Searching journal content for articles similar to Blechschmidt et al. 9 (2): 158.

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Resource: The ggRibo single-gene viewer reveals insights into translatome and other nucleotide-resolution omics data
- Hsin-Yen Larry Wu,
- Isaiah D. Kaufman,
- and Polly Yingshan Hsu
Genome Res. September 2025 35: 2130-2142; Published in Advance July 22, 2025, doi:10.1101/gr.280480.125
...to ggRibo, GWIPS-viz plots Ribo-seq reads in a single color, which hinders the intuitive interpretation of reading frames (Supplemental Fig. S2B). Although RiboCrypt offers color-coded reading frames in the “gene” view, the reading frame is assigned based on the genomic sequence, and therefore...
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Research: Xist upstream deletion leads to dysregulation of Xist and autosomal gene expression
- Sudeshna Majumdar,
- Lakshmi Sowjanya Bammidi,
- Hemant C. Naik,
- Avinchal Manhas,
- Runumi Baro,
- Akash Kalita,
- Amlan Jyoti Naskar,
- Sundarraj Nidharshan,
- Girija S. Bariha,
- Dimple Notani,
- and Srimonta Gayen
Genome Res. September 2025 35: 1992-2010; Published in Advance August 6, 2025, doi:10.1101/gr.279822.124
...upstream sequence imparts a multifaceted role in regulation beyond the XCI.X-Chromosome inactivation (XCI) is a process by which female mammals compensate for the dosage of X-linked gene expression between sexes (Lyon 1961; Gayen et al. 2015, 2016). XCI is an excellent model system for understanding...
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Research: Oxygen-induced stress reveals context-specific gene regulatory effects in human brain organoids
- Benjamin D. Umans and
- Yoav Gilad
Genome Res. August 2025 35: 1689-1700; Published in Advance June 2, 2025, doi:10.1101/gr.280219.124
...NovaSeq 6000 instrument at the University of Chicago Genomics Core Facility (RRID:SCR_019196).Differential expression analysisTo identify genes differentially expressed between treatment conditions, we relied on well-established methods for analyzing bulk RNA sequencing data. Single-cell transcriptomes...
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Method: Factors impacting target-enriched long-read sequencing of resistomes and mobilomes
- Ilya B. Slizovskiy,
- Nathalie Bonin,
- Jonathan E. Bravo,
- Peter M. Ferm,
- Jacob Singer,
- Christina Boucher,
- and Noelle R. Noyes
Genome Res. November 2024 34: 2048-2060; Published in Advance November 5, 2024, doi:10.1101/gr.279226.124
..., Florida 32611, USA; 4Department of Computer Science, University of Maryland, College Park, Maryland 20742, USA Corresponding author: nnoyes@umn.eduAbstractWe investigated the efficiency of target-enriched long-read sequencing (TELSeq) for detecting antimicrobial resistance genes (ARGs) and mobile genetic...
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Method: Evaluation of N⁶-methyldeoxyadenosine antibody-based genomic profiling in eukaryotes
- Brian M. Debo,
- Benjamin J. Mallory,
- and Andrew B. Stergachis
Genome Res. March 2023 33: 427-434; Published in Advance February 14, 2023, doi:10.1101/gr.276696.122
...embryo and A. thaliana cauline leaf samples, but only a single replicate was used for analyses.DNA-m6A loci genomic positionsA. thaliana gene and transposable element TSSs were identified using the “TAIR9_GFF3_genes_transposons.gff” annotation file downloaded from The Arabidopsis Information Resource...
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Resource: The fine-scale recombination rate variation and associations with genomic features in a butterfly
- Aleix Palahí i Torres,
- Lars Höök,
- Karin Näsvall,
- Daria Shipilina,
- Christer Wiklund,
- Roger Vila,
- Peter Pruisscher,
- and Niclas Backström
Genome Res. May 2023 33: 810-823; Published in Advance June 12, 2023, doi:10.1101/gr.277414.122
.... Associations between the recombination rate and base composition (A) and gene density (B) in 1-Mb genomic windows. (A) Association between the recombination rate and the nucleotide composition (GC content). (B) Association between the recombination rate and the density of coding sequences (CDS).Because we...
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Method: Simultaneous profiling of host expression and microbial abundance by spatial metatranscriptome sequencing
- Lin Lyu,
- Xue Li,
- Ru Feng,
- Xin Zhou,
- Tuhin K. Guha,
- Xiaofei Yu,
- Guo Qiang Chen,
- Yufeng Yao,
- Bing Su,
- Duowu Zou,
- Michael P. Snyder,
- and Lei Chen
Genome Res. March 2023 33: 401-411; Published in Advance March 27, 2023, doi:10.1101/gr.277178.122
...sequence capture with or without the additional lysozyme step. (D) Violin plots of host gene UMI count, gene count, and mitochondria percentage (common measurements to QC single-cell and ST data) with or without lysozyme treatment, no significant difference could be observed. (E) Spatial dim plots showing...
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Method: Data integration and inference of gene regulation using single-cell temporal multimodal data with scTIE
- Yingxin Lin,
- Tung-Yu Wu,
- Xi Chen,
- Sheng Wan,
- Brian Chao,
- Jingxue Xin,
- Jean Y.H. Yang,
- Wing H. Wong,
- and Y.X. Rachel Wang
Genome Res. January 2024 34: 119-133; Published in Advance December 15, 2023, doi:10.1101/gr.277960.123
.... Nuclei were isolated by following the protocol provided by 10x Genomics (nuclei isolation for single-cell multiome ATAC + gene expression sequencing, CG00365, Rev A). The final nuclei concentration was adjusted to 3000 cell/µL in 1× nuclei buffer (10x Genomics). The sample was immediately submitted...
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Research: tRNA-derived small RNAs are embedded in the gene regulatory network instructing Drosophila metamorphosis
- Junling Shi,
- Jiaqi Xu,
- Jun Ma,
- and Feng He
Genome Res. December 2023 33: 2119-2132; Published in Advance November 16, 2023, doi:10.1101/gr.278128.123
...RNAs in early pupae exert regulatory activities on their putative target genes during normal development, we analyzed our mRNA-seq data of WT across different stages. Enriched GO groups of genes with an increased mRNA level include “mitochondrion organization” (GO:0007005), “cuticle development” (GO:0042335...
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Resource: Native RNA sequencing in fission yeast reveals frequent alternative splicing isoforms
- José Carlos Montañés,
- Marta Huertas,
- Simone G. Moro,
- William R. Blevins,
- Mercè Carmona,
- José Ayté,
- Elena Hidalgo,
- and M. Mar Albà
Genome Res. June 2022 32: 1215-1227; Published in Advance May 26, 2022, doi:10.1101/gr.276516.121
...by different combinations of exons and introns, which cannot be accurately solved by Illumina reads. At the same time, the cost and scalability it offers is comparable to that of Illumina sequencing. We generated around 7 million dRNA reads in an organism with about 7000 genes. This high coverage and the lack...

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