brouner
   27. Lyudmila Shulga
   28. Melissa Reding
   29. Patrick Latimer
   30. Raymond Sanchez
   31. Stuard Barta
   32. Tom Egdorf
   33. Zachary Madigan
   34. Chelsea M Pagan
   35. Jennie L Close
   36. Brian Long
   37. Michael Kunst
   38. Ed S Lein
   39. Hongkui Zeng
   40. Delissa McMillen
   41. Jack Waters

   This article has been curated by 1 group:

   • Curated by eLife

     eLife Assessment

     This valuable study describes MerQuaCo, a computational and automatic quality control tool for spatial transcriptomics datasets. The authors have collected a remarkable number of tissues to construct the main algorithm. The exceptional strength of the evidence is demonstrated through a combination of empirical observations, automated computational approaches, and validation against existing software packages. MerQuaCo will interest researchers who routinely perform spatial transcriptomic imaging (especially MERSCOPE), as it provides an imperfection detector and quality control measures for reliable and reproducible downstream analysis.

   Reviewed by eLife

7. Thrifty wide-context models of B cell receptor somatic hypermutation

   This article has 7 authors:

   1. Kevin Sung
   2. Mackenzie M Johnson
   3. Will Dumm
   4. Noah Simon
   5. Hugh Haddox
   6. Julia Fukuyama
   7. Frederick A Matsen

   This article has been curated by 1 group:

   • Curated by eLife

     eLife Assessment

     This study provides an important method to model the statistical biases of hypermutations during the affinity maturation of antibodies. The authors show convincingly that their model outperforms previous methods with fewer parameters; this is made possible by the use of machine learning to expand the context dependence of the mutation bias. They also show that models learned from nonsynonymous mutations and from out-of-frame sequences are different, prompting new questions about germinal center function. Strengths of the study include an open-access tool for using the model, a careful curation of existing datasets, and a rigorous benchmark; it is also shown that current machine-learning methods are currently limited by the availability of data, which explains the only modest gain in model performance afforded by modern machine learning.

   Reviewed by eLife

8. Ezh2 Delays Activation of Differentiation Genes During Normal Cerebellar Granule Neuron Development and in Medulloblastoma

   This article has 13 authors:

   1. James Purzner
   2. Alexander S Brown
   3. Teresa Purzner
   4. Lauren Ellis
   5. Sara Broski
   6. Ulrike Litzenburger
   7. Kaytlin Andrews
   8. Aryaman Sharma
   9. Xin Wang
   10. Michael D Taylor
   11. Yoon-Jae Cho
   12. Margaret T Fuller
   13. Matthew P Scott

   This article has been curated by 1 group:

   • Curated by eLife

     eLife Assessment

     Using an unbiased approach, this important study discovered a role of Ezh2 in the differentiation of granule neuron precursors, the cell of origin for Shh group of medulloblastoma. Furthermore, the authors also provided solid evidence that combined inhibition of Ezh2 and CDK4/6 likely represents a promising strategy for the treatment of this subgroup of MB. Validation of these findings using the FDA-approved Ezh2 inhibitor is needed to further strengthen this preclinical study.

   Reviewed by eLife

9. The title and authors for this article are not available from our external data provider yet:
   10.48550/arxiv.2409.19469v1

10. Late maturation of semantic control promotes conceptual development

    This article has 3 authors:

    1. Rebecca L Jackson
    2. Matthew A Lambon Ralph
    3. Timothy T Rogers

    This article has been curated by 1 group:

    • Curated by eLife

      eLife Assessment

      This study presents valuable findings suggesting that the late maturation of prefrontal cortex-based control processes enhances conceptual learning by allowing a period of less-constrained knowledge acquisition. The authors provide convincing computational evidence that delayed semantic control promotes learning without compromising representation integrity, with the strongest benefits emerging when control connections target intermediate layers of the model. However, the model's narrow scope raises concerns about scalability to more complex, real-world learning environments, and the meta-analysis, while supporting the developmental trajectory, does not directly test the model's specific predictions regarding task outcomes or error patterns.

    Reviewed by eLife