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View article: <i>C. elegans</i> transgenerational avoidance of <i>P. fluorescens</i> is mediated by the Pfs1 sRNA and <i>vab-1</i>
<i>C. elegans</i> transgenerational avoidance of <i>P. fluorescens</i> is mediated by the Pfs1 sRNA and <i>vab-1</i> Open
In its natural habitat, Caenorhabditis elegans must distinguish friend from foe. Pseudomonas are abundant in the worm’s environment and can be nutritious or pathogenic. Previously, we found that worms learn to avoid Pseudomonas aeruginosa …
View article: Integrative Computational Framework,<i>Dyscovr</i>, Links Mutated Driver Genes to Expression Dysregulation Across 19 Cancer Types
Integrative Computational Framework,<i>Dyscovr</i>, Links Mutated Driver Genes to Expression Dysregulation Across 19 Cancer Types Open
SUMMARY Though somatic mutations play a critical role in driving cancer initiation and progression, the systems-level functional impacts of these mutations—particularly, how they alter expression across the genome and give rise to cancer h…
View article: <i>Pseudomonas fluorescens 15</i>small RNA Pfs1 mediates transgenerational epigenetic inheritance of pathogen avoidance in<i>C. elegans</i>through the Ephrin receptor VAB-1
<i>Pseudomonas fluorescens 15</i>small RNA Pfs1 mediates transgenerational epigenetic inheritance of pathogen avoidance in<i>C. elegans</i>through the Ephrin receptor VAB-1 Open
C. elegans are exposed to a variety of pathogenic and non-pathogenic bacteria species in their natural environment. Correspondingly, C. elegans has evolved an ability to discern between nutritive and infectious bacterial food sources. Here…
View article: Convergent selection on hormone signaling shaped social evolution in bees
Convergent selection on hormone signaling shaped social evolution in bees Open
Sweat bees have repeatedly gained and lost eusociality, a transition from individual to group reproduction. Here, we generate chromosome-length genome assemblies for 17 species and identify genomic signatures of evolutionary trade-offs ass…
View article: AccuCor2 Isotope Natural Abundance Correction for Dual-Isotope Tracer Experiments
AccuCor2 Isotope Natural Abundance Correction for Dual-Isotope Tracer Experiments Open
Stable isotope labeling techniques have been widely applied in the field of metabolomics and proteomics. Before the measured mass spectrum data can be used for quantitative analysis, it must be accurately corrected for isotope natural abun…
View article: AccuCor2 Isotope Natural Abundance Correction for Dual-Isotope Tracer Experiments
AccuCor2 Isotope Natural Abundance Correction for Dual-Isotope Tracer Experiments Open
Stable isotope labeling techniques have been widely applied in the field of metabolomics and proteomics. Before the measured mass spectrum data can be used for quantitative analysis, it must be accurately corrected for isotope natural abun…
View article: Genome Sequence of the Virulent Model Herpes Simplex Virus 1 Strain McKrae Demonstrates the Presence of at Least Two Widely Used Variant Strains
Genome Sequence of the Virulent Model Herpes Simplex Virus 1 Strain McKrae Demonstrates the Presence of at Least Two Widely Used Variant Strains Open
Herpes simplex virus 1 (HSV-1) strain McKrae was isolated in 1965 and has been utilized by many laboratories. Three HSV-1 strain McKrae stocks have been sequenced previously, revealing discrepancies in key genes. We sequenced the genome of…
View article: Horizontal and vertical transmission of transgenerational memories via the<i>Cer1</i>transposon
Horizontal and vertical transmission of transgenerational memories via the<i>Cer1</i>transposon Open
Animals face both external and internal dangers: pathogens threaten from the environment, and unstable genomic elements threaten from within. Previously, we discovered that C. elegans protects itself from pathogens by “reading” bacterial s…
View article: <i>C. elegans</i>“reads” bacterial non-coding RNAs to learn pathogenic avoidance
<i>C. elegans</i>“reads” bacterial non-coding RNAs to learn pathogenic avoidance Open
C. elegans is exposed to many different bacteria in its environment, and must distinguish pathogenic from nutritious bacterial food sources. Here, we show that a single exposure to purified small RNAs isolated from pathogenic Pseudomonas a…
View article: Conservation of cell-intrinsic immune responses in diverse nonhuman primate species
Conservation of cell-intrinsic immune responses in diverse nonhuman primate species Open
Differences in immune responses across species can contribute to the varying permissivity of species to the same viral pathogen. Understanding how our closest evolutionary relatives, nonhuman primates (NHPs), confront pathogens and how the…
View article: Cross-kingdom recognition of bacterial small RNAs induces transgenerational pathogenic avoidance
Cross-kingdom recognition of bacterial small RNAs induces transgenerational pathogenic avoidance Open
We recently discovered that C. elegans can pass on a learned avoidance of pathogenic Pseudomonas aeruginosa (PA14) to four generations of its progeny. This transgenerational inheritance is bacterial species-specific, but how C. elegans rec…
View article: Analysis of Host Responses to Hepatitis B and Delta Viral Infections in a Micro‐scalable Hepatic Co‐culture System
Analysis of Host Responses to Hepatitis B and Delta Viral Infections in a Micro‐scalable Hepatic Co‐culture System Open
Hepatitis B virus (HBV) remains a major global health problem with 257 million chronically infected individuals worldwide, of whom approximately 20 million are co‐infected with hepatitis delta virus (HDV). Progress toward a better understa…
View article: ElucidataInc/ElMaven: v0.4.0-beta.1
ElucidataInc/ElMaven: v0.4.0-beta.1 Open
Fixed Isotopic detection in shift-drag integration #781 Groups with zero peaks will not be bookmarked on shift-drag integration Fixed a bug in changing compound database from the drop-down Getting Started window will not open behind the ma…
View article: Treeview 3.0 (beta 1) - Visualization and analysis of large data matrices
Treeview 3.0 (beta 1) - Visualization and analysis of large data matrices Open
Treeview 3.0 is an open-source Java app for visualizing large data matrices. It enables the user to load a dataset, navigate it, cluster it, customize its appearance and export it (or parts of it) into a figure. This upload corresponds to …
View article: ElucidataInc/ElMaven: El-MAVEN v0.2.4
ElucidataInc/ElMaven: El-MAVEN v0.2.4 Open
LC-MS data processing engine for large-scale metabolomic experiments.
View article: ElucidataInc/ElMaven: El-MAVEN v0.2.2
ElucidataInc/ElMaven: El-MAVEN v0.2.2 Open
LC-MS data processing engine for large-scale metabolomic experiments.
View article: Bioconda: A sustainable and comprehensive software distribution for the life sciences
Bioconda: A sustainable and comprehensive software distribution for the life sciences Open
We present Bioconda ( https://bioconda.github.io ), a distribution of bioinformatics software for the lightweight, multiplatform and language-agnostic package manager Conda. Currently, Bioconda offers a collection of over 3000 software pac…
View article: Whole-Genome Sequence and Variant Analysis of W303, a Widely-Used Strain of <i>Saccharomyces cerevisiae</i>
Whole-Genome Sequence and Variant Analysis of W303, a Widely-Used Strain of <i>Saccharomyces cerevisiae</i> Open
The yeast Saccharomyces cerevisiae has emerged as a superior model organism. Selection of distinct laboratory strains of S. cerevisiae with unique phenotypic properties, such as superior mating or sporulation efficiencies, has facilitated …
View article: Galaxy Planemo 0.35.0
Galaxy Planemo 0.35.0 Open
Command-line utilities to assist in developing tools for the Galaxy Project. http://galaxyproject.org
View article: Genome-wide Purification of Extrachromosomal Circular DNA from Eukaryotic Cells
Genome-wide Purification of Extrachromosomal Circular DNA from Eukaryotic Cells Open
Extrachromosomal circular DNAs (eccDNAs) are common genetic elements in Saccharomyces cerevisiae and are reported in other eukaryotes as well. EccDNAs contribute to genetic variation among somatic cells in multicellular organisms and to ev…
View article: Formation of Extrachromosomal Circular DNA from Long Terminal Repeats of Retrotransposons in<i>Saccharomyces cerevisiae</i>
Formation of Extrachromosomal Circular DNA from Long Terminal Repeats of Retrotransposons in<i>Saccharomyces cerevisiae</i> Open
Extrachromosomal circular DNA (eccDNA) derived from chromosomal Ty retrotransposons in yeast can be generated in multiple ways. Ty eccDNA can arise from the circularization of extrachromosomal linear DNA during the transpositional life cyc…
View article: Comparison of key ciliate macronuclear genomes.
Comparison of key ciliate macronuclear genomes. Open
The phylogeny represents the bootstrap consensus of 100 replicates from PhyML (with the HKY85 substitution model) based on a MUSCLE multiple sequence alignment of 18S rRNA genes from seven ciliates (Oxytricha trifallax—FJ545743; Stylonychi…
View article: Rapid Genome Assembly and Comparison Decode Intrastrain Variation in Human Alphaherpesviruses
Rapid Genome Assembly and Comparison Decode Intrastrain Variation in Human Alphaherpesviruses Open
Herpes simplex virus (HSV) is a widespread pathogen that causes epithelial lesions with recurrent disease that manifests over a lifetime. The lifelong aspect of infection results from latent viral infection of neurons, a reservoir from whi…