Searching journal content for articles similar to Qian et al. 27 (2): 185.

Displaying results 1-10 of 6309

For checked items

view abstracts
download to citation manager

Select this article
Method: OMKar automates genome karyotyping using optical maps to identify constitutional abnormalities
- Siavash Raeisi Dehkordi,
- Zhaoyang Jia,
- Joey Estabrook,
- Jen Hauenstein,
- Neil Miller,
- Naz Güleray-Lafci,
- Jürgen Neesen,
- Alex Hastie,
- Alka Chaubey,
- Andy Wing Chun Pang,
- Paul Dremsek,
- and Vineet Bafna
Genome Res. December 2025 35: 2671-2681; Published in Advance November 14, 2025, doi:10.1101/gr.280536.125
...OGMThe molecular karyotype of a donor can be described as a collection of genomic sequences, each sequence corresponding to one donor chromosome. Traditionally, the karyotype information was captured by cytogenetics, albeit at low resolution, and helped identify balanced and unbalanced rearrangements...
OPEN ACCESS ARTICLE
Select this article
Research: Long-read single-cell RNA sequencing enables the study of cancer subclone-specific genotypes and phenotypes in chronic lymphocytic leukemia
- Gage S. Black,
- Xiaomeng Huang,
- Yi Qiao,
- Philip Moos,
- Deepa Sampath,
- Deborah M. Stephens,
- Jennifer A. Woyach,
- and Gabor T. Marth
Genome Res. April 2025 35: 686-697; Published in Advance February 18, 2025, doi:10.1101/gr.279049.124
...subclone-specific gene expression, we find that in one patient, BTK-mutated subclones are transcriptionally distinct from the rest of the malignant B cell population with an overexpression of CLL-relevant genes.Chronic lymphocytic leukemia (CLL) is the most prevalent subtype of leukemia in adults...
Select this article
Method: Spatially resolved whole transcriptome profiling in human and mouse tissue using Digital Spatial Profiling
- Stephanie M. Zimmerman,
- Robin Fropf,
- Bridget R. Kulasekara,
- Maddy Griswold,
- Oliver Appelbe,
- Arya Bahrami,
- Rich Boykin,
- Derek L. Buhr,
- Kit Fuhrman,
- Margaret L. Hoang,
- Quoc Huynh,
- Lesley Isgur,
- Andrew Klock,
- Alecksandr Kutchma,
- Alexa E. Lasley,
- Yan Liang,
- Jill McKay-Fleisch,
- Jeffrey S. Nelson,
- Karen Nguyen,
- Erin Piazza,
- Aric Rininger,
- Daniel R. Zollinger,
- Michael Rhodes,
- and Joseph M. Beechem
Genome Res. October 2022 32: 1892-1905; Published in Advance September 13, 2022, doi:10.1101/gr.276206.121
.... In total, these results demonstrate the feasibility of whole transcriptome profiling of specific organ substructures to detect spatially variable disease-related abnormalities.Identifying organ substructure–specific transcriptomes in the developing mouse embryoAnother anticipated use of WTA is to catalog...
OPEN ACCESS ARTICLE
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
...a sample, reverse-transcribing it into stable cDNA, and finally sequencing using (mostly) Illumina technology (Bentley et al. 2008). RNA-seq has multiple technical variations, either to identify specific types of transcripts or to characterize other RNA products. For instance, small RNA sequencing (s...
Select this article
Perspective: Unraveling the hidden complexity of cancer through long-read sequencing
- Qiuhui Li,
- Ayse G. Keskus,
- Justin Wagner,
- Michal B. Izydorczyk,
- Winston Timp,
- Fritz J. Sedlazeck,
- Alison P. Klein,
- Justin M. Zook,
- Mikhail Kolmogorov,
- and Michael C. Schatz
Genome Res. April 2025 35: 599-620; Published in Advance March 20, 2025, doi:10.1101/gr.280041.124
...genomics studies aiming to identify and catalog driver mutations (Cortés-Ciriano et al. 2021), study tumor evolution (Gerstung et al. 2020), stratify cancers into clinical subtypes (Chakravarty and Solit 2021), and inform patient treatment (Sosinsky et al. 2024). Somatic variation in cancer is a result...
OPEN ACCESS ARTICLE
Select this article
Method: Autoencoders for genomic variation analysis
- Margarita Geleta,
- Daniel Mas Montserrat,
- Xavier Giro-i-Nieto,
- and Alexander G. Ioannidis
Genome Res. February 2026 36: 348-360; Published in Advance January 20, 2026, doi:10.1101/gr.280086.124
..., Stanford University School of Engineering, Stanford, California 94305, USA Corresponding author: geleta@berkeley.eduAbstractModern biobanks are providing numerous high-resolution genomic sequences of diverse populations. In order to account for diverse and admixed populations, new algorithmic tools...
OPEN ACCESS ARTICLE
Select this article
Method: PoreMeth2 for decoding the evolution of methylome alterations with nanopore sequencing
- Gianluca Mattei,
- Marta Baragli,
- Barbara Gega,
- Alessandra Mingrino,
- Martina Chieca,
- Tommaso Ducci,
- Gianmaria Frigè,
- Luca Mazzarella,
- Romina D'Aurizio,
- Francesco De Logu,
- Romina Nassini,
- Pier Giuseppe Pelicci,
- and Alberto Magi
Genome Res. November 2025 35: 2501-2512; Published in Advance October 20, 2025, doi:10.1101/gr.280259.124
...), allow to produce sequences in the order of tens to hundreds of kilobases and to directly recognize base modifications, such as 5mC, thus allowing concomitant analyses of genomic and epigenomic changes (Magi et al. 2017, 2018, 2023a).Using Oxford Nanopore Technologies (ONT) and a novel computational...
Select this article
Research: Long-read sequencing reveals HBV integration patterns and oncogenic impact on early-onset hepatocellular carcinoma
- Yao Wang,
- Dong Yu,
- Yue Mei,
- ZhiDa Fu,
- Jian Lin,
- Di Wu,
- Yuan Yang,
- and Hongli Yan
Genome Res. November 2025 35: 2389-2405; Published in Advance September 16, 2025, doi:10.1101/gr.279889.124
...aberrant oncogene expression, which is dependent on both the genomic integration site and viral sequence composition. Beyond the well-characterized TERT promoter integration in sample T1, we identified a clinically significant HBV integration cluster upstream of the MYC TSS in sample T2 (56 supporting...
Select this article
Method: Single-cell Rapid Capture Hybridization sequencing reliably detects isoform usage and coding mutations in targeted genes
- Hongke Peng,
- Jafar S. Jabbari,
- Luyi Tian,
- Changqing Wang,
- Yupei You,
- Chong Chyn Chua,
- Natasha S. Anstee,
- Noorul Amin,
- Andrew H. Wei,
- Nadia M. Davidson,
- Andrew W. Roberts,
- David C.S. Huang,
- Matthew E. Ritchie,
- and Rachel Thijssen
Genome Res. April 2025 35: 942-955; Published in Advance January 10, 2025, doi:10.1101/gr.279322.124
...for these altered transcripts was low (Fig. 4A,B). A comparison of scRaCH-seq efficiency in capturing the SF3B1 K700E mutation with whole transcriptome short-read sequencing (scRNA-seq) and long-read sequencing (scFLT-seq) revealed that scRaCH-seq significantly increased the capture of cells carrying the mutation...
OPEN ACCESS ARTICLE
Select this article
Research: Pangenome analysis reveals families of ubiquitin-ligase adaptors as key genomic divergence drivers that lead to hybrid incompatibility
- Dongying Xie,
- Pohao Ye,
- Yiming Ma,
- and Zhongying Zhao
Genome Res. March 2026 36: 506-521; Published in Advance February 17, 2026, doi:10.1101/gr.280885.125
...is primarily driven by differences in unalignable regionsWe next investigated the sequence divergences underpinning the larger sizes of C. nigoni strains relative to C. briggsae strains. To this end, we leveraged the genomic variation detection tool SyRI (Goel et al. 2019), which systematically identifies...

For checked items

view abstracts
download to citation manager

Searching journal content for articles similar to Qian et al. 27 (2): 185.

Search Results

Modify Results

This search

Preprint Server

Current Issue

In This Issue

Citation format:
Results / page:
Results order: