Genomics

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 multi-omic and clinical health information as the Korean population multi-omic reference dataset

1. Kyungwhan An
2. Sungwon Jeon
3. Yoonsung Kwon
4. Changhan Yoon
5. Yookyung Choi
6. Yeonsu Jeon
7. Hyoung-Jin Choi
8. Jihun Bhak
9. Dong-Hyun Shin
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. Jongbum Jeon
19. Soobok Joe
20. Jin Ok Yang
21. Jong-Hwan Kim
22. Byoung-Chul Kim
23. Jungeun Kim
24. Neung-Hwa Park
25. Siwoo Lee
26. Hee-jeong Jin
27. Younghwa Baek
28. Dooyoung Jung
29. Yunsung Cho
30. Yong Min Ahn
31. Hyung-Tae Jung
32. Byungjoo Ham
33. Yoon Young Choi
34. Seung Ah Choi
35. Seung-Ki Kim
36. Ji Hoon Phi
37. Heon Yung Gee
38. Borah Kim
39. Woojae Myung
40. Chong Kun Cheon
41. Dong Uk Kim
42. Gang-Nam Jin
43. Hojune Lee
44. Kyun Shik Chae
45. Chang Geun Kim
46. BongHee Lee
47. Jaesuk Lee
48. Semin Lee
49. George Church
50. Haeyoung Jeong
51. 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

Breaking Through Biology's Data Wall: Expanding the Known Tree of Life by Over 10x using a Global Biodiscovery Pipeline

1. Oliver Vince
2. Phoebe Oldach
3. Valerio Pereno
4. Marcus H Y Leung
5. Carla Greco
6. Gus Minto-Cowcher
7. Saif Ur-Rehman
8. Keith Y K Kam
9. William Chow
10. Emma Bolton
11. Bupe R Mwambingu
12. Nadine L Greenhalgh
13. Ineke E Knot
14. Leif Christoffersen
15. Marlon Clark
16. Robert Pecoraro
17. Aaron W Kollasch
18. Tanggis Bohnuud
19. Matthew Bakalar
20. Philipp Lorenz
21. Glen Gowers

Reviewed by Arcadia Science

Mechanistic dissection of GRHL2 and PR transcriptional co-regulation in breast cells

1. M.T. Aarts
2. A. Nordin
3. C. Cantù
4. A.L. van Boxtel
5. R. van Amerongen

Reviewed by Review Commons

Multimodal single-cell analyses reveal distinct fusion-regulated transcriptional programs in Ewing sarcoma

1. Olivia G Waltner
2. April A Apfelbaum
3. Emma D Wrenn
4. Shruti S Bhise
5. Sami B Kanaan
6. Rula Green Gladden
7. Mark A Mendoza
8. Roger Volden
9. Zev Kronenberg
10. Anand Patel
11. Michael Dyer
12. Jay F Sarthy
13. Elizabeth R Lawlor
14. Scott N Furlan

• Curated by eLife

  eLife Assessment

  This valuable study presents an analysis of the gene regulatory networks that contribute to tumour heterogeneity and tumor plasticity in Ewing sarcoma, with key implications for other fusion-driven sarcomas. The authors convincingly employed orthogonal approaches, including single-cell sequencing and xenografts, to reveal the existence and plasticity of specific gene regulatory networks (e.g., TGF-beta signaling) within Ewing sarcoma, as well as significant differences that exist between cell lines and patient tumors.

Reviewed by eLife

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 attempt to use sequencing of nascent DNA (DNA linked to an RNA primer, "SNS-Seq") to localise DNA replication origins in Trypanosoma brucei, but they analyse the results for only part of the genome. There are also significant discrepancies between their results and those from other origin mapping methods which have not been addressed, meaning that SNS-seq has not been validated for origin mapping in T. brucei. For this reason, the evidence that origins are distributed as the authors claim - and not where previously mapped - is inadequate. This work will be of interest to those studying DNA replication.

Reviewed by eLife