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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
...@cuhk.edu.hkAbstractThe discovery of circulating fetal and tumor cell-free DNA (cfDNA) molecules in plasma has opened up tremendous opportunities in noninvasive diagnostics such as the detection of fetal chromosomal aneuploidies and cancers and in posttransplantation monitoring. The advent of high-throughput sequencing...
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Research: Environmentally induced plasticity of programmed DNA elimination boosts somatic variability in Paramecium tetraurelia
- Valerio Vitali,
- Rebecca Hagen,
- and Francesco Catania
Genome Res. October 2019 29: 1693-1704; Published in Advance September 23, 2019, doi:10.1101/gr.245332.118
...that environmentally induced developmental thermoplasticity contributes to genotypic diversification in Paramecium.The DNA that is perpetuated by the germline is not always carried over to the soma in its entirety. In a broad range of eukaryotes, germline DNA sequences are reproducibly discarded at each round...
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Method: Efficient identification of Y chromosome sequences in the human and Drosophila genomes
- Antonio Bernardo Carvalho and
- Andrew G. Clark
Genome Res. November 2013 23: 1894-1907; Published in Advance August 6, 2013, doi:10.1101/gr.156034.113
...by a straight comparison of the short DNA words (k-mers) present in the assembled and female short-reads. We successfully applied the YGS method to two very different s, D. virilis and human. Genome Research 1895 www..org Efficient identification of Y chromosome sequences other sequenced Drosophila; its D...
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Method: Multisample motif discovery and visualization for tandem repeats
- Yaran Zhang,
- Marc Hulsman,
- Alex Salazar,
- Niccolò Tesi,
- Lydian Knoop,
- Sven van der Lee,
- Sanduni Wijesekera,
- Jana Krizova,
- Erik-Jan Kamsteeg,
- and Henne Holstege
Genome Res. April 2025 35: 850-862; Published in Advance November 13, 2024, doi:10.1101/gr.279278.124
...of repeats is tandem repeats (TRs), which are DNA sequences characterized by the contiguous repetition of at least one nucleotide, accounting for ∼6%–8% of the human (Cui et al. 2024; English et al. 2024; Rajan-Babu et al. 2024). TRs are broadly classified based on the size of their repetitive motif: TRs...
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Research: Historical RNA expression profiles from the extinct Tasmanian tiger
- Emilio Mármol-Sánchez,
- Bastian Fromm,
- Nikolay Oskolkov,
- Zoé Pochon,
- Panagiotis Kalogeropoulos,
- Eli Eriksson,
- Inna Biryukova,
- Vaishnovi Sekar,
- Erik Ersmark,
- Björn Andersson,
- Love Dalén,
- and Marc R. Friedländer
Genome Res. August 2023 33: 1299-1316; Published in Advance July 18, 2023, doi:10.1101/gr.277663.123
....marmol.sanchez@gmail.comAbstractPaleogenomics continues to yield valuable insights into the evolution, population dynamics, and ecology of our ancestors and other extinct species. However, DNA sequencing cannot reveal tissue-specific gene expression, cellular identity, or gene regulation, which are only attainable at the transcriptional level...
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Research: Machine learning identifies activation of RUNX/AP-1 as drivers of mesenchymal and fibrotic regulatory programs in gastric cancer
- Milad Razavi-Mohseni,
- Weitai Huang,
- Yu A. Guo,
- Dustin Shigaki,
- Shamaine Wei Ting Ho,
- Patrick Tan,
- Anders J. Skanderup,
- and Michael A. Beer
Genome Res. May 2024 34: 680-695; Published in Advance May 22, 2024, doi:10.1101/gr.278565.123
...for protein-coding genes whose expression and CN correlate. CN values are obtained by DNA sequencing, in which “−2” marks deep DNA deletion, “0” shows a normal diploid , and “+2” is for deep DNA amplification in the gene locus. Mann–Whitney U test P < 0.05. (E) CN variation is consistent with altered GATA4...
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Method: The Nubeam reference-free approach to analyze metagenomic sequencing reads
- Hang Dai and
- Yongtao Guan
Genome Res. September 2020 30: 1364-1375; Published in Advance September 3, 2020, doi:10.1101/gr.261750.120
...distance matrix and the case control status.The unmapped reads from WGS sequencing are more prone to artifacts produced in DNA handling and sequencing. Since Nubeam is a reference-free approach, we paid extraordinary attention to guard against possible artifacts. We performed additional quality controls...
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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
...regions, influenced by the unique tertiary structures of these regions, thereby affecting the sequencing output. In contrast, linear regression analysis was not applicable to data obtained from the oligo(dT)-based protocol. This method uses a poly(T) primer to initiate cDNA synthesis, focusing almost...
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Resource: A chromosome-scale epigenetic map of the Hydra genome reveals conserved regulators of cell state
- Jack F. Cazet,
- Stefan Siebert,
- Hannah Morris Little,
- Philip Bertemes,
- Abby S. Primack,
- Peter Ladurner,
- Matthias Achrainer,
- Mark T. Fredriksen,
- R. Travis Moreland,
- Sumeeta Singh,
- Suiyuan Zhang,
- Tyra G. Wolfsberg,
- Christine E. Schnitzler,
- Andreas D. Baxevanis,
- Oleg Simakov,
- Bert Hobmayer,
- and Celina E. Juliano
Genome Res. February 2023 33: 283-298; Published in Advance January 13, 2023, doi:10.1101/gr.277040.122
...promoter regions.Hydra chromatin is organized into localized contact domainsThe three-dimensional organization of DNA molecules in the nucleus is tightly linked to regulation (Szabo et al. 2019). Although several cnidarian Hi-C data sets have been published (Supplemental Table S4; Li et al. 2020; Nong et...
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Research: Transposable element accumulation drives size differences among polymorphic Y Chromosomes in Drosophila
- Alison H. Nguyen,
- Weixiang Wang,
- Emily Chong,
- Kamalakar Chatla,
- and Doris Bachtrog
Genome Res. June 2022 32: 1074-1088; Published in Advance May 2, 2022, doi:10.1101/gr.275996.121
..., which replicate all the DNA, including heterochromatin. We found that YL males had a higher proportion of DNA underreplicated in thoracic cells compared with the YS males (i.e., the sequenced strain male) and females from the sequenced strain; YM had intermediate levels of underreplicated DNA (Fig. 1D...

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