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ASCancer Atlas: a comprehensive knowledgebase of alternative splicing in human cancers
2022
Nucleic Acids Research
Preserved Fulltext
network, and a suit of multi-scale online analysis tools. ...
Additionally, a user-friendly web interface was built to enable users to easily browse, search, visualize, analyze, and download all splicing events. ...
We also appreciate a number of users and two anonymous reviewers for reporting bugs and providing constructive feedback.
FUNDING ...
doi:10.1093/nar/gkac955
pmid:36318242
pmcid:PMC9825479
fatcat:5rprd3kea5g7pcf4kxpdeer3sq
Widespread germline genetic heterogeneity of human ribosomal RNA genes
[article]
2021
bioRxiv
pre-print
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Pairwise alignment of the rRNA coding sequences of these copies showed differences in sequence and length. ...
We employed whole genome sequencing (WGS) data from the 1000 Genomes Project phase 3 and analyzed variants in 2,504 individuals from 26 populations. ...
Steven Salzberg for helpful discussions and Maryland Advanced Research Computing Center (MARCC) for access to the high computing resource. ...
doi:10.1101/2021.07.21.453267
fatcat:46huzdfpwrao3l3z5pneslh2nu
A real data-based simulation procedure to select an imputation strategy for mixed-type trait data
[article]
2022
bioRxiv
pre-print
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Using a reptile dataset comprised of both numerical and categorical trait data, we employed a real data-based simulation strategy to select an optimal imputation method for the dataset. ...
It also remains to be explored whether the type of genetic data used affects imputation accuracy. ...
Tyler Elliott for his valuable comments on the manuscript and code. Finally, we thank many researchers who have collected trait and sequence data and made them publicly available. ...
doi:10.1101/2022.05.03.490388
fatcat:facyhm62i5hdxio6hxaxixtmkq
GAST proteins evolved through successive conjugation of novel motifs and their sub-functionalization
2019
Plant Physiology
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Here, using a customized workflow, we report genes encoding GAST proteins, identify novel motifs and evolutionary patterns contributing to the subfunctionalization of GAST domains, and explore functional ...
, and that they might act as signaling molecules in a complex feedback loop. ...
We thank the Arabidopsis Biological Resource Center for Arabidopsis seeds and Shalini Mukherjee, Swati Verma, Archita Singh, and Sandeep Yadav for critical review of the article. ...
doi:10.1104/pp.19.00305
pmid:30971449
pmcid:PMC6548256
fatcat:62ey7xwmhzhd3owxgmjbw2febu
CBF transcription factors involved in the cold response of Camellia japonica (Naidong)
2021
PeerJ
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Using full-length transcriptome data, we identified four CjCBF genes that respond to cold stress and analyzed their evolutionary relationships, domains, and expression patterns. ...
A yeast two-hybrid assay revealed an interaction between CjCBF1, CjCBF2, and CjCBF5, and subcellular localization confirmed this finding. ...
MAFFT was used for sequence alignment according to default parameters (FASTA format, auto). The R package ggmsa was used to visualize the sequence alignment. ...
doi:10.7717/peerj.12155
pmid:34589310
pmcid:PMC8435204
fatcat:eaedt5ytafeajnxdgabrdiwnbm
Phylogenomics of scorpions reveal contemporaneous diversification of scorpion mammalian predators and mammal-active sodium channel toxins
[article]
2022
Zenodo
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Scorpions constitute a charismatic lineage of arthropods and comprise more than 2,500 described species. ...
Found throughout various tropical and temperate habitats, these predatory arachnids have a long evolutionary history, with a fossil record that began in the Silurian. ...
Gene trees and multiple sequence alignment were plotted using the extended R package ggmsa v.1.0.2 from ggplot2 v. 3.3.5 (Wickham, 2016) with the function geom_facet. ...
doi:10.5281/zenodo.5639711
fatcat:ytjl2nz3ivglvjptd46c7n6rrq
Geminiviral genomes encode additional proteins with specific subcellular localizations and virulence function
[article]
2021
bioRxiv
pre-print
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We prove that the largest of these new ORFs, which we name V3, is required for full viral infection, and that the V3 protein localizes in the Golgi apparatus and functions as an RNA silencing suppressor ...
Geminivirus-encoded proteins were identified applying a 10-kDa arbitrary threshold; however, it is increasingly clear that small proteins play relevant roles in biological systems, which calls for the ...
Multiple sequence alignments were constructed by ClustalW and visualized by the R 395 package ggmsa (https://cran.r-project.org/web/packages/ggmsa/vignettes/ggmsa.html). ...
doi:10.1101/2021.03.01.433473
fatcat:xifce2ri2jcdtgn2pz7opgkvxu
HNRNPH1 destabilizes the G-quadruplex structures formed by G-rich RNA sequences that regulate the alternative splicing of an oncogenic fusion transcript
2022
Nucleic Acids Research
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The file type is application/pdf.
analysis of tumor data, long-read sequencing, and minigene studies. ...
Specifically, HNRNPH1 associates and dissociates from G4-folded RNA faster than the identical sequences in a non-G4 state. ...
Data Science (BIDS), Frederick National Laboratory for Cancer Research (FNLCR) for the performance of the long-read sequencing and their assistance with the analysis of these data. ...
doi:10.1093/nar/gkac409
pmid:35639772
pmcid:PMC9226515
fatcat:ffcfyhijhfhxtgdrt6vv4fqzw4
The S Protein of Group B Streptococcus Is a Critical Virulence Determinant That Impacts the Cell Surface Virulome
2021
Frontiers in Microbiology
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These results expand the key roles S protein plays in streptococcal pathogenesis and introduces a new GBS virulence determinant and potential target for therapy development. ...
In our efforts to expand the knowledge base required for targeted anti-virulence therapies, we identified a GBS homolog for a recently identified virulence determinant of group A Streptococcus, S protein ...
These alignment of these sequences was visualized via construction of a circular dendrogram (Figure 2B ). ...
doi:10.3389/fmicb.2021.729308
pmid:34721327
pmcid:PMC8551713
fatcat:rribfr4ch5bkxnae7umaiyq3p4
HNRNPH1 destabilizes the G-quadruplex structures formed by G-rich RNA sequences that regulate the alternative splicing of an oncogenic fusion transcript
[article]
2022
bioRxiv
pre-print
Preserved Fulltext
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The file type is application/pdf.
analysis of tumor data, long-read sequencing, and minigene studies. ...
Specifically, HNRNPH1 associates and dissociates from G4-folded RNA faster than the identical sequences in a non-G4 state. ...
The protein alignments of HNRNPH1, HNRNPH2, and HNRNPF were generated using ggmsa: a visual exploration tool for multiple sequence alignment and associated data (https://github.com/YuLab-SMU/ggmsa). ...
doi:10.1101/2022.04.18.488656
fatcat:kjvsnwbsgbhrxamz4ois2x3u3m
Genomic landscape of drug response reveals mediators of anthelmintic resistance
2022
Cell Reports
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This gene is within a locus under selection in ivermectin-resistant populations worldwide; expression analyses and functional validation using knockdown experiments support that cky-1 is associated with ...
Here, we use an in vivo genetic cross between drug-susceptible and multi-drug-resistant strains of Haemonchus contortus in a natural host-parasite system to simultaneously map resistance loci for the three ...
We also thank Pathogen Informatics and DNA Pipelines (WSI) for their support and expertise and the Biosciences Division at the Moredun Research Institute for expert care and animal assistance. ...
doi:10.1016/j.celrep.2022.111522
pmid:36261007
pmcid:PMC9597552
fatcat:3ggw777m55epbk6pijpts3opaq
Uncovering the Role of Hydroxycinnamoyl Transferase in Boosting Chlorogenic Acid Accumulation in Carthamus tinctorius Cells under Methyl Jasmonate Elicitation
2024
International Journal of Molecular Sciences
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Secondly, the transcriptome data revealed 3637 new genes previously unannotated in the Carthamus tinctorius genome and 3653 differentially expressed genes. ...
The genes involved in the plant signaling pathway and the biosynthesis of CGAs and their precursors showed a general up-regulation, especially the HCT gene family, which ultimately promoted CGA biosynthesis ...
Additionally, multiple sequence alignment analyses of the amino acid sequence of CtHCT protein and its highly homologous sequences were performed using the ggmsa and ggplot2 packages in R studio software ...
doi:10.3390/ijms25052710
pmid:38473957
pmcid:PMC10931740
fatcat:k5q6ziabrve5dj337cladsmncu
Genome-encoded ABCF factors implicated in intrinsic antibiotic resistance in Gram-positive bacteria: VmlR2, Ard1 and CplR
[article]
2022
bioRxiv
pre-print
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The file type is application/pdf.
Finally, assisted by our novel tool for detection of upstream open reading frames, we dissect the translational attenuation mechanism that controls the induction of cplR expression upon an antibiotic challenge ...
We show that CplR contributes to intrinsic pleuromutilin, lincosamide and streptogramin A resistance in Clostridioides, and demonstrate that C. difficile CplR (CDIF630_02847) synergises with the transposon-encoded ...
ACKNOWLEDGMENTS We thank Michael Hall for help with cryo-EM data collection and grid preparation, Farren Isaacs for providing the pRK24 plasmid (Ma et al., 2014) ...
doi:10.1101/2022.12.05.519065
fatcat:ukykhh6scffihfcrynrzzralau
The Influenza B Virus Victoria and Yamagata Lineages Display Distinct Cell Tropism and Infection-Induced Host Gene Expression in Human Nasal Epithelial Cell Cultures
2023
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While ciliated epithelial cells were the dominant cell type infected by both lineages, B/Victoria lineages had a slight preference for MUC5AC-positive cells, and B/Yamagata lineages infected more basal ...
Finally, while both lineages induced a strong interferon response 48 h after infection of hNEC cultures, the B/Victoria lineages showed a much stronger induction of interferon-related signaling pathways ...
We gratefully acknowledge all data contributors, i.e., the Authors and their Originating laboratories responsible for obtaining the specimens, and their Submitting laboratories for generating the genetic ...
doi:10.3390/v15091956
pmid:37766362
pmcid:PMC10537232
fatcat:n6ouo4kd5jbzdmzrifwwexjq4a