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Research: Timescale and genetic linkage explain the variable impact of defense systems on horizontal gene transfer
- Yang Liu,
- João Botelho,
- and Jaime Iranzo
Genome Res. February 2025 35: 268-278; Published in Advance January 10, 2025, doi:10.1101/gr.279300.124
..., using the presence or absence of each defense system as predictors and the species trees as guides to generate the covariance matrix.For each species, the PGLMM assumes that the response variable, Yi, follows a Poisson distribution with mean μi, that is, . The expected gene abundance, μi, is modeled...
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Research: Distinct classes of lamina-associated domains are defined by differential patterns of repressive histone methylation
- Caden J. Martin,
- Elizabeth A. Oser,
- Prabakaran Nagarajan,
- Liudmila V. Popova,
- Benjamin D. Sunkel,
- Benjamin Z. Stanton,
- and Mark R. Parthun
Genome Res. September 2025 35: 1959-1974; Published in Advance August 5, 2025, doi:10.1101/gr.280380.124
...of individual LADs or groups of LADs. To address this, we clustered LADs by scaling them all to a uniform size and dividing the chromatin signal into 24 bins across each LAD, then performing k-means clustering on the resulting matrix. A plot of silhouette scores suggested two or three clusters to be optimal...
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Method: Examining the dynamics of three-dimensional genome organization with multitask matrix factorization
- Da-Inn Lee and
- Sushmita Roy
Genome Res. May 2025 35: 1179-1193; Published in Advance March 20, 2025, doi:10.1101/gr.279930.124
...Examining the dynamics of three-dimensional organization with multitask matrix factorization Da-Inn Lee1 and Sushmita Roy1,2 1Department of Biostatistics and Medical Informatics, University of Wisconsin–Madison, Madison, Wisconsin 53715, USA; 2Wisconsin Institute for Discovery, Madison, Wisconsin...
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Research: Translation-dependent and -independent mRNA decay occur through mutually exclusive pathways defined by ribosome density during T cell activation
- Blandine C. Mercier,
- Emmanuel Labaronne,
- David Cluet,
- Laura Guiguettaz,
- Nicolas Fontrodona,
- Alicia Bicknell,
- Antoine Corbin,
- Mélanie Wencker,
- Fabien Aube,
- Laurent Modolo,
- Karina Jouravleva,
- Didier Auboeuf,
- Melissa J. Moore,
- and Emiliano P. Ricci
Genome Res. March 2024 34: 394-409; Published in Advance March 20, 2024, doi:10.1101/gr.277863.123
...).Taken together, our results suggest that TDD and TID occur through mutually exclusive pathways that compete for the same substrate and are defined by ribosome density as well as transcript cis-acting features that participate in modulating the efficiency of each pathway.DiscussionTDD has emerged as an important...
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Method: Diffusion-enhanced characterization of 3D chromatin structure reveals its linkage to gene regulatory networks and the interactome
- Yueying He,
- Yue Xue,
- Jingyao Wang,
- Yupeng Huang,
- Lu Liu,
- Yanyi Huang,
- and Yi Qin Gao
Genome Res. August 2023 33: 1354-1368; Published in Advance July 25, 2023, doi:10.1101/gr.277737.123
...of each genomic locus to all other genomic loci by integrating k-step (k = 1, 2, 3, ……) transition probability matrices derived from a Hi-C contact matrix (see Methods). Taking all other genomic loci into consideration, the diffusion property is hence defined based on global information of the Hi...
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Method: Copolymerization of single-cell nucleic acids into balls of acrylamide gel
- Siran Li,
- Jude Kendall,
- Sarah Park,
- Zihua Wang,
- Joan Alexander,
- Andrea Moffitt,
- Nissim Ranade,
- Cassidy Danyko,
- Bruno Gegenhuber,
- Stephan Fischer,
- Brian D. Robinson,
- Herbert Lepor,
- Jessica Tollkuhn,
- Jesse Gillis,
- Eric Brouzes,
- Alex Krasnitz,
- Dan Levy,
- and Michael Wigler
Genome Res. January 2020 30: 49-61; Published in Advance November 14, 2019, doi:10.1101/gr.253047.119
...in oil, the aqueous droplet forms a gel ball with the Acrydite primer covalently incorporated into the matrix.View larger version: In this window In a new window Figure 1. Schematic of single-cell DNA or RNA BAG-seq workflow. The star between first split and second split indicating the place where more...
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Research: Spatial organization of chromosomes leads to heterogeneous chromatin motion and drives the liquid- or gel-like dynamical behavior of chromatin
- Hossein Salari,
- Marco Di Stefano,
- and Daniel Jost
Genome Res. January 2022 32: 28-43; Published in Advance December 28, 2021, doi:10.1101/gr.275827.121
...fundamental processes such as gene transcription and DNA repair. Experiments unveiled that chromatin motion is highly heterogeneous inside cell nuclei, ranging from a liquid-like, mobile state to a gel-like, rigid regime. Using polymer modeling, we investigate how these different physical states and dynamical...
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Research: A DNA methylation haplotype block landscape in human tissues and preimplantation embryos reveals regulatory elements defined by comethylation patterns
- Yan Feng,
- Zhiqiang Zhang,
- Yuyang Hong,
- Yi Ding,
- Leiqin Liu,
- Siqi Gao,
- Hai Fang,
- and Jiantao Shi
Genome Res. December 2023 33: 2041-2052; Published in Advance November 8, 2023, doi:10.1101/gr.278146.123
...aggregates the detected signal, WGBS has the potential to characterize DNA methylation haplotypes (MHAPs) (Zhang et al. 2021b). These MHAPs are defined as CpGs on the same read fragment originating from a single chromosome. Several read-level metrics have been proposed to quantify the characteristics...
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Research: Expanding heterochromatin reveals discrete subtelomeric domains delimited by chromatin landscape transitions
- Antoine Hocher,
- Myriam Ruault,
- Petra Kaferle,
- Marc Descrimes,
- Mickaël Garnier,
- Antonin Morillon,
- and Angela Taddei
Genome Res. December 2018 28: 1867-1881; Published in Advance October 24, 2018, doi:10.1101/gr.236554.118
...'s correlation matrix between Sir3 binding and histone marks, SIR3 oe corresponds to yAT1254 and SIR2 and SIR3 oe to yAT1668. Histone modification data from Weiner et al. (2015) for all marks except H3K79me2 (Schulze et al. 2009). (B) Genome browser visualization of Sir3 binding in WT, pGPD-SIR2 pGPD-SIR3...
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Resource: Phosphoproteomic profiling reveals a defined genetic program for osteoblastic lineage commitment of human bone marrow–derived stromal stem cells
- Inigo Barrio-Hernandez,
- Abbas Jafari,
- Kristoffer T.G. Rigbolt,
- Philip Hallenborg,
- Virginia Sanchez-Quiles,
- Ida Skovrind,
- Vyacheslav Akimov,
- Irina Kratchmarova,
- Joern Dengjel,
- Moustapha Kassem,
- and Blagoy Blagoev
Genome Res. January 2020 30: 127-137; Published in Advance December 12, 2019, doi:10.1101/gr.248286.119
...tissue constantly undergoing bone matrix resorption and formation, two coupled processes mediated by osteoclastic and osteoblastic cells, respectively (Parfitt et al. 2011). Decreased osteoblastic bone formation relative to osteoclastic bone resorption is the cellular basis of age- and osteoporosis...

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