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Method: Accurate typing of short tandem repeats from genome-wide sequencing data and its applications
- Arkarachai Fungtammasan,
- Guruprasad Ananda,
- Suzanne E. Hile,
- Marcia Shu-Wei Su,
- Chen Sun,
- Robert Harris,
- Paul Medvedev,
- Kristin Eckert,
- and Kateryna D. Makova
Genome Res. May 2015 25: 736-749; Published in Advance March 30, 2015, doi:10.1101/gr.185892.114
...STRs with consecutive repeat numbers. Applying our model and pipeline to Illumina sequencing data with 100-bp reads, we could confidently genotype several disease-related long trinucleotide STRs. Utilizing this pipeline, for the first time we determined the genome-wide STR germline mutation rate from...
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LETTER: Genome-wide analysis of microsatellite polymorphism in chicken circumventing the ascertainment bias
- Mikael Brandström and
- Hans Ellegren
Genome Res. June 2008 18: 881-887; Published in Advance March 20, 2008, doi:10.1101/gr.075242.107
...Genome-wide analysis of microsatellite polymorphism in chicken circumventing the ascertainment bias Mikael Brandström and Hans Ellegren 1 Department of Evolutionary Biology, Evolutionary Biology Centre, Uppsala University, Norbyvägen 18D, SE-752 36 Uppsala...
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Research: Genome-wide parent-of-origin DNA methylation analysis reveals the intricacies of human imprinting and suggests a germline methylation-independent mechanism of establishment
- Franck Court,
- Chiharu Tayama,
- Valeria Romanelli,
- Alex Martin-Trujillo,
- Isabel Iglesias-Platas,
- Kohji Okamura,
- Naoko Sugahara,
- Carlos Simón,
- Harry Moore,
- Julie V. Harness,
- Hans Keirstead,
- Jose Vicente Sanchez-Mut,
- Eisuke Kaneki,
- Pablo Lapunzina,
- Hidenobu Soejima,
- Norio Wake,
- Manel Esteller,
- Tsutomu Ogata,
- Kenichiro Hata,
- Kazuhiko Nakabayashi,
- and David Monk
Genome Res. April 2014 24: 554-569; Published in Advance January 8, 2014, doi:10.1101/gr.164913.113
...331 gene, and the second coincides with exon 2 of DIRAS3 (Supplemental Fig. S2C). Genome-wide methylation profiling identifies novel imprinted domains To determine if there are additional imprintedDMRs in the human , we screened for regions of intermediate methylation common to lymphocyte, brain...
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Methods: Genome-wide nucleotide-level mammalian ancestor reconstruction
- Benedict Paten,
- Javier Herrero,
- Stephen Fitzgerald,
- Kathryn Beal,
- Paul Flicek,
- Ian Holmes,
- and Ewan Birney
Genome Res. November 2008 18: 1829-1843; Published in Advance October 10, 2008, doi:10.1101/gr.076521.108
...Genome-wide nucleotide-level mammalian ancestor reconstruction Benedict Paten 1 , 4 , Javier Herrero 2 , Stephen Fitzgerald 2 , Kathryn Beal 2 , Paul Flicek 2 , Ian Holmes 3 , and Ewan Birney 2 , 4 1...
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Research: A genome-wide analysis of common fragile sites: What features determine chromosomal instability in the human genome?
- Arkarachai Fungtammasan,
- Erin Walsh,
- Francesca Chiaromonte,
- Kristin A. Eckert,
- and Kateryna D. Makova
Genome Res. June 2012 22: 993-1005; Published in Advance March 28, 2012, doi:10.1101/gr.134395.111
...A genome-wide analysis of common fragile sites: What features determine chromosomal instability in the human genome? Arkarachai Fungtammasan 1 , 2 , 3 , Erin Walsh 3 , 4 , Francesca Chiaromonte 3 , 5 , 7 , Kristin A. Eckert 3 , 6 , 7...
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ARTICLE: Extensive Genome-wide Linkage Disequilibrium in Cattle
- Frédéric Farnir,
- Wouter Coppieters,
- Juan-José Arranz,
- Paulette Berzi,
- Nadine Cambisano,
- Bernard Grisart,
- Latifa Karim,
- Fabienne Marcq,
- Laurence Moreau,
- Myriam Mni,
- Carine Nezer,
- Patricia Simon,
- Pascal Vanmanshoven,
- Danny Wagenaar,
- and Michel Georges
Genome Res. February 1, 2000 10: 220-227; doi:10.1101/gr.10.2.220
...those that are known to harbor QTL, influencing milk yield and composition (e.g., Georges et al. 1995 ; Coppieters et al. 1998 ). View larger version: In this window In a new window Figure 5. Genome-wide linkage disequilibrium map. Microsatellite markers are ordered along the X and Y-axis by chromosome...
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LETTER: Genome-wide definitive haplotypes determined using a collection of complete hydatidiform moles
- Yoji Kukita,
- Katsuyuki Miyatake,
- Renee Stokowski,
- David Hinds,
- Koichiro Higasa,
- Norio Wake,
- Toshio Hirakawa,
- Hidenori Kato,
- Takao Matsuda,
- Krishna Pant,
- David Cox,
- Tomoko Tahira,
- and Kenshi Hayashi
Genome Res. November 2005 15: 1511-1518; doi:10.1101/gr.4371105
...Genome-wide definitive haplotypes determined using a collection of complete hydatidiform moles Yoji Kukita 1 , 4 , Katsuyuki Miyatake 1 , 4 , Renee Stokowski 2 , 4 , David Hinds 2 , 4 , Koichiro Higasa 1 , 4 , Norio Wake 3...
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Research: Repeat associated mechanisms of genome evolution and function revealed by the Mus caroli and Mus pahari genomes
- David Thybert,
- Maša Roller,
- Fábio C.P. Navarro,
- Ian Fiddes,
- Ian Streeter,
- Christine Feig,
- David Martin-Galvez,
- Mikhail Kolmogorov,
- Václav Janoušek,
- Wasiu Akanni,
- Bronwen Aken,
- Sarah Aldridge,
- Varshith Chakrapani,
- William Chow,
- Laura Clarke,
- Carla Cummins,
- Anthony Doran,
- Matthew Dunn,
- Leo Goodstadt,
- Kerstin Howe,
- Matthew Howell,
- Ambre-Aurore Josselin,
- Robert C. Karn,
- Christina M. Laukaitis,
- Lilue Jingtao,
- Fergal Martin,
- Matthieu Muffato,
- Stefanie Nachtweide,
- Michael A. Quail,
- Cristina Sisu,
- Mario Stanke,
- Klara Stefflova,
- Cock Van Oosterhout,
- Frederic Veyrunes,
- Ben Ward,
- Fengtang Yang,
- Golbahar Yazdanifar,
- Amonida Zadissa,
- David J. Adams,
- Alvis Brazma,
- Mark Gerstein,
- Benedict Paten,
- Son Pham,
- Thomas M. Keane,
- Duncan T. Odom,
- and Paul Flicek
Genome Res. April 2018 28: 448-459; Published in Advance March 21, 2018, doi:10.1101/gr.234096.117
...Repeat associated mechanisms of evolution and function revealed by the Mus caroli and Mus pahari s David Thybert1,2, Maša Roller1, Fábio C.P. Navarro3, Ian Fiddes4, Ian Streeter1, Christine Feig5, David Martin-Galvez1, Mikhail Kolmogorov6, Václav Janoušek7, Wasiu Akanni1, Bronwen Aken1, Sarah...
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LETTER: Differential Alu Mobilization and Polymorphism Among the Human and Chimpanzee Lineages
- Dale J. Hedges,
- Pauline A. Callinan,
- Richard Cordaux,
- Jinchuan Xing,
- Erin Barnes,
- and Mark A. Batzer
Genome Res. June 2004 14: 1068-1075; doi:10.1101/gr.2530404
...retroposition dynamics and associated polymorphism between chimpanzees and humans. We have surveyed common chimpanzee chromosome 22, and its human homolog, chromosome 21, for lineage-specific Alu sequences and determined the insertion polymorphism associated with each of these insertions. We also examined...
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LETTER: Selection on Human Genes as Revealed by Comparisons to Chimpanzee cDNA
- Ines Hellmann,
- Sebastian Zöllner,
- Wolfgang Enard,
- Ingo Ebersberger,
- Birgit Nickel,
- and Svante Pääbo
Genome Res. May 1, 2003 13: 831-837; doi:10.1101/gr.944903
...to their human counterparts. In conjunction with intergenic chimpanzee DNA sequences and data on human single-nucleotide polymorphisms in the genes studied, this allows us to gauge the extent to which selection affects human genes at a genome-wide scale. The comparison to intergenic DNA sequences indicates...

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