Searching journal content for articles similar to Nekrutenko and Li 10 (12): 1986.

Displaying results 1-10 of 296

For checked items

view abstracts
download to citation manager

Select this article
Method: GeneMark-ETP significantly improves the accuracy of automatic annotation of large eukaryotic genomes
- Tomáš Brůna,
- Alexandre Lomsadze,
- and Mark Borodovsky
Genome Res. May 2024 34: 757-768; Published in Advance June 12, 2024, doi:10.1101/gr.278373.123
..., Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA Corresponding author: borodovsky@gatech.eduAbstractLarge-scale genomic initiatives, such as the Earth BioGenome Project, require efficient methods for eukaryotic annotation. Here we present an automatic gene finder, GeneMark-ETP, integrating...
OPEN ACCESS ARTICLE
Select this article
Method: Probing the eukaryotic microbes of ruminants with a deep-learning classifier and comprehensive protein databases
- Ming Yan,
- Thea O. Andersen,
- Phillip B. Pope,
- and Zhongtang Yu
Genome Res. February 2025 35: 368-378; Published in Advance December 27, 2024, doi:10.1101/gr.279825.124
...and assessing the significance of rumen eukaryotes in rumen functions (Andersen et al. 2023). Given that reference search databases are a major bottleneck in metaproteomic studies of complex microbiomes, and considering the previously demonstrated high genomic and functional diversity of the rumen eukaryotes...
Select this article
Research: Diverse evolutionary trajectories of mitocoding DNA in mammalian and avian nuclear genomes
- Yu-Chi Chen,
- David L.J. Vendrami,
- Maximilian L. Huber,
- Luisa E.Y. Handel,
- Christopher R. Cooney,
- Joseph I. Hoffman,
- and Toni I. Gossmann
Genome Res. June 2025 35: 1313-1324; Published in Advance March 31, 2025, doi:10.1101/gr.279428.124
...contribute to genomic diversification driven by the acquisition of adaptive elements across species.An intriguing possibility for the acquisition of novel, genetically adapted elements is the transfer of organelle DNA (Popadin et al. 2022; Butenko et al. 2024). In many eukaryotic species, organelles...
Select this article
Method: Inferring and comparing metabolism across heterogeneous sets of annotated genomes using AuCoMe
- Arnaud Belcour,
- Jeanne Got,
- Méziane Aite,
- Ludovic Delage,
- Jonas Collén,
- Clémence Frioux,
- Catherine Leblanc,
- Simon M. Dittami,
- Samuel Blanquart,
- Gabriel V. Markov,
- and Anne Siegel
Genome Res. June 2023 33: 972-987; Published in Advance July 19, 2023, doi:10.1101/gr.277056.122
...distant algae, underlining the potential of AuCoMe to accelerate the broad exploration of metabolic evolution across the tree of life.The comparison of genomic data gave rise to today's view of the three domains of life: bacteria, archaea, and eukaryotes, which are divided into several supergroups (Burki...
Select this article
Method: Mapping and characterizing N6-methyladenine in eukaryotic genomes using single-molecule real-time sequencing
- Shijia Zhu,
- John Beaulaurier,
- Gintaras Deikus,
- Tao P. Wu,
- Maya Strahl,
- Ziyang Hao,
- Guanzheng Luo,
- James A. Gregory,
- Andrew Chess,
- Chuan He,
- Andrew Xiao,
- Robert Sebra,
- Eric E. Schadt,
- and Gang Fang
Genome Res. July 2018 28: 1067-1078; Published in Advance May 15, 2018, doi:10.1101/gr.231068.117
...% methylation across all molecules. However, epigenetic heterogeneity is often observed in both bacteria (Casadesús and Low 2013; Manso et al. 2014; Beaulaurier et al. 2015) and eukaryotic species (Heng et al. 2009; Smallwood et al. 2014), where only a fraction of cells are methylated at each genomic locus, i...
Select this article
Method: Haplotype diversity and sequence heterogeneity of human telomeres
- Kirill Grigorev,
- Jonathan Foox,
- Daniela Bezdan,
- Daniel Butler,
- Jared J. Luxton,
- Jake Reed,
- Miles J. McKenna,
- Lynn Taylor,
- Kerry A. George,
- Cem Meydan,
- Susan M. Bailey,
- and Christopher E. Mason
Genome Res. July 2021 31: 1269-1279; Published in Advance June 23, 2021, doi:10.1101/gr.274639.120
...and Applied Genomics, University of Tübingen, 72076 Tübingen, Germany; 5NGS Competence Center Tübingen, University of Tübingen, 72076 Tübingen, Germany; 6Department of Environmental and Radiological Health Sciences, Colorado State University, Fort Collins, Colorado 80523, USA; 7Cell and Molecular Biology...
OPEN ACCESS ARTICLE
Select this article
Review: Accurate and complete genomes from metagenomes
- Lin-Xing Chen,
- Karthik Anantharaman,
- Alon Shaiber,
- A. Murat Eren,
- and Jillian F. Banfield
Genome Res. March 2020 30: 315-333; Published in Advance March 18, 2020, doi:10.1101/gr.258640.119
...Supplemental Fig. S2). Overall, it is essential for our community to note that computational analyses that rely heavily on SCGs to assess the quality of MAGs can promote erroneous insights.Genome curation: moving toward complete sThe opportunity to recover huge numbers of new s from metagenomic data sets...
OPEN ACCESS ARTICLE
Select this article
Method: Accurate reconstruction of bacterial pan- and core genomes with PEPPAN
- Zhemin Zhou,
- Jane Charlesworth,
- and Mark Achtman
Genome Res. November 2020 30: 1667-1679; Published in Advance October 14, 2020, doi:10.1101/gr.260828.120
...work on eukaryotic s. PEPPAN could therefore be extended for use on eukaryotes with collaboration from experts in eukaryotic genomics.Relevance to MLST schemesAlikhan et al. (2018) described a pan for all of Salmonella based on 537 s that had been derived by a precursor of PEPPAN in 2015. That pan...
OPEN ACCESS ARTICLE
Select this article
Method: Transcriptome reconstruction and functional analysis of eukaryotic marine plankton communities via high-throughput metagenomics and metatranscriptomics
- Alexey Vorobev,
- Marion Dupouy,
- Quentin Carradec,
- Tom O. Delmont,
- Anita Annamalé,
- Patrick Wincker,
- and Eric Pelletier
Genome Res. April 2020 30: 647-659; Published in Advance March 23, 2020, doi:10.1101/gr.253070.119
..., the analysis of the MGTs closely related to organisms which have sequenced representatives may lead to a re-evaluation of their genomic potential and provide additional information on their ecology.DMSP biosynthesis and degradation by eukaryotesWe demonstrated the ability of the MGT approach to assess...
Select this article
Research: Gene duplication and genetic innovation in cereal genomes
- Hui Guo,
- Yuannian Jiao,
- Xu Tan,
- Xiyin Wang,
- Xianzhong Huang,
- Huizhe Jin,
- and Andrew H. Paterson
Genome Res. February 2019 29: 261-269; Published in Advance January 16, 2019, doi:10.1101/gr.237511.118
...MCL: identification of ortholog groups for eukaryotic s. Genome Res 13: 2178–2189. doi:10.1101/gr.1224503 ↵Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, Marth G, Abecasis G, Durbin R; 1000 Genome Project Data Processing Subgroup. 2009. The Sequence Alignment/Map format and SAMtools. Bioinformatics 25...

For checked items

view abstracts
download to citation manager

Searching journal content for articles similar to Nekrutenko and Li 10 (12): 1986.

Search Results

Modify Results

This search

Preprint Server

Current Issue

In This Issue

Citation format:
Results / page:
Results order: