Genomics

The Open Pediatric Cancer Project

1. Zhuangzhuang Geng
2. Eric Wafula
3. Ryan J Corbett
4. Yuanchao Zhang
5. Run Jin
6. Krutika S Gaonkar
7. Sangeeta Shukla
8. Komal S Rathi
9. Dave Hill
10. Aditya Lahiri
11. Daniel P Miller
12. Alex Sickler
13. Kelsey Keith
14. Christopher Blackden
15. Antonia Chroni
16. Miguel A Brown
17. Adam A Kraya
18. Kaylyn L Clark
19. Brian R Rood
20. Adam C Resnick
21. Nicholas Van Kuren
22. John M Maris
23. Alvin Farrel
24. Mateusz P Koptyra
25. Gerri R Trooskin
26. Noel Coleman
27. Yuankun Zhu
28. Stephanie Stefankiewicz
29. Zied Abdullaev
30. Asif T Chinwalla
31. Mariarita Santi
32. Ammar S Naqvi
33. Jennifer L Mason
34. Carl J Koschmann
35. Xiaoyan Huang
36. Sharon J Diskin
37. Kenneth Aldape
38. Bailey K Farrow
39. Weiping Ma
40. Bo Zhang
41. Brian M Ennis
42. Sarah Tasian
43. Saksham Phul
44. Matthew R Lueder
45. Chuwei Zhong
46. Joseph M Dybas
47. Pei Wang
48. Deanne Taylor
49. Jo Lynne Rokita

Reviewed by GigaScience

A comprehensive water buffalo pangenome reveals extensive structural variation linked to population specific signatures of selection

1. Fazeela Arshad
2. Siddharth Jayaraman
3. Andrea Talenti
4. Rachel Owen
5. Muhammad Mohsin
6. Shahid Mansoor
7. Muhammad Asif
8. James Prendergast

Reviewed by GigaScience

OpenSpliceAI provides an efficient modular implementation of SpliceAI enabling easy retraining across nonhuman species

1. Kuan-Hao Chao
2. Alan Mao
3. Anqi Liu
4. Steven L Salzberg
5. Mihaela Pertea

• Curated by eLife

  eLife Assessment

  This valuable study introduces a modern and accessible PyTorch reimplementation of the widely used SpliceAI model for splice site prediction. The authors provide convincing evidence that their OpenSpliceAI implementation matches the performance of the original while improving usability and enabling flexible retraining across species. These advances are likely to be of broad interest to the computational genomics community.

Reviewed by eLife

Cell type-specific network analysis in Diversity Outbred mice identifies genes potentially responsible for human bone mineral density GWAS associations

1. Luke J Dillard
2. Gina Calabrese
3. Larry Mesner
4. Charles Farber

• Curated by eLife

  eLife Assessment

  This is an important study that provides compelling data from a diverse set of approaches from single cell transcriptome data and network analysis from genetically diverse mouse cells to identify novel driver genes underlying human GWAS associations. The authors present evidence that network analysis of scRNA-seq data from genetically diverse mouse bone-marrow derived stromal cells can be informative for identifying human BMD GWAS driver genes. Their approach should be broadly used and applicable to other GWAS studies.

Reviewed by eLife

The RNA-binding protein HuR modulates the expression of the disease-linked CCL2 rs1024611G-rs13900T haplotype

1. Feroz Akhtar
2. Joselin Hernandez Ruiz
3. Ya-Guang Liu
4. Roy G Resendez
5. Denis Feliers
6. Liza D Morales
7. Alvaro Diaz-Badillo
8. Donna M Lehman
9. Rector Arya
10. Juan Carlos Lopez Alvarenga
11. John Blangero
12. Ravindranath Duggirala
13. Srinivas Mummidi

• Curated by eLife

  eLife Assessment

  CCL2 is a chemokine with immune cell chemoattractant properties, and it appears to play a role in several chronic inflammatory diseases. The RNA-binding protein HuR controls the stability and translation of CCL2 mRNA. This paper presents convincing evidence that a relatively common genetic variant tied to several disease phenotypes affects the interaction between the mRNA of CCL2 and the RNA-binding protein HuR. While the experiments cannot definitively distinguish between effects on RNA transcription and stability, CCL2 is thought to be relevant for leukocyte migration in various conditions, including chronic inflammation and cancer, and the study presents important findings that may be relevant to a broad audience.

Reviewed by eLife

Telomere-to-telomere African wild rice ( Oryza longistaminata ) reference genome reveals segmental and structural variation

1. Xuanmin Guang
2. Jingnan Yang
3. Shilai Zhang
4. Fei Guo
5. Linzhou Li
6. Xiaoping Lian
7. Tao Zeng
8. Chongyang Cai
9. Fushu Liu
10. Zhihao Li
11. Yangzi Hu
12. Dongming Fang
13. Weiming He
14. Sunil Kumar Sahu
15. Wangsheng Li
16. Haorong Lu
17. Yuxiang Li
18. Huan Liu
19. Xun Xu
20. Ying Gu
21. Fengyi Hu
22. Yuliang Dong
23. Tong Wei

Reviewed by GigaScience

A telomere to telomere phased genome assembly and annotation for the Australian central bearded dragon Pogona vitticeps

1. Hardip R. Patel
2. Kirat Alreja
3. Andre L.M. Reis
4. J King Chang
5. Zahra A. Chew
6. Hyungtaek Jung
7. Jillian M. Hammond
8. Ira W. Deveson
9. Aurora Ruiz-Herrera
10. Laia Marin-Gual
11. Clare E. Holleley
12. Xiuwen Zhang
13. Nicholas C. Lister
14. Sarah Whiteley
15. Lei Xiong
16. Duminda S.B. Dissanayake
17. Paul D. Waters
18. Arthur Georges

Reviewed by GigaScience

Human cytomegalovirus infection coopts chromatin organization to diminish TEAD1 transcription factor activity

1. Khund Sayeed
2. Sreeja Parameswaran
3. Matthew J Beucler
4. Lee E Edsall
5. Andrew VonHandorf
6. Audrey Crowther
7. Omer A Donmez
8. Matthew R Hass
9. Scott Richards
10. Carmy R Forney
11. Hayley K Hesse
12. Sydney H Jones
13. Katelyn A Dunn
14. Jay Wright
15. Merrin Man Long Leong
16. Laura A Murray-Nerger
17. Vijay Yechoor
18. Ben E Gewurz
19. Kenneth M Kaufman
20. John B Harley
21. Bo Zhao
22. William E Miller
23. Leah C Kottyan
24. Matthew T Weirauch

• Curated by eLife

  eLife Assessment

  This interesting study presents important information on how human cytomegalovirus (HCMV) infection disrupts the activity of the TEAD1 transcription factor, leading to widespread chromatin alterations. The strength of evidence in revised manuscript is convincing, and includes additional functional data teasing out how TEAD1-driven chromatin changes might influence HCMV replication. This work will be of interest to the virology, chromosome biology and transcriptional co-regulation fields.

Reviewed by eLife

A near-complete genome assembly of the bearded dragon Pogona vitticeps provides insights into the origin of Pogona sex chromosomes

1. Qunfei Guo
2. Youliang Pan
3. Wei Dai
4. Fei Guo
5. Tao Zeng
6. Wanyi Chen
7. Yaping Mi
8. Yanshu Zhang
9. Shuaizhen Shi
10. Wei Jiang
11. Huimin Cai
12. Beiying Wu
13. Yang Zhou
14. Ying Wang
15. Chentao Yang
16. Xiao Shi
17. Xu Yan
18. Junyi Chen
19. Chongyang Cai
20. Jingnan Yang
21. Xun Xu
22. Ying Gu
23. Yuliang Dong
24. Qiye Li

Reviewed by GigaScience

DNA methylation insulates genic regions from CTCF loops near nuclear speckles

1. Shelby A Roseman
2. Allison P Siegenfeld
3. Ceejay Lee
4. Nicholas Z Lue
5. Amanda L Waterbury
6. Brian B Liau

• Curated by eLife

  eLife Assessment

  This valuable study tested the impact of DNA methylation on CTCF binding in two cancer cell lines. Increased CTCF binding sites are enriched in gene bodies, and associate with nuclear speckles, indicating a role in increased transcription. In the revised work, the inferred association with nuclear speckles has been supported with more solid data. These results will be of interest to the epigenetics field.

Reviewed by eLife