Genomics

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

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

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

A high-coverage genome from a 200,000-year-old Denisovan

1. Stéphane Peyrégne
2. Diyendo Massilani
3. Yaniv Swiel
4. Michael James Boyle
5. Leonardo N. M. Iasi
6. Arev P. Sümer
7. Alba Bossoms Mesa
8. Cesare de Filippo
9. Bence Viola
10. Elena Essel
11. Sarah Nagel
12. Julia Richter
13. Antje Weihmann
14. Barbara Schellbach
15. Hugo Zeberg
16. Johann Visagie
17. Maxim B. Kozlikin
18. Michael V. Shunkov
19. Anatoly P. Derevianko
20. Kay Prüfer
21. Benjamin M. Peter
22. Matthias Meyer
23. Svante Pääbo
24. Janet Kelso

Reviewed by preLights

Beyond the transcript: chromatin implications in trans-splicing in Trypanosomatids

1. Romina Trinidad Zambrano Siri
2. Paula Beati
3. Lucas Inchausti
4. Pablo Smircich
5. Guillermo Daniel Alonso
6. Josefina Ocampo

Reviewed by Review Commons

Evolutionary remodeling of non-canonical ORF translation in mammals

1. Yue Chang
2. Tianyu Lei
3. Feng Zhou
4. Jiawen Jiang
5. Yu Huang
6. Ziyang Zhu
7. Hong Zhang

• Curated by eLife

  eLife Assessment

  This study presents a large, systematically curated catalog of non-canonical open reading frames (ncORFs) in human and mouse by reanalyzing nearly 400 Ribo-seq datasets using a standardized pipeline; the resulting atlas consolidates ncORF annotations across tissues and provides a valuable reference for understanding non-canonical translation and ORF emergence. The main conclusions are supported by consistent data processing and multiple computational measures of translation and conservation. While the pipeline is transparent and robust, several downstream analyses are descriptive, and some evolutionary interpretations remain correlative; dataset heterogeneity, uneven tissue representation, and limited experimental validation also constrain the strength of a subset of the findings. Overall, the evidence is solid, and the resource will be broadly used by the community.

Reviewed by eLife

RNA-SeqEZPZ: A Point-and-Click Pipeline for Comprehensive Transcriptomics Analysis with Interactive Visualizations

1. Cenny Taslim
2. Yuan Zhang
3. Genevieve C. Kendall
4. Emily R. Theisen

Reviewed by GigaScience

Neisseria gonorrhoeae LIN codes: a Robust, Multi-Resolution Lineage Nomenclature

1. Anastasia Unitt
2. Made Krisna
3. Kasia M Parfitt
4. Keith A Jolley
5. Martin CJ Maiden
6. Odile B Harrison

• Curated by eLife

  eLife Assessment

  This important study introduces the Life Identification Number (LIN) coding system as a powerful and versatile approach for classifying Neisseria gonorrhoeae lineages. The authors show that LIN codes capture both previously defined lineages and their relationships in a way that aligns with the species' phylogenetic structure. The compelling evidence presented, together with its integration into the PubMLST platform, underscores its strong potential to enhance epidemiological surveillance and advance our understanding of gonococcal population biology.

Reviewed by eLife