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Manipulation of FASTQ data with Galaxy

https://doi.org/10.1093/bioinformatics/btq281

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What this work says

Outgoing claims: the papers this work cites, builds on, or argues with.

inferredcites →https://doi.org/10.1002/0471142727.mb1910s89openalex-snapshot

Galaxy: A Web‐Based Genome Analysis Tool for Experimentalists

inferredcites →https://doi.org/10.1002/0471250953.bi1005s19openalex-snapshot

Using Galaxy to Perform Large‐Scale Interactive Data Analyses

inferredcites →https://doi.org/10.1093/nar/gkp1137openalex-snapshot

The Sanger FASTQ file format for sequences with quality scores, and the Solexa/Illumina FASTQ variants

inferredcites →https://doi.org/10.1101/gr.5578007openalex-snapshot

A framework for collaborative analysis of ENCODE data: Making large-scale analyses biologist-friendly

What points at this work

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RNA-Seq analysis of the toxicant-induced transcriptome of the marine diatom, Ceratoneis closterium

inferred← citeshttps://doi.org/10.1016/j.margen.2014.08.003openalex-snapshot

Next generation sequence analysis of the transcriptome of Sydney rock oysters (Saccostrea glomerata) exposed to a range of environmental stressors

inferred← citeshttps://doi.org/10.1016/j.margen.2017.08.002openalex-snapshot

Skin Transcriptomes of common bottlenose dolphins (Tursiops truncatus) from the northern Gulf of Mexico and southeastern U.S. Atlantic coasts

inferred← citeshttps://doi.org/10.1016/j.matbio.2022.08.006openalex-snapshot

Obesity impairs skeletal muscle repair through NID-1 mediated extracellular matrix remodeling by mesenchymal progenitors

inferred← citeshttps://doi.org/10.1016/j.mce.2017.10.016openalex-snapshot

High-fat diet exposure, regardless of induction of obesity, is associated with altered expression of genes critical to normal ovulatory function

inferred← citeshttps://doi.org/10.1016/j.mce.2020.110701openalex-snapshot

Interplay of ERα binding and DNA methylation in the intron-2 determines the expression and estrogen regulation of cystatin A in breast cancer cells

inferred← citeshttps://doi.org/10.1016/j.meegid.2017.07.009openalex-snapshot

Whole-genome characterization of Uruguayan strains of avian infectious bronchitis virus reveals extensive recombination between the two major South American lineages

inferred← citeshttps://doi.org/10.1016/j.neuron.2019.01.015openalex-snapshot

Transcriptional Feedback Links Lipid Synthesis to Synaptic Vesicle Pools in Drosophila Photoreceptors

inferred← citeshttps://doi.org/10.1016/j.neuron.2021.05.020openalex-snapshot

C9orf72 deficiency promotes microglial-mediated synaptic loss in aging and amyloid accumulation

inferred← citeshttps://doi.org/10.1016/j.neuropharm.2014.03.013openalex-snapshot

Chronic LSD alters gene expression profiles in the mPFC relevant to schizophrenia

inferred← citeshttps://doi.org/10.1016/j.onehlt.2015.08.002openalex-snapshot

Comparative Usutu and West Nile virus transmission potential by local Culex pipiens mosquitoes in north-western Europe

inferred← citeshttps://doi.org/10.1016/j.plaphy.2016.08.008openalex-snapshot

Transcriptome and proteome analyses provide insight into laticifer's defense of Euphorbia tirucalli against pests

inferred← citeshttps://doi.org/10.1016/j.plaphy.2017.11.013openalex-snapshot

Small RNA differential expression and regulation in Tuxpeño maize embryogenic callus induction and establishment

inferred← citeshttps://doi.org/10.1016/j.protis.2019.06.001openalex-snapshot

Integrated Genomic and Transcriptomic Analysis of the Peridinin Dinoflagellate Amphidinium carterae Plastid

inferred← citeshttps://doi.org/10.1016/j.repbio.2021.100577openalex-snapshot

Identification of genes associated with susceptibility to persistent breeding-induced endometritis by RNA-sequencing of uterine cytobrush samples

inferred← citeshttps://doi.org/10.1016/j.repbio.2021.100598openalex-snapshot

Transcriptomic analysis of MA-10 tumor Leydig cells treated with adipose derived hormones adiponectin and resistin

inferred← citeshttps://doi.org/10.1016/j.scienta.2023.112628openalex-snapshot

Identification of genes involved in almond scion tree architecture influenced by rootstock genotype using transcriptome analysis

inferred← citeshttps://doi.org/10.1016/j.scitotenv.2021.150020openalex-snapshot

Demonstration of an aggregated biomarker response approach to assess the impact of point and diffuse contaminant sources in feral fish in a small river case study

inferred← citeshttps://doi.org/10.1016/j.softx.2020.100535openalex-snapshot

GTO: A toolkit to unify pipelines in genomic and proteomic research

inferred← citeshttps://doi.org/10.1016/j.syapm.2015.09.003openalex-snapshot

Burkholderia kirstenboschensis sp. nov. nodulates papilionoid legumes indigenous to South Africa

inferred← citeshttps://doi.org/10.1016/j.ydbio.2013.02.014openalex-snapshot

Interaction between DMRT1 function and genetic background modulates signaling and pluripotency to control tumor susceptibility in the fetal germ line

inferred← citeshttps://doi.org/10.1016/j.ydbio.2015.10.016openalex-snapshot

Ribbon regulates morphogenesis of the Drosophila embryonic salivary gland through transcriptional activation and repression

inferred← citeshttps://doi.org/10.1016/j.yexmp.2020.104577openalex-snapshot

Analysis of latent T-cell epitopes in Epstein-Barr virus isolated from extranodal nasal-type natural killer/T-cell lymphoma in Taiwanese population

inferred← citeshttps://doi.org/10.1016/j.ymeth.2013.03.022openalex-snapshot

Transcriptome-wide identification of RNA binding sites by CLIP-seq

inferred← citeshttps://doi.org/10.1016/j.ympev.2015.06.003openalex-snapshot

Detecting reticulate relationships among diploid Leucanthemum Mill. (Compositae, Anthemideae) taxa using multilocus species tree reconstruction methods and AFLP fingerprinting

inferred← citeshttps://doi.org/10.1016/j.ympev.2025.108322openalex-snapshot

Transcriptomic analyses in thirteen Tephritidae species provide insights into the ecological driving force behind odorant receptor evolution

inferred← citeshttps://doi.org/10.1021/acs.jproteome.8b00610openalex-snapshot

In-Depth Venome of the Brazilian Rattlesnake Crotalus durissus terrificus: An Integrative Approach Combining Its Venom Gland Transcriptome and Venom Proteome

inferred← citeshttps://doi.org/10.1021/acsnano.4c00925openalex-snapshot

A Polymer-Based Antigen Carrier Activates Two Innate Immune Pathways for Adjuvant-Free Subunit Vaccines

inferred← citeshttps://doi.org/10.1021/acssynbio.4c00657openalex-snapshot

MOSAIC: A Highly Efficient, One-Step Recombineering Approach to Plasmid Editing and Diversification

inferred← citeshttps://doi.org/10.1021/acssynbio.6c00166openalex-snapshot

Combinatorial Optimization of Protein Systems in Synthetic Cells

inferred← citeshttps://doi.org/10.1021/jacs.8b02618openalex-snapshot

miCLIP-MaPseq, a Substrate Identification Approach for Radical SAM RNA Methylating Enzymes

inferred← citeshttps://doi.org/10.1021/jacsau.4c01189openalex-snapshot

Prediction of Single-Mutation Effects for Fluorescent Immunosensor Engineering with an End-to-End Trained Protein Language Model

inferred← citeshttps://doi.org/10.1038/ismej.2013.195openalex-snapshot

Ectomycorrhizal fungi contribute to soil organic matter cycling in sub-boreal forests

inferred← citeshttps://doi.org/10.1038/mt.2015.68openalex-snapshot

CNTF Gene Therapy Confers Lifelong Neuroprotection in a Mouse Model of Human Retinitis Pigmentosa

inferred← citeshttps://doi.org/10.1038/nature17664openalex-snapshot

Efficient introduction of specific homozygous and heterozygous mutations using CRISPR/Cas9

inferred← citeshttps://doi.org/10.1038/ncb2701openalex-snapshot

Polycomb Cbx family members mediate the balance between haematopoietic stem cell self-renewal and differentiation

inferred← citeshttps://doi.org/10.1038/ncomms15790openalex-snapshot

Improving the DNA specificity and applicability of base editing through protein engineering and protein delivery

inferred← citeshttps://doi.org/10.1038/ncomms9213openalex-snapshot

RNA regulatory networks diversified through curvature of the PUF protein scaffold

inferred← citeshttps://doi.org/10.1038/nm.3963openalex-snapshot

Viral variants that initiate and drive maturation of V1V2-directed HIV-1 broadly neutralizing antibodies

inferred← citeshttps://doi.org/10.1038/s41380-022-01497-8openalex-snapshot

Differential vulnerability of adult neurogenic niches to dosage of the neurodevelopmental-disorder linked gene Foxg1

inferred← citeshttps://doi.org/10.1038/s41419-023-06224-xopenalex-snapshot

Lamin A upregulation reorganizes the genome during rod photoreceptor degeneration

inferred← citeshttps://doi.org/10.1038/s41435-026-00377-3openalex-snapshot

Association of tumour-associated macrophage states with nonconserved lncRNAs in lung cancer

inferred← citeshttps://doi.org/10.1038/s41467-017-01342-5openalex-snapshot

Mammalian γ2 AMPK regulates intrinsic heart rate

inferred← citeshttps://doi.org/10.1038/s41467-018-06659-3openalex-snapshot

Immune-suppression by OsHV-1 viral infection causes fatal bacteraemia in Pacific oysters

inferred← citeshttps://doi.org/10.1038/s41467-018-07310-xopenalex-snapshot

Orthogonal Cas9–Cas9 chimeras provide a versatile platform for genome editing

inferred← citeshttps://doi.org/10.1038/s41467-019-09152-7openalex-snapshot

Sterol regulatory element binding protein 1 couples mechanical cues and lipid metabolism

inferred← citeshttps://doi.org/10.1038/s41467-019-12400-5openalex-snapshot

Distinct transcriptional roles for Histone H3-K56 acetylation during the cell cycle in Yeast

inferred← citeshttps://doi.org/10.1038/s41467-020-17531-8openalex-snapshot

DNA sequence-dependent activity and base flipping mechanisms of DNMT1 regulate genome-wide DNA methylation

inferred← citeshttps://doi.org/10.1038/s41467-020-20784-yopenalex-snapshot

UPRmt scales mitochondrial network expansion with protein synthesis via mitochondrial import in Caenorhabditis elegans

inferred← citeshttps://doi.org/10.1038/s41467-021-23775-9openalex-snapshot

HIRA stabilizes skeletal muscle lineage identity

inferred← citeshttps://doi.org/10.1038/s41467-021-23922-2openalex-snapshot

Mapping chromatin accessibility and active regulatory elements reveals pathological mechanisms in human gliomas

inferred← citeshttps://doi.org/10.1038/s41467-022-31455-5openalex-snapshot

Comparative genomics of Acinetobacter baumannii and therapeutic bacteriophages from a patient undergoing phage therapy

inferred← citeshttps://doi.org/10.1038/s41467-024-52711-wopenalex-snapshot

Private benefit of β-lactamase dictates selection dynamics of combination antibiotic treatment

inferred← citeshttps://doi.org/10.1038/s41526-018-0061-0openalex-snapshot

Comparison of Bacillus subtilis transcriptome profiles from two separate missions to the International Space Station

inferred← citeshttps://doi.org/10.1038/s41556-021-00840-5openalex-snapshot

LONP-1 and ATFS-1 sustain deleterious heteroplasmy by promoting mtDNA replication in dysfunctional mitochondria

inferred← citeshttps://doi.org/10.1038/s41559-018-0719-8openalex-snapshot

The genome of the jellyfish Aurelia and the evolution of animal complexity

inferred← citeshttps://doi.org/10.1038/s41559-022-01705-2openalex-snapshot

Intra- and interpopulation transposition of mobile genetic elements driven by antibiotic selection

inferred← citeshttps://doi.org/10.1038/s41586-019-1076-8openalex-snapshot

Precise therapeutic gene correction by a simple nuclease-induced double-stranded break

inferred← citeshttps://doi.org/10.1038/s41589-021-00961-wopenalex-snapshot

Modulation of microbial community dynamics by spatial partitioning

inferred← citeshttps://doi.org/10.1038/s41593-021-00905-6openalex-snapshot

Neuroinflammatory astrocyte subtypes in the mouse brain

inferred← citeshttps://doi.org/10.1038/s41598-017-03534-xopenalex-snapshot

Identification of novel dysregulated key genes in Breast cancer through high throughput ChIP-Seq data analysis

inferred← citeshttps://doi.org/10.1038/s41598-017-05422-wopenalex-snapshot

Deficient Vitamin E Uptake During Development Impairs Neural Tube Closure in Mice Lacking Lipoprotein Receptor SR-BI

inferred← citeshttps://doi.org/10.1038/s41598-017-11574-6openalex-snapshot

Acute doses of caffeine shift nervous system cell expression profiles toward promotion of neuronal projection growth

inferred← citeshttps://doi.org/10.1038/s41598-017-11800-1openalex-snapshot

Differential landscape of non-CpG methylation in embryonic stem cells and neurons caused by DNMT3s

inferred← citeshttps://doi.org/10.1038/s41598-018-29278-wopenalex-snapshot

Temporal analysis of Arabidopsis genes activated by Eucalyptus grandis NAC transcription factors associated with xylem fibre and vessel development

inferred← citeshttps://doi.org/10.1038/s41598-018-31866-9openalex-snapshot

Child Weight Gain Trajectories Linked To Oral Microbiota Composition

inferred← citeshttps://doi.org/10.1038/s41598-018-32818-zopenalex-snapshot

Meta-analysis of data from spaceflight transcriptome experiments does not support the idea of a common bacterial “spaceflight response”

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