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Research: The role of transposon activity in shaping cis-regulatory element evolution after whole-genome duplication
- Øystein Monsen,
- Lars Grønvold,
- Alex Datsomor,
- Thomas Harvey,
- James Kijas,
- Alexander Suh,
- Torgeir R. Hvidsten,
- and Simen Rød Sandve
Genome Res. March 2025 35: 475-488; Published in Advance February 12, 2025, doi:10.1101/gr.278931.124
...-Aid package (https://github.com/clemgoub/TE-Aid) on each consensus to help guide curation efforts and check each consensus according to its annotation profile and self-alignment. This helped screen for technical noise such as microsatellite sequences near sites of local annotation enrichment...
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Method: Haplotype and population structure inference using neural networks in whole-genome sequencing data
- Jonas Meisner and
- Anders Albrechtsen
Genome Res. August 2022 32: 1542-1552; Published in Advance July 6, 2022, doi:10.1101/gr.276813.122
...Haplotype and population structure inference using neural networks in whole- sequencing data Jonas Meisner and Anders Albrechtsen Department of Biology, Bioinformatics Center, University of Copenhagen, DK-2200 Copenhagen, Denmark Corresponding author: jonas...
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Research: An atlas of fish genome evolution reveals delayed rediploidization following the teleost whole-genome duplication
- Elise Parey,
- Alexandra Louis,
- Jérôme Montfort,
- Yann Guiguen,
- Hugues Roest Crollius,
- and Camille Berthelot
Genome Res. September 2022 32: 1685-1697; Published in Advance August 12, 2022, doi:10.1101/gr.276953.122
...@bio.ens.psl.eu, camille.berthelot@pasteur.frAbstractTeleost fishes are ancient tetraploids descended from an ancestral whole- duplication that may have contributed to the impressive diversification of this clade. Whole- duplications can occur via self-doubling (autopolyploidy) or via hybridization between different...
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Research: Whole-genome resequencing of temporally stratified samples reveals substantial loss of haplotype diversity in the highly inbred Scandinavian wolf population
- Agnese Viluma,
- Øystein Flagstad,
- Mikael Åkesson,
- Camilla Wikenros,
- Håkan Sand,
- Petter Wabakken,
- and Hans Ellegren
Genome Res. March 2022 32: 449-458; Published in Advance February 8, 2022, doi:10.1101/gr.276070.121
..., including loss of segregating variants. However, there is a shortage of quantitative studies of how genetic diversity changes over time in natural populations, especially on -wide scales. Here, we analyzed whole- sequences from 76 wolves of a highly inbred Scandinavian population, founded by only one female...
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Method: Gene discovery by chemical mutagenesis and whole-genome sequencing in Dictyostelium
- Cheng-Lin Frank Li,
- Balaji Santhanam,
- Amanda Nicole Webb,
- Blaž Zupan,
- and Gad Shaulsky
Genome Res. September 2016 26: 1268-1276; Published in Advance June 15, 2016, doi:10.1101/gr.205682.116
...Gene discovery by chemical mutagenesis and whole-genome sequencing in Dictyostelium Cheng-Lin Frank Li 1 , Balaji Santhanam 2 , Amanda Nicole Webb 1 , Blaž Zupan 1 , 3 and Gad Shaulsky 1 1Department of Molecular and Human...
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Resource: Whole-genome analysis of the methylome and hydroxymethylome in normal and malignant lung and liver
- Xin Li,
- Yun Liu,
- Tal Salz,
- Kasper D. Hansen,
- and Andrew Feinberg
Genome Res. December 2016 26: 1730-1741; Published in Advance October 13, 2016, doi:10.1101/gr.211854.116
.... The ten-eleven translocation (TET) gene family oxidizes 5mC to 5-hydroxymethylcytosine (5hmC), providing an active mechanism for DNA demethylation, and it may also provide its own regulatory function. Here we applied oxidative bisulfite sequencing to generate whole-genome DNA methylation...
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Research: Model-based analyses of whole-genome data reveal a complex evolutionary history involving archaic introgression in Central African Pygmies
- PingHsun Hsieh,
- August E. Woerner,
- Jeffrey D. Wall,
- Joseph Lachance,
- Sarah A. Tishkoff,
- Ryan N. Gutenkunst,
- and Michael F. Hammer
Genome Res. March 2016 26: 291-300; Published in Advance February 17, 2016, doi:10.1101/gr.196634.115
...@email.arizona.edu Abstract Comparisons of whole-genome sequences from ancient and contemporary samples have pointed to several instances of archaic admixture through interbreeding between the ancestors of modern non-Africans and now extinct hominids such as Neanderthals and Denisovans. One implication of these findings...
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Research: Comparison against 186 canid whole-genome sequences reveals survival strategies of an ancient clonally transmissible canine tumor
- Brennan Decker,
- Brian W. Davis,
- Maud Rimbault,
- Adrienne H. Long,
- Eric Karlins,
- Vidhya Jagannathan,
- Rebecca Reiman,
- Heidi G. Parker,
- Cord Drögemüller,
- Jason J. Corneveaux,
- Erica S. Chapman,
- Jeffery M. Trent,
- Tosso Leeb,
- Matthew J. Huentelman,
- Robert K. Wayne,
- Danielle M. Karyadi,
- and Elaine A. Ostrander
Genome Res. November 2015 25: 1646-1655; Published in Advance July 31, 2015, doi:10.1101/gr.190314.115
...Comparison against 186 canid whole- sequences reveals survival strategies of an ancient clonally transmissible canine tumor Brennan Decker,1,2,7 Brian W. Davis,1,7 Maud Rimbault,1 Adrienne H. Long,3 Eric Karlins,1 Vidhya Jagannathan,4 Rebecca Reiman,5 Heidi G. Parker,1 Cord Drögemüller,4 Jason J...
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Research: Whole-genome and multisector exome sequencing of primary and post-treatment glioblastoma reveals patterns of tumor evolution
- Hoon Kim,
- Siyuan Zheng,
- Seyed S. Amini,
- Selene M. Virk,
- Tom Mikkelsen,
- Daniel J. Brat,
- Jonna Grimsby,
- Carrie Sougnez,
- Florian Muller,
- Jian Hu,
- Andrew E. Sloan,
- Mark L. Cohen,
- Erwin G. Van Meir,
- Lisa Scarpace,
- Peter W. Laird,
- John N. Weinstein,
- Eric S. Lander,
- Stacey Gabriel,
- Gad Getz,
- Matthew Meyerson,
- Lynda Chin,
- Jill S. Barnholtz-Sloan,
- and Roel G.W. Verhaak
Genome Res. March 2015 25: 316-327; Published in Advance February 3, 2015, doi:10.1101/gr.180612.114
...Whole-genome and multisector exome sequencing of primary and post-treatment glioblastoma reveals patterns of tumor evolution Hoon Kim 1 , 12 , Siyuan Zheng 1 , 2 , 12 , Seyed S. Amini 1 , Selene M. Virk 3 , Tom Mikkelsen 4...
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Method: Detection and phasing of single base de novo mutations in biopsies from human in vitro fertilized embryos by advanced whole-genome sequencing
- Brock A. Peters,
- Bahram G. Kermani,
- Oleg Alferov,
- Misha R. Agarwal,
- Mark A. McElwain,
- Natali Gulbahce,
- Daniel M. Hayden,
- Y. Tom Tang,
- Rebecca Yu Zhang,
- Rick Tearle,
- Birgit Crain,
- Renata Prates,
- Alan Berkeley,
- Santiago Munné,
- and Radoje Drmanac
Genome Res. March 2015 25: 426-434; Published in Advance February 11, 2015, doi:10.1101/gr.181255.114
...Detection and phasing of single base de novo mutations in biopsies from human in vitro fertilized embryos by advanced whole-genome sequencing Brock A. Peters 1 , 2 , Bahram G. Kermani 1 , Oleg Alferov 1 , Misha R. Agarwal 1 , Mark A...
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