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Research: AGAP duplicons associate with structural diversity at Chromosome 10q11.22
- Stefania Fornezza,
- Vincenza Simona Delvecchio,
- William T. Harvey,
- Philip C. Dishuck,
- Evan E. Eichler,
- and Giuliana Giannuzzi
Genome Res. October 2024 34: 1487-1499; Published in Advance September 25, 2024, doi:10.1101/gr.279454.124
...structural variation at the Chromosome 10q11.22 region and gain insights into the molecular mechanisms of its genomic instability.ResultsDuplicon and gene annotation at Chromosome 10q11.22 in the T2T-CHM13 assemblyWe assessed SDs, protein-coding genes, and pseudogenes annotated at Chr 10: 46...
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Research: Interchromosomal core duplicons drive both evolutionary instability and disease susceptibility of the Chromosome 8p23.1 region
- Kiana Mohajeri,
- Stuart Cantsilieris,
- John Huddleston,
- Bradley J. Nelson,
- Bradley P. Coe,
- Catarina D. Campbell,
- Carl Baker,
- Lana Harshman,
- Katherine M. Munson,
- Zev N. Kronenberg,
- Milinn Kremitzki,
- Archana Raja,
- Claudia Rita Catacchio,
- Tina A. Graves,
- Richard K. Wilson,
- Mario Ventura,
- and Evan E. Eichler
Genome Res. November 2016 26: 1453-1467; Published in Advance October 7, 2016, doi:10.1101/gr.211284.116
...Nelson, BJ Mohajeri, K 1549-5469 genome;gr.211284.116 10.1101/gr.211284.116 1088-9051 Interchromosomal core duplicons drive both evolutionary instability and disease susceptibility of the Chromosome 8p23.1 region Mohajeri et al. Evolution of the Chromosome 8p23.1 region Interchromosomal core duplicons...
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LETTER: Neocentromeres in 15q24-26 Map to Duplicons Which Flanked an Ancestral Centromere in 15q25
- Mario Ventura,
- Jonathan M. Mudge,
- Valeria Palumbo,
- Sally Burn,
- Elisabeth Blennow,
- Mauro Pierluigi,
- Roberto Giorda,
- Orsetta Zuffardi,
- Nicoletta Archidiacono,
- Michael S. Jackson,
- and Mariano Rocchi
Genome Res. September 2003 13: 2059-2068; Published in Advance January 1, 2003, doi:10.1101/gr.1155103
...emergence have been reported, and it harbors a high density of chromosome-specific duplicons, rearrangements of which have been implicated as a susceptibility factor for panic and phobic disorders with joint laxity. We investigated the evolutionary history of this region in primates and found...
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LETTER: Additional Complexity on Human Chromosome 15q: Identification of a Set of Newly Recognized Duplicons (LCR15) on 15q11–q13, 15q24, and 15q26
- Miguel Angel Pujana,
- Marga Nadal,
- Mònica Gratacòs,
- Belén Peral,
- Katalin Csiszar,
- Rogelio González-Sarmiento,
- Lauro Sumoy,
- and Xavier Estivill
Genome Res. January 1, 2001 11: 98-111; doi:10.1101/gr.155601
...-like protein ( GLP ) and the SH3 domain-containing protein ( SH3P18 ) gene sequences and have the characteristics of duplicons. Because duplicons flank chromosome regions that are rearranged in human genomic disorders, the LCR15 described here could represent new elements of rearrangements affecting different...
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LETTER: Evolutionary dynamics of segmental duplications from human Y-chromosomal euchromatin/heterochromatin transition regions
- Stefan Kirsch,
- Claudia Münch,
- Zhaoshi Jiang,
- Ze Cheng,
- Lin Chen,
- Christiane Batz,
- Evan E. Eichler,
- and Werner Schempp
Genome Res. July 2008 18: 1030-1042; Published in Advance April 29, 2008, doi:10.1101/gr.076711.108
...and other great apes will undoubtedly reveal additional Y-derivative duplicons that could serve as genomic markers for subspecies identification in the great apes. Human Y-chromosomal SDs, for example, are absent on the rhesus macaque Y chromosome as the Old World monkeys diverged at the onset...
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METHODS: Sequence-Based Design of Single-Copy Genomic DNA Probes for Fluorescence In Situ Hybridization
- Peter K. Rogan,
- Patricia M. Cazcarro,
- and Joan H.M. Knoll
Genome Res. June 1, 2001 11: 1086-1094; doi:10.1101/gr.171701
.... ( 2000 ) The DNA sequence of human chromosome 21. Nature 405 : 311 – 319 . ↵ Ji Y. , Eichler E.E. , Schwartz S. , Nicholls R.D. ( 2000 ) Structure of chromosomal duplicons and their role in mediating human genomic disorders. Genome Res. 10 : 597 – 610 . ↵ Jurka J. ( 1998 ) Repeats in genomic DNA: mining...
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LETTER: Nonrecurrent MECP2 duplications mediated by genomic architecture-driven DNA breaks and break-induced replication repair
- Marijke Bauters,
- Hilde Van Esch,
- Michael J. Friez,
- Odile Boespflug-Tanguy,
- Martin Zenker,
- Angela M. Vianna-Morgante,
- Carla Rosenberg,
- Jaakko Ignatius,
- Martine Raynaud,
- Karen Hollanders,
- Karen Govaerts,
- Kris Vandenreijt,
- Florence Niel,
- Pierre Blanc,
- Roger E. Stevenson,
- Jean-Pierre Fryns,
- Peter Marynen,
- Charles E. Schwartz,
- and Guy Froyen
Genome Res. June 2008 18: 847-858; Published in Advance April 2, 2008, doi:10.1101/gr.075903.107
...Nonrecurrent MECP2 duplications mediated by genomic architecture-driven DNA breaks and break-induced replication repair Marijke Bauters 1 , 2 , 10 , Hilde Van Esch 3 , 10 , Michael J. Friez 4 , Odile Boespflug-Tanguy 5 , Martin Zenker 6...
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ARTICLE: Large-Scale Variation Among Human and Great Ape Genomes Determined by Array Comparative Genomic Hybridization
- Devin P. Locke,
- Richard Segraves,
- Lucia Carbone,
- Nicoletta Archidiacono,
- Donna G. Albertson,
- Daniel Pinkel,
- and Evan E. Eichler
Genome Res. March 1, 2003 13: 347-357; doi:10.1101/gr.1003303
...: 113 – 123 . ↵ Jain A.N. , Tokuyasu T.A. , Snijders A.M. , Segraves R. , Albertson D.G. , Pinkel D. ( 2002 ) Fully automatic quantification of microarray image data. Genome Res. 12 : 325 – 332 . ↵ Ji Y. , Eichler E.E. , Schwartz S. , Nicholls R.D. ( 2000 ) Structure of chromosomal duplicons...
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Research: Multiple paralogs and recombination mechanisms contribute to the high incidence of 22q11.2 deletion syndrome
- Lisanne Vervoort,
- Nicolas Dierckxsens,
- Marta Sousa Santos,
- Senne Meynants,
- Erika Souche,
- Ruben Cools,
- Tracy Heung,
- Koen Devriendt,
- Hilde Peeters,
- Donna M. McDonald-McGinn,
- Ann Swillen,
- Jeroen Breckpot,
- Beverly S. Emanuel,
- Hilde Van Esch,
- Anne S. Bassett,
- and Joris R. Vermeesch
Genome Res. April 2025 35: 786-797; Published in Advance November 13, 2024, doi:10.1101/gr.279331.124
...Genetics, Sapienza University, Rome 00185, Italy Corresponding author: joris.vermeesch@kuleuven.beAbstractThe 22q11.2 deletion syndrome (22q11.2DS) is the most common microdeletion disorder. Why the incidence of 22q11.2DS is much greater than that of other genomic disorders remains unknown. Short...
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Resource: Analysis of copy number variations among diverse cattle breeds
- George E. Liu,
- Yali Hou,
- Bin Zhu,
- Maria Francesca Cardone,
- Lu Jiang,
- Angelo Cellamare,
- Apratim Mitra,
- Leeson J. Alexander,
- Luiz L. Coutinho,
- Maria Elena Dell'Aquila,
- Lou C. Gasbarre,
- Gianni Lacalandra,
- Robert W. Li,
- Lakshmi K. Matukumalli,
- Dan Nonneman,
- Luciana C. de A. Regitano,
- Tim P.L. Smith,
- Jiuzhou Song,
- Tad S. Sonstegard,
- Curt P. Van Tassell,
- Mario Ventura,
- Evan E. Eichler,
- Tara G. McDaneld,
- and John W. Keele
Genome Res. May 2010 20: 693-703; Published in Advance March 8, 2010, doi:10.1101/gr.105403.110
...that these chromosomes also have the highest SD content (Liu et al. 2009). Furthermore, similar to the human, mouse, rat, and dog s, there are a greater proportion of CNVs near pericentromeric and subtelomeric regions. Excluding unmapped contigs, pericentromeric and subtelomeric regions each represent 3.4% of genomic...

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