Searching journal content for articles similar to Wuchty 14 (7): 1310.

Displaying results 1-10 of 156

For checked items

view abstracts
download to citation manager

Select this article
Review: The structure, function, and evolution of plant centromeres
- Matthew Naish and
- Ian R. Henderson
Genome Res. February 2024 34: 161-178; Published in Advance March 14, 2024, doi:10.1101/gr.278409.123
...; Talbert et al. 2002; Allshire and Karpen 2008). In humans and yeast, the kinetochore consists of approximately 30 core subunits, within which CENP-A/Cse4 recruits the constitutive centromere-associated network (CCAN) (Yu et al. 2000; Yan et al. 2019; Pesenti et al. 2022; Yatskevich et al. 2022). CCAN...
OPEN ACCESS ARTICLE
Select this article
Research: Functional characterization of enhancer activity during a long terminal repeat's evolution
- Alan Y. Du,
- Xiaoyu Zhuo,
- Vasavi Sundaram,
- Nicholas O. Jensen,
- Hemangi G. Chaudhari,
- Nancy L. Saccone,
- Barak A. Cohen,
- and Ting Wang
Genome Res. October 2022 32: 1840-1851; Published in Advance October 3, 2022, doi:10.1101/gr.276863.122
...expected under a neutral model of evolution. To obtain the background motif conservation rates, we adapted a method previously used in yeast (Doniger et al. 2005). Briefly, we take the sum of probabilities for all sequences that match a motif PWM, with each sequence probability calculated starting from...
OPEN ACCESS ARTICLE
Select this article
Research: Extensive sampling of Saccharomyces cerevisiae in Taiwan reveals ecology and evolution of predomesticated lineages
- Tracy Jiaye Lee,
- Yu-Ching Liu,
- Wei-An Liu,
- Yu-Fei Lin,
- Hsin-Han Lee,
- Huei-Mien Ke,
- Jen-Pan Huang,
- Mei-Yeh Jade Lu,
- Chia-Lun Hsieh,
- Kuo-Fang Chung,
- Gianni Liti,
- and Isheng Jason Tsai
Genome Res. May 2022 32: 864-877; Published in Advance March 31, 2022, doi:10.1101/gr.276286.121
...yeast Saccharomyces cerevisiae before human domestication remain poorly understood. Taiwan is regarded as part of this yeast's geographic birthplace, where the most divergent natural lineage was discovered. Here, we extensively sampled the broadleaf forests across this continental island to probe...
OPEN ACCESS ARTICLE
Select this article
Research: Intergenic ORFs as elementary structural modules of de novo gene birth and protein evolution
- Chris Papadopoulos,
- Isabelle Callebaut,
- Jean-Christophe Gelly,
- Isabelle Hatin,
- Olivier Namy,
- Maxime Renard,
- Olivier Lespinet,
- and Anne Lopes
Genome Res. December 2021 31: 2303-2315; Published in Advance November 22, 2021, doi:10.1101/gr.275638.121
..., thus participating in protein structure diversity and evolution. We showed that amino acid sequences encoded by most yeast intergenic ORFs contain the elementary building blocks of protein structures. Moreover, they encompass the large structural state diversity of canonical proteins, with the majority...
Select this article
Method: ERC2.0 evolutionary rate covariation update improves inference of functional interactions across large phylogenies
- Jordan H. Little,
- Guillermo Hoffmann Meyer,
- Aakash Grover,
- Alex Michael Francette,
- Raghavendran Partha,
- Karen M. Arndt,
- Martin Smith,
- Nathan Clark,
- and Maria Chikina
Genome Res. September 2025 35: 2041-2051; Published in Advance August 7, 2025, doi:10.1101/gr.280586.125
...to nonmodel organisms lacking the extensive experimental data sets found in yeasts and mammals, and it can be done using sequence information alone for a relatively minuscule cost.ERC2.0 networks best predict organism-level cluster interactions in mammals compared to cellular processes in yeast...
Select this article
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
...a multi–cell type extension of the weighted gene coexpression network analysis (WGCNA) framework, termed mWGCNA. Applying mWGCNA to RNA-seq data from six sorted immune cell populations (15 SLE, 10 healthy donors), we identify a coexpression module with interferon-stimulated genes (ISGs) among all cell...
Select this article
Research: Deep learning of the regulatory grammar of yeast 5′ untranslated regions from 500,000 random sequences
- Josh T. Cuperus,
- Benjamin Groves,
- Anna Kuchina,
- Alexander B. Rosenberg,
- Nebojsa Jojic,
- Stanley Fields,
- and Georg Seelig
Genome Res. December 2017 27: 2015-2024; Published in Advance November 2, 2017, doi:10.1101/gr.224964.117
...model on native 5′ UTRs. (A) Native 5′ UTR sequences were synthesized in 50-nt fragments and introduced into the HIS3-based selection system. (B) Correlation of a native library with the predictions from our convolutional neural network built from random sequences.In silico evolution of 5′ UTRs...
Select this article
Research: Population genomics and the evolution of virulence in the fungal pathogen Cryptococcus neoformans
- Christopher A. Desjardins,
- Charles Giamberardino,
- Sean M. Sykes,
- Chen-Hsin Yu,
- Jennifer L. Tenor,
- Yuan Chen,
- Timothy Yang,
- Alexander M. Jones,
- Sheng Sun,
- Miriam R. Haverkamp,
- Joseph Heitman,
- Anastasia P. Litvintseva,
- John R. Perfect,
- and Christina A. Cuomo
Genome Res. July 2017 27: 1207-1219; Published in Advance June 13, 2017, doi:10.1101/gr.218727.116
...). Evolution of virulence in Cryptococcus neoformans Genome Research 1209 www..org VNBII isolates are enriched for clinical isolation source relative to VNBI Although the VNB lineage was previously associated with a high frequency of environmental samples and the a mating type, we found differences between...
OPEN ACCESS ARTICLE
Select this article
Research: Global deceleration of gene evolution following recent genome hybridizations in fungi
- Sira Sriswasdi,
- Masako Takashima,
- Ri-ichiroh Manabe,
- Moriya Ohkuma,
- Takashi Sugita,
- and Wataru Iwasaki
Genome Res. August 2016 26: 1081-1090; Published in Advance July 20, 2016, doi:10.1101/gr.205948.116
...Trichosporon yeasts as a model platform for interrogating early consequences of hybridization, but also highlight its multistage nature (Aury et al. 2006; Conant 2014), filling in a critical gap in the current understanding of eukaryotic evolution. Methods Genome sequencing and assembly T. coremiiforme JCM...
Select this article
Method: Unveiling the functional fate of duplicated genes through expression profiling and structural analysis
- Alex Warwick Vesztrocy,
- Natasha Glover,
- Paul D. Thomas,
- Christophe Dessimoz,
- and Irene Julca
Genome Res. October 2025 35: 2273-2284; Published in Advance August 14, 2025, doi:10.1101/gr.280166.124
...(LDO) conjecture.” This study explores this conjecture, using a novel method to identify asymmetric evolution of paralogs and applying it to all gene families across the Tree of Life in the PANTHER database. Structural data for over 1 million proteins and expression data for 16 animals and 20 plants...

For checked items

view abstracts
download to citation manager

Searching journal content for articles similar to Wuchty 14 (7): 1310.

Search Results

Modify Results

This search

Preprint Server

Current Issue

In This Issue

Citation format:
Results / page:
Results order: