Searching journal content for articles similar to Li et al. 18 (1): 113.

Displaying results 1-10 of 6309

For checked items

view abstracts
download to citation manager

Select this article
Research: Long-read genome assembly of the insect model organism Tribolium castaneum reveals spread of satellite DNA in gene-rich regions by recurrent burst events
- Marin Volarić,
- Evelin Despot-Slade,
- Damira Veseljak,
- Brankica Mravinac,
- and Nevenka Meštrović
Genome Res. November 2024 34: 1878-1894; Published in Advance October 22, 2024, doi:10.1101/gr.279225.124
...with a reference-guided assembly approach to generate an improved, high-quality assembly, TcasONT, of the model beetle Tribolium castaneum. Enriched by 45 Mb in repetitive regions, the new assembly comprises almost the entire sequence. We use the enhanced assembly to conduct global and in-depth analyses...
OPEN ACCESS ARTICLE
Select this article
Research: Dynamic evolution of satellite DNAs drastically differentiates the genomes of Tribolium sibling species
- Damira Veseljak,
- Evelin Despot-Slade,
- Marin Volarić,
- Lucija Horvat,
- Tanja Vojvoda Zeljko,
- Nevenka Meštrović,
- and Brankica Mravinac
Genome Res. November 2025 35: 2445-2460; Published in Advance September 16, 2025, doi:10.1101/gr.280516.125
...DNAs are particularly useful.The flour beetle Tribolium freemani belongs to the genus that includes some of the most important pests of stored agricultural products (Sokoloff 1972). The economically important Tribolium species are also an excellent platform for the study of satellite DNAs, which occupy up to 60...
Select this article
Research: Developmental transcriptomics in Pristionchus reveals the environmental responsiveness of a plasticity gene-regulatory network
- Shelley Reich,
- Tobias Loschko,
- Julie Jung,
- Samantha Nestel,
- Ralf J. Sommer,
- and Michael S. Werner
Genome Res. July 2025 35: 1560-1573; Published in Advance June 9, 2025, doi:10.1101/gr.279783.124
...expectations for when differential gene expression should matter. Here, we collated existing data into a gene-regulatory network (GRN) and performed developmental transcriptomics across different environmental conditions, genetic backgrounds, and mutants to assess the regulatory logic of mouth-form plasticity...
OPEN ACCESS ARTICLE
Select this article
Editorial: Revolutionizing genomics and medicine—one long molecule at a time
- Ana Conesa,
- Alexander Hoischen,
- and Fritz J. Sedlazeck
Genome Res. November 2024 34: ix-xi; doi:10.1101/gr.280179.124
....279351.124 ↵Volarić M, Despot-Slade E, Veseljak D, Mravinac B, Meštrović N. 2024. Long-read assembly of the insect model organism Tribolium castaneum reveals spread of satellite DNA in gene-rich regions by recurrent burst events. Genome Res (this issue) 34: 1878–1894. doi:10.1101/gr.279225.124 ↵Zeglinski...
Select this article
Method: Integration of transcriptomics and long-read genomics prioritizes structural variants in rare disease
- Tanner D. Jensen,
- Bohan Ni,
- Chloe M. Reuter,
- John E. Gorzynski,
- Sarah Fazal,
- Devon Bonner,
- Rachel A. Ungar,
- Pagé C. Goddard,
- Archana Raja,
- Euan A. Ashley,
- Jonathan A. Bernstein,
- Stephan Zuchner,
- Undiagnosed Diseases Network,
- Michael D. Greicius,
- Stephen B. Montgomery,
- Michael C. Schatz,
- Matthew T. Wheeler,
- and Alexis Battle
Genome Res. April 2025 35: 914-928; Published in Advance March 20, 2025, doi:10.1101/gr.279323.124
...enrichments were observed for single-tissue outliers but not multitissue outliers (Supplemental Fig. S5E).Watershed-SV integrates genomic annotations and transcriptomic signals to prioritize rare functional SVsThe co-occurrence of expression outliers with rare SVs provides the opportunity to jointly use...
OPEN ACCESS ARTICLE
Select this article
Research: MicroRNA evolution, expression, and function during short germband development in Tribolium castaneum
- Maria Ninova,
- Matthew Ronshaugen,
- and Sam Griffiths-Jones
Genome Res. January 2016 26: 85-96; Published in Advance October 30, 2015, doi:10.1101/gr.193367.115
...gastrulation by growth and cell division, and patterning occurs in a cellularized environment via an oscillatory mechanism (Sarrazin et al. 2012). Inmany respects, short germband embryogenesis therefore more closely resembles the segmentation of vertebrate embryos. The red flour beetleTribolium castaneum...
OPEN ACCESS ARTICLE
Select this article
Method: Unified integration of spatial transcriptomics across platforms with LLOKI
- Ellie Haber,
- Ajinkya Deshpande,
- Jian Ma,
- and Spencer Krieger
Genome Res. December 2025 35: 2722-2733; Published in Advance November 13, 2025, doi:10.1101/gr.280803.125
..., Pittsburgh, Pennsylvania 15213, USA Corresponding authors: jianma@cs.cmu.edu, skrieger@andrew.cmu.eduAbstractSpatial transcriptomics (ST) has transformed our understanding of tissue architecture and cellular interactions, but integrating ST data across platforms remains challenging due to differences in gene...
OPEN ACCESS ARTICLE
Select this article
Method: Iterative improvement of deep learning models using synthetic regulatory genomics
- André M. Ribeiro-dos-Santos and
- Matthew T. Maurano
Genome Res. November 2025 35: 2539-2549; Published in Advance October 22, 2025, doi:10.1101/gr.280540.125
...the reference, such as disease- and trait-associated variants or engineered sequences. Recent work has applied synthetic regulatory genomics to characterized dozens of deletions, inversions, and rearrangements of DNase I hypersensitive sites (DHSs). Here, we use the state-of-the-art model Enformer to predict...
Select this article
Method: spRefine denoises and imputes spatial transcriptomics with a reference-free framework powered by genomic language model
- Tianyu Liu,
- Tinglin Huang,
- Wengong Jin,
- Tinyi Chu,
- Rex Ying,
- and Hongyu Zhao
Genome Res. February 3, 2026 gr.281001.125; Published in Advance February 3, 2026, doi:10.1101/gr.281001.125
...spRefine denoises and imputes spatial1 transcriptomics with a reference-free framework2 powered by genomic language model3 Tianyu Liu1,2, Tinglin Huang3, Wengong Jin4,5, Tinyi Chu2, Rex4 Ying3, Hongyu Zhao1,2*5 1Interdepartmental Program in Computational Biology &6 Bioinformatics, Yale University...
- Abstract
- Full Text (PDF)
OPEN ACCESS ARTICLEACCEPTED MANUSCRIPT
Select this article
Research: Functional genomics analysis of developing zebrafish and human endoderm reveals highly conserved cis-regulatory modules acting during vertebrate organogenesis
- Daniela M Riley,
- Randa Elsayed,
- Mark D Walsh,
- Simaran Johal,
- Ying Lin,
- Harry Walton,
- Till Bretschneider,
- Sascha Ott,
- and Andrew C Nelson
Genome Res. March 4, 2026 gr.280838.125; Published in Advance March 4, 2026, doi:10.1101/gr.280838.125
...1 Functional genomics analysis of developing zebrafish and human endoderm reveals 1 highly conserved cis-regulatory modules acting during vertebrate organogenesis 2 3 Daniela M. Riley1,†, Randa Elsayed1,†, Mark D. Walsh2,†, Simaran Johal2, Ying Lin3,4, Harry 4 Walton1, Till Bretschneider5, Sascha...
- Abstract
- Full Text (PDF)
ACCEPTED MANUSCRIPT

For checked items

view abstracts
download to citation manager

Searching journal content for articles similar to Li et al. 18 (1): 113.

Search Results

Modify Results

This search

Preprint Server

Current Issue

In This Issue

Citation format:
Results / page:
Results order: