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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
...and transfected into the HCC cell lines HuH-7 and Hep G2, and the luciferase activity was measured 32 h later. As expected, HBV-Enh I increased MYOCD promoter-Luc-reporter activity (Fig. 8C). The following stable MYOCD-overexpressing HCC cell lines (HuH7-MYOCD-OE and Hep G2-MYOCD-OE) were subsequently constructed...
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Resource: Binding profiles for 961 Drosophila and C. elegans transcription factors reveal tissue-specific regulatory relationships
- Michelle Kudron,
- Louis Gevirtzman,
- Alec Victorsen,
- Bridget C. Lear,
- Jiahao Gao,
- Jinrui Xu,
- Swapna Samanta,
- Emily Frink,
- Adri Tran-Pearson,
- Chau Huynh,
- Dionne Vafeados,
- Ann Hammonds,
- William Fisher,
- Martha Wall,
- Greg Wesseling,
- Vanessa Hernandez,
- Zhichun Lin,
- Mary Kasparian,
- Kevin White,
- Ravi Allada,
- Mark Gerstein,
- LaDeana Hillier,
- Susan E. Celniker,
- Valerie Reinke,
- and Robert H. Waterston
Genome Res. December 2024 34: 2319-2334; Published in Advance October 22, 2024, doi:10.1101/gr.279037.124
...total data sets) were generated after Kudron et al. (2018). A total of 356 worm TFs (56% of targeted TFs) in 525 different experiments have ChIP-seq data (Table 1), of which 350 were included in later analyses. Of these TF data sets, 166 (174 total data sets) were generated after Kudron et al. (2018...
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Research: Vertebrates show coordinated elevated expression of mitochondrial and nuclear genes after birth
- Hadar Medini and
- Dan Mishmar
Genome Res. March 2025 35: 459-474; Published in Advance March 4, 2025, doi:10.1101/gr.279700.124
...DNA genes expression was observed at 585 min postfertilization (mpf), whereas elevated expression of nuclear DNA-encoded structural OXPHOS genes was observed shortly later, 645 mpf (Fig. 6A; Supplemental Figs. S49, S50); the elevated expression of both s preceded the onset of muscle twitching (840 mpf; i...
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Method: Robust analysis of prokaryotic pangenome gene gain and loss rates with Panstripe
- Gerry Tonkin-Hill,
- Rebecca A. Gladstone,
- Anna K. Pöntinen,
- Sergio Arredondo-Alonso,
- Stephen D. Bentley,
- and Jukka Corander
Genome Res. January 2023 33: 129-140; Published in Advance January 20, 2023, doi:10.1101/gr.277340.122
...and Microbes, Wellcome Sanger Institute, Cambridge CB10 1RQ, United Kingdom; 3Helsinki Institute for Information Technology HIIT, Department of Mathematics and Statistics, University of Helsinki, 00014 Helsinki, Finland Corresponding author: gerryt@uio.noAbstractHorizontal gene transfer (HGT) plays a critical...
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Research: Kinetic networks identify TWIST2 as a key regulatory node in adipogenesis
- Arun B. Dutta,
- Daniel S. Lank,
- Roza K. Przanowska,
- Piotr Przanowski,
- Lixin Wang,
- Bao Nguyen,
- Ninad M. Walavalkar,
- Fabiana M. Duarte,
- and Michael J. Guertin
Genome Res. March 2023 33: 314-331; Published in Advance February 21, 2023, doi:10.1101/gr.277559.122
...significantly between two time points to infer binding or dissociation; (4) the direction of accessibility changes must match with the molecular function of the TF as defined in Figure 1; (5) members of the TF family must be expressed at the appropriate time point (e.g., the TF must be expressed at the later...
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Research: Local nucleosome dynamics and eviction following a double-strand break are reversible by NHEJ-mediated repair in the absence of DNA replication
- Vinay Tripuraneni,
- Gonen Memisoglu,
- Heather K. MacAlpine,
- Trung Q. Tran,
- Wei Zhu,
- Alexander J. Hartemink,
- James E. Haber,
- and David M. MacAlpine
Genome Res. May 2021 31: 775-788; Published in Advance April 2, 2021, doi:10.1101/gr.271155.120
...-establishment of the prelesion chromatin landscape suggests that a DNA replication-independent mechanism exists to preserve epi organization following DSB repair.Failure to repair DNA double-strand breaks (DSBs) results in cell cycle arrest and ultimately programmed cell death, whereas improper repair can lead to profound...
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Resource: The EnteroBase user's guide, with case studies on Salmonella transmissions, Yersinia pestis phylogeny, and Escherichia core genomic diversity
- Zhemin Zhou,
- Nabil-Fareed Alikhan,
- Khaled Mohamed,
- Yulei Fan,
- the Agama Study Group,
- and Mark Achtman
Genome Res. January 2020 30: 138-152; Published in Advance December 6, 2019, doi:10.1101/gr.251678.119
...Base tools GrapeTree (Zhou et al. 2018a) and Dendrogram, which in turn can transfer data to external websites such as Microreact (Argimón et al. 2016).View this table: In this window In a new window Table 1. Basic statistics on EnteroBaseResultsOverview of EnteroBaseThe EnteroBase back end consists...
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Research: Somatic structural variation targets neurodevelopmental genes and identifies SHANK2 as a tumor suppressor in neuroblastoma
- Gonzalo Lopez,
- Karina L. Conkrite,
- Miriam Doepner,
- Komal S. Rathi,
- Apexa Modi,
- Zalman Vaksman,
- Lance M. Farra,
- Eric Hyson,
- Moataz Noureddine,
- Jun S. Wei,
- Malcolm A. Smith,
- Shahab Asgharzadeh,
- Robert C. Seeger,
- Javed Khan,
- Jaime Guidry Auvil,
- Daniela S. Gerhard,
- John M. Maris,
- and Sharon J. Diskin
Genome Res. September 2020 30: 1228-1242; Published in Advance August 13, 2020, doi:10.1101/gr.252106.119
...at the University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA ↵13 These authors contributed equally to this work. Corresponding author: diskin@email.chop.eduAbstractNeuroblastoma is a malignancy of the developing sympathetic nervous system that accounts for 12% of childhood cancer deaths. Like many...
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Resource: GenTree, an integrated resource for analyzing the evolution and function of primate-specific coding genes
- Yi Shao,
- Chunyan Chen,
- Hao Shen,
- Bin Z. He,
- Daqi Yu,
- Shuai Jiang,
- Shilei Zhao,
- Zhiqiang Gao,
- Zhenglin Zhu,
- Xi Chen,
- Yan Fu,
- Hua Chen,
- Ge Gao,
- Manyuan Long,
- and Yong E. Zhang
Genome Res. April 2019 29: 682-696; Published in Advance March 12, 2019, doi:10.1101/gr.238733.118
...by promoting immune cell death (Than et al. 2009). LGALS16 shows strong LD in African population as shown by an outlier iHS score (1.81, Supplemental Table S13), suggesting that this gene may be subject to local adaptation. In contrast, HM7, which contains adult brain-biased genes, shows a significant deficit...
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Method: A graph neural network model to estimate cell-wise metabolic flux using single-cell RNA-seq data
- Norah Alghamdi,
- Wennan Chang,
- Pengtao Dang,
- Xiaoyu Lu,
- Changlin Wan,
- Silpa Gampala,
- Zhi Huang,
- Jiashi Wang,
- Qin Ma,
- Yong Zang,
- Melissa Fishel,
- Sha Cao,
- and Chi Zhang
Genome Res. October 2021 31: 1867-1884; Published in Advance July 22, 2021, doi:10.1101/gr.271205.120
...of information transfer in belief propagation, which has been commonly used in analyzing cyclic networks such as Markov random field (Lan et al. 2006). Specifically, L is minimized by iteratively minimizing the flux imbalance of Ck and the weighted sum of the flux imbalance of the Hop-2 neighbors of Ck...
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