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Research: The role of transposon activity in shaping cis-regulatory element evolution after whole-genome duplication
- Øystein Monsen,
- Lars Grønvold,
- Alex Datsomor,
- Thomas Harvey,
- James Kijas,
- Alexander Suh,
- Torgeir R. Hvidsten,
- and Simen Rød Sandve
Genome Res. March 2025 35: 475-488; Published in Advance February 12, 2025, doi:10.1101/gr.278931.124
...,267,201 million unique DNA fragments from open chromatin in liver were assayed. Thirty-four percent of these fragments (1,456,914) could be assigned to a specific TE insertion site (>50% overlap with a TE annotation) (Fig. 6B). Of the TE-derived sequence fragments assayed, 1.2% had transcriptional regulatory...
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Method: Integration of high-throughput proteomic data and complementary omics layers with PriOmics
- Robin Kosch,
- Katharina Limm,
- Annette M. Staiger,
- Nadine S. Kurz,
- Nicole Seifert,
- Bence Oláh,
- Stefan Solbrig,
- Viola Poeschel,
- Gerhard Held,
- Marita Ziepert,
- Norbert Schmitz,
- Emil Chteinberg,
- Reiner Siebert,
- Rainer Spang,
- Helena U. Zacharias,
- German Ott,
- Peter J. Oefner,
- and Michael Altenbuchinger
Genome Res. January 2026 36: 197-213; Published in Advance November 18, 2025, doi:10.1101/gr.279487.124
...lymphoma (DLBCL) data set in which we integrate SWATH-MS-based proteomics with transcriptomic and phenotypic data.State-of-the-art proteomic approaches such as liquid chromatography coupled to quadrupole-time of flight tandem mass spectrometry (LC-QTOF-MS/MS) facilitate the high-throughput characterization...
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Method: Nanopore sequencing identifies high-frequency somatic structural variations in laryngeal squamous cell carcinoma genomes
- Xuyan Liu,
- Lin Xia,
- Yixin Qiao,
- Yang Li,
- Yan Huang,
- Bingyan Yue,
- Xi Liang,
- Xin Yang,
- Honghui Zhang,
- Jiaxun Zhang,
- Xiao Chen,
- Dan Xie,
- and Jifeng Liu
Genome Res. April 8, 2026 gr.281046.125; Published in Advance April 8, 2026, doi:10.1101/gr.281046.125
...evaluation of simple somatic variants (e.g., INS, DEL, DUP), 527 as type-agnostic matching may misclassify genuine events. However, recent innovations 528 in high-throughput ultra-long-read sequencing technologies (Wang et al. 2021) and 529 graph-based or assembly-based long-read alignment algorithms (Li...
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Research: Assessing the readiness of Oxford Nanopore sequencing for clinical genomics applications
- Judith Arres,
- Santosh Elavalli,
- Shalini Behl,
- Daniel Matias Sanchez,
- Ayesha Al Ali,
- Abdelrahman Ahmed Yehia Abdelaziz Saad,
- Azza Attia,
- Cyla Minas,
- Sharika Pariyachery,
- Shariq Ahmed,
- Fatmah Aldhuhoori,
- Nitu Thulasidharan,
- Gurunath Katagi,
- Omar Soliman,
- Shilp Purohit,
- Vinay Kusuma,
- Raony Cardenas,
- Thyago Cardoso,
- Luis F. Paulin,
- Philippe Sanio,
- Joseph Mafofo,
- Haiguo Wu,
- Val Zvereff,
- Albarah El-Khani,
- Fahed Al Marzooqi,
- Tiago R. Magalhães,
- Fritz J. Sedlazeck,
- and Javier Quilez
Genome Res. March 2026 36: 460-471; Published in Advance February 11, 2026, doi:10.1101/gr.280134.124
...Coriell reference samples to evaluate the performance of high-throughput sequencing (HTS) technologies in accurately detecting genetic variants. The samples were ordered from the Coriell Institute for Medical Research, which provides well-characterized reference materials with publicly available genetic...
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Research: Transposon accumulation at xenobiotic gene family loci in aphids
- Tobias Baril,
- Adam Pym,
- Chris Bass,
- and Alex Hayward
Genome Res. October 2023 33: 1718-1733; Published in Advance October 18, 2023, doi:10.1101/gr.277820.123
.... There is no mechanistic basis to suggest that TEs specifically target the regions surrounding XGFs as insertion sites compared with other genomic locations. Instead, under this model, TE insertions at XGFs are more likely to be retained and spread through the host population (compared with TE insertions at other loci...
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Research: Genetic effects on chromatin accessibility uncover mechanisms of liver gene regulation and quantitative traits
- Kevin W. Currin,
- Hannah J. Perrin,
- Gautam K. Pandey,
- Abdalla A. Alkhawaja,
- Swarooparani Vadlamudi,
- Annie E. Musser,
- Amy S. Etheridge,
- K. Alaine Broadaway,
- Jonathan D. Rosen,
- Arushi Varshney,
- Amarjit S. Chaudhry,
- Paul J. Gallins,
- Fred A. Wright,
- Yi-hui Zhou,
- Stephen C.J. Parker,
- Laura M. Raffield,
- Erin G. Schuetz,
- Federico Innocenti,
- and Karen L. Mohlke
Genome Res. July 2025 35: 1485-1502; Published in Advance May 20, 2025, doi:10.1101/gr.279741.124
...of Michigan, Ann Arbor, Michigan 48109, USA; 9Department of Biostatistics, Center for Statistical Genetics, University of Michigan, Ann Arbor, Michigan 48109, USA Corresponding author: mohlke@med.unc.eduAbstractChromatin accessibility quantitative trait locus (caQTL) studies have identified regulatory...
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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
...nested PCR or high-throughput sequencing (HTS), which may introduce bias and is restricted to detecting junctions between HBV and host s. Recently, the advancement of long-read sequencing has improved our understanding of HBV integration and its role in HCC development. HBV can integrate into the human...
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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
...), and the development of microarrays first (Schena et al. 1995) and high-throughput sequencing later (Margulies et al. 2005) boosted our capacity to analyze transcriptomes. Nowadays, the most common technique to analyze gene expression is RNA sequencing (RNA-seq). This technique consists of first isolating RNA from...
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Research: Expanded methylome and quantitative trait loci detection by long-read profiling of personal DNA
- Cristian Groza,
- Bing Ge,
- Warren A. Cheung,
- Tomi Pastinen,
- and Guillaume Bourque
Genome Res. April 2025 35: 644-652; Published in Advance March 20, 2025, doi:10.1101/gr.279240.124
...methylation level in these bins (Methods). Then, we identified SV alleles and methylation bins within 100 kbp flanking sequence and performed 124.9 × 106 SVs act as methylation quantitative trait loci (SV-mQTL) tests (Supplemental Fig. S12). We detected 230,464 methylation bins that were in QTL with 76,677 SV...
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Method: Genome skimming with nanopore sequencing precisely determines global and transposon DNA methylation in vertebrates
- Christopher Faulk
Genome Res. June 2023 33: 948-956; Published in Advance July 13, 2023, doi:10.1101/gr.277743.123
...pyrosequencing, which amplifies a random mixture of transposons of a particular family and quantitates methylation at few specific CpG sites that are of unknown conservation in the bisulfite amplicon, leading to error and poor replication. Even at 0.001× coverage, equating to just 3 Mb of sequence, I was able...

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