Searching journal content for articles similar to Blanchette et al. 14 (12): 2412.

Displaying results 1-10 of 66

For checked items

view abstracts
download to citation manager

Select this article
Research: MHC in newts illuminates the evolutionary dynamics of complex regions in giant genomes
- Wiesław Babik,
- Katarzyna Dudek,
- Gemma Palomar,
- Marzena Marszałek,
- Grzegorz Dubin,
- Maximina H. Yun,
- and Magdalena Migalska
Genome Res. February 2026 36: 303-317; Published in Advance January 12, 2026, doi:10.1101/gr.281127.125
...understood. Here, we use comparative genomics, expression across multiple ontogenetic stages and tissues, as well as polymorphism data to investigate MHC evolution in newts. Contrary to earlier suggestions of a massively expanded MHC in salamanders, we find that the core MHC region remains relatively compact...
Select this article
Research: De novo genome assemblies of two cryptodiran turtles with ZZ/ZW and XX/XY sex chromosomes provide insights into patterns of genome reshuffling and uncover novel 3D genome folding in amniotes
- Basanta Bista,
- Laura González-Rodelas,
- Lucía Álvarez-González,
- Zhi-qiang Wu,
- Eugenia E. Montiel,
- Ling Sze Lee,
- Daleen B. Badenhorst,
- Srihari Radhakrishnan,
- Robert Literman,
- Beatriz Navarro-Dominguez,
- John B. Iverson,
- Simon Orozco-Arias,
- Josefa González,
- Aurora Ruiz-Herrera,
- and Nicole Valenzuela
Genome Res. October 2024 34: 1553-1569; Published in Advance October 16, 2024, doi:10.1101/gr.279443.124
...open chromatin in the face of warmer mammalian body temperatures, in genomic regions not already stabilized by compact chromatin structure (Saccone et al. 2002). In turn, avian microchromosomes were proposed to be counterparts of these mammalian GC-rich chromosomal segments found within chromosomes...
OPEN ACCESS ARTICLE
Select this article
Methods: Reconstructing contiguous regions of an ancestral genome
- Jian Ma,
- Louxin Zhang,
- Bernard B. Suh,
- Brian J. Raney,
- Richard C. Burhans,
- W. James Kent,
- Mathieu Blanchette,
- David Haussler,
- and Webb Miller
Genome Res. December 2006 16: 1557-1565; Published in Advance September 18, 2006, doi:10.1101/gr.5383506
....J. , Eichler, E.E. ( 2001 ) Segmental duplications: Organization and impact within the current human project assembly . Genome Res. 11 : 1005 – 1017 . ↵ Blanchette, M. , Green, E.D. , Miller, W. , Haussler, D. ( 2004 ) Reconstructing large regions of an ancestral mammalian in silico . Genome Res. 14 : 2412...
OPEN ACCESS ARTICLE
Select this article
Research: Noncoding regions underpin avian bill shape diversification at macroevolutionary scales
- Leeban Yusuf,
- Matthew C. Heatley,
- Joseph P.G. Palmer,
- Henry J. Barton,
- Christopher R. Cooney,
- and Toni I. Gossmann
Genome Res. April 2020 30: 553-565; Published in Advance April 8, 2020, doi:10.1101/gr.255752.119
...that the genomic regions are trans-acting factors. Identifying the mechanisms underlying trans-acting factors is however very difficult to approach in vitro as well as in silico, and our approach to detect the role of trans-acting factors over macroevolutionary time is novel. We opted for an in silico approach...
Select this article
Methods: Reconstructing ancestral gene content by coevolution
- Tamir Tuller,
- Hadas Birin,
- Uri Gophna,
- Martin Kupiec,
- and Eytan Ruppin
Genome Res. January 2010 20: 122-132; Published in Advance November 30, 2009, doi:10.1101/gr.096115.109
..., these errors are difficult to abolish by using longer genomic sequences or by analyzing more taxa. This study describes a new approach for improving ancestral genome reconstruction, the ancestral coevolver (ACE), which utilizes coevolutionary information to improve the accuracy of such reconstructions over...
Select this article
Resource: A high-resolution map of small-scale inversions in the gibbon genome
- Ludovica Mercuri,
- Donato Palmisano,
- Alberto L'Abbate,
- Pietro D'Addabbo,
- Francesco Montinaro,
- Claudia Rita Catacchio,
- Patrick Hasenfeld,
- Mario Ventura,
- Jan O. Korbel,
- Ashley D. Sanders,
- Flavia Angela Maria Maggiolini,
- and Francesca Antonacci
Genome Res. October 2022 32: 1941-1951; Published in Advance September 30, 2022, doi:10.1101/gr.276960.122
...or millions of years and often involve large genomic regions that may contain important genes for intraspecific divergence and speciation (Wellenreuther and Bernatchez 2018).Despite the important role of inversions in evolution, they are difficult to detect and analyze in mammalian s owing to their balanced...
Select this article
Research: Evolution of gene regulation in ruminants differs between evolutionary breakpoint regions and homologous synteny blocks
- Marta Farré,
- Jaebum Kim,
- Anastasia A. Proskuryakova,
- Yang Zhang,
- Anastasia I. Kulemzina,
- Qiye Li,
- Yang Zhou,
- Yingqi Xiong,
- Jennifer L. Johnson,
- Polina L. Perelman,
- Warren E. Johnson,
- Wesley C. Warren,
- Anna V. Kukekova,
- Guojie Zhang,
- Stephen J. O'Brien,
- Oliver A. Ryder,
- Alexander S. Graphodatsky,
- Jian Ma,
- Harris A. Lewin,
- and Denis M. Larkin
Genome Res. April 2019 29: 576-589; Published in Advance February 13, 2019, doi:10.1101/gr.239863.118
...of the genomic or epigenomic features. Herein we reconstructed the ancestral chromosome organization for several mammalian ancestral clades to investigate the functional role of EBRs in the context of changes that occurred for 60 million years (My) in the lineage leading to cattle.We used ruminants as a model...
Select this article
Method: In silico phylogenomics using complete genomes: a case study on the evolution of hominoids
- Igor Rodrigues Costa,
- Francisco Prosdocimi,
- and W. Bryan Jennings
Genome Res. September 2016 26: 1257-1267; Published in Advance July 19, 2016, doi:10.1101/gr.203950.115
...In silico phylogenomics using complete genomes: a case study on the evolution of hominoids Igor Rodrigues Costa 1 , 3 , Francisco Prosdocimi 1 , 3 and W. Bryan Jennings 2 1Laboratório de Genômica e Biodiversidade, Instituto de Bioquímica...
Select this article
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...
OPEN ACCESS ARTICLE
Select this article
Research: Epigenetic maintenance of topological domains in the highly rearranged gibbon genome
- Nathan H. Lazar,
- Kimberly A. Nevonen,
- Brendan O'Connell,
- Christine McCann,
- Rachel J. O'Neill,
- Richard E. Green,
- Thomas J. Meyer,
- Mariam Okhovat,
- and Lucia Carbone
Genome Res. July 2018 28: 983-997; Published in Advance June 18, 2018, doi:10.1101/gr.233874.117
..., however, that these putative translocations were not experimentally validated and may simply reflect errors in the assemblies.We observed that genomic regions that were syntenic in the ancestral chromosome sometimes maintained their interaction even after loss of synteny occurred in gibbon due...

For checked items

view abstracts
download to citation manager

Searching journal content for articles similar to Blanchette et al. 14 (12): 2412.

Search Results

Modify Results

This search

Preprint Server

Current Issue

In This Issue

Citation format:
Results / page:
Results order: