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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
...are substrates for nonallelic homologous recombination (NAHR) that generates structural changes of the SDs themselves as well as of the flanking unique regions (Carvalho and Lupski 2016).Given their impact on genetic diversity, these genomic intervals are expected to significantly influence phenotypic variation...
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Research: Genome-wide analysis of polymerase III–transcribed Alu elements suggests cell-type–specific enhancer function
- Xiao-Ou Zhang,
- Thomas R. Gingeras,
- and Zhiping Weng
Genome Res. September 2019 29: 1402-1414; Published in Advance August 14, 2019, doi:10.1101/gr.249789.119
...window Figure 1. Genome-wide identification of expressed Alu elements using RAMPAGE data. (A) A computational pipeline to call RAMPAGE peaks and annotate expressed Alu elements. Paired-end RAMPAGE reads (R1 and R2, black; N, read pairs in total) with uniquely mapping R2 reads were first clustered to call...
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Research: Characterizing nucleotide variation and expansion dynamics in human-specific variable number tandem repeats
- Meredith M. Course,
- Arvis Sulovari,
- Kathryn Gudsnuk,
- Evan E. Eichler,
- and Paul N. Valdmanis
Genome Res. August 2021 31: 1313-1324; Published in Advance July 9, 2021, doi:10.1101/gr.275560.121
..., Jazin E. 2005. Genome-wide prediction of human VNTRs. Genomics 85: 24–35. doi:10.1016/j.ygeno.2004.10.009 ↵Örd T, Puurand T, Örd D, Annilo T, Möls M, Remm M, Örd T. 2020. A human-specific VNTR in the TRIB3 promoter causes gene expression variation between individuals. PLoS Genet 16: e1008981. doi:10...
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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
...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 1 , 15 , Chiharu Tayama 2 , 15 , Valeria Romanelli 1 , 15 , Alex...
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Research: Novel H3K4me3 marks are enriched at human- and chimpanzee-specific cytogenetic structures
- Giuliana Giannuzzi,
- Eugenia Migliavacca,
- and Alexandre Reymond
Genome Res. September 2014 24: 1455-1468; Published in Advance June 10, 2014, doi:10.1101/gr.167742.113
...Novel H3K4me3 marks are enriched at human- and chimpanzee-specific cytogenetic structures Giuliana Giannuzzi 1 , Eugenia Migliavacca 1 , 2 and Alexandre Reymond 1 1 Center for Integrative Genomics, University of Lausanne, 1015 Lausanne...
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Research: Genome-wide search for novel human uORFs and N-terminal protein extensions using ribosomal footprinting
- Claudia Fritsch,
- Alexander Herrmann,
- Michael Nothnagel,
- Karol Szafranski,
- Klaus Huse,
- Frank Schumann,
- Stefan Schreiber,
- Matthias Platzer,
- Michael Krawczak,
- Jochen Hampe,
- and Mario Brosch
Genome Res. November 2012 22: 2208-2218; Published in Advance August 9, 2012, doi:10.1101/gr.139568.112
...Genome-wide search for novel human uORFs and N-terminal protein extensions using ribosomal footprinting Claudia Fritsch 1 , Alexander Herrmann 1 , Michael Nothnagel 2 , Karol Szafranski 3 , Klaus Huse 3 , Frank Schumann 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
...]) GC content Average Genome-wide screen (− [Mishmar et al. 1998]) (+ [Tsantoulis et al. 2008]) Distance to the telomere Distance Genome-wide screen Distance to the centromere Distance Genome-wide screen Gene expression/chromatin structure CpG islands Coverage (Karolchik et al. 2003) (Rhead et al. 2009...
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Research: Shifts in the intensity of purifying selection: An analysis of genome-wide polymorphism data from two closely related yeast species
- Eyal Elyashiv,
- Kevin Bullaughey,
- Shmuel Sattath,
- Yosef Rinott,
- Molly Przeworski,
- and Guy Sella
Genome Res. November 2010 20: 1558-1573; Published in Advance September 4, 2010, doi:10.1101/gr.108993.110
...Shifts in the intensity of purifying selection: An analysis of genome-wide polymorphism data from two closely related yeast species Eyal Elyashiv 1 , Kevin Bullaughey 2 , Shmuel Sattath 1 , Yosef Rinott 3 , Molly Przeworski 2 , 4 , 5...
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Research: Impact of the X Chromosome and sex on regulatory variation
- Kimberly R. Kukurba,
- Princy Parsana,
- Brunilda Balliu,
- Kevin S. Smith,
- Zachary Zappala,
- David A. Knowles,
- Marie-Julie Favé,
- Joe R. Davis,
- Xin Li,
- Xiaowei Zhu,
- James B. Potash,
- Myrna M. Weissman,
- Jianxin Shi,
- Anshul Kundaje,
- Douglas F. Levinson,
- Philip Awadalla,
- Sara Mostafavi,
- Alexis Battle,
- and Stephen B. Montgomery
Genome Res. June 2016 26: 768-777; Published in Advance April 21, 2016, doi:10.1101/gr.197897.115
...al. 2014). However, no studies to date have systematically investigated the contribution of the X Chromosome in the context of both regulatory variation and its interaction with sex.By leveraging a recent, large genetic study of gene expression (Battle et al. 2014), we comprehensively survey...
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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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