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 11

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

Molecular epidemiology of O139 Vibrio cholerae: mutation, lateral gene transfer, and founder flush.

PMID 12890320 · PMC3023423 · Emerging infectious diseases · 2003 · 8 claims · 4 setups

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Lateral gene transfer (LGT) produced roughly three times as many nucleotide changes as point mutation among the 96 O139 isolates.

vibrio same novel aligned multilocus pcr blast
Codon usage comparison of novel genes in clinical isolates of Haemophilus influenzae.

PMID 15983137 · PMC1160521 · Nucleic acids research · 2005 · 8 claims · 4 setups

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A codon usage similarity statistic (ε, based on squared/absolute differences of codon frequencies with an optimized amino acid usage factor) was developed to compare ORFs against a set of 80 reference genomes.

influenzae novel reference codon phylogenetic comparative
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
Integrating alternative splicing detection into gene prediction.

PMID 15705189 · PMC550657 · BMC bioinformatics · 2005 · 8 claims · 4 setups

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An integrative intrinsic/extrinsic method was implemented in the gene finder EuGÈNE (as EuGÈNE-M) to detect AS evidence from aligned transcripts and generate alternative optimal gene predictions consistent with each detected AS event.

arabidopsis araset thaliana transcript-to-genome initio comparative
A third approach to gene prediction suggests thousands of additional human transcribed regions.

PMID 16543943 · PMC1391917 · PLoS computational biology · 2006 · 8 claims · 7 setups

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A third basic concept for gene prediction exists, based on detecting strand-specific 'transcription footprints' (mutational and selectional biases) rather than gene structure or sequence similarity.

genome 4.4-mb known nucleotide repeat polyadenylation
The diploid genome sequence of an Asian individual.

PMID 18987735 · PMC2716080 · Nature · 2008 · 8 claims · 8 setups

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First diploid genome sequence of an Asian (Han Chinese) individual generated using massively parallel Illumina sequencing

han donor genome genomic whole-genome g-banded snp
Comparative genomics.

PMID 14624258 · PMC261895 · PLoS biology · 2003 · 8 claims · 7 setups

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Conserved DNA between species tends to encode shared functional features, while divergent DNA underlies species differences

caenorhabditis yeast mammalian vertebrate whole-genome comparative interspecies-similarity-informed
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
NEIBank: genomics and bioinformatics resources for vision research.

PMID 18648525 · PMC2480482 · Molecular vision · 2008 · 8 claims · 7 setups

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NEIBank is an integrated genomics and bioinformatics resource for vision research, combining EST/cDNA clone data, SAGE expression data, and eye disease gene databases.

dissected eye retina cdna est serial sequence
Exome sequencing of a multigenerational human pedigree.

PMID 20011588 · PMC2788131 · PloS one · 2009 · 8 claims · 6 setups

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Microarray-based exome capture combined with 454 GS FLX NGS is an efficient and reliable method to enrich for chromosomal regions of interest, validated on eight individuals from a three-generation pedigree

genomic eluted captured pcr microarray-based qpcr next-generation
Inventory and analysis of the protein subunits of the ribonucleases P and MRP provides further evidence of homology between the yeast and human enzymes.

PMID 16998185 · PMC1636426 · Nucleic acids research · 2006 · 8 claims · 6 setups

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Fungal Pop8 is evolutionarily related to the Rpp14/Pop5 protein family, suggesting Pop8 is the fungal orthologue of Rpp14

sequences sequence eukaryotic mrp psi-blast phylogenetic hmm

Experiments

Molecular epidemiology of O139 Vibrio cholerae: mutation, lateral gene transfer, and founder flush.

Codon usage comparison of novel genes in clinical isolates of Haemophilus influenzae.

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

Integrating alternative splicing detection into gene prediction.

A third approach to gene prediction suggests thousands of additional human transcribed regions.

The diploid genome sequence of an Asian individual.

Comparative genomics.

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

NEIBank: genomics and bioinformatics resources for vision research.

Exome sequencing of a multigenerational human pedigree.

Inventory and analysis of the protein subunits of the ribonucleases P and MRP provides further evidence of homology between the yeast and human enzymes.