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49 matching publication(s)

Publication	Journal	Year	Score	Verdict
RNA-sequence analysis of primary alveolar macrophages after in vitro infection with porcine reproductive and respiratory syndrome virus strains of differing vir ⚑ PMID 24643046	PLoS One	2014	41	41/100 ⚑
A comparative study of techniques for differential expression analysis on RNA-Seq data. PMID 25119138	PLoS One	2014	58	L1 58/100
RNA-Seq transcriptome profiling identifies CRISPLD2 as a glucocorticoid responsive gene that modulates cytokine function in airway smooth muscle cells. PMID 24926665	PLoS One	2014	87	L1 87/100
The Li2 mutation results in reduced subgenome expression bias in elongating fibers of allotetraploid cotton (Gossypium hirsutum L.). PMID 24598808	PLoS One	2014	58	L1 58/100
Transcriptome analysis reveals differential splicing events in IPF lung tissue. PMID 24647608	PLoS One	2014	81	L1 81/100
HTSstation: a web application and open-access libraries for high-throughput sequencing data analysis. PMID 24475057	PLoS One	2014	66	L1 66/100
Exploring candidate genes for pericarp russet pigmentation of sand pear (Pyrus pyrifolia) via RNA-Seq data in two genotypes contrasting for pericarp color. PMID 24400075	PLoS One	2014	74	L1 74/100
Transcriptome profiling of radish (Raphanus sativus L.) root and identification of genes involved in response to Lead (Pb) stress with next generation sequencin ⚑ PMID 23840502	PLoS One	2013	27	L1 27/100 ⚑
Identifying and classifying trait linked polymorphisms in non-reference species by walking coloured de bruijn graphs. ⚑ PMID 23536903	PLoS One	2013	45	L1 45/100 ⚑
Ordinal-level phylogenomics of the arthropod class Diplopoda (millipedes) based on an analysis of 221 nuclear protein-coding loci generated using next-generatio PMID 24236165	PLoS One	2013	82	L1 82/100
Sequencing mRNA from cryo-sliced Drosophila embryos to determine genome-wide spatial patterns of gene expression. PMID 23951250	PLoS One	2013	67	L1 67/100
Compression of structured high-throughput sequencing data. ⚑ PMID 24260313	PLoS One	2013	43	L1 43/100 ⚑
Combining evidence of preferential gene-tissue relationships from multiple sources. PMID 23950964	PLoS One	2013	53	L1 53/100
An extensive evaluation of read trimming effects on Illumina NGS data analysis. PMID 24376861	PLoS One	2013	85	L1 85/100
RNA-Seq transcriptome profiling of upland cotton (Gossypium hirsutum L.) root tissue under water-deficit stress. ⚑ PMID 24324815	PLoS One	2013	38	L1 38/100 ⚑
Optimal scaling of digital transcriptomes. PMID 24223126	PLoS One	2013	67	L1 67/100
A case study for large-scale human microbiome analysis using JCVI's metagenomics reports (METAREP). PMID 22719821	PLoS One	2012	78	L1 78/100
RAGER: A user-friendly computational platform for integrated analysis of RNA-Seq and ATAC-seq data. PMID 42172220	PLoS One	2026	63	L1 63/100
Investigating epigenetic biomarkers of age, sex, and disease in captive South African cheetahs (Acinonyx jubatus jubatus). PMID 41528985	PLoS One	2026	58	L1 58/100
Manual curation for improved genome annotation of the functionally extinct northern white rhinoceros (Ceratotherium simum cottoni). PMID 41490125	PLoS One	2026	69	L1 69/100
What defines a photosynthetic microbial mat in western Antarctica? PMID 40043057	PLoS One	2025	85	L1 85/100
SEMdag: Fast learning of Directed Acyclic Graphs via node or layer ordering. PMID 39775401	PLoS One	2025	81	L1 81/100
Transcriptome and machine learning analysis of the impact of COVID-19 on mitochondria and multiorgan damage. PMID 38295140	PLoS One	2024	71	L1 71/100
Stemness genes and miR-1247-3p expression associate with clinicopathological parameters and prognosis in lung adenocarcinoma. PMID 37948380	PLoS One	2023	90	L1 90/100
Identification of immune-related signatures and pathogenesis differences between thoracic aortic aneurysm patients with bicuspid versus tricuspid valves via wei PMID 37883426	PLoS One	2023	97	L1 97/100
Genomic capacities for Reactive Oxygen Species metabolism across marine phytoplankton. ⚑ PMID 37098087	PLoS One	2023	38	L1 38/100 ⚑
The selection of software and database for metagenomics sequence analysis impacts the outcome of microbial profiling and pathogen detection. PMID 37027361	PLoS One	2023	86	L1 86/100
Analyzing biomarker discovery: Estimating the reproducibility of biomarker sets. PMID 35901020	PLoS One	2022	83	L1 83/100
Gene module regulation in dilated cardiomyopathy and the role of Na/K-ATPase. ⚑ PMID 35901050	PLoS One	2022	55	L1 55/100 ⚑
Comparative analysis of molecular signatures reveals a hybrid approach in breast cancer: Combining the Nottingham Prognostic Index with gene expressions into a ⚑ PMID 35143511	PLoS One	2022	48	L1 48/100 ⚑
Pathway-targeting gene matrix for Drosophila gene set enrichment analysis. PMID 34710184	PLoS One	2021	95	L1 95/100
miRbiom: Machine-learning on Bayesian causal nets of RBP-miRNA interactions successfully predicts miRNA profiles. PMID 34637468	PLoS One	2021	100	L1 100/100
Identification and analysis of genes associated with epithelial ovarian cancer by integrated bioinformatics methods. PMID 34143800	PLoS One	2021	75	L1 75/100
Regulatory and evolutionary adaptation of yeast to acute lethal ethanol stress. PMID 33170850	PLoS One	2020	68	L1 68/100
Evaluation of classification and forecasting methods on time series gene expression data. PMID 33156855	PLoS One	2020	74	L1 74/100
Unveiling prognostics biomarkers of tyrosine metabolism reprogramming in liver cancer by cross-platform gene expression analyses. ⚑ PMID 32542016	PLoS One	2020	51	L1 51/100 ⚑
RNAmountAlign: Efficient software for local, global, semiglobal pairwise and multiple RNA sequence/structure alignment. PMID 31978147	PLoS One	2020	71	L1 71/100
All of gene expression (AOE): An integrated index for public gene expression databases. ⚑ PMID 31978081	PLoS One	2020	—	not yet assessed
Predicting position along a looping immune response trajectory. PMID 30296270	PLoS One	2018	98	L1 98/100
A methyl-sensitive element induces bidirectional transcription in TATA-less CpG island-associated promoters. PMID 30332484	PLoS One	2018	63	L1 63/100
Verrucomicrobia are prevalent in north-temperate freshwater lakes and display class-level preferences between lake habitats. PMID 29590198	PLoS One	2018	99	L1 99/100
De novo transcriptomic analysis of leaf and fruit tissue of Cornus officinalis using Illumina platform. ⚑ PMID 29451882	PLoS One	2018	45	L1 45/100 ⚑
Invasive bacterial disease trends and characterization of group B streptococcal isolates among young infants in southern Mozambique, 2001-2015. PMID 29351318	PLoS One	2018	97	L1 97/100
Metavisitor, a Suite of Galaxy Tools for Simple and Rapid Detection and Discovery of Viruses in Deep Sequence Data. PMID 28045932	PLoS One	2017	78	L1 78/100
Gene-Expression Profiling Suggests Impaired Signaling via the Interferon Pathway in Cstb-/- Microglia. ⚑ PMID 27355630	PLoS One	2016	54	54/100 ⚑
Genetic Dissection of Tissue-Specific Apolipoprotein E Function for Hypercholesterolemia and Diet-Induced Obesity PMID 26695075	PLoS ONE	2015	—	L1 No computation
A Deluge of Complex Repeats: The Solanum Genome. PMID 26241045	PLoS One	2015	94	L1 94/100
Conservation and losses of non-coding RNAs in avian genomes. PMID 25822729	PLoS One	2015	100	L1 100/100
A method for selectively enriching microbial DNA from contaminating vertebrate host DNA. PMID 24204593	PLoS One	2013	71	71/100