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Research: A high-resolution gene expression atlas links dedicated meristem genes to key architectural traits
- Steffen Knauer,
- Marie Javelle,
- Lin Li,
- Xianran Li,
- Xiaoli Ma,
- Kokulapalan Wimalanathan,
- Sunita Kumari,
- Robyn Johnston,
- Samuel Leiboff,
- Robert Meeley,
- Patrick S. Schnable,
- Doreen Ware,
- Carolyn Lawrence-Dill,
- Jianming Yu,
- Gary J. Muehlbauer,
- Michael J. Scanlon,
- and Marja C.P. Timmermans
Genome Res. December 2019 29: 1962-1973; Published in Advance November 19, 2019, doi:10.1101/gr.250878.119
...the preferential, differential expression of individual members within gene families functioning in a plethora of cellular processes. Subfunctionalization thus emerges as a fundamental feature underlying cell identity. Moreover, we show that adult plant characters are, to a significant degree, regulated by gene...
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Research: Genetic analysis in the Collaborative Cross breeding population
- Vivek M. Philip,
- Greta Sokoloff,
- Cheryl L. Ackert-Bicknell,
- Martin Striz,
- Lisa Branstetter,
- Melissa A. Beckmann,
- Jason S. Spence,
- Barbara L. Jackson,
- Leslie D. Galloway,
- Paul Barker,
- Ann M. Wymore,
- Patricia R. Hunsicker,
- David C. Durtschi,
- Ginger S. Shaw,
- Sarah Shinpock,
- Kenneth F. Manly,
- Darla R. Miller,
- Kevin D. Donohue,
- Cymbeline T. Culiat,
- Gary A. Churchill,
- William R. Lariviere,
- Abraham A. Palmer,
- Bruce F. O'Hara,
- Brynn H. Voy,
- and Elissa J. Chesler
Genome Res. August 2011 21: 1223-1238; Published in Advance July 6, 2011, doi:10.1101/gr.113886.110
...are at http://www..org/cgi/doi/10.1101/gr.113886.110. Freely available online through the Genome Research Open Access option. 21:1223–1238 2011 by Cold Spring Harbor Laboratory Press; ISSN 1088-9051/11; www..org Genome Research 1223 www..org The Collaborative Cross (CC) is an emerging mouse recombinant...
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Method: Multi–cell type gene coexpression network analysis reveals coordinated interferon response and cross–cell type correlations in systemic lupus erythematosus
- Bharat Panwar,
- Benjamin J. Schmiedel,
- Shu Liang,
- Brandie White,
- Enrique Rodriguez,
- Kenneth Kalunian,
- Andrew J. McKnight,
- Rachel Soloff,
- Gregory Seumois,
- Pandurangan Vijayanand,
- and Ferhat Ay
Genome Res. April 2021 31: 659-676; Published in Advance March 5, 2021, doi:10.1101/gr.265249.120
...disproportionately affecting women. A major obstacle in finding targeted therapies for SLE is its remarkable heterogeneity in clinical manifestations as well as in the involvement of distinct cell types. To identify cell-specific targets as well as cross-correlation relationships among expression programs...
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Method: ML-MAGES enables multivariate genetic association analyses with genes and effect size shrinkage
- Xiran Liu,
- Lorin Crawford,
- and Sohini Ramachandran
Genome Res. December 2025 35: 2691-2700; Published in Advance November 19, 2025, doi:10.1101/gr.280440.125
...such as height, molecular biomarkers, or diseases. With advancements in sequencing technologies and the emergence of biobank data sets that sample hundreds of thousands of individuals, GWA studies have proven powerful in detecting potential causal variants for various traits and diseases. More than 45,000 GWA...
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Research: Collaborative Cross mice and their power to map host susceptibility to Aspergillus fumigatus infection
- Caroline Durrant,
- Hanna Tayem,
- Binnaz Yalcin,
- James Cleak,
- Leo Goodstadt,
- Fernando Pardo-Manuel de Villena,
- Richard Mott,
- and Fuad A. Iraqi
Genome Res. August 2011 21: 1239-1248; Published in Advance April 14, 2011, doi:10.1101/gr.118786.110
..., Buus RJ, Verdugo RA, Baric RS, Ferris MT, Frelinger JA, Heise M, Frieman MB, et al. 2011. Genetic analysis of complex traits in the emerging Collaborative cross. Genome Res (in press). doi: 10.1101/gr.111310.110. Beck JA, Lloyd S, Hafezparast M, Lennon-Pierce M, Eppig JT, Festing MF, Fisher EM. 2000...
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Resource: Integrative chromatin state annotation of 234 human ENCODE4 cell types using Segway
- Marjan Farahbod,
- Aboud Diab,
- Paul Sud,
- Meenakshi S. Kagda,
- Ian Whaling,
- Mehdi Foroozandeh,
- Ishan Goel,
- Habib Daneshpajouh,
- Benjamin Hitz,
- J. Michael Cherry,
- and Maxwell W. Libbrecht
Genome Res. October 6, 2025 gr.280633.125; Published in Advance October 6, 2025, doi:10.1101/gr.280633.125
...University, Stanford, CA 94305, United States Abstract The fourth and final phase of the ENCODE consortium has newly profiled epigenetic activity in hundreds of human tissues. Chromatin state annotations created by segmentation and annotation (SAGA) methods, such as Segway, have emerged as the predominant...
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Method: EnDeep4mC predicts DNA N⁴-methylcytosine sites using a dual-adaptive feature encoding framework in deep ensembles
- Shuyu Zhang,
- Quan Zou,
- Mengting Niu,
- Zhibin Lv,
- Antony Stalin,
- and Ximei Luo
Genome Res. March 2026 36: 589-599; Published in Advance February 17, 2026, doi:10.1101/gr.280977.125
...-model cross-evaluation. The purpose of this stage is to realize the joint analysis of species model traits by constructing a 3D evaluation matrix. Specifically, for each species s ∈ {A. thaliana, C. elegans, …} and DL base model k ∈ {CNN, BLSTM, Transformer}, the utility of 14 candidate feature encoding...
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Review: Contrasting genetic architectures in different mouse reference populations used for studying complex traits
- David A. Buchner and
- Joseph H. Nadeau
Genome Res. June 2015 25: 775-791; Published in Advance May 7, 2015, doi:10.1101/gr.187450.114
...mapping and gene identification, but they are also leading to strikingly different pictures of the genetic architecture of complex traits. Collaborative Cross (CC) The CC sought to improve QTL mapping efficiency by increasing statistical power, improving mapping resolution, and enhancing genetic diversity...
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Research: Epigenetic drift score captures directional methylation variability and links aging to transcriptional, metabolic, and genetic alterations
- Xiu Fan,
- Qili Qian,
- Wenran Li,
- Tianzi Liu,
- Changqing Zeng,
- Peilin Jia,
- Huandong Lin,
- Xin Gao,
- Li Jin,
- Mingfeng Xia,
- Sijia Wang,
- and Fan Liu
Genome Res. October 2025 35: 2173-2188; Published in Advance August 1, 2025, doi:10.1101/gr.280155.124
...at loci related to malignancy and can be predictive of cancer emergence (Landau et al. 2014; Feinberg and Levchenko 2023). In contrast, the phenotype enrichment for negative drift underscored aging as the most significantly associated trait (P = 1.3 × 10−36 after FDR), followed by Down syndrome...
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Research: Pangenome analysis reveals families of ubiquitin-ligase adaptors as key genomic divergence drivers that lead to hybrid incompatibility
- Dongying Xie,
- Pohao Ye,
- Yiming Ma,
- and Zhongying Zhao
Genome Res. March 2026 36: 506-521; Published in Advance February 17, 2026, doi:10.1101/gr.280885.125
...studies may overlook. On the other hand, analyses of genomic variation frequently reveal a complex interplay among sequence changes, including single-nucleotide polymorphisms (SNPs) and structural variations (SVs), which are associated with altered gene expression and phenotypic traits (Collins et al...

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