Experiments

Searchable full-text extractions: founding hypothesis, core claims, experimental setups, key results and statistics — pulled out of each paper as structure. Search a cell line, an assay or an entity (e.g. HUH7) and find every paper that worked with it. This corpus stands on its own: most entries carry no reproduction assessment (yet).

Publications 1.3k Datasets 392.5k Experiments 33

System / cell line: novel ✕ Assay: annotation ✕ Clear

Benchmarking methods for genome annotation using nanopore direct RNA in a non-model crop plant.

PMID 41800382 · PMC12967217 · Bioinformatics advances · 2026 · 6 claims · 8 setups

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Annotation tools show substantial variation in isoform detection, structural completeness, splicing classification, and handling of 5' read truncation when applied to plant dRNA-seq data.

barley extracted tool novel nanopore illumina transcriptome
Annotation and analysis of 10,000 expressed sequence tags from developing mouse eye and adult retina.

PMID 14519200 · PMC328454 · Genome biology · 2003 · 8 claims · 5 setups

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Annotation of 8,633 high-quality non-mitochondrial/non-ribosomal ESTs shows 57% represent known genes and 43% are unknown or novel, with M15E having the highest proportion of novel ESTs

embryonic high-quality unique m15e est sequence comparative
GENCODE: producing a reference annotation for ENCODE.

PMID 16925838 · PMC1810553 · Genome biology · 2006 · 8 claims · 8 setups

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GENCODE annotation combines initial manual annotation by HAVANA, experimental validation, and refinement based on results to identify protein-coding genes in ENCODE regions

tissues encode rt-pcr comparative automated
Large-Scale Phylogenomics of the Lactobacillus casei Group Highlights Taxonomic Inconsistencies and Reveals Novel Clade-Associated Features.

PMID 28845461 · PMC5566788 · mSystems · 2017 · 8 claims · 8 setups

Has reproduction · 94

Many strains currently classified as L. casei or L. paracasei are taxonomically misclassified; reclassifying them to their closest type strain improves functional predictive power

novel casei genomes selected whole-genome maximum-likelihood pairwise
Genome-wide analysis of small RNA and novel MicroRNA discovery in human acute lymphoblastic leukemia based on extensive sequencing approach.

PMID 19724645 · PMC2731166 · PloS one · 2009 · 7 claims · 5 setups

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159 novel miRNAs and 116 novel miRNA*s were identified from ALL patient and normal donor small RNA libraries

pooled sequenced analysis predicted small bioinformatic qrt-pcr
miRge 2.0 for comprehensive analysis of microRNA sequencing data.

PMID 30153801 · PMC6112139 · BMC bioinformatics · 2018 · 8 claims · 6 setups

Has reproduction · 89

An SVM-based novel miRNA detection model achieves an average MCC of 0.939 across 32 human cell datasets and outperforms miRDeep2 and miRAnalyzer on phylogenetic conservation of predicted miRNAs

unmapped pooled colon adipose small novel a-to-i
Identification of Novel Therapeutic Candidates Against SARS-CoV-2 Infections: An Application of RNA Sequencing Toward mRNA Based Nanotherapeutics.

PMID 35983322 · PMC9378778 · Frontiers in microbiology · 2022 · 6 claims · 7 setups

Has reproduction · 75

RPL29 (60S ribosomal protein L29) is highly/consistently expressed across all COVID-19 infected groups regardless of severity, suggesting it as a novel host therapeutic target for mRNA-based nanomedicines.

pbmcs pbmc aligned bulk read transcript
Systematic identification of pseudogenes through whole genome expression evidence profiling.

PMID 16945953 · PMC1636364 · Nucleic acids research · 2006 · 8 claims · 8 setups

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Developed a novel bioinformatics method that identifies pseudogenes by profiling whole-genome transcript and protein expression evidence

genome ensembl vega celera spliced protein-to-genome pseudogene
EGASP: the human ENCODE Genome Annotation Assessment Project.

PMID 16925836 · PMC1810551 · Genome biology · 2006 · 8 claims · 6 setups

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Best-performing computational gene prediction methods correctly predict at least one transcript for close to 70% of annotated genes in the ENCODE regions.

encode computational manual rt-pcr
Polymorphism identification and improved genome annotation of Brassica rapa through Deep RNA sequencing.

PMID 25122667 · PMC4232532 · G3 (Bethesda, Md.) · 2014 · 8 claims · 8 setups

Has reproduction · 50

330,995 SNPs were identified in transcribed regions between B. rapa genotypes R500 and IMB211, at an average frequency of one SNP per 200 bases.

brassica r500 rapa genomic bulk reference-based snp
The vertebrate genome annotation (Vega) database.

PMID 18003653 · PMC2238886 · Nucleic acids research · 2008 · 8 claims · 8 setups

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Vega is a database for viewing manual genome annotation of human, mouse and zebrafish genomic sequences produced at the Wellcome Trust Sanger Institute.

genome zebrafish pig nod manual comparative transcript
FusionQ: a novel approach for gene fusion detection and quantification from paired-end RNA-Seq.

PMID 23768108 · PMC3691734 · BMC bioinformatics · 2013 · 8 claims · 8 setups

Has reproduction · 65

FusionQ is a novel tool that detects gene fusions, constructs chimerical transcript structures, and estimates their abundances from paired-end RNA-Seq data.

simulated four rna-seq randomly simulated paired-end read-mappability
Systematic analysis of human kinase genes: a large number of genes and alternative splicing events result in functional and structural diversity.

PMID 16351747 · PMC1866387 · BMC bioinformatics · 2005 · 8 claims · 7 setups

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Systematic in silico search identified 5 novel human kinase genes (on chromosomes 1, 11, 13, 15, 16) and 1 pseudogene (chromosome X) absent from KinBase

genome genomic kinase psi-blast comparative genscan
The mammalian phenotype ontology: enabling robust annotation and comparative analysis.

PMID 20052305 · PMC2801442 · Wiley interdisciplinary reviews. Systems biology and medicine · 2009 · 8 claims · 6 setups

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The Mammalian Phenotype (MP) Ontology enables classification and organization of phenotypic data for mouse and other mammalian species in a computationally useful, standardized manner.

genotypes neural inbred viable phenotype phylogenetic comparative
Discovery of novel human transcript variants by analysis of intronic single-block EST with polyadenylation site.

PMID 19906316 · PMC2784480 · BMC genomics · 2009 · 8 claims · 7 setups

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Intronic single-block ESTs with poly(A/T) tails reveal previously unidentified novel transcript variants missed by existing databases.

genome poly est cdna est blast cdna
annotate_my_genomes: an easy-to-use pipeline to improve genome annotation and uncover neglected genes by hybrid RNA sequencing.

PMID 36472574 · PMC9724561 · GigaScience · 2022 · 7 claims · 8 setups

Has reproduction · 78

annotate_my_genomes is an easy-to-use genome-guided pipeline that uses hybrid (PacBio+Illumina) assembled transcripts to distinguish coding genes from long non-coding RNAs and reconcile them with prior annotations.

chick real simulated pacbio illumina hybrid
AgBase: a functional genomics resource for agriculture.

PMID 16961921 · PMC1618847 · BMC genomics · 2006 · 8 claims · 7 setups

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AgBase is a curated, web-accessible database providing structural and functional (GO) annotation for agricultural genomes and their pathogens.

pasteurella chicken maize gene proteogenomic mudpit differential
RAId_DbS: mass-spectrometry based peptide identification web server with knowledge integration.

PMID 18954448 · PMC2605478 · BMC genomics · 2008 · 7 claims · 4 setups

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Constructed enhanced protein databases integrating annotated SAPs, PTMs, and disease associations for 17 organisms.

consensus sap query all-against-all blast cross-database
Integration of a neuronal RNAseq dataset with the draft Gryllus bimaculatus transcriptome refines gene predictions and highlights potential systematic response to injury.

PMID 42054377 · PMC13127959 · PloS one · 2026 · 8 claims · 7 setups

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Integrating prothoracic ganglion RNAseq data with the draft genome refines gene predictions, adding 3,868 novel genes and 9,172 new transcript isoforms (including non-coding transcripts)

bimaculatus prothoracic differentially gbig rna-seq genome differential
Genome-wide identification of conserved and novel microRNAs in one bud and two tender leaves of tea plant (Camellia sinensis) by small RNA sequencing, microarray-based hybridization and genome survey scaffold sequences.

PMID 29157210 · PMC5697157 · BMC plant biology · 2017 · 8 claims · 8 setups

Has reproduction · 91

175 conserved miRNAs (39 families) and 83 novel miRNAs were identified in C. sinensis one bud and two tender leaves using small RNA sequencing combined with genome survey scaffold data

one sinensis small-molecular-weight leaves small genome mirna

Experiments

Benchmarking methods for genome annotation using nanopore direct RNA in a non-model crop plant.

Annotation and analysis of 10,000 expressed sequence tags from developing mouse eye and adult retina.

GENCODE: producing a reference annotation for ENCODE.

Large-Scale Phylogenomics of the Lactobacillus casei Group Highlights Taxonomic Inconsistencies and Reveals Novel Clade-Associated Features.

Genome-wide analysis of small RNA and novel MicroRNA discovery in human acute lymphoblastic leukemia based on extensive sequencing approach.

miRge 2.0 for comprehensive analysis of microRNA sequencing data.

Identification of Novel Therapeutic Candidates Against SARS-CoV-2 Infections: An Application of RNA Sequencing Toward mRNA Based Nanotherapeutics.

Systematic identification of pseudogenes through whole genome expression evidence profiling.

EGASP: the human ENCODE Genome Annotation Assessment Project.

Polymorphism identification and improved genome annotation of Brassica rapa through Deep RNA sequencing.

The vertebrate genome annotation (Vega) database.

FusionQ: a novel approach for gene fusion detection and quantification from paired-end RNA-Seq.

Systematic analysis of human kinase genes: a large number of genes and alternative splicing events result in functional and structural diversity.

The mammalian phenotype ontology: enabling robust annotation and comparative analysis.

Discovery of novel human transcript variants by analysis of intronic single-block EST with polyadenylation site.

annotate_my_genomes: an easy-to-use pipeline to improve genome annotation and uncover neglected genes by hybrid RNA sequencing.

AgBase: a functional genomics resource for agriculture.

RAId_DbS: mass-spectrometry based peptide identification web server with knowledge integration.

Integration of a neuronal RNAseq dataset with the draft Gryllus bimaculatus transcriptome refines gene predictions and highlights potential systematic response to injury.

Genome-wide identification of conserved and novel microRNAs in one bud and two tender leaves of tea plant (Camellia sinensis) by small RNA sequencing, microarray-based hybridization and genome survey scaffold sequences.