Searching journal content for articles similar to Cozma et al. 12 (6): 969.

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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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Method: TFcomb identifies transcription factor combinations for cellular reprogramming based on single-cell multiomics data
- Chen Li,
- Sijie Chen,
- Yixin Chen,
- Haiyang Bian,
- Minsheng Hao,
- Lei Wei,
- and Xuegong Zhang
Genome Res. June 2025 35: 1429-1439; Published in Advance April 10, 2025, doi:10.1101/gr.279955.124
...–based methods (D'Alessio et al. 2015; Hammelman et al. 2022; Qiu et al. 2022) can also be a solution to identify the reprogramming TFs. For example, the differentially expressed TFs between target states and source states can be a candidate list of reprograming TFs. Although these TFs may be important during...
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Method: A new compression strategy to reduce the size of nanopore sequencing data
- Kavindu Jayasooriya,
- Sasha P. Jenner,
- Pasindu Marasinghe,
- Udith Senanayake,
- Hassaan Saadat,
- David Taubman,
- Roshan Ragel,
- Hasindu Gamaarachchi,
- and Ira W. Deveson
Genome Res. July 2025 35: 1574-1582; Published in Advance May 15, 2025, doi:10.1101/gr.280090.124
...be analyzed directly to identify ‘modified’ DNA (Simpson et al. 2017; Zhang et al. 2023) or RNA (Jain et al. 2022) bases, DNA damage (An et al. 2015), RNA secondary structures (Bizuayehu et al. 2022; Stephenson et al. 2022), or other features beyond the primary nucleotide sequence (Wan et al. 2022). Because...
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Research: Loss of epigenetic suppression of retrotransposons with oncogenic potential in aging mammary luminal epithelial cells
- Parijat Senapati,
- Masaru Miyano,
- Rosalyn W. Sayaman,
- Mudaser Basam,
- Amy Leung,
- Mark A. LaBarge,
- and Dustin E. Schones
Genome Res. August 2023 33: 1229-1241; Published in Advance July 18, 2023, doi:10.1101/gr.277511.122
.... Furthermore, because of a higher cost associated with WGBS experiments, we were able to profile a limited number of individual samples. In the future, a more targeted approach will be needed that will use candidate regions identified in our study to detect DNA methylation changes in a larger number of samples...
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Research: The Chinese longsnout catfish genome provides novel insights into the feeding preference and corresponding metabolic strategy of carnivores
- Yulong Liu,
- Gang Zhai,
- Jingzhi Su,
- Yulong Gong,
- Bingyuan Yang,
- Qisheng Lu,
- Longwei Xi,
- Yutong Zheng,
- Jingyue Cao,
- Haokun Liu,
- Junyan Jin,
- Zhimin Zhang,
- Yunxia Yang,
- Xiaoming Zhu,
- Zhongwei Wang,
- Gaorui Gong,
- Jie Mei,
- Zhan Yin,
- Rodolphe E. Gozlan,
- Shouqi Xie,
- and Dong Han
Genome Res. July 2024 34: 981-996; Published in Advance August 9, 2024, doi:10.1101/gr.278476.123
...preference and the corresponding metabolic strategies that differentiate feeding habits remain elusive. Here, by comparing the whole of a typical carnivorous fish (Leiocassis longirostris Günther) with that of herbivorous fish, we identify 250 genes through both positive selection and rapid evolution...
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Research: Analysis of canine gene constraint identifies new variants for orofacial clefts and stature
- Reuben M. Buckley,
- Nüket Bilgen,
- Alexander C. Harris,
- Peter Savolainen,
- Cafer Tepeli,
- Metin Erdoğan,
- Aitor Serres Armero,
- Dayna L. Dreger,
- Frank G. van Steenbeek,
- Marjo K. Hytönen,
- Heidi G. Parker,
- Jessica Hale,
- Hannes Lohi,
- Bengi Çınar Kul,
- Adam R. Boyko,
- and Elaine A. Ostrander
Genome Res. May 2025 35: 1080-1093; Published in Advance March 24, 2025, doi:10.1101/gr.280092.124
...metrics (Gough et al. 2018; Plassais et al. 2019; Dutrow et al. 2022; Morrill et al. 2022).In humans, candidate trait and disease variants are generally identified using a combination of strategies, including multiple species alignment, protein structure predictions, gene mutation tolerance, and machine...
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Research: Optical genome mapping identifies rare structural variants in neural tube defects
- Nikhil S. Sahajpal,
- Jane Dean,
- Benjamin Hilton,
- Timothy Fee,
- Cindy Skinner,
- Alex Hastie,
- Barbara R. DuPont,
- Alka Chaubey,
- Michael J. Friez,
- and Roger E. Stevenson
Genome Res. April 2025 35: 798-809; Published in Advance March 19, 2025, doi:10.1101/gr.279318.124
...was identified in this case. Additional comprehensive genomic/epigenomic analysis in a cohort of cases with pathogenic VANGL2 variants would be needed to identify candidate modifiers, if any.The anencephalic fetus with cervical rachischisis and multiple abnormalities (bilateral cleft lip and palate...
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Research: A hidden layer of structural variation in transposable elements reveals potential genetic modifiers in human disease-risk loci
- Elisabeth J. van Bree,
- Rita L.F.P. Guimarães,
- Mischa Lundberg,
- Elena R. Blujdea,
- Jimi L. Rosenkrantz,
- Fred T.G. White,
- Josse Poppinga,
- Paula Ferrer-Raventós,
- Anne-Fleur E. Schneider,
- Isabella Clayton,
- David Haussler,
- Marcel J.T. Reinders,
- Henne Holstege,
- Adam D. Ewing,
- Colette Moses,
- and Frank M.J. Jacobs
Genome Res. April 2022 32: 656-670; Published in Advance March 24, 2022, doi:10.1101/gr.275515.121
...of the GWAS-identified disease-risk loci, our data present structural variation in SVAs and other TEs as novel potential genetic modifiers of gene regulation in these loci.DiscussionOur study reveals that structural variations in SVAs are previously unknown candidates for causal genetic variants not captured...
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Resource: Modeling molecular development of breast cancer in canine mammary tumors
- Kiley Graim,
- Dmitriy Gorenshteyn,
- David G. Robinson,
- Nicholas J. Carriero,
- James A. Cahill,
- Rumela Chakrabarti,
- Michael H. Goldschmidt,
- Amy C. Durham,
- Julien Funk,
- John D. Storey,
- Vessela N. Kristensen,
- Chandra L. Theesfeld,
- Karin U. Sorenmo,
- and Olga G. Troyanskaya
Genome Res. February 2021 31: 337-347; Published in Advance December 23, 2020, doi:10.1101/gr.256388.119
...: non-neoplastic mammary gland tissues (normal), benign/premalignant, and malignant. We consider the three types of CMT samples in each of our patients as progression-ordered groups, enabling us for the first time to identify distinct signatures of gene expression reflective of progression from normal...
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Method: QuadST identifies cell–cell interaction–changed genes in spatially resolved transcriptomics data
- Xiaoyu Song,
- Yuqing Shang,
- Michelle E. Ehrlich,
- Panos Roussos,
- Guo-Cheng Yuan,
- and Pei Wang
Genome Res. August 2025 35: 1821-1831; Published in Advance June 23, 2025, doi:10.1101/gr.279859.124
...QuadST identifies cell–cell interaction–changed genes in spatially resolved transcriptomics data Xiaoyu Song1, Yuqing Shang1, Michelle E. Ehrlich2, Panos Roussos3,4, Guo-Cheng Yuan5 and Pei Wang6 1Centre for Quantitative Medicine, Duke-NUS Medical School, Singapore 169857; 2Departments of Neurology...
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