Searching journal content for articles similar to López-Cortegano et al. 35 (1): 43.

Displaying results 1-10 of 32

For checked items

view abstracts
download to citation manager

Select this article
Research: Integrating short-read and long-read single-cell RNA sequencing for comprehensive transcriptome profiling in mouse retina
- Meng Wang,
- Yumei Li,
- Jun Wang,
- Soo Hwan Oh,
- Yexuan Cao,
- and Rui Chen
Genome Res. April 2025 35: 740-754; Published in Advance March 6, 2025, doi:10.1101/gr.279167.124
...a systematic comparison between single-cell long-read and conventional short-read RNA sequencing techniques. The transcriptome of approximately 30,000 mouse retina cells was profiled using 1.54 billion Illumina short reads and 1.40 billion Oxford Nanopore Technologies long reads. Consequently, we identify 44...
Select this article
Research: Modest increase in the de novo single-nucleotide mutation rate in house mice born by assisted reproduction
- Laura Blanco-Berdugo,
- Alexis Garretson,
- and Beth L. Dumont
Genome Res. January 2026 36: 50-60; Published in Advance November 13, 2025, doi:10.1101/gr.281180.125
....5%–56%) increase in the dnSNV rate with ART compared with naturally conceived mice (P = 0.017). Analysis of the dnSNV mutation spectrum identifies signatures attributable to germline DNA repair activity but reveals no differentially enriched signatures between cohorts. We observe no enrichment of dn...
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
...in the Twinkle subjects were more evenly distributed across the mitochondrial . The distribution of fusion event locations was distinct from the distribution of mtDNA deletion mutations breakpoints reported in long-read sequencing of normal aging muscle and in available online mtDNA mutation databases (Fig. 2C...
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
..., Spain; 10Gene Expression and mRNA Metabolism Laboratory, CIPF, 46012 Valencia, Spain ↵11 Joint first authorship. Corresponding author: aconesa@ufl.edu, aconesa@cipf.esAbstractHigh-throughput sequencing of full-length transcripts using long reads has paved the way for the discovery of thousands of novel...
OPEN ACCESS ARTICLE
Select this article
Method: Measuring X-Chromosome inactivation skew for X-linked diseases with adaptive nanopore sequencing
- Sena A. Gocuk,
- James Lancaster,
- Shian Su,
- Jasleen K. Jolly,
- Thomas L. Edwards,
- Doron G. Hickey,
- Matthew E. Ritchie,
- Marnie E. Blewitt,
- Lauren N. Ayton,
- and Quentin Gouil
Genome Res. November 2024 34: 1954-1965; Published in Advance September 16, 2024, doi:10.1101/gr.279396.124
...by nanopore sequencing of Cas9-targeted native DNA. DNA modifications trigger recognizable variation in the electrical current measured at the nanopore, enabling base-level modification analysis in long reads. Although this targeted test improves quantitation accuracy, it suffers from most of the same...
Select this article
Method: PRAM: a novel pooling approach for discovering intergenic transcripts from large-scale RNA sequencing experiments
- Peng Liu,
- Alexandra A. Soukup,
- Emery H. Bresnick,
- Colin N. Dewey,
- and Sündüz Keleş
Genome Res. November 2020 30: 1655-1666; Published in Advance September 21, 2020, doi:10.1101/gr.252445.119
...on the same strand regardless of frame (Supplemental Table 19; Supplemental Fig. 31).Comparison with Pacific Biosciences (PacBio) long reads revealed that a substantial fraction of PRAM transcripts overlapped with these long reads and had matching splice junctions (Supplemental Fig. 32). Collectively...
OPEN ACCESS ARTICLE
Select this article
Research: Burkholderia pseudomallei sequencing identifies genomic clades with distinct recombination, accessory, and epigenetic profiles
- Tannistha Nandi,
- Matthew T.G. Holden,
- Xavier Didelot,
- Kurosh Mehershahi,
- Justin A. Boddey,
- Ifor Beacham,
- Ian Peak,
- John Harting,
- Primo Baybayan,
- Yan Guo,
- Susana Wang,
- Lee Chee How,
- Bernice Sim,
- Angela Essex-Lopresti,
- Mitali Sarkar-Tyson,
- Michelle Nelson,
- Sophie Smither,
- Catherine Ong,
- Lay Tin Aw,
- Chua Hui Hoon,
- Stephen Michell,
- David J. Studholme,
- Richard Titball,
- Swaine L. Chen,
- Julian Parkhill,
- and Patrick Tan
Genome Res. January 2015 25: 129-141; Published in Advance September 18, 2014, doi:10.1101/gr.177543.114
...strains within a clade, then this would serve to homogenize the recombining sequences across strains, whereas nonrecombining regions would accumulate mutations independently in different strains (Fig. 4A, ‘‘Ongoing Recombination’’). Thus, the within-clade nucleotide divergence of recombined regions would...
Select this article
Research: APOBEC3A drives deaminase mutagenesis in human gastric epithelium
- Yohan An,
- Ji-Hyun Lee,
- Joonoh Lim,
- Jeonghwan Youk,
- Seongyeol Park,
- Ji-Hyung Park,
- Kijong Yi,
- Taewoo Kim,
- Chang Hyun Nam,
- Won Hee Lee,
- Soo A Oh,
- Yoo Jin Bae,
- Thomas M. Klompstra,
- Haeun Lee,
- Jinju Han,
- Junehwak Lee,
- Jung Woo Park,
- Jie-Hyun Kim,
- Hyunki Kim,
- Hugo Snippert,
- Bon-Kyoung Koo,
- and Young Seok Ju
Genome Res. October 2025 35: 2158-2172; Published in Advance August 26, 2025, doi:10.1101/gr.280338.124
...inactivation. Further analysis of the mutational landscape following APOBEC3A upregulation reveals a detailed spectrum of APOBEC3A-associated mutations, including indels, primarily 1 bp deletions, clustered mutations, and evidence of selective pressures acting on cells carrying the mutations. Our observations...
OPEN ACCESS ARTICLE
Select this article
Research: Whole-exome sequencing of human pancreatic cancers and characterization of genomic instability caused by MLH1 haploinsufficiency and complete deficiency
- Linghua Wang,
- Shuichi Tsutsumi,
- Tokuichi Kawaguchi,
- Koichi Nagasaki,
- Kenji Tatsuno,
- Shogo Yamamoto,
- Fei Sang,
- Kohtaro Sonoda,
- Minoru Sugawara,
- Akio Saiura,
- Seiko Hirono,
- Hiroki Yamaue,
- Yoshio Miki,
- Minoru Isomura,
- Yasushi Totoki,
- Genta Nagae,
- Takayuki Isagawa,
- Hiroki Ueda,
- Satsuki Murayama-Hosokawa,
- Tatsuhiro Shibata,
- Hiromi Sakamoto,
- Yae Kanai,
- Atsushi Kaneda,
- Tetsuo Noda,
- and Hiroyuki Aburatani
Genome Res. February 2012 22: 208-219; Published in Advance December 7, 2011, doi:10.1101/gr.123109.111
...to a mean coverage of 56-fold. This study identified a total of 1517 somatic mutations and validated 934 mutations by transcriptome sequencing. We detected recurrent mutations in 56 genes. Among them, 41 have not been described. The mutation rates varied widely among cell lines. The diversity...
Select this article
Research: Unexpectedly low recombination rates and presence of hotspots in termite genomes
- Turid Everitt,
- Tilman Rönneburg,
- Daniel Elsner,
- Anna Olsson,
- Yuanzhen Liu,
- Tuuli Larva,
- Judith Korb,
- and Matthew T. Webster
Genome Res. May 2025 35: 1124-1137; Published in Advance March 20, 2025, doi:10.1101/gr.279180.124
...in length. However, little is known about the prevalence of recombination hotspots in insect s. Here we infer recombination rate and its fine-scale variation across the s of two social species from the insect order Blattodea: the termites Macrotermes bellicosus and Cryptotermes secundus. We used linkage...

For checked items

view abstracts
download to citation manager

Searching journal content for articles similar to López-Cortegano et al. 35 (1): 43.

Search Results

Modify Results

This search

Preprint Server

Current Issue

In This Issue

Citation format:
Results / page:
Results order: