Genomics

Recurrent loss of crossover interference punctuates the recombination landscape across yeast species

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

Multicellular, IVT-derived, unmodified human transcriptome for nanopore-direct RNA analysis

1. Caroline A. McCormick
2. Stuart Akeson
3. Sepideh Tavakoli
4. Dylan Bloch
5. Isabel N. Klink
6. Miten Jain
7. Sara H. Rouhanifard

• 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

Enhancer-driven cell type comparison reveals similarities between the mammalian and bird pallium

1. Nikolai Hecker
2. Niklas Kempynck
3. David Mauduit
4. Darina Abaffyová
5. Roel Vandepoel
6. Sam Dieltiens
7. Lars Borm
8. Ioannis Sarropoulos
9. Carmen Bravo González-Blas
10. Julie De Man
11. Kristofer Davie
12. Elke Leysen
13. Jeroen Vandensteen
14. Rani Moors
15. Gert Hulselmans
16. Lynette Lim
17. Joris De Wit
18. Valerie Christiaens
19. Suresh Poovathingal
20. Stein Aerts

Reviewed by preLights

Exploring polymorphic interspecies structural variants in Eucalyptus: Unravelling Their Role in Reproductive Isolation and Adaptive Divergence

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

Genomic decoding of Theobroma grandiflorum (cupuassu) at chromosomal scale: Evolutionary insights for horticultural innovation

1. Rafael Moysés Alves
2. Vinicius A. C. de Abreu
3. Rafaely Pantoja Oliveira
4. João Victor dos Anjos Almeida
5. Mauro de Medeiros de Oliveira
6. Saura R. Silva
7. Alexandre R. Paschoal
8. Sintia S. de Almeida
9. Pedro A. F. de Souza
10. Jesus A. Ferro
11. Vitor F. O. Miranda
12. Antonio Figueira
13. Douglas S. Domingues
14. Alessandro M. Varani

Reviewed by GigaScience

Chromatin accessibility variation provides insights into missing regulation underlying immune-mediated diseases

1. Raehoon Jeong
2. Martha L Bulyk

• Curated by eLife

  eLife assessment

  This paper addresses a question regarding the low overlap between genetic variants linked to human complex diseases and variants linked to differences in gene expression. Some of the analyses supporting the main claims are convincing, and the key conclusions are valuable and of interest to readers in the fields of human genetics and functional genomics. However, chromatin accessibility QTL (caQTL) also carry the limitation of not identifying the genes that directly mediate the influence on disease phenotypes.

Reviewed by eLife

The whole blood microbiome of Indonesians reveals translocated and pathogenic microbiota

1. Katalina Bobowik
2. Muhamad Fachrul
3. Chelzie Crenna Darusallam
4. Pradiptajati Kusuma
5. Herawati Sudoyo
6. Clarissa A. Febinia
7. Safarina G. Malik
8. Christine Wells
9. Irene Gallego Romero

Reviewed by Review Commons

Comparative analysis of multiplexed in situ gene expression profiling technologies

1. Austin Hartman
2. Rahul Satija

• Curated by eLife

  eLife assessment

  Hartman et al.'s important research examines six commonly utilized imaging-based multiplexed transcriptomic techniques and introduces a novel specificity metric, "MECR," to streamline platform evaluations. The authors highlight the crucial influence of cell segmentation methodologies on outcomes, offering insight into the field. Nonetheless, the substantiation for the principal assertions remains incomplete, as the comparisons across platforms seem uneven due to variations in gene panels.

Reviewed by eLife

Frequent lack of repressive capacity of promoter DNA methylation identified through genome-wide epigenomic manipulation

1. Ethan Ford
2. Matthew R. Grimmer
3. Sabine Stolzenburg
4. Ozren Bogdanovic
5. Alex de Mendoza
6. Peggy J. Farnham
7. Pilar Blancafort
8. Ryan Lister

Reviewed by PREreview

Unraveling the genetic legacy of commercial whaling in bowhead whales and narwhals

1. Evelien de Greef
2. Claudio Müller
3. Matt J. Thorstensen
4. Steven H. Ferguson
5. Cortney A. Watt
6. Marianne Marcoux
7. Stephen D. Petersen
8. Colin J. Garroway

Reviewed by PREreview