Genomics

Stranded short nascent strand sequencing reveals the topology of DNA replication origins in Trypanosoma brucei

1. Slavica Stanojcic
2. Bridlin Barckmann
3. Pieter Monsieurs
4. Lucien Crobu
5. Simon George
6. Yvon Sterkers

• Curated by eLife

  eLife Assessment

  The authors use sequencing of nascent DNA (DNA linked to an RNA primer, “SNS-Seq”) to localise DNA replication origins in Trypanosoma brucei, so this work will be of interest to those studying either Kinetoplastids or DNA replication. The paper presents the SNS-seq results for only part of the genome, and there are significant discrepancies between the SNS-Seq results and those from other, previously-published results obtained using other origin mapping methods. The reasons for the differences are unknown and from the data available, it is not possible to assess which origin-mapping method is most suitable for origin mapping in T. brucei. Thus at present, the evidence that origins are distributed as the authors claim - and not where previously mapped - is inadequate.

Reviewed by eLife

Expression-Driven Genetic Dependency Reveals Targets for Precision Medicine

1. Abdulkadir Elmas
2. Hillary M. Layden
3. Jacob D. Ellis
4. Luke N. Bartlett
5. Xian Zhao
6. Reika Kawabata-Iwakawa
7. Hideru Obinata
8. Scott W. Hiebert
9. Kuan-lin Huang

Reviewed by GigaScience

CellCover Defines Marker Gene Panels Capturing Developmental Progression in Neocortical Neural Stem Cell Identity

1. Lanlan Ji
2. An Wang
3. Shreyash Sonthalia
4. Seungmae Seo
5. Daniel Q Naiman
6. Laurent Younes
7. Carlo Colantuoni
8. Donald Geman

• Curated by eLife

  eLife Assessment

  This study offers a valuable methodological advance by introducing a gene panel selection approach that captures combinatorial specificity to define cell identity. The findings address key limitations of current single-gene marker methods. The evidence is compelling, but would be strengthened by further validation of rare cell states and unexpected marker categories.

Reviewed by eLife

Single-cell transcriptomics of X-ray irradiated Drosophila wing discs reveals heterogeneity related to cell-cycle status and cell location

1. Joyner Cruz
2. William Y Sun
3. Alexandra Verbeke
4. Iswar K Hariharan

• Curated by eLife

  eLife Assessment

  This important study uses standard single-cell RNA-seq analyses combined with methods from the social sciences to reduce heterogeneity in gene expression in Drosophila imaginal wing disc cells treated with 4000 rads of ionizing radiation. The use of this methodology from social sciences is novel in Drosophila and allows them to identify a subpopulation of cells that is disproportionately responsible for much of the radiation-induced gene expression. Their compelling analyses reveal genes that are expressed regionally after irradiation, including ligands and transcription factors that have been associated with regeneration, as well as others whose roles in response to irradiation are unknown. This paper would be of interest to researchers in the field of DNA damage responses, regeneration, and development.

Reviewed by eLife

Haplotype-resolved chromosome-level genome assemblies of four Diamesa species reveal the genetic basis of cold tolerance and high-altitude adaptations in arctic chironomids

1. Sarah L.F. Martin
2. Renato La Torre
3. Bram Danneels
4. Ave Tooming-Klunderud
5. Morten Skage
6. Spyridon Kollias
7. Ole Kristian Tørresen
8. Mohsen Falahati Anbaran
9. Elisabeth Stur
10. Kjetill S. Jakobsen
11. Michael D. Martin
12. Torbjørn Ekrem

Reviewed by GigaScience

Raman2RNA: Live-cell label-free prediction of single-cell RNA expression profiles by Raman microscopy

1. Koseki J. Kobayashi-Kirschvink
2. Shreya Gaddam
3. Taylor James-Sorenson
4. Emanuelle Grody
5. Johain R. Ounadjela
6. Baoliang Ge
7. Ke Zhang
8. Jeon Woong Kang
9. Ramnik Xavier
10. Peter T. C. So
11. Tommaso Biancalani
12. Jian Shu
13. Aviv Regev

Reviewed by Arcadia Science

Integrating bulk and single cell RNA-seq refines transcriptomic profiles of individual C. elegans neurons

1. Alec Barrett
2. Erdem Varol
3. Alexis Weinreb
4. Seth R Taylor
5. Rebecca M McWhirter
6. Cyril Cros
7. Berta Vidal
8. Manasa Basaravaju
9. Abigail Poff
10. John A Tipps
11. Maryam Majeed
12. Chen Wang
13. Emily A Bayer
14. Molly Reilly
15. Eviatar Yemini
16. HaoSheng Sun
17. Oliver Hobert
18. David M Miller
19. Marc Hammarlund

• Curated by eLife

  eLife Assessment

  This paper uses a new computational method that integrates bulk sequencing and single-cell sequencing data to provide refined gene expression datasets for 52 neuron classes in C. elegans. The paper's findings are convincing, presenting an approach that alleviates a key shortcoming of single-cell RNA sequencing. While the datasets have some limitations that the authors acknowledge, the new methodology and refined datasets will be important resources for those interested in understanding how gene expression shapes neuronal morphology and physiology.

Reviewed by eLife

10,239 whole genomes with multiomic and clinical health information as the Korean Multiomics Reference dataset

1. Kyungwhan An
2. Sungwon Jeon
3. Yoonsung Kwon
4. Yookyung Choi
5. Changhan Yoon
6. Yeonsu Jeon
7. Jihun Bhak
8. Dong-Hyun Shin
9. Hyoung-Jin Choi
10. Hyomin Lee
11. Yeo Jin Kim
12. Eun-Seok Shin
13. Hyojung Ryu
14. Asta Blazyte
15. Sangsoo Park
16. Juok Cho
17. Dan Bolser
18. Soobok Joe
19. Jin Ok Yang
20. Jongbum Jeon
21. Jong-Hwan Kim
22. Jungeun Kim
23. Dooyoung Jung
24. Yun Sung Cho
25. Kiyuk Chang
26. Eun Ho Choo
27. Eunmin Kim
28. Sang Yeub Lee
29. Weon Kim
30. Min Gyu Kang
31. Ae-Young Her
32. Suk Chon
33. Jeong-Taek Woo
34. Sang Youl Rhee
35. Siwoo Lee
36. Hyo-Jeong Ban
37. Hee-Jeong Jin
38. Younghwa Baek
39. Yong Min Ahn
40. Sang Jin Rhee
41. Min Ji Kim
42. Sang Yeol Lee
43. Chan-Mo Yang
44. Se-Hoon Shim
45. Seong-Jin Cho
46. Shin Gyeom Kim
47. Hyung-Tae Jung
48. Byung-Joo Ham
49. Yoon Young Choi
50. Jae-Ho Cheong
51. Seung-Ki Kim
52. Ji Hoon Phi
53. Seung Ah Choi
54. Heon Yung Gee
55. Sun Young Joo
56. Jinsei Jung
57. Wonsuk Shin
58. Sang-Hyuk Lee
59. Borah Kim
60. Woojae Myung
61. Chong Kun Cheon
62. Dong Uk Kim
63. Seok-Soo Byun
64. Gangnam Jin
65. Hojune Lee
66. Kyun Shik Chae
67. Chang Geun Kim
68. Bonghee Lee
69. Jaesuk Lee
70. Kwangwoo Kim
71. Semin Lee
72. Neung-Hwa Park
73. Haeyoung Jeong
74. George M. Church
75. Jong Bhak

Reviewed by Arcadia Science

Single-cell co-mapping reveals relationship between chromatin state and gene expression in early zebrafish development

1. Vivek Bhardwaj
2. Alberto Griffa
3. Helena Viñas Gaza
4. Peter Zeller
5. Alexander van Oudenaarden

Reviewed by Review Commons

Nanopore genome skimming with Illumina polishing yields highly accurate mitogenome sequences: a case study of Niphargus amphipods

1. Alice Salussolia
2. Ninon Lecoquierre
3. Fabio Stoch
4. Jean-François Flot

Reviewed by Peer Community In Zoology