Searching journal content for articles similar to Kampa et al. 14 (3): 331.

Displaying results 1-10 of 143

For checked items

view abstracts
download to citation manager

Select this article
Research: Panoramic transcriptome analysis and functional screening of long noncoding RNAs in mouse spermatogenesis
- Kai Li,
- Jiayue Xu,
- Yanyun Luo,
- Dingfeng Zou,
- Ruiqin Han,
- Shunshun Zhong,
- Qing Zhao,
- Xinyu Mang,
- Mengzhen Li,
- Yanmin Si,
- Yan Lu,
- Pengyu Li,
- Cheng Jin,
- Zhipeng Wang,
- Fang Wang,
- Shiying Miao,
- Bo Wen,
- Linfang Wang,
- Yanni Ma,
- Jia Yu,
- and Wei Song
Genome Res. January 2021 31: 13-26; Published in Advance December 16, 2020, doi:10.1101/gr.264333.120
.... 2016; Jan et al. 2017; Rolland et al. 2019; Gamble et al. 2020; Tan et al. 2020). Further in-depth genomic examination of spermatogenesis reveals individual features of lnRNAs, including germ cell specificity, longer exon length, or high representation of antisense (AS) lncRNAs, which have shown...
Select this article
Method: Parallel bimodal single-cell sequencing of transcriptome and chromatin accessibility
- Qiao Rui Xing,
- Chadi A El Farran,
- Ying Ying Zeng,
- Yao Yi,
- Tushar Warrier,
- Pradeep Gautam,
- James J. Collins,
- Jian Xu,
- Peter Dröge,
- Cheng-Gee Koh,
- Hu Li,
- Li-Feng Zhang,
- and Yuin-Han Loh
Genome Res. July 2020 30: 1027-1039; Published in Advance July 22, 2020, doi:10.1101/gr.257840.119
..., their high-throughput nature results in rare sequencing reads for each profiled cell and extensive loss of information (Xing et al. 2020). In comparison, scNMT-seq and scCAT-seq are applicable for studies with the intention of mining in-depth molecular distinctions between subpopulations (Clark et al. 2018...
OPEN ACCESS ARTICLE
Select this article
Research: LTR retroelement expansion of the human cancer transcriptome and immunopeptidome revealed by de novo transcript assembly
- Jan Attig,
- George R. Young,
- Louise Hosie,
- David Perkins,
- Vesela Encheva-Yokoya,
- Jonathan P. Stoye,
- Ambrosius P. Snijders,
- Nicola Ternette,
- and George Kassiotis
Genome Res. October 2019 29: 1578-1590; Published in Advance September 19, 2019, doi:10.1101/gr.248922.119
...with molecular subclasses, previously identified by in-depth genomic and transcriptomic analyses (Fig. 4B–E; The Cancer Genome Atlas Network 2015; Robertson et al. 2017). Indeed, expression of CLTs associated with SKCM survival formed four distinct clusters, three of which matched clusters identified by TCGA...
OPEN ACCESS ARTICLE
Select this article
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
...for analyzing frame-specific distributions (Supplemental Fig. S4B). One data set is processed at a time for in-depth examination.ggRibo_tx: single-transcript visualizationggRibo_tx visualizes RNA-seq and Ribo-seq data in the context of mature RNA for a selected transcript isoform (Supplemental Fig. S4C), which...
OPEN ACCESS ARTICLE
Select this article
Method: SQANTI: extensive characterization of long-read transcript sequences for quality control in full-length transcriptome identification and quantification
- Manuel Tardaguila,
- Lorena de la Fuente,
- Cristina Marti,
- Cécile Pereira,
- Francisco Jose Pardo-Palacios,
- Hector del Risco,
- Marc Ferrell,
- Maravillas Mellado,
- Marissa Macchietto,
- Kenneth Verheggen,
- Mariola Edelmann,
- Iakes Ezkurdia,
- Jesus Vazquez,
- Michael Tress,
- Ali Mortazavi,
- Lennart Martens,
- Susana Rodriguez-Navarro,
- Victoria Moreno-Manzano,
- and Ana Conesa
Genome Res. March 2018 28: 396-411; Published in Advance February 9, 2018, doi:10.1101/gr.222976.117
...analysis workflowThe SQANTI pipeline was developed for an in-depth characterization and curation of long-reads transcriptomes. SQANTI takes as input a transcripts data set, together with annotation and, if available, quantification data, to return a reference corrected transcriptome together with a wide...
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
...in the common ancestor of the two species.F-box genes have undergone a remarkable expansion in C. nigoni compared with C. briggsaeGiven the substantial expansion and the largest numerical differences in F-box genes between C. nigoni and C. briggsae, we conducted an in-depth analysis of these genes in both...
Select this article
Perspective: Notable challenges posed by long-read sequencing for the study of transcriptional diversity and genome annotation
- Carolina Monzó,
- Adam Frankish,
- and Ana Conesa
Genome Res. April 2025 35: 583-592; Published in Advance March 3, 2025, doi:10.1101/gr.279865.124
...to differentiate it from technical noise and condition-specific transcript isoforms.Recent efforts have moved beyond annotating alternative isoforms to conducting in-depth analysis of transcriptional diversity per gene. For instance, Reese et al. (2023) evaluate non-FSM reads based on three diversity mechanisms...
OPEN ACCESS ARTICLE
Select this article
Method: A scalable computational framework for predicting gene expression from candidate cis-regulatory elements
- Qinhu Zhang,
- Siguo Wang,
- Zhipeng Li,
- Wenzheng Bao,
- Wenjian Liu,
- and De-Shuang Huang
Genome Res. February 2026 36: 361-374; Published in Advance January 16, 2026, doi:10.1101/gr.281219.125
...+ perturbation) discovers all validated enhancers, outperforming other methods in capturing active enhancers.Categorization of ScPGE's predictions shows distinct patternsAlthough several computational methods for predicting gene expression have been proposed, there is little in-depth analysis...
OPEN ACCESS ARTICLE
Select this article
Resource: Epigenomics of embryogenesis in turbot
- Oscar Aramburu,
- Belen G Pardo,
- Ada Jimenez-Gonzalez,
- Andrés Blanco-Hortas,
- Daniel Macqueen,
- Carmen Bouza,
- and Paulino Martinez
Genome Res. November 4, 2025 gr.280355.124; Published in Advance November 4, 2025, doi:10.1101/gr.280355.124
...key 116 developmental stages. Full information on samples and metadata is shown in 117 Supplemental tables S1 and S2. 118 Transcriptomic profiling of turbot embryogenesis 119 RNA-seq was used to compare transcriptomic profiles across different stages of 120 turbot development. On average, 64...
- Abstract
- Full Text (PDF)
OPEN ACCESS ARTICLEACCEPTED MANUSCRIPT
Select this article
Research: Synergistic regulation by H3K36 and H3K27 methylation defines the chromatin landscape to control virulence and secondary metabolism in a fungal pathogen
- Xingmin Han,
- Chenghui Xu,
- Yiyi Ren,
- Meiling Guo,
- Jiayue Yan,
- Xuan Wang,
- Chao Liu,
- Qin Gu,
- Xing-Xing Shen,
- Zhonghua Ma,
- and Yun Chen
Genome Res. November 2025 35: 2472-2487; Published in Advance October 14, 2025, doi:10.1101/gr.280560.125
...proteins in Fusarium graminearum, a globally significant fungal pathogen, reveals diverse roles in growth, development, and virulence. In-depth analyses of two H3K36-specific methyltransferases, Set2 and Ash1, uncover their distinct regulatory functions. Set2-mediated H3K36me3 is enriched in gene bodies...

For checked items

view abstracts
download to citation manager

Searching journal content for articles similar to Kampa et al. 14 (3): 331.

Search Results

Modify Results

This search

Preprint Server

Current Issue

In This Issue

Citation format:
Results / page:
Results order: