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Research: Chromosome-wide profiling of X-chromosome inactivation and epigenetic states in fetal brain and placenta of the opossum, Monodelphis domestica
- Xu Wang,
- Kory C. Douglas,
- John L. VandeBerg,
- Andrew G. Clark,
- and Paul B. Samollow
Genome Res. January 2014 24: 70-83; Published in Advance September 24, 2013, doi:10.1101/gr.161919.113
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Research: A comparative analysis of whole genome sequencing of esophageal adenocarcinoma pre- and post-chemotherapy
- Ayesha Noorani,
- Jan Bornschein,
- Andy G. Lynch,
- Maria Secrier,
- Achilleas Achilleos,
- Matthew Eldridge,
- Lawrence Bower,
- Jamie M.J. Weaver,
- Jason Crawte,
- Chin-Ann Ong,
- Nicholas Shannon,
- Shona MacRae,
- Nicola Grehan,
- Barbara Nutzinger,
- Maria O'Donovan,
- Richard Hardwick,
- Simon Tavaré,
- Rebecca C. Fitzgerald,
- and on behalf of the Oesophageal Cancer Clinical and Molecular Stratification (OCCAMS) Consortium
Genome Res. June 2017 27: 902-912; Published in Advance May 2, 2017, doi:10.1101/gr.214296.116
...provided written consent for participation in this study and the staff at all participating sites. References The 1000Genomes Project Consortium. 2015. A global reference for human genetic variation. Nature 526: 6874. Alderson D, Langley RE, Nankivell MG, Blazeby JM, Griffin M, Crellin A, Grabsch HI ...
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Method: Parente2: a fast and accurate method for detecting identity by descent
- Jesse M. Rodriguez,
- Sivan Bercovici,
- Lin Huang,
- Roy Frostig,
- and Serafim Batzoglou
Genome Res. February 2015 25: 280-289; Published in Advance October 1, 2014, doi:10.1101/gr.173641.114
...a Creative Commons License (Attribution-NonCommercial 4.0 International), as described at http://creativecommons.org/licenses/by-nc/4.0/ . Huang, L Bercovici, S Sivan Frostig Roy Lin Huang JesseM Rodriguez Rodriguez, J.M Serafim Batzoglou Frostig, Roy L Huang Batzoglou Bercovici Bercovici Sivan ...
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Method: taxMaps: comprehensive and highly accurate taxonomic classification of short-read data in reasonable time
- André Corvelo,
- Wayne E. Clarke,
- Nicolas Robine,
- and Michael C. Zody
Genome Res. May 2018 28: 751-758; Published in Advance March 27, 2018, doi:10.1101/gr.225276.117
..., Bernstein N, Maritz JM, Reeves D, Gandara J, Chhangawala S, et al. 2015. Geospatial resolution of human and bacterial diversity with city-scale metagenomics. Cell Syst 1: 7287. Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ. 1990. Basic local alignment search tool. J Mol Biol 215: 403410. Bik HM ...
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Method: CRISPR RNAs trigger innate immune responses in human cells
- Sojung Kim,
- Taeyoung Koo,
- Hyeon-Gun Jee,
- Hee-Yeon Cho,
- Gyeorae Lee,
- Dong-Gyun Lim,
- Hyoung Shik Shin,
- and Jin-Soo Kim
Genome Res. March 2018 28: 367-373; Published in Advance February 22, 2018, doi:10.1101/gr.231936.117
...Laboratory Press This article, published in Genome Research, is available under a Creative Commons License (Attribution-NonCommercial 4.0 International), as described at http://creativecommons.org/licenses/by-nc/4.0/.References Cho SW, Kim S, Kim JM, Kim JS. 2013a. Targeted engineering in human cells ...
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Resource: Benchmarking small-variant genotyping in polyploids
- Daniel P. Cooke,
- David C. Wedge,
- and Gerton Lunter
Genome Res. February 2022 32: 403-408; Published in Advance December 29, 2021, doi:10.1101/gr.275579.121
...variant calling. Nat Biotechnol 39: 885892. doi:10.1038/s41587-021-00861-3 D'Hont A, Denoeud F, Aury J-M, Baurens F-C, Carreel F, Garsmeur O, Noel B, Bocs S, Droc G, Rouard M, Da Silva C, et al. 2012. The banana (Musa acuminata) and the evolution of monocotyledonous plants. Nature 488: 213217. doi:10 ...
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Method: Targeted, programmable, and precise tandem duplication in the mammalian genome
- Yaoge Jiao,
- Min Li,
- Xingyu He,
- Yanhong Wang,
- Junwei Song,
- Yun Hu,
- Li Li,
- Lifang Zhou,
- Lurong Jiang,
- Junyan Qu,
- Lifang Xie,
- Qiang Chen,
- and Shaohua Yao
Genome Res. May 2023 33: 779-786; Published in Advance June 9, 2023, doi:10.1101/gr.277261.122
...- and nuclease-based prime editing in human and mouse cells. Nucleic Acids Res 49: 1078510795. doi:10.1093/nar/gkab792 Anzalone AV, Randolph PB, Davis JR, Sousa AA, Koblan LW, Levy JM, Chen PJ, Wilson C, Newby GA, Raguram A, et al. 2019. Search-and-replace editing without double-strand breaks or donor DNA ...
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Research: Integration site-dependent HIV-1 promoter activity shapes host chromatin conformation
- Jack A. Collora and
- Ya-Chi Ho
Genome Res. June 9, 2023 gr.277698.123; Published in Advance June 9, 2023, doi:10.1101/gr.277698.123
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Research: Evolution of genome structure in the Drosophila simulans species complex
- Mahul Chakraborty,
- Ching-Ho Chang,
- Danielle E. Khost,
- Jeffrey Vedanayagam,
- Jeffrey R. Adrion,
- Yi Liao,
- Kristi L. Montooth,
- Colin D. Meiklejohn,
- Amanda M. Larracuente,
- and J.J. Emerson
Genome Res. March 2021 31: 380-396; Published in Advance February 9, 2021, doi:10.1101/gr.263442.120
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Resource: Visualization and analysis of medically relevant tandem repeats in nanopore sequencing of control cohorts with pathSTR
- Wouter De Coster,
- Ida Höijer,
- Inge Bruggeman,
- Svenn D'Hert,
- Malin Melin,
- Adam Ameur,
- and Rosa Rademakers
Genome Res. November 2024 34: 2074-2080; Published in Advance August 15, 2024, doi:10.1101/gr.279265.124
...Chiu R, Rajan-Babu I-S, Friedman JM, Birol I. 2021. Straglr: discovering and genotyping tandem repeat expansions using whole long-read sequences. Genome Biol 22: 224. doi:10.1186/s13059-021-02447-3 Cortese A, Beecroft SJ, Facchini S, Curro R, Cabrera-Serrano M, Stevanovski I, Chintalaphani SR ...
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