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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
...Hsin-Yen Larry Wu, Isaiah D. Kaufman and Polly Yingshan Hsu Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan 48824, USA Corresponding author: pollyhsu@msu.eduAbstractVisualizing Ribo-seq and other sequencing data within genes of interest...
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Method: Deep structural clustering reveals hidden systematic biases in RNA sequencing data
- Qiang Su,
- Yi Long,
- Deming Gou,
- Junmin Quan,
- Xiaoming Zhou,
- and Qizhou Lian
Genome Res. November 2025 35: 2563-2577; Published in Advance September 19, 2025, doi:10.1101/gr.280713.125
...biological functions (Le and Maizel 1997; Cheng et al. 2001). The VAE-GMM k-mer clustering model, by combining deep neural networks with probabilistic clustering and dimensionality reduction techniques, offers a promising framework for decoding high-dimensional RNA sequence structures and uncovering latent...
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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
...Nanopore sequencing identifies high-frequency somatic structural 1 variations in laryngeal squamous cell carcinoma s 2 Xuyan Liu1#, Lin Xia1#, Yixin Qiao2#, Yang Li1, Yan Huang1, Bingyan Yue2, Xi Liang2, Xin 3 Yang2, Honghui Zhang2, Jiaxun Zhang1, Xiao Chen1, Dan Xie1*, Jifeng Liu2,3* 4 1...
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Research: Centromeric instability and chromoanasynthesis observed in nine supernumerary marker chromosomes resolved with long-read genome sequencing
- Kristine Bilgrav Saether,
- Angelo Salazar Mantero,
- Marlene Ek,
- Maria Pettersson,
- Elisabeth Syk Lundberg,
- Christopher M. Grochowski,
- Claudia M.B. Carvalho,
- Jesper Eisfeldt,
- and Anna Lindstrand
Genome Res. April 2026 36: 661-670; Published in Advance March 25, 2026, doi:10.1101/gr.281175.125
...structure of the derivative Chromosome 7 identified in RD_P328. (B) Integrative Genomics Viewer images of short-read sequencing (srGS) and long-read sequencing (lrGS) data for each BPJ. (C) Breakpoint sequences of the two BPJs with the chimeric sequence in the center aligned to the reference sequences shown...
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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
...1, Raony Cardenas1, Thyago Cardoso1, Luis F. Paulin2, Philippe Sanio2, Joseph Mafofo1, Haiguo Wu1, Val Zvereff1, Albarah El-Khani1, Fahed Al Marzooqi1, Tiago R. Magalhães1, Fritz J. Sedlazeck2,3,4 and Javier Quilez1 1M42, Abu Dhabi, United Arab Emirates; 2Human Genome Sequencing Center, Baylor...
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Research: Long-read DNA and cDNA sequencing identify cancer-predisposing deep intronic variation in tumor-suppressor genes
- Suleyman Gulsuner,
- Amal AbuRayyan,
- Jessica B. Mandell,
- Ming K. Lee,
- Greta V. Bernier,
- Barbara M. Norquist,
- Sarah B. Pierce,
- Mary-Claire King,
- and Tom Walsh
Genome Res. November 2024 34: 1825-1831; Published in Advance September 13, 2024, doi:10.1101/gr.279158.124
...are benign, but some extremely rare or private deep intronic variants lead to exonification of intronic sequence with abnormal transcriptional consequences. Damaging variants of this class are likely underreported as causes of disease for several reasons: Most clinical DNA and RNA testing does not include...
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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
...; however, its oncogenic mechanisms remain incompletely understood because of limitations in detection methods and sample availability. In this study, we employ Oxford Nanopore Technologies (ONT) whole- sequencing and full-length transcriptome sequencing to characterize HBV integration events at the genomic...
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Resource: Whole-genome sequencing of diverse 351 cultured prokaryotes including as-yet-unsequenced type strains
- Shingo Kato,
- Sachiko Masuda,
- Arisa Shibata,
- Takashi Itoh,
- Mitsuo Sakamoto,
- Ken Shirasu,
- and Moriya Ohkuma
Genome Res. April 2026 36: 875-884; Published in Advance April 7, 2026, doi:10.1101/gr.281026.125
...Whole- sequencing of diverse 351 cultured prokaryotes including as-yet-unsequenced type strains Shingo Kato1, Sachiko Masuda2, Arisa Shibata2, Takashi Itoh1, Mitsuo Sakamoto1, Ken Shirasu2 and Moriya Ohkuma1 1Japan Collection of Microorganisms, RIKEN BioResource Research Center, Tsukuba, Ibaraki...
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Method: Ultra-long sequencing for contiguous haplotype resolution of the human immunoglobulin heavy-chain locus
- Mari B. Gornitzka,
- Egil Røsjø,
- Uddalok Jana,
- Easton E. Ford,
- Alan Tourancheau,
- William D. Lees,
- Zachary Vanwinkle,
- Melissa L. Smith,
- Corey T. Watson,
- and Andreas Lossius
Genome Res. October 2025 35: 2240-2251; Published in Advance August 21, 2025, doi:10.1101/gr.280400.125
...antibody repertoire and susceptibility to infectious and autoimmune diseases. However, repetitive sequences and complex structural variation pose significant challenges for large-scale characterization. Here, we introduce a method that combines Oxford Nanopore Technologies ultra-long sequencing...
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Method: Incorporating valuable prior knowledge to improve deep learning prediction of genetic perturbation responses
- Xiuhao Fu,
- Chao Yang,
- Chunyan Cui,
- Aoyun Geng,
- Yidi Sun,
- Chao Zha,
- Feifei Cui,
- Leyi Wei,
- Quan Zou,
- Xin Gao,
- and Zilong Zhang
Genome Res. March 26, 2026 gr.281523.125; Published in Advance March 26, 2026, doi:10.1101/gr.281523.125
....gao@kaust.edu.sa) Abstract 1 Genetic perturbation response prediction plays a critical role in virtual cell research, 2 yet the performance of current deep learning models still leaves room for 3 improvement. In this study, we present a prior-guided response inference model 4 (PRIM) that leverages a valuable priori...
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