Sequence analysis
View article: Repetitive DNA Dynamics, Phylogenetic Relationships and Divergence Times in Andean Ctenomys (Rodentia: Ctenomyidae).
Repetitive DNA Dynamics, Phylogenetic Relationships and Divergence Times in Andean Ctenomys (Rodentia: Ctenomyidae). Open
The genus Ctenomys comprises a group of rodents with remarkable karyotypic variability linked to the distribution of repetitive sequences and rearrangements. We analyzed the distribution and variation of repetitive DNA in tw…
View article: De novo assembled transcriptome of Red Rubin (Ocimum basilicum) cultivar
De novo assembled transcriptome of Red Rubin (Ocimum basilicum) cultivar Open
RNA-Seq libraries were prepared and sequenced on an Illumina NovaSeq platform (Genewiz, Leipzig, Germany), generating 150 bp paired-end reads. Raw sequencing reads are available in the National Center for Biotechnology Information (N…
View article: Supplemental Data for "High-throughput screening for class I peptide–MHC binding via yeast surface display" (Holec et al., 2025)
Supplemental Data for "High-throughput screening for class I peptide–MHC binding via yeast surface display" (Holec et al., 2025) Open
This dataset contains the full supplementary materials for the study “High-throughput screening for class I peptide–MHC binding via yeast surface display” (Holec et al., 2025). It includes raw and processed data, reference sequences, oligo…
View article: Spatial transcriptomics analysis code
Spatial transcriptomics analysis code Open
This repository contains the code used for the spatial transcriptomics analysis of mouse lung tissue samples included in the study. The analysis was performed on three experimental groups: (1) unvaccinated mice, (2) mice vaccinated with GL…
View article: Supplemental Data for "High-throughput screening for class I peptide–MHC binding via yeast surface display" (Holec et al., 2025)
Supplemental Data for "High-throughput screening for class I peptide–MHC binding via yeast surface display" (Holec et al., 2025) Open
This dataset contains the full supplementary materials for the study “High-throughput screening for class I peptide–MHC binding via yeast surface display” (Holec et al., 2025). It includes raw and processed data, reference sequenc…
View article: Molecular Detection and Genetic Characterization of Anaplasma phagocytophilum in Canine Blood Samples via Real-Time PCR from Kerman, Iran
Molecular Detection and Genetic Characterization of Anaplasma phagocytophilum in Canine Blood Samples via Real-Time PCR from Kerman, Iran Open
Anaplasmosis is an emerging tick-borne disease caused by obligate intracellular bacteria of the genus Anaplasma, capable of infecting both animals and humans. Due to the increasing stray dog population in Kerman city, Iran, and associated …
View article: Whole-genome bisulfite sequencing (WGBS) of the giant panda
Whole-genome bisulfite sequencing (WGBS) of the giant panda Open
Raw sequencing data from whole-genome bisulfite sequencing (WGBS) of the giant panda
View article: 241Whole Genome Sequencing of Qingyuan Partridge Chicken Blood Samples
241Whole Genome Sequencing of Qingyuan Partridge Chicken Blood Samples Open
241Whole Genome Sequencing of Qingyuan Partridge Chicken Blood Samples
View article: 16S sequencing
16S sequencing Open
Microbial diversity is based on the Illumina NovaSeq sequencing platform, using paired end sequencing to construct small fragment libraries for sequencing. By concatenating and filtering Reads, clustering or denoising, and performing speci…
View article: Transcriptome-wide prediction of heat-sensitive RNA structures in Zea mays
Transcriptome-wide prediction of heat-sensitive RNA structures in Zea mays Open
Introduction As global temperatures rise, understanding the potential effects on agriculture and food security is critical. Plant heat stress responses are finely controlled at transcriptional and post-transcriptional levels, with RNA seco…
View article: Comparative metagenomics using pan-metagenomics graphs
Comparative metagenomics using pan-metagenomics graphs Open
Identifying microbial genomic factors underlying human phenotypes is a key goal of microbiome research. Sequence graphs are a highly effective tool for genome comparisons because they enable high-resolution de novo analyses that capture an…
View article: Supplementary Table 2 from Characterization of Leukemic Resistance to CD19-Targeted CAR T-cell Therapy through Deep Genomic Sequencing
Supplementary Table 2 from Characterization of Leukemic Resistance to CD19-Targeted CAR T-cell Therapy through Deep Genomic Sequencing Open
Details of SNVs and small indels detected from deep whole-exome sequencing in CD19 and selected genes associated with genomic instability.
View article: Unraveling VP2 mutations in Infectious Bursal Disease Virus (IBDV) associated with potential vaccine escape in poultry flocks in Shandong, China
Unraveling VP2 mutations in Infectious Bursal Disease Virus (IBDV) associated with potential vaccine escape in poultry flocks in Shandong, China Open
Background Infectious bursal disease virus (IBDV) remains a major threat to the global poultry industry, causing significant economic losses. Recent surveillance data indicate that genetically diverse strains of IBDV are circulating in dif…
View article: Molecular and serological detection of equine infectious anemia virus and equine herpesvirus 1 in selected sites in Ethiopia
Molecular and serological detection of equine infectious anemia virus and equine herpesvirus 1 in selected sites in Ethiopia Open
Infectious diseases are an important constraint to the health and productivity of working equids. However, data quantifying the occurrence and distribution of many viral diseases in working equids in Ethiopia are limited. Thus, this study …
View article: Christiangramia qingdaonensis sp. nov., a novel polysaccharide-degrading Bacteroidota bacterium, isolated from intertidal sediment
Christiangramia qingdaonensis sp. nov., a novel polysaccharide-degrading Bacteroidota bacterium, isolated from intertidal sediment Open
A novel polysaccharide-degrading bacterial strain, designated ASW11-125 T , was isolated from intertidal sediments in Aoshan Bay, Qingdao, China. The strain was strictly aerobic, Gram-stain-negative, catalase-positive but oxidas…
View article: Draft genome sequence of <i>Muricoccus roseus</i> DSM 14916 <sup>T</sup> , isolated from a children’s care center in Finland
Draft genome sequence of <i>Muricoccus roseus</i> DSM 14916 <sup>T</sup> , isolated from a children’s care center in Finland Open
Muricoccus roseus DSM 14916 T , a strain also reported as Roseomonas rosea and Pararoseomonas rosea , was isolated from a water-damaged childcare center in Finland. We report the whole-genome sequence and annotation, identifying genes asso…
View article: Molecular Survey and Genetic Characterization of Hop Stunt Viroid (HSVd) in Fruit Trees in Kazakhstan
Molecular Survey and Genetic Characterization of Hop Stunt Viroid (HSVd) in Fruit Trees in Kazakhstan Open
Hop stunt viroid (HSVd) infects a variety of natural hosts, including fruit trees, leading to significant economic losses worldwide. This survey aimed to assess the incidence of HSVd in fruit trees in southern Kazakhstan. Out of 482 fruit …
View article: An Insight into Strain-Specificity of Streptomyces chrestomyceticus ADP4 and Identification of a Novel Peptide with Potential Antiviral Activities Against Significant Human Viruses, Including SARS-CoV2, HCV, and HIV
An Insight into Strain-Specificity of Streptomyces chrestomyceticus ADP4 and Identification of a Novel Peptide with Potential Antiviral Activities Against Significant Human Viruses, Including SARS-CoV2, HCV, and HIV Open
This study aimed to unravel the genomic uniqueness of Streptomyces chrestomyceticus ADP4 using whole-genome sequence analysis, with a focus on identifying strain-specific genes/proteins associated with a novel therapeutic source. The genom…
View article: Structural and functional characterization of a metagenomically derived γ‐type carbonic anhydrase and its engineering into a hyperthermostable esterase
Structural and functional characterization of a metagenomically derived γ‐type carbonic anhydrase and its engineering into a hyperthermostable esterase Open
The 16S microbial community profiling of a metagenomics library from geothermal spring at Lisvori (Lesvos island, Greece) enabled the identification of a putative sequence exhibiting 95% identity to the γ‐type carbonic anhydrase (γ‐CA) fro…
View article: Genetic identification of the selenate reductase in <i>Enterobacter cloacae</i> SLD1a-1
Genetic identification of the selenate reductase in <i>Enterobacter cloacae</i> SLD1a-1 Open
Bacterial selenate reduction is a key microbial process that affects the speciation and mobility of selenium in the environment. In this study, we identified the selenate reductase gene in the facultative anaerobe Enterobacter cloacae SLD1…
View article: Molecular and Phylogenetic Analyses of Lumpy Skin Disease Virus (LSDV) Outbreak (2021/22) in Pakistan Indicate Involvement of a Clade 1.2 LSDV Strain
Molecular and Phylogenetic Analyses of Lumpy Skin Disease Virus (LSDV) Outbreak (2021/22) in Pakistan Indicate Involvement of a Clade 1.2 LSDV Strain Open
Livestock is the backbone of the economy in an agricultural country like Pakistan, with cattle serving as a milk and protein source. In 2021/22, Pakistan was hit by the first major outbreak of lumpy skin disease (LSD) in cattle, in all fou…
View article: 12S rRNA V5 (Fish-12S-Riaz) amplicon reference sequence database
12S rRNA V5 (Fish-12S-Riaz) amplicon reference sequence database Open
12S rRNA Riaz amplicon reference sequence database in QIIME2 .qza format. Includes a newly developed rCRUX database leveraging NCBI nt sequences as of September. 2024 (Curd et al. 2023), sequences from MitoFish database (Zhu et al., 2023),…
View article: Phylogenomic analysis and genetic mechanisms of antifungal resistance in clinical isolates of <i>Candida glabrata</i> ( <i>Nakaseomyces glabratus</i> ) from across Canada, 2013–2020
Phylogenomic analysis and genetic mechanisms of antifungal resistance in clinical isolates of <i>Candida glabrata</i> ( <i>Nakaseomyces glabratus</i> ) from across Canada, 2013–2020 Open
Candida glabrata ( Nakaseomyces glabratus ) is an important cause of invasive fungal infections and may exhibit reduced susceptibility toward antifungal drugs. Here, we used whole-genome sequencing to investigate the genomic phylogeny and …
View article: First Isolation and Genomic Characterization of Escherichia ruysiae in Togo from a Five-Year-Old Patient with Gastroenteritis and Bloody Diarrhea
First Isolation and Genomic Characterization of Escherichia ruysiae in Togo from a Five-Year-Old Patient with Gastroenteritis and Bloody Diarrhea Open
Escherichia ruysiae is a recently characterized species within the Escherichia genus, often misclassified as E. coli due to limitations in existing operating procedures and diagnostic databases. In this study, we report the first isolation…
View article: Enrichment of root-associated Streptomyces strains in response to drought is driven by diverse functional traits and does not predict beneficial effects on plant growth
Enrichment of root-associated Streptomyces strains in response to drought is driven by diverse functional traits and does not predict beneficial effects on plant growth Open
The genus Streptomyces has consistently been found enriched in drought-stressed plant root microbiomes, yet the ecological basis and functional variation underlying this enrichment at the strain and isolate level remain unclear. Using two …
View article: Fig S8 from Dynamics of Sequence and Structural Cell-Free DNA Landscapes in Small-Cell Lung Cancer
Fig S8 from Dynamics of Sequence and Structural Cell-Free DNA Landscapes in Small-Cell Lung Cancer Open
Longitudinal changes in cfTL were re-analyzed for each patient, considering all plasma variants independent of origin. Survival analyses revealed that CH-unfiltered ctDNA responses were not associated with either (A) overall survival-OS or…
View article: Emergence of a novel reassorted high pathogenicity avian influenza A(H5N2) virus associated with severe pneumonia in a young adult
Emergence of a novel reassorted high pathogenicity avian influenza A(H5N2) virus associated with severe pneumonia in a young adult Open
Background Infection of backyard and poultry with low pathogenicity avian influenza LPAI A(H5N2) viruses has occurred in Mexico since 1994, and the first human infection caused by this influenza virus was detected in 2024. Since its emerge…
View article: Fig S4 from Dynamics of Sequence and Structural Cell-Free DNA Landscapes in Small-Cell Lung Cancer
Fig S4 from Dynamics of Sequence and Structural Cell-Free DNA Landscapes in Small-Cell Lung Cancer Open
(A) Genome-wide log2 copy ratios derived from targeted error-correction sequencing (TEC-Seq) data using CNVkit (Methods) are shown for each plasma sample, with copy number gains indicated in red and losses indicated in blue. Each row corre…
View article: Reviewer #1 (Public review): Heterogeneity of Genetic Sequence within Quasi-species of Influenza Virus Revealed by Single-Molecule Sequencing
Reviewer #1 (Public review): Heterogeneity of Genetic Sequence within Quasi-species of Influenza Virus Revealed by Single-Molecule Sequencing Open
View article: Global geographic and genomic epidemiology analysis of carbapenem-resistant <i>Escherichia coli</i> carrying <i>bla</i> <sub>NDM-9</sub>
Global geographic and genomic epidemiology analysis of carbapenem-resistant <i>Escherichia coli</i> carrying <i>bla</i> <sub>NDM-9</sub> Open
Carbapenem-resistant Escherichia coli (CREC), particularly strains producing New Delhi metallo-β-lactamase-9 (NDM-9), pose a growing threat as agents of nosocomial infections. Despite their emergence since 2013, a comprehensive global phyl…