Searching journal content for articles similar to Zeglinski et al. 34 (11): 1966.

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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
...committee of Changhai Hospital. Written consent was obtained from the patients. The clinicopathological information of the patients is listed in Supplemental Table S1.DNA and RNA extractionHigh-molecular-weight (HMW) gDNA and total RNA were extracted from fresh-frozen tumor and matched nontumor tissues...
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Resource: High-quality sika deer omics data and integrative analysis reveal genic and cellular regulation of antler regeneration
- Zihe Li,
- Ziyu Xu,
- Lei Zhu,
- Tao Qin,
- Jinrui Ma,
- Zhanying Feng,
- Huishan Yue,
- Qing Guan,
- Botong Zhou,
- Ge Han,
- Guokun Zhang,
- Chunyi Li,
- Shuaijun Jia,
- Qiang Qiu,
- Dingjun Hao,
- Yong Wang,
- and Wen Wang
Genome Res. January 2025 35: 188-201; Published in Advance November 14, 2024, doi:10.1101/gr.279448.124
....07%–1.53%) (Supplemental Table S3) sika deer assemblies (Han et al. 2022; Xing et al. 2023). Utilizing a range of methods, including RNA-seq and Iso-Seq transcriptome data (Supplemental Table S4), gene projection based on alignment, protein homology annotation, and de novo annotation, we annotated a total of 22...
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Research: Long-read transcriptome sequencing of CLL and MDS patients uncovers molecular effects of SF3B1 mutations
- Alicja Pacholewska,
- Matthias Lienhard,
- Mirko Brüggemann,
- Heike Hänel,
- Lorina Bilalli,
- Anja Königs,
- Felix Heß,
- Kerstin Becker,
- Karl Köhrer,
- Jesko Kaiser,
- Holger Gohlke,
- Norbert Gattermann,
- Michael Hallek,
- Carmen D. Herling,
- Julian König,
- Christina Grimm,
- Ralf Herwig,
- Kathi Zarnack,
- and Michal R. Schweiger
Genome Res. November 2024 34: 1832-1848; Published in Advance September 13, 2024, doi:10.1101/gr.279327.124
....Splicing is a fundamental step in eukaryotic gene expression in which noncoding introns are removed from premessenger RNA (pre-mRNA) transcripts and exons are joined to form mature mRNAs. This intricate process is often disrupted in cancer, either by mutations in spliceosomal genes or by other mechanisms that affect normal...
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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...
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Method: Accurate typing of short tandem repeats from genome-wide sequencing data and its applications
- Arkarachai Fungtammasan,
- Guruprasad Ananda,
- Suzanne E. Hile,
- Marcia Shu-Wei Su,
- Chen Sun,
- Robert Harris,
- Paul Medvedev,
- Kristin Eckert,
- and Kateryna D. Makova
Genome Res. May 2015 25: 736-749; Published in Advance March 30, 2015, doi:10.1101/gr.185892.114
...preparation protocol (hereafter called “PCR−”) is expected to improve STR genotyping accuracy. The direct advantage of limiting PCR steps during NGS is the increased uniformity of the sequencing depth (Kozarewa et al. 2009). Also, this protocol eliminates duplicate reads that obscure allele frequency...
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Method: High-throughput phenotyping using parallel sequencing of RNA interference targets in the African trypanosome
- Sam Alsford,
- Daniel J. Turner,
- Samson O. Obado,
- Alejandro Sanchez-Flores,
- Lucy Glover,
- Matthew Berriman,
- Christiane Hertz-Fowler,
- and David Horn
Genome Res. June 2011 21: 915-924; Published in Advance March 1, 2011, doi:10.1101/gr.115089.110
....’’ Full exploitation of the TriTryp sequences requires the continued development of versatile approaches for -scale functional analyses. RNA interference (RNAi) mediated knockdown has proven to be an excellent functional analysis tool for T. brucei but has been largely limited to a piecemeal gene-by-gene...
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Method: Long-read Ribo-STAMP simultaneously measures transcription and translation with isoform resolution
- Pratibha Jagannatha,
- Alexandra T. Tankka,
- Daniel A. Lorenz,
- Tao Yu,
- Brian A. Yee,
- Kristopher W. Brannan,
- Cathy J. Zhou,
- Jason G. Underwood,
- and Gene W. Yeo
Genome Res. November 2024 34: 2012-2024; Published in Advance June 21, 2024, doi:10.1101/gr.279176.124
...to simultaneously profile translation and transcription at both the gene and mRNA isoform levels. We also developed the EditsC metric to quantify editing and leverage the single-molecule, full-length transcript information provided by long-read sequencing. Here, we report concordance between gene-level translation...
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Resource: Charting the regulatory landscape of TP53 on transposable elements in cancer
- Xuan Qu,
- Yonghao Liang,
- Colin McCornack,
- Xiaoyun Xing,
- Heather Schmidt,
- Chad Tomlinson,
- Catrina Fronick,
- Edward A. Belter, Jr.,
- Juan F. Macias-Velasco,
- and Ting Wang
Genome Res. June 2025 35: 1456-1471; Published in Advance May 13, 2025, doi:10.1101/gr.279398.124
...ECL Imager (Thermo Fisher Scientific, 62236).Library preparation for ONT cDNA long-read sequencingTotal RNA was extracted with the RNeasy mini kit (Qiagen, 74104). Two hundred nanograms of total RNA was input into the PCR-cDNA Barcoding kit (Oxford Nanopore Technologies, SQK-PCB111.24). A custom primer...
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Review: Artificial intelligence and machine learning in cell-free-DNA-based diagnostics
- W.H. Adrian Tsui,
- Spencer C. Ding,
- Peiyong Jiang,
- and Y.M. Dennis Lo
Genome Res. January 2025 35: 1-19; doi:10.1101/gr.278413.123
...et al. 2019; Jiang et al. 2020a), cfDNA tissue-of-origin deconvolution (Li et al. 2023b), and direct methylation analysis in single-molecule real-time (SMRT) sequencing (Tse et al. 2021).An essential component in ML is to find the best model parameters that achieve the desired performance...
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Review: Navigating the landscape of epitranscriptomics and host immunity
- Elaine Huang,
- Clara Frydman,
- and Xinshu Xiao
Genome Res. April 2024 34: 515-529; Published in Advance May 3, 2024, doi:10.1101/gr.278412.123
...et al. 2023), are capable of quantitatively estimating the modification level of each site based on nucleotide deletion signatures.In addition to these antibody and chemical-based detection methods, nanopore direct sequencing of full-length native RNA molecules is increasingly receiving attention...

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