Searching journal content for articles similar to Karttunen et al. 6 (5): 392.

Displaying results 1-10 of 6158

For checked items

view abstracts
download to citation manager

Select this article
Research: Confounding factors in assessing the enriched expression of somatic mutant alleles in bulk tumor samples
- Kohei Hagiwara,
- Andrew Thrasher,
- Nadezhda V. Terekhanova,
- and Jinghui Zhang
Genome Res. March 4, 2026 ; Published in Advance March 4, 2026, doi:10.1101/gr.281003.125
...of attenuating (including silencing) or enhancing (including activation) the transcription of one specific allele (Ge et al. 2009). A conventional approach to characterize ASE is to test if the variant allele fraction (VAF) in RNA (VAFRNA) is significantly deviated from its expected VAF in DNA (VAFDNA...
OPEN ACCESS ARTICLE
Select this article
Method: Highly accurate assembly polishing with DeepPolisher
- Mira Mastoras,
- Mobin Asri,
- Lucas Brambrink,
- Prajna Hebbar,
- Alexey Kolesnikov,
- Daniel E. Cook,
- Maria Nattestad,
- Julian Lucas,
- Taylor S. Won,
- Pi-Chuan Chang,
- Andrew Carroll,
- Benedict Paten,
- Kishwar Shafin,
- and and the Human Pangenome Reference Consortium
Genome Res. July 2025 35: 1595-1608; Published in Advance May 19, 2025, doi:10.1101/gr.280149.124
...The first affiliated hospital of Xi'an Jiaotong University, Xi'an Jiaotong University, Xi'an, Shaanxi, 710049, China; Corresponding authors: awcarroll@google.com, bpaten@ucsc.edu, shafin@google.comAbstractAccurate assemblies are essential for biological research, but even the highest...
Select this article
Method: Accurate fusion transcript identification from long- and short-read isoform sequencing at bulk or single-cell resolution
- Qian Qin,
- Victoria Popic,
- Kirsty Wienand,
- Houlin Yu,
- Emily White,
- Akanksha Khorgade,
- Asa Shin,
- Christophe Georgescu,
- Catarina D. Campbell,
- Arthur Dondi,
- Niko Beerenwinkel,
- Francisca Vazquez,
- Aziz M. Al'Khafaji,
- and Brian J. Haas
Genome Res. April 2025 35: 967-986; Published in Advance March 14, 2025, doi:10.1101/gr.279200.124
...in diverse adult and pediatric cancers. Accurate detection of fusion transcripts is essential in cancer clinical diagnostics and prognostics and for guiding therapeutic development. Most currently available methods for fusion transcript detection are compatible with Illumina RNA-seq involving highly accurate...
OPEN ACCESS ARTICLE
Select this article
Method: Mapping and quantifying nascent transcript start sites using TT-TSS-seq
- Eleanor Elgood Hunt,
- Claudia Vivori,
- Richard Mitter,
- Vedis Agnadottir,
- and Folkert J. van Werven
Genome Res. March 2026 36: 600-610; Published in Advance February 17, 2026, doi:10.1101/gr.280726.125
...involving the coordinated action of transcription factors, chromatin remodelers, and RNA polymerase, which determine where and when transcription begins. Accurately mapping and quantifying transcription start sites (TSSs) from nascently transcribed RNAs remains a key area of interest, as it provides...
OPEN ACCESS ARTICLE
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
...be formulated as searching for a cycle in the graph with maximized bottleneck weight. We then evaluate the accuracy of EquiRep compared with leading methods across a variety of data sets over the two aforementioned applications, reconstructing repeat units from satellite DNA and circular RNAs from RCA data...
OPEN ACCESS ARTICLE
Select this article
Research: Chimeric mitochondrial RNA transcripts predict mitochondrial genome deletion mutations in mitochondrial genetic diseases and aging
- Amy R. Vandiver,
- Allen Herbst,
- Paul Stothard,
- and Jonathan Wanagat
Genome Res. January 2025 35: 55-65; Published in Advance November 27, 2024, doi:10.1101/gr.279072.124
...be found through application of established chimeric RNA detection software, we first analyzed RNA-seq of two human fibroblast lines previously documented to contain low levels of a single clonal genomic deletion (Majora et al. 2009) and a control neonatal dermal fibroblast cell line. Chimeric mt...
Select this article
Research: Deciphering the largest disease-associated transcript isoforms in the human neural retina with advanced long-read sequencing approaches
- Merel Stemerdink,
- Tabea Riepe,
- Nick Zomer,
- Renee Salz,
- Michael Kwint,
- Jaap Oostrik,
- Raoul Timmermans,
- Barbara Ferrari,
- Stefano Ferrari,
- Alfredo Dueñas Rey,
- Emma Delanote,
- Suzanne E. de Bruijn,
- Hannie Kremer,
- Susanne Roosing,
- Frauke Coppieters,
- Alexander Hoischen,
- Frans P.M. Cremers,
- Peter A.C. ‘t Hoen,
- Erwin van Wijk,
- and Erik de Vrieze
Genome Res. April 2025 35: 725-739; Published in Advance March 4, 2025, doi:10.1101/gr.280060.124
..., as it facilitates the development of therapeutic strategies and enables accurate classification of genetic variants linked to the disorder. To this end, we aimed to provide an overview of the Usher syndrome–associated transcript isoforms in the human neural retina, using the PacBio long-read mRNA Iso-Seq data set...
Select this article
Method: Highly accurate reference and method selection for universal cross–data set cell type annotation with CAMUS
- Qunlun Shen,
- Shuqin Zhang,
- and Shihua Zhang
Genome Res. November 2025 35: 2527-2538; Published in Advance October 1, 2025, doi:10.1101/gr.280821.125
...in accuracy, a 49.4% increase in macro F1 score, and a 57.3% increase in weighted F1 score compared with the random selection (Fig. 3C).View larger version: In this window In a new window Figure 3. Application of CAMUS for method selection in 672 pairs of cross-species cell type annotations. (A) Dot plot...
Select this article
Perspective: Challenges in identifying mRNA transcript starts and ends from long-read sequencing data
- Ezequiel Calvo-Roitberg,
- Rachel F. Daniels,
- and Athma A. Pai
Genome Res. November 2024 34: 1719-1734; doi:10.1101/gr.279559.124
...(Jia et al. 2020) among many other applications. However, SRS technologies are usually limited by their inability to sequence more than 100–300 contiguous nucleotides (nt). Although SRS offers robust and accurate solutions for detecting and characterizing local features within the sequenced fragment...
OPEN ACCESS ARTICLE
Select this article
Research: A prospective trial comparing programmable targeted long-read sequencing and short-read genome sequencing for genetic diagnosis of cerebellar ataxia
- Haloom Rafehi,
- Liam G. Fearnley,
- Justin Read,
- Penny Snell,
- Kayli C. Davies,
- Liam Scott,
- Greta Gillies,
- Genevieve C. Thompson,
- Tess A. Field,
- Aleena Eldo,
- Simon Bodek,
- Ernest Butler,
- Luke Chen,
- John Drago,
- Himanshu Goel,
- Anna Hackett,
- G. Michael Halmagyi,
- Andrew Hannaford,
- Katya Kotschet,
- Kishore R. Kumar,
- Smitha Kumble,
- Matthew Lee-Archer,
- Abhishek Malhotra,
- Mark Paine,
- Michael Poon,
- Kate Pope,
- Katrina Reardon,
- Steven Ring,
- Anne Ronan,
- Matthew Silsby,
- Renee Smyth,
- Chloe Stutterd,
- Mathew Wallis,
- John Waterston,
- Thomas Wellings,
- Kirsty West,
- Christine Wools,
- Kathy H.C. Wu,
- David J. Szmulewicz,
- Martin B. Delatycki,
- Melanie Bahlo,
- and Paul J. Lockhart
Genome Res. April 2025 35: 769-785; Published in Advance February 27, 2025, doi:10.1101/gr.279634.124
...are shown as colored circles. (C) Concordance plot showing a comparison of the FGF14 STR EH5 genotypes from SR-GS compared to PCR sizing (longer allele only). The pathogenic (≥250 repeats) and VUS (≥180 repeats) thresholds are shown as dashed red lines. A 1:1 correlation is shown as a dashed blue line...

For checked items

view abstracts
download to citation manager

Searching journal content for articles similar to Karttunen et al. 6 (5): 392.

Search Results

Modify Results

This search

Preprint Server

Current Issue

In This Issue

Citation format:
Results / page:
Results order: