Searching journal content for articles similar to Freyhult et al. 17 (1): 117.

Displaying results 1-10 of 25

For checked items

view abstracts
download to citation manager

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
...-regulatory elements because they focus on genes nearby to noncoding regions. Hence, we conducted a second strategy to gain further insights into the role of the identified noncoding regions as possible trans-acting elements. For this, we searched for short enriched motifs in the set of 39,806 genomic regions using...
Select this article
Research: A long-term demasculinization of X-linked intergenic noncoding RNAs in Drosophila melanogaster
- Ge Gao,
- Maria D. Vibranovski,
- Li Zhang,
- Zheng Li,
- Ming Liu,
- Yong E. Zhang,
- Xinmin Li,
- Wenxia Zhang,
- Qichang Fan,
- Nicholas W. VanKuren,
- Manyuan Long,
- and Liping Wei
Genome Res. April 2014 24: 629-638; Published in Advance January 9, 2014, doi:10.1101/gr.165837.113
...on the mammalian X chromosome. Science 303: 537–540. ↵ Freyhult EK, Bollback JP, Gardner PP Freyhult EK, Bollback JP, Gardner PP. 2007. Exploring genomic dark matter: A critical assessment of the performance of homology search methods on noncoding RNA. Genome Res 17: 117–125. ↵ Gnad F, Parsch J Gnad F, Parsch J...
OPEN ACCESS ARTICLE
Select this article
Resource: Assemblathon 1: A competitive assessment of de novo short read assembly methods
- Dent Earl,
- Keith Bradnam,
- John St. John,
- Aaron Darling,
- Dawei Lin,
- Joseph Fass,
- Hung On Ken Yu,
- Vince Buffalo,
- Daniel R. Zerbino,
- Mark Diekhans,
- Ngan Nguyen,
- Pramila Nuwantha Ariyaratne,
- Wing-Kin Sung,
- Zemin Ning,
- Matthias Haimel,
- Jared T. Simpson,
- Nuno A. Fonseca,
- İnanç Birol,
- T. Roderick Docking,
- Isaac Y. Ho,
- Daniel S. Rokhsar,
- Rayan Chikhi,
- Dominique Lavenier,
- Guillaume Chapuis,
- Delphine Naquin,
- Nicolas Maillet,
- Michael C. Schatz,
- David R. Kelley,
- Adam M. Phillippy,
- Sergey Koren,
- Shiaw-Pyng Yang,
- Wei Wu,
- Wen-Chi Chou,
- Anuj Srivastava,
- Timothy I. Shaw,
- J. Graham Ruby,
- Peter Skewes-Cox,
- Miguel Betegon,
- Michelle T. Dimon,
- Victor Solovyev,
- Igor Seledtsov,
- Petr Kosarev,
- Denis Vorobyev,
- Ricardo Ramirez-Gonzalez,
- Richard Leggett,
- Dan MacLean,
- Fangfang Xia,
- Ruibang Luo,
- Zhenyu Li,
- Yinlong Xie,
- Binghang Liu,
- Sante Gnerre,
- Iain MacCallum,
- Dariusz Przybylski,
- Filipe J. Ribeiro,
- Shuangye Yin,
- Ted Sharpe,
- Giles Hall,
- Paul J. Kersey,
- Richard Durbin,
- Shaun D. Jackman,
- Jarrod A. Chapman,
- Xiaoqiu Huang,
- Joseph L. DeRisi,
- Mario Caccamo,
- Yingrui Li,
- David B. Jaffe,
- Richard E. Green,
- David Haussler,
- Ian Korf,
- and Benedict Paten
Genome Res. December 2011 21: 2224-2241; Published in Advance September 16, 2011, doi:10.1101/gr.126599.111
...of a genomic assembly by checking the extent to which the assembly recapitulates the transcriptome. When a reference or sequence is available, a comparison between the assembly and reference can be performed. This has previously been accomplished by studies using several different alignment methods, including...
OPEN ACCESS ARTICLE
Select this article
Research: Transcription and potential functions of a novel XIST isoform in male peripheral glia
- Kevin S. O'Leary,
- Meng-Yen Li,
- Kevyn Jackson,
- Lijie Shi,
- Elena Ezhkova,
- Bernice E. Morrow,
- and Deyou Zheng
Genome Res. February 2026 36: 257-274; Published in Advance December 12, 2025, doi:10.1101/gr.280832.125
....Zheng@einsteinmed.eduAbstractThe XIST RNA is known for its critical roles in X Chromosome inactivation (XCI). It is thought to be expressed exclusively from one copy of the X Chromosome and silence it by recruiting various chromatin factors in female cells. In this study, we find XIST expression in male peripheral glia after...
OPEN ACCESS ARTICLE
Select this article
Review: De novo gene birth and the conundrum of ORFan genes in bacteria
- Md. Hassan uz-Zaman and
- Howard Ochman
Genome Res. August 2025 35: 1679-1688; Published in Advance July 10, 2025, doi:10.1101/gr.280157.124
...postulated to originate from either horizontal transfer, rapid divergence from pre-existing genes, or de novo emergence from noncoding sequences. We assess the body of research that explores each of these hypotheses and demonstrate that the mystery of the origin of bacterial ORFans still remains unresolved...
Select this article
Method: Strain-level metagenomic profiling using pangenome graphs with PanTax
- Wenhai Zhang,
- Yuansheng Liu,
- Guangyi Li,
- Jialu Xu,
- Enlian Chen,
- Alexander Schönhuth,
- and Xiao Luo
Genome Res. February 2026 36: 405-420; Published in Advance January 14, 2026, doi:10.1101/gr.280858.125
...that are indicative of species. For example, whereas the 16S rRNA sequence is commonly used in some microbiome analysis methods due to its high conservation (Edgar 2018), tools like MetaPhlAn4 and mOTUs rely on a broader set of specific taxon-specific markers. Although these methods are computationally efficient...
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
.... cerevisiae with the aim of (1) exploring whether the structural states’ diversity of proteomes is already present in noncoding sequences, and (2) estimating the potential of the noncoding to produce novel protein bricks that could either give rise to novel genes or be integrated into pre-existing proteins...
Select this article
Research: The population genomics of rhesus macaques (Macaca mulatta) based on whole-genome sequences
- Cheng Xue,
- Muthuswamy Raveendran,
- R. Alan Harris,
- Gloria L. Fawcett,
- Xiaoming Liu,
- Simon White,
- Mahmoud Dahdouli,
- David Rio Deiros,
- Jennifer E. Below,
- William Salerno,
- Laura Cox,
- Guoping Fan,
- Betsy Ferguson,
- Julie Horvath,
- Zach Johnson,
- Sree Kanthaswamy,
- H. Michael Kubisch,
- Dahai Liu,
- Michael Platt,
- David G. Smith,
- Binghua Sun,
- Eric J. Vallender,
- Feng Wang,
- Roger W. Wiseman,
- Rui Chen,
- Donna M. Muzny,
- Richard A. Gibbs,
- Fuli Yu,
- and Jeffrey Rogers
Genome Res. December 2016 26: 1651-1662; Published in Advance October 17, 2016, doi:10.1101/gr.204255.116
...Mature miRNA 650 Population genomics of rhesus macaques Genome Research 1655 www..org but more similar between species than the counts of synonymous variants (7810.1 in rhesus versus 6551.7 in humans; t-test P = 7.66 × 10−47) (see also Yuan et al. 2012). Consequently, the ratio of nonsynonymous...
OPEN ACCESS ARTICLE
Select this article
Method: A general calculus of fitness landscapes finds genes under selection in cancers
- Teng-Kuei Hsu,
- Jennifer Asmussen,
- Amanda Koire,
- Byung-Kwon Choi,
- Mayur A. Gadhikar,
- Eunna Huh,
- Chih-Hsu Lin,
- Daniel M. Konecki,
- Young Won Kim,
- Curtis R. Pickering,
- Marek Kimmel,
- Lawrence A. Donehower,
- Mitchell J. Frederick,
- Jeffrey N. Myers,
- Panagiotis Katsonis,
- and Olivier Lichtarge
Genome Res. May 2022 32: 916-929; Published in Advance March 17, 2022, doi:10.1101/gr.275811.121
...–phenotype relationship describes how genetic variations induce biological change (Manolio et al. 2009). Experimental screens tracking the effect of these variations include RNA interference (RNAi) (Boutros and Ahringer 2008), CRISPR-Cas9 knockouts (Mali et al. 2013; Koike-Yusa et al. 2014; Wang et al. 2014b; Hart et al...
OPEN ACCESS ARTICLE
Select this article
ARTICLE: Evolutionarily conserved elements in vertebrate, insect, worm, and yeast genomes
- Adam Siepel,
- Gill Bejerano,
- Jakob S. Pedersen,
- Angie S. Hinrichs,
- Minmei Hou,
- Kate Rosenbloom,
- Hiram Clawson,
- John Spieth,
- LaDeana W. Hillier,
- Stephen Richards,
- George M. Weinstock,
- Richard K. Wilson,
- Richard A. Gibbs,
- W. James Kent,
- Webb Miller,
- and David Haussler
Genome Res. August 2005 15: 1034-1050; Published in Advance July 15, 2005, doi:10.1101/gr.3715005
...tremendous progress in vertebrate genomics, it is still not clear how much of the human and other vertebrate s are directly functional, in the sense of encoding proteins or RNAs helping to regulate transcription and translation, enabling replication, altering chromatin structure, or performing other...

For checked items

view abstracts
download to citation manager

Searching journal content for articles similar to Freyhult et al. 17 (1): 117.

Search Results

Modify Results

This search

Preprint Server

Current Issue

In This Issue

Citation format:
Results / page:
Results order: