Searching journal content for articles similar to Miller et al. 9 (11): 1143.

Displaying results 1-10 of 355

For checked items

view abstracts
download to citation manager

Select this article
Method: STCC enhances spatial domain detection through consensus clustering of spatial transcriptomics data
- Congcong Hu,
- Nana Wei,
- Jiyuan Yang,
- Hua-Jun Wu,
- and Xiaoqi Zheng
Genome Res. June 2025 35: 1415-1428; Published in Advance May 12, 2025, doi:10.1101/gr.280031.124
...benchmark data sets, including sequencing technologies, species, organism/disease types, numbers of spots, genes, and cell types, etc.To comprehensively assess the performance of these diverse consensus strategies, we have collected seven SRT data sets with manual annotations by pathologists as ground truth...
Select this article
Method: Aggregation of recount3 RNA-seq data improves inference of consensus and tissue-specific gene coexpression networks
- Prashanthi Ravichandran,
- Princy Parsana,
- Rebecca Keener,
- Kasper D. Hansen,
- and Alexis Battle
Genome Res. September 2025 35: 2087-2103; Published in Advance July 17, 2025, doi:10.1101/gr.280808.125
...-specific networks. Central genes in consensus networks are enriched for evolutionarily constrained genes and ubiquitous biological pathways, whereas context-specific central nodes include tissue-specific transcription factors. The increased statistical power from data aggregation facilitates the derivation...
OPEN ACCESS ARTICLE
Select this article
Method: scSHEFT enables multiomics label transfer from scRNA-seq to scATAC-seq through dual alignment
- Zhitao Huang,
- Ruiqing Zheng,
- Pengzhen Jia,
- Xuhua Yan,
- Jinmiao Chen,
- and Min Li
Genome Res. February 2026 36: 387-396; Published in Advance January 20, 2026, doi:10.1101/gr.280410.125
...(Ashuach et al. 2023). For example, GLUE is a representative method of this category, which integrates gene expression and peak count data and leverages prior regulatory knowledge to guide cross-omics alignment (Cao and Gao 2022). This approach preserves as much information as possible in the raw sc...
Select this article
Method: Nanopore-based consensus sequencing enables accurate multimodal tumor cell-free DNA profiling
- Li-Ting Chen,
- Myrthe Jager,
- Dàmi Rebergen,
- Geertruid J. Brink,
- Tom van den Ende,
- Willem Vanderlinden,
- Pauline Kolbeck,
- Marc Pagès-Gallego,
- Ymke van der Pol,
- Nicolle Besselink,
- Norbert Moldovan,
- Nizar Hami,
- Wigard P. Kloosterman,
- Hanneke van Laarhoven,
- Florent Mouliere,
- Ronald Zweemer,
- Jan Lipfert,
- Sarah Derks,
- Alessio Marcozzi,
- and Jeroen de Ridder
Genome Res. April 2025 35: 886-899; Published in Advance January 13, 2025, doi:10.1101/gr.279144.124
...the genomic position on the chromosomes (1 Mb bins), and the y-axis indicates copy numbers. (C) Correlation of CNA-derived TF between NanoRCS and NovaSeq. (D) NanoRCS copy number of genes often amplified (red) and deleted (blue) according to literature. The boxplots show the observed copy number distribution...
OPEN ACCESS ARTICLE
Select this article
Resource: Quadrupia provides a comprehensive catalog of G-quadruplexes across genomes from the tree of life
- Nikol Chantzi,
- Akshatha Nayak,
- Fotis A. Baltoumas,
- Eleni Aplakidou,
- Shiau Wei Liew,
- Jesslyn Elvaretta Galuh,
- Michail Patsakis,
- Austin Montgomery,
- Camille Moeckel,
- Ioannis Mouratidis,
- Saiful Arefeen Sazed,
- Wilfried Guiblet,
- Panagiotis Karmiris-Obratański,
- Guliang Wang,
- Apostolos Zaravinos,
- Karen M. Vasquez,
- Chun Kit Kwok,
- Georgios A. Pavlopoulos,
- and Ilias Georgakopoulos-Soares
Genome Res. November 2025 35: 2578-2600; Published in Advance August 26, 2025, doi:10.1101/gr.279790.124
..., lead to the formation of G4 structures (Fig. 1A; Spiegel et al. 2020). Their presence and formation in telomeric regions provided early evidence that G4s are a native DNA conformation (Parkinson et al. 2002). Furthermore, an array of studies have shown that G4s are involved in processes such as gene...
OPEN ACCESS ARTICLE
Select this article
Review: A systematic guide for identifying transcription factors that directly regulate the expression of a gene of interest
- Andrew D. Bates,
- Dawid Grzela,
- Maciej Studzian,
- Louise Brennan,
- Moli Williams,
- Conor Fawcett,
- Beth Hammond,
- Manreen Grewal,
- Marcin Ratajewski,
- Lukasz Pulaski,
- and Urszula L. McClurg
Genome Res. March 2026 36: 433-459; Published in Advance February 17, 2026, doi:10.1101/gr.281154.125
...sequence is functional, the reporter gene is expressed/induced and the cellular concentration of the gene product is measured (Smale 2010).TF binding predictionTFs bind DNA in a sequence-specific manner based on motifs, with each binding site having a consensus sequence that indicates prerequisites...
OPEN ACCESS ARTICLE
Select this article
Method: Partial alignment of multislice spatially resolved transcriptomics data
- Xinhao Liu,
- Ron Zeira,
- and Benjamin J. Raphael
Genome Res. July 2023 33: 1124-1132; Published in Advance August 8, 2023, doi:10.1101/gr.277670.123
...spot of ≈2000, compared to ≈4000 spots and ≈5000 median UMI per spot in the 10x Visium DLPFC data set. They derived the cell type of each spot by unsupervised clustering of gene expression followed by annotation based on marker genes. The publication used PASTE to align all slices from the same stage...
Select this article
Method: Deciphering context-specific gene programs from single-cell and spatial transcriptomics data with DeCEP
- Lin Li,
- Xianbin Su,
- and Ze-Guang Han
Genome Res. October 2025 35: 2300-2315; Published in Advance August 21, 2025, doi:10.1101/gr.279689.124
...of the three simulated data sets into four clusters, with each data set containing clusters labeled from zero to three (Supplemental Fig. S1). We applied consensus clustering (Wilkerson and Hayes 2010) to the highly variable genes in each data set to generate functional gene lists and performed De...
Select this article
Method: Assessing and mitigating privacy risks of sparse, noisy genotypes by local alignment to haplotype databases
- Prashant S. Emani,
- Maya N. Geradi,
- Gamze Gürsoy,
- Monica R. Grasty,
- Andrew Miranker,
- and Mark B. Gerstein
Genome Res. December 2023 33: 2156-2173; Published in Advance December 14, 2023, doi:10.1101/gr.278322.123
...sequence-based variant discovery (Gürsoy et al. 2020), and inference using gene expression values and associated loci (Harmanci and Gerstein 2016). The ubiquity of large-scale omics projects make this source of variants especially concerning (Gürsoy et al. 2020). Several studies have showed identification...
OPEN ACCESS ARTICLE
Select this article
Resource: Comprehensive assessment of 11 de novo HiFi assemblers on complex eukaryotic genomes and metagenomes
- Wenjuan Yu,
- Haohui Luo,
- Jinbao Yang,
- Shengchen Zhang,
- Heling Jiang,
- Xianjia Zhao,
- Xingqi Hui,
- Da Sun,
- Liang Li,
- Xiu-qing Wei,
- Stefano Lonardi,
- and Weihua Pan
Genome Res. February 2024 34: 326-340; Published in Advance March 1, 2024, doi:10.1101/gr.278232.123
...length distribution for various choices of the NGx fraction threshold. (D) Quality value scores. (E) Running time analysis. (F) Memory usage analysis (legend on panel D also applies to panels E,F).Second, the completeness was assessed by BUSCO. The set of conserved genes in gramineae (4896 genes in total...

For checked items

view abstracts
download to citation manager

Searching journal content for articles similar to Miller et al. 9 (11): 1143.

Search Results

Modify Results

This search

Preprint Server

Current Issue

In This Issue

Citation format:
Results / page:
Results order: