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Research: Complete genomes of Asgard archaea reveal diverse integrated and mobile genetic elements
- Luis E. Valentin-Alvarado,
- Ling-Dong Shi,
- Kathryn E. Appler,
- Alexander Crits-Christoph,
- Valerie De Anda,
- Benjamin A. Adler,
- Michael L. Cui,
- Lynn Ly,
- Pedro Leão,
- Richard J. Roberts,
- Rohan Sachdeva,
- Brett J. Baker,
- David F. Savage,
- and Jillian F. Banfield
Genome Res. October 2024 34: 1595-1609; Published in Advance October 15, 2024, doi:10.1101/gr.279480.124
...://github.com/christophertbrown/iRep). We classified complete MGE s as viruses if they contained viral structural genes. Genomes lacking viral structural genes were categorized as plasmids or other MGEs (such as transposons or conjugative elements) based on length, the presence of transposases (classified using ISFinder) (Siguier et al...
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Method: Complete genetic and epigenetic architecture of D4Z4 macrosatellites in FSHD, BAMS, and reference cohorts with D4Z4End2End
- Lucinda C. Xiao,
- Ayush Semwal,
- Brianna St John,
- Kathleen Zeglinski,
- Shian Su,
- James Lancaster,
- Shifeng Xue,
- Bruno Reversade,
- Matthew E. Ritchie,
- Frédérique Magdinier,
- Marnie E. Blewitt,
- and Quentin Gouil
Genome Res. March 23, 2026 ; Published in Advance March 23, 2026, doi:10.1101/gr.280907.125
...from two controls, four FSHD1 patients, four FSHD2 patients, and two patients with Bosma arhinia microphthalmia syndrome (BAMS) caused by SMCHD1 variants, as well as publicly available data from 30 B-lymphoblastoid cell lines from the 1000 Genomes Project and Human Pan Reference Consortium. We attain...
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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
...). In the absence of another Triturus assembly or cytogenetic FISH evidence, we cannot completely rule out the possibility that the apparent translocation is an assembly error. However, genes flanking the additional MHC region from both sides map to a continuous genomic region in other newt assemblies, rendering...
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Research: Stable genome structures in living fossil fishes
- Cheng Wang,
- Chase D. Brownstein,
- Wenjun Chen,
- Zufa Ding,
- Dan Yu,
- Yu Deng,
- Chenguang Feng,
- Thomas J. Near,
- Shunping He,
- and Liandong Yang
Genome Res. February 2026 36: 318-329; Published in Advance January 13, 2026, doi:10.1101/gr.280800.125
...contributed equally to this work. Corresponding authors: thomas.near@yale.edu, clad@ihb.ac.cn, yangliandong1987@163.comAbstractGenomic evolution can propel and restrict species diversification. Rapid molecular evolution and genomic rearrangement is often associated with increased species diversification...
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Method: Secure phasing of private genomes in a trusted execution environment with TX-Phase
- Natnatee Dokmai,
- Kaiyuan Zhu,
- S. Cenk Sahinalp,
- and Hyunghoon Cho
Genome Res. December 2025 35: 2626-2636; Published in Advance November 12, 2025, doi:10.1101/gr.280558.125
...poses a significant challenge in maintaining practical performance under privacy constraints. Here, we introduce TX-Phase, a secure haplotype phasing method based on the framework of trusted execution environments (TEEs). TX-Phase allows users’ private genomic data to be phased while ensuring data...
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Method: Pangenome-based genome inference using integer programming
- Ghanshyam Chandra,
- Md Helal Hossen,
- Stephan Scholz,
- Alexander T. Dilthey,
- Daniel Gibney,
- and Chirag Jain
Genome Res. December 2025 35: 2661-2670; Published in Advance August 21, 2025, doi:10.1101/gr.280567.125
..., Rautiainen M, Bzikadze AV, Mikheenko A, Vollger MR, Altemose N, Uralsky L, Gershman A, et al. 2022. The complete sequence of a human . Science 376: 44–53. doi:10.1126/science.abj6987 ↵Paten B, Novak AM, Eizenga JM, Garrison E. 2017. Genome graphs and the evolution of inference. Genome Res 27: 665–676. doi:10...
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Research: Rearrangements of viral and human genomes at human papillomavirus integration events and their allele-specific impacts on cancer genome regulation
- Vanessa L. Porter,
- Michelle Ng,
- Kieran O'Neill,
- Signe MacLennan,
- Richard D. Corbett,
- Luka Culibrk,
- Zeid Hamadeh,
- Marissa Iden,
- Rachel Schmidt,
- Shirng-Wern Tsaih,
- Carolyn Nakisige,
- Martin Origa,
- Jackson Orem,
- Glenn Chang,
- Jeremy Fan,
- Ka Ming Nip,
- Vahid Akbari,
- Simon K. Chan,
- James Hopkins,
- Richard A. Moore,
- Eric Chuah,
- Karen L. Mungall,
- Andrew J. Mungall,
- Inanc Birol,
- Steven J.M. Jones,
- Janet S. Rader,
- and Marco A. Marra
Genome Res. April 2025 35: 653-670; Published in Advance December 5, 2024, doi:10.1101/gr.279041.124
...,8 and Marco A. Marra1,2,3 1Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, British Columbia V5Z 4S6, Canada; 2Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada; 3Michael Smith Laboratories, University of British Columbia, Vancouver...
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Research: Dynamic evolution of satellite DNAs drastically differentiates the genomes of Tribolium sibling species
- Damira Veseljak,
- Evelin Despot-Slade,
- Marin Volarić,
- Lucija Horvat,
- Tanja Vojvoda Zeljko,
- Nevenka Meštrović,
- and Brankica Mravinac
Genome Res. November 2025 35: 2445-2460; Published in Advance September 16, 2025, doi:10.1101/gr.280516.125
...on this comparison, we also draw conclusions about the genomic architecture, evolutionary dynamics, and the main molecular mechanisms that most significantly differentiated their satellitomes.ResultsIdentification of T. freemani satDNAsThe first step was to characterize the T. freemani satellitome. For assembly...
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Resource: Quadrupia provides a comprehensive catalog of G-quadruplexes across genomes from the tree of life
- Nikol Chantzi,
- Akshatha Nayak,
- Fotis A. Baltoumas,
- Eleni Aplakidou,
- Shiau Wei Liew,
- Jesslyn Elvaretta Galuh,
- Michail Patsakis,
- Austin Montgomery,
- Camille Moeckel,
- Ioannis Mouratidis,
- Saiful Arefeen Sazed,
- Wilfried Guiblet,
- Panagiotis Karmiris-Obratański,
- Guliang Wang,
- Apostolos Zaravinos,
- Karen M. Vasquez,
- Chun Kit Kwok,
- Georgios A. Pavlopoulos,
- and Ilias Georgakopoulos-Soares
Genome Res. November 2025 35: 2578-2600; Published in Advance August 26, 2025, doi:10.1101/gr.279790.124
...at Austin, Dell Pediatric Research Institute, Austin, Texas 78723, USA; 9Department of Life Sciences, School of Sciences, European University Cyprus, Nicosia 1516, Cyprus; 10Cancer Genetics, Genomics and Systems Biology Laboratory, Basic and Translational Cancer Research Center (BTCRC), Nicosia 1516, Cyprus...
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Research: Contiguous and complete assemblies of Blastocystis gut microbiome–associated protists reveal evolutionary diversification to host ecology
- Abigail L. Lind,
- Nathan A. McDonald,
- Elias R. Gerrick,
- Ami S. Bhatt,
- and Katherine S. Pollard
Genome Res. June 2025 35: 1377-1390; Published in Advance April 22, 2025, doi:10.1101/gr.279080.124
...BAT 2, but MetaEuk and EukRep were performed as described above to identify potential contaminating sequences. This resulted in two contigs being removed from the BT1 assembly and no contigs being removed from Nand or JDR assemblies.Genome completeness was determined with sequenced-based and gene...
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