Searching journal content for articles similar to Muilu et al. 11 (1): 179.

Displaying results 1-10 of 5778

For checked items

view abstracts
download to citation manager

Select this article
Method: Real-time analysis and visualization of nanopore metagenomic samples with MARTi
- Ned Peel,
- Samuel Martin,
- Darren Heavens,
- Douglas W. Yu,
- Matthew D. Clark,
- and Richard M. Leggett
Genome Res. November 2025 35: 2488-2500; Published in Advance October 27, 2025, doi:10.1101/gr.280550.125
...their own databases. As an offline tool with low memory options, MARTi can be used for in-field taxonomic composition and AMR gene analysis in real-time on a standard laptop. MARTi can also carry out larger scale, complex analyses using a high performance computing (HPC) cluster. Finally, MARTi features...
OPEN ACCESS ARTICLE
Select this article
Method: Multisample motif discovery and visualization for tandem repeats
- Yaran Zhang,
- Marc Hulsman,
- Alex Salazar,
- Niccolò Tesi,
- Lydian Knoop,
- Sven van der Lee,
- Sanduni Wijesekera,
- Jana Krizova,
- Erik-Jan Kamsteeg,
- and Henne Holstege
Genome Res. April 2025 35: 850-862; Published in Advance November 13, 2024, doi:10.1101/gr.279278.124
.... To visualize the motif composition, motifs are colored based on their sequence similarity to each other. The sequences are then clustered based on their motif composition. It also offers the option to perform multiple sequence alignment (MSA) based on motif compositions.Accuracy and efficiencyTo evaluate...
OPEN ACCESS ARTICLE
Select this article
Resource: Visualization and analysis of medically relevant tandem repeats in nanopore sequencing of control cohorts with pathSTR
- Wouter De Coster,
- Ida Höijer,
- Inge Bruggeman,
- Svenn D'Hert,
- Malin Melin,
- Adam Ameur,
- and Rosa Rademakers
Genome Res. November 2024 34: 2074-2080; Published in Advance August 15, 2024, doi:10.1101/gr.279265.124
...a consensus of the repeat allele is generated using a partial overlap alignment (SPOA) (Vaser et al. 2017), as implemented in rust-bio. In the absence of phasing information, STRdust will perform pairwise alignment of the insertions and hierarchical clustering to identify the reads that make up the two...
OPEN ACCESS ARTICLE
Select this article
Method: Interactive visualization and interpretation of pangenome graphs by linear reference–based coordinate projection and annotation integration
- Zepu Miao and
- Jia-Xing Yue
Genome Res. February 2025 35: 296-310; Published in Advance January 13, 2025, doi:10.1101/gr.279461.124
.... Information of the highlighted path regarding nodes’ traversing order and orientation is further reported (in GAF-specified style) in VRPG's path information panel.Application demonstration 1: visualizing a pan graph derived from 163 yeast assembliesTo demonstrate the application of VRPG in real world...
OPEN ACCESS ARTICLE
Select this article
Method: Theoretical framework for the difference of two negative binomial distributions and its application in comparative analysis of sequencing data
- Alicia Petrany,
- Ruoyu Chen,
- Shaoqiang Zhang,
- and Yong Chen
Genome Res. October 2024 34: 1636-1650; Published in Advance October 15, 2024, doi:10.1101/gr.278843.123
...properties. As a state-of-the-art application of DOTNB, we introduce DEGage, a computational method for detecting differentially expressed genes (DEGs) in scRNA-seq data. DEGage calculates the mean of the sample-wise differences of gene expression levels as the test statistic and determines significant...
OPEN ACCESS ARTICLE
Select this article
Method: Linear-time cluster ensembles of large-scale single-cell RNA-seq and multimodal data
- Van Hoan Do,
- Francisca Rojas Ringeling,
- and Stefan Canzar
Genome Res. April 2021 31: 677-688; Published in Advance February 24, 2021, doi:10.1101/gr.267906.120
...that form nonconvex regions. On a variety of data types, this flexibility has allowed spectral clustering methods to produce more accurate clusterings than competing methods (Shi and Malik 2000). The high computational complexity, however, renders its application to large-scale problems infeasible. For n...
Select this article
Method: GrapeTree: visualization of core genomic relationships among 100,000 bacterial pathogens
- Zhemin Zhou,
- Nabil-Fareed Alikhan,
- Martin J. Sergeant,
- Nina Luhmann,
- Cátia Vaz,
- Alexandre P. Francisco,
- João André Carriço,
- and Mark Achtman
Genome Res. September 2018 28: 1395-1404; Published in Advance July 26, 2018, doi:10.1101/gr.232397.117
..., the genetic relationships of legacy STs were represented by phylograms based on hierarchical clustering methods, an approach which can be very useful for visualizing deeper branching structures. Phylograms may, however, be problematic for the presentation of large numbers of genotypes because each genotype...
OPEN ACCESS ARTICLE
Select this article
Method: Background-suppressed live visualization of genomic loci with an improved CRISPR system based on a split fluorophore
- Narendra Chaudhary,
- Si-Hyeong Nho,
- Hayoon Cho,
- Narangerel Gantumur,
- Jae Sun Ra,
- Kyungjae Myung,
- and Hajin Kim
Genome Res. September 2020 30: 1306-1316; Published in Advance September 4, 2020, doi:10.1101/gr.260018.119
...in living cells. Genome imaging based on the CRISPR system is a powerful approach but has limited applicability due to background signals and nonspecific aggregation of fluorophores within nuclei. To address this issue, we developed a novel visualization scheme combining tripartite fluorescent proteins...
Select this article
Methods: The Multiassembly Problem: Reconstructing Multiple Transcript Isoforms From EST Fragment Mixtures
- Yi Xing,
- Alissa Resch,
- and Christopher Lee
Genome Res. March 2004 14: 426-441; Published in Advance February 12, 2004, doi:10.1101/gr.1304504
...). Another major source of transcript information is EST fragment data. However, these data require software assembly to reconstruct full-length transcript sequences. There are ∼4 million human EST sequences in public databases. Clustering ( Schuler 1997 ; Christoffels et al. 2001 ), indexing (Liang et al...
Select this article
RESOURCE: Development and Application of a Salmonid EST Database and cDNA Microarray: Data Mining and Interspecific Hybridization Characteristics
- Matthew L. Rise,
- Kristian R. von Schalburg,
- Gordon D. Brown,
- Melanie A. Mawer,
- Robert H. Devlin,
- Nathanael Kuipers,
- Maura Busby,
- Marianne Beetz-Sargent,
- Roberto Alberto,
- A. Ross Gibbs,
- Peter Hunt,
- Robert Shukin,
- Jeffrey A. Zeznik,
- Colleen Nelson,
- Simon R.M. Jones,
- Duane E. Smailus,
- Steven J.M. Jones,
- Jacqueline E. Schein,
- Marco A. Marra,
- Yaron S.N. Butterfield,
- Jeff M. Stott,
- Siemon H.S. Ng,
- William S. Davidson,
- and Ben F. Koop
Genome Res. March 2004 14: 478-490; Published in Advance February 12, 2004, doi:10.1101/gr.1687304
.... clupeaformis ) were assembled by using PHRAP under high stringency to identify EST clusters (contiguous sequences, or contigs) representing redundant transcripts (Tables 1 , 2 ). The average trimmed PHRED20 length of these ESTs is 546 bases. The 61,819 S. salar ESTs were assembled into 11,560 contigs (with 17...

For checked items

view abstracts
download to citation manager

Searching journal content for articles similar to Muilu et al. 11 (1): 179.

Search Results

Modify Results

This search

Preprint Server

Current Issue

In This Issue

Citation format:
Results / page:
Results order: