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Research: Identification of the male-specific region on the guppy Y Chromosome from a haplotype-resolved assembly
- Kang Du,
- Oliver Deusch,
- Ilja Bezrukov,
- Christa Lanz,
- Yann Guiguen,
- Margarete Hoffmann,
- Anette Habring,
- Detlef Weigel,
- Manfred Schartl,
- and Christine Dreyer
Genome Res. March 2025 35: 489-498; Published in Advance March 5, 2025, doi:10.1101/gr.279582.124
.... Alignment of reconstructed X Chromosomes to Ygua and Ymac haplotypes. Ygua and Ymac assembled as described in Supplemental Table S2 are aligned to Xgua and a virtual Xmac. Both X Chromosomes were rescaffolded from the female Guanapo contigs using Ygua and Ymac as templates.Identification of the male...
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Resource: Genome-wide identification of tandem repeats associated with splicing variation across 49 tissues in humans
- Kohei Hamanaka,
- Daisuke Yamauchi,
- Eriko Koshimizu,
- Kei Watase,
- Kaoru Mogushi,
- Kinya Ishikawa,
- Hidehiro Mizusawa,
- Naomi Tsuchida,
- Yuri Uchiyama,
- Atsushi Fujita,
- Kazuharu Misawa,
- Takeshi Mizuguchi,
- Satoko Miyatake,
- and Naomichi Matsumoto
Genome Res. March 2023 33: 435-447; Published in Advance March 27, 2023, doi:10.1101/gr.277335.122
...City University Hospital, Yokohama, Kanagawa 236-0004, Japan; 8Clinical Genetics Department, Yokohama City University Hospital, Yokohama, Kanagawa 236-0004, Japan Corresponding author: naomat@yokohama-cu.ac.jpAbstractTandem repeats (TRs) are one of the largest sources of polymorphism, and their length...
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RESOURCE: Large-Scale Validation of Single Nucleotide Polymorphisms in Gene Regions
- Matthew R. Nelson,
- George Marnellos,
- Stefan Kammerer,
- Carolyn R. Hoyal,
- Michael M. Shi,
- Charles R. Cantor,
- and Andreas Braun
Genome Res. August 2004 14: 1664-1668; doi:10.1101/gr.2421604
...Sequenom Inc., San Diego, California 92121 USA Abstract Genome-wide association studies using large numbers of bi-allelic single nucleotide polymorphisms (SNPs) have been proposed as a potentially powerful method for identifying genes involved in common diseases. To assemble a SNP collection...
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RESOURCE: Single Nucleotide Polymorphisms Associated With Rat Expressed Sequences
- Victor Guryev,
- Eugene Berezikov,
- Rainer Malik,
- Ronald H.A. Plasterk,
- and Edwin Cuppen
Genome Res. July 2004 14: 1438-1443; doi:10.1101/gr.2154304
...on naturally occurring polymorphisms are mostly lacking. We have used publicly available sequences consisting of whole- shotgun (WGS), expressed sequence tag (EST), and mRNA data as a source for the in silico identification of SNPs in gene-coding regions and have identified a large collection of 33,305 high...
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RESOURCE: Large-Scale Identification and Analysis of Genome-Wide Single-Nucleotide Polymorphisms for Mapping in Arabidopsis thaliana
- Karl J. Schmid,
- Thomas Rosleff Sörensen,
- Ralf Stracke,
- Ottó Törjék,
- Thomas Altmann,
- Tom Mitchell-Olds,
- and Bernd Weisshaar
Genome Res. June 2003 13: 1250-1257; doi:10.1101/gr.728603
...Large-Scale Identification and Analysis of Genome-Wide Single-Nucleotide Polymorphisms for Mapping in Arabidopsis thaliana Karl J. Schmid 1 , Thomas Rosleff Sörensen 2 , Ralf Stracke 2 , Ottó Törjék 3 , Thomas Altmann 3 , Tom Mitchell...
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Next-Generation DNA Sequencing/Review: Next-generation DNA sequencing of paired-end tags (PET) for transcriptome and genome analyses
- Melissa J. Fullwood,
- Chia-Lin Wei,
- Edison T. Liu,
- and Yijun Ruan
Genome Res. April 2009 19: 521-532; doi:10.1101/gr.074906.107
.... The underlying concept was that the nucleotide composition of a short DNA stretch is sufficiently specific to represent a longer DNA fragment. Expressed sequence tag (EST) was the first example of tag-based sequencing concept, by using single Sanger sequencing reads to tag cDNA sequences reverse transcribed from...
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Methods: A genotyping system capable of simultaneously analyzing >1000 single nucleotide polymorphisms in a haploid genome
- Hui-Yun Wang,
- Minjie Luo,
- Irina V. Tereshchenko,
- Danielle M. Frikker,
- Xiangfeng Cui,
- James Y. Li,
- Guohong Hu,
- Yi Chu,
- Marco A. Azaro,
- Yong Lin,
- Li Shen,
- Qifeng Yang,
- Manousos E. Kambouris,
- Richeng Gao,
- Weichung Shih,
- and Honghua Li
Genome Res. February 2005 15: 276-283; doi:10.1101/gr.2885205
...A genotyping system capable of simultaneously analyzing &gt;1000 single nucleotide polymorphisms in a haploid genome Hui-Yun Wang 1 , 4 , Minjie Luo 1 , 4 , Irina V. Tereshchenko 1 , Danielle M. Frikker 1 , Xiangfeng Cui 1 , James Y...
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LETTER: Identification, Characterization, and Mapping of Expressed Sequence Tags from an Embryonic Zebrafish Heart cDNA Library
- Christopher Ton,
- David M. Hwang,
- Adam A. Dempsey,
- Hong-Chang Tang,
- Jennifer Yoon,
- Mindy Lim,
- John D. Mably,
- Mark C. Fishman,
- and Choong-Chin Liew
Genome Res. December 1, 2000 10: 1915-1927; doi:10.1101/gr.154000
...Identification, Characterization, and Mapping of Expressed Sequence Tags from an Embryonic Zebrafish Heart cDNA Library Christopher Ton 1 , David M. Hwang 1 , Adam A. Dempsey 1 , Hong-Chang Tang 1 , Jennifer Yoon 1 , Mindy Lim 1...
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RESOURCE: Expression-based Genetic/Physical Maps of Single-Nucleotide Polymorphisms Identified by the Cancer Genome Anatomy Project
- Robert Clifford,
- Michael Edmonson,
- Ying Hu,
- Cu Nguyen,
- Titia Scherpbier,
- and Kenneth H. Buetow
Genome Res. August 1, 2000 10: 1259-1265; doi:10.1101/gr.10.8.1259
...containing single nucleotide polymorphisms in genes expressed in breast, colon, kidney, liver, lung, or prostate tissue. The integrated maps, a SNP search engine, and a Java-based tool for viewing candidate SNPs in the context of EST assemblies can be accessed via the CGAP-GAI web site ( http...
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LETTER: Accounting for Human Polymorphisms Predicted to Affect Protein Function
- Pauline C. Ng and
- Steven Henikoff
Genome Res. March 1, 2002 12: 436-446; doi:10.1101/gr.212802
...L.P. , et al. ( 1995 ) A candidate genetic risk factor for vascular disease: A common mutation in methylenetetrahydrofolate reductase. Nat. Genet. 10 : 111 – 113 . ↵ Garg K. , Green P. , Nickerson D.A. ( 1999 ) Identification of candidate coding region single nucleotide polymorphisms in 165 human...

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