Searching journal content for articles similar to Ulrich et al. 2 (3): 241.

Displaying results 1-10 of 6127

For checked items

view abstracts
download to citation manager

Select this article
Method: Analysis of coding gene expression from small RNA sequencing
- Aygun Azadova,
- Anthonia Ekperuoh,
- Greg N. Brooke,
- and Antonio Marco
Genome Res. March 2026 36: 611-618; Published in Advance February 10, 2026, doi:10.1101/gr.281364.125
....Although the computational prediction of miRNA targets has been relatively successful in the past (see Introduction), experimental techniques have improved our ability to detect/confirm bona fide targets. These techniques are diverse and include variations of immunoprecipitation and expression analysis (for review, see...
Select this article
Research: Enhanced detection of RNA modifications and read mapping with high-accuracy nanopore RNA basecalling models
- Gregor Diensthuber,
- Leszek P. Pryszcz,
- Laia Llovera,
- Morghan C. Lucas,
- Anna Delgado-Tejedor,
- Sonia Cruciani,
- Jean-Yves Roignant,
- Oguzhan Begik,
- and Eva Maria Novoa
Genome Res. November 2024 34: 1865-1877; Published in Advance September 13, 2024, doi:10.1101/gr.278849.123
...at high stoichiometries. Here, we demonstrate that the use of alternative RNA basecalling models, trained with fully unmodified sequences, increases the “error” signal of m6A, leading to enhanced detection and improved sensitivity even at low stoichiometries. Moreover, we find that high...
Select this article
Research: Nanopore direct RNA sequencing reveals METTL2A-mediated m³C sites in poly(A) RNA
- Shuhei Mitsutomi,
- Anzu Sugawara,
- Masahide Seki,
- Yutaka Suzuki,
- Sotaro Miyao,
- Haozhe Du,
- Kenji Takahashi,
- Yusuke Mizukami,
- Kenzui Taniue,
- and Nobuyoshi Akimitsu
Genome Res. November 2025 35: 2406-2417; Published in Advance October 30, 2025, doi:10.1101/gr.280269.124
...detected in polyadenylated (poly[A]) RNA by mass spectrometric analysis; however, its transcriptome-wide distribution and functions remain unknown because of its low abundance and technical challenges. Here, we show that METTL2A, an m3C writer, is upregulated and associated with poor prognosis...
Select this article
Method: Statistically rigorous and computationally efficient chromatin stripe detection with Quagga
- Fan Feng,
- Sean Moran,
- Anders S. Hansen,
- Xiaotian Zhang,
- and Jie Liu
Genome Res. January 2026 36: 159-168; Published in Advance November 12, 2025, doi:10.1101/gr.280132.124
...determination. Therefore, integrated analysis of stripes with genomic and epigenomic features at a -wide scale shows vast potential in understanding the cooperation between regulatory elements in 3D nucleome. To this end, we present Quagga, a computational tool for detection and statistical verification...
OPEN ACCESS ARTICLE
Select this article
Method: Efficient integration of spatial omics data for joint domain detection, matching, and alignment with stMSA
- Han Shu,
- Jing Chen,
- Chang Xu,
- Jialu Hu,
- Yongtian Wang,
- Jiajie Peng,
- Qinghua Jiang,
- Xuequn Shang,
- and Tao Wang
Genome Res. October 2025 35: 2285-2299; Published in Advance August 14, 2025, doi:10.1101/gr.280584.125
..., providing detailed views of the transcriptome in spatial perspective (Asp et al. 2020). Recently, cellular indexing of transcriptomes and epitopes by sequencing (spatial CITE-seq) (Liu et al. 2023) has emerged as a significant advancement in SOs. This technique integrates RNA sequencing with the measurement...
Select this article
Research: Dynamic A-to-I RNA editing in response to gut microbiome in honeybees
- Yuange Duan,
- Min Huang,
- Lin Ye,
- Ling Ma,
- Yashuai Wu,
- Yating Du,
- Jiyao Liu,
- Fan Song,
- Li Tian,
- Wanzhi Cai,
- Hu Li,
- Xin Zhou,
- and Shiqi Luo
Genome Res. March 4, 2026 ; Published in Advance March 4, 2026, doi:10.1101/gr.280291.124
...for a set of reliable editing sites (Supplemental Fig. S3). The validation of individual RNA editing sites (and the corresponding positions in DNA) was performed by Sanger sequencing in subsequent sections. In parallel, we also utilized a DNA-free method to identify hyperediting sites in the transcriptome...
Select this article
Research: Transcriptome-wide systematic search does not detect A-to-I RNA editing in cis-antisense RNA duplexes
- Zohar Rosenwasser,
- Roni Cohen-Fultheim,
- Ofir Shliefer,
- Erez Y. Levanon,
- and Eli Eisenberg
Genome Res. March 12, 2026 gr.280820.125; Published in Advance March 12, 2026, doi:10.1101/gr.280820.125
...in the intricate balance of the immune system. Many viruses are made of dsRNA, or produce dsRNA. Sensing of viral dsRNA by pattern recognition receptors, such as melanoma differentiationassociated protein 5 (MDA5), triggers the innate immune response through the mitochondrial antiviral signaling protein (MAVS...
- Abstract
- Full Text (PDF)
OPEN ACCESS ARTICLEACCEPTED MANUSCRIPT
Select this article
Method: Accurate detection of tandem repeats from error-prone sequences with EquiRep
- Zhezheng Song,
- Tasfia Zahin,
- Xiang Li,
- and Mingfu Shao
Genome Res. December 2025 35: 2714-2721; Published in Advance August 21, 2025, doi:10.1101/gr.280750.125
...several kilobases in certain contexts. RCA followed by Pacific Biosciences (PacBio) or Oxford Nanopore Technologies (ONT) sequencing is a popular protocol adopted in many recent studies, especially for detection of full-length circular RNAs (Liu et al. 2021; Xin et al. 2021; Zhang et al. 2021). A crucial...
OPEN ACCESS ARTICLE
Select this article
Method: De novo detection of somatic variants in high-quality long-read single-cell RNA sequencing data
- Arthur Dondi,
- Nico Borgsmüller,
- Pedro F. Ferreira,
- Brian J. Haas,
- Francis Jacob,
- Viola Heinzelmann-Schwarz,
- Tumor Profiler Consortium,
- and Niko Beerenwinkel
Genome Res. April 2025 35: 900-913; Published in Advance March 19, 2025, doi:10.1101/gr.279281.124
....beerenwinkel@bsse.ethz.chAbstractIn cancer, genetic and transcriptomic variations generate clonal heterogeneity, leading to treatment resistance. Long-read single-cell RNA sequencing (LR scRNA-seq) has the potential to detect genetic and transcriptomic variations simultaneously. Here, we present LongSom, a computational workflow leveraging...
OPEN ACCESS ARTICLE
Select this article
Method: Tree-based differential testing using inferential uncertainty for RNA-seq
- Noor Pratap Singh,
- Euphy Y. Wu,
- Jason Fan,
- Michael I. Love,
- and Rob Patro
Genome Res. October 2025 35: 2326-2338; Published in Advance August 21, 2025, doi:10.1101/gr.279981.124
...-aware differential transcript/gene expression methods. Our method detects inner nodes that show a strong signal for differential expression, which would have been overlooked when analyzing the transcripts alone.RNA-seq has become the de facto technology for measuring the expression profiles of different genomic...
OPEN ACCESS ARTICLE

For checked items

view abstracts
download to citation manager

Searching journal content for articles similar to Ulrich et al. 2 (3): 241.

Search Results

Modify Results

This search

Preprint Server

Current Issue

In This Issue

Citation format:
Results / page:
Results order: