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Research: Multisite long-read sequencing reveals the early contributions of somatic structural variations to HBV-related hepatocellular carcinoma tumorigenesis
- Tianfu Zeng,
- Haotian Liao,
- Lin Xia,
- Siyao You,
- Yanqun Huang,
- Jiaxun Zhang,
- Yahui Liu,
- Xuyan Liu,
- and Dan Xie
Genome Res. April 2025 35: 671-685; Published in Advance March 4, 2025, doi:10.1101/gr.279617.124
...half of HCC cases globally occur in China, where chronic hepatitis B virus (HBV) infection is the major etiological factor, accounting for over 60% of cases (Llovet et al. 2021; Bray et al. 2024; Chen et al. 2024a). Somatic DNA alterations are known as pivotal drivers of HCC tumorigenesis...
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Method: High-throughput single-cell functional elucidation of neurodevelopmental disease–associated genes reveals convergent mechanisms altering neuronal differentiation
- Matthew A. Lalli,
- Denis Avey,
- Joseph D. Dougherty,
- Jeffrey Milbrandt,
- and Robi D. Mitra
Genome Res. September 2020 30: 1317-1331; Published in Advance September 4, 2020, doi:10.1101/gr.262295.120
...Matthew A. Lalli1,2, Denis Avey1,2, Joseph D. Dougherty1,3, Jeffrey Milbrandt1 and Robi D. Mitra1,2 1Department of Genetics, Washington University in St. Louis School of Medicine, St. Louis, Missouri 63110, USA; 2Edison Family Center for Genome Sciences and Systems Biology, Washington University...
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Research: Single-cell gene expression analysis reveals regulators of distinct cell subpopulations among developing human neurons
- Jiaxu Wang,
- Piroon Jenjaroenpun,
- Akshay Bhinge,
- Vladimir Espinosa Angarica,
- Antonio Del Sol,
- Intawat Nookaew,
- Vladimir A. Kuznetsov,
- and Lawrence W. Stanton
Genome Res. November 2017 27: 1783-1794; Published in Advance October 13, 2017, doi:10.1101/gr.223313.117
...cells were transfected with plko.1, psPAX2, and VSVg at the ratio of 4:3:1. Culture medium was changed 12 h after transfection. Virus was collected after an additional 36 h and used for NPC infection. NPCs were changed to fresh medium. Short hairpin RNAs cloned in PLKO.1 vector are shown in Supplemental...
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Research: mRNA deep sequencing reveals 75 new genes and a complex transcriptional landscape in Mimivirus
- Matthieu Legendre,
- Stéphane Audic,
- Olivier Poirot,
- Pascal Hingamp,
- Virginie Seltzer,
- Deborah Byrne,
- Audrey Lartigue,
- Magali Lescot,
- Alain Bernadac,
- Julie Poulain,
- Chantal Abergel,
- and Jean-Michel Claverie
Genome Res. May 2010 20: 664-674; Published in Advance April 1, 2010, doi:10.1101/gr.102582.109
..., Genoscope, FR-91057 Evry, France Abstract Mimivirus, a virus infecting Acanthamoeba , is the prototype of the Mimiviridae , the latest addition to the nucleocytoplasmic large DNA viruses. The Mimivirus genome encodes close to 1000 proteins, many of them never before encountered in a virus...
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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
...the accuracy of the IGH assemblies using Pacific Biosciences HiFi reads, demonstrating near-complete sequence congruence, with only some residual indel errors. Moreover, when applied to the reference material HG002, our pipeline reveals no base differences and a limited number of indels compared...
ARTICLE: Genetic subtyping of human immunodeficiency virus using a heteroduplex mobility assay.
- E L Delwart,
- B Herring,
- A G Rodrigo,
- and J I Mullins
Genome Res. April 1995 4: S202-S216
....L. Mullins, J.I. and Rübsamen-Waigmann. H. 1994 . Genetic analysis of human immunodeficiency virus type 1 and 2 (HIV-1 and HIV-2) mixed infections in India reveals a recent spread of HIV-1 and HIV-2 from a single ancestor for each of these viruses. J. Virol. 68 : 2161 – 2168 . 59. Kuiken, C., Zwart, G. Baan...
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Review: Understanding isoform expression by pairing long-read sequencing with single-cell and spatial transcriptomics
- Natan Belchikov,
- Justine Hsu,
- Xiang Jennie Li,
- Julien Jarroux,
- Wen Hu,
- Anoushka Joglekar,
- and Hagen U. Tilgner
Genome Res. November 2024 34: 1735-1746; doi:10.1101/gr.279640.124
...(Wang et al. 2024).The central nervous system features multiple cell types arranged in complex networks that vary and even migrate during development. Our analysis of the prefrontal cortex and hippocampus of the postnatal mouse revealed the predominance of cell-type specificity in driving isoform...
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Research: Mapping genome variation of SARS-CoV-2 worldwide highlights the impact of COVID-19 super-spreaders
- Alberto Gómez-Carballa,
- Xabier Bello,
- Jacobo Pardo-Seco,
- Federico Martinón-Torres,
- and Antonio Salas
Genome Res. October 2020 30: 1434-1448; Published in Advance September 2, 2020, doi:10.1101/gr.266221.120
...Cauley 2017) provides public access to the most complete collection of genetic sequences of several viruses, with special emphasis on influenza viruses. In 2020, GISAID started to compile sequence data from the virus causing COVID-19, and now it makes thousands of genomic sequences of the virus available...
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Method: De novo assembly of viral quasispecies using overlap graphs
- Jasmijn A. Baaijens,
- Amal Zine El Aabidine,
- Eric Rivals,
- and Alexander Schönhuth
Genome Res. May 2017 27: 835-848; Published in Advance April 10, 2017, doi:10.1101/gr.215038.116
...tools. We also apply SAVAGE on two deep-coverage samples of patients infected by the Zika and the hepatitis C virus, respectively, which sheds light on the genetic structures of the respective viral quasispecies. [Supplemental material is available for this article.] Viruses such as HIV, Zika, and Ebola...
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Method: Massively parallel cis-regulatory analysis in the mammalian central nervous system
- Susan Q. Shen,
- Connie A. Myers,
- Andrew E.O. Hughes,
- Leah C. Byrne,
- John G. Flannery,
- and Joseph C. Corbo
Genome Res. February 2016 26: 238-255; Published in Advance November 17, 2015, doi:10.1101/gr.193789.115
...of species. We reasoned that adeno-associated virus (AAV), a nonpathogenic virus commonly used for gene therapy studies, would be suitable for this purpose. AAV causes long-lasting infection in rodents and primates, and its tissue tropism ranges by serotype from promiscuous Cis -regulome analysis in the CNS...

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