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).
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Evidence for a novel gene associated with human influenza A viruses.
PMID 19917120 · PMC2780412 · Virology journal · 2009 · 8 claims · 8 setups
A 167-codon ORF (NEG8) on the negative-sense genomic strand of segment 8 is associated with early-20th-century human influenza A isolates
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Has reproduction · 76
Estimation of peptide elongation times from ribosome profiling spectra.
PMID 33885812 · PMC8136808 · Nucleic acids research · 2021 · 8 claims · 3 setups
A maximum-likelihood model that separates context-dependent bias factors from elongation-time factors enables bias-corrected estimation of peptide elongation times at single-codon resolution from Ribo-Seq spectra.
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Comparison of characteristics and function of translation termination signals between and within prokaryotic and eukaryotic organisms.
PMID 16614446 · PMC1435984 · Nucleic acids research · 2006 · 8 claims · 5 setups
A core termination signal of 4 nt (stop codon plus the following nucleotide) is preferred across most prokaryotic and eukaryotic genomes
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Has reproduction · 71
Utilizing the codon adaptation index to evaluate the susceptibility to HIV-1 and SARS-CoV-2 related coronaviruses in possible target cells in humans.
PMID 36760235 · PMC9905242 · Frontiers in cellular and infection microbiology · 2022 · 7 claims · 8 setups
CAI is positively correlated with translational efficiency, supporting its use as a proxy for viral mRNA translation in cell types.
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Comparative genomics and understanding of microbial biology.
PMID 10998382 · PMC2627966 · Emerging infectious diseases · 2000 · 8 claims · 7 setups
GC content varies widely among prokaryotic genomes (29% in B. burgdorferi to 68% in M. tuberculosis) and shapes codon usage and amino acid composition.
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PRNP variation in UK sporadic and variant Creutzfeldt Jakob disease highlights genetic risk factors and a novel non-synonymous polymorphism.
PMID 20035629 · PMC2806268 · BMC medical genetics · 2009 · 8 claims · 7 setups
All UK vCJD cases tested (147/147) are methionine homozygous (MM) at PRNP codon 129
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The human L-threonine 3-dehydrogenase gene is an expressed pseudogene.
PMID 12361482 · PMC131051 · BMC genetics · 2002 · 8 claims · 7 setups
The human TDH gene is located at chromosome 8p23-22, spans 10 kb, and has 8 exons that would be expected to encode a 369-residue ORF.
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A genome-wide survey demonstrates widespread non-linear mRNA in expressed sequences from multiple species.
PMID 16237125 · PMC1258171 · Nucleic acids research · 2005 · 8 claims · 6 setups
A genome-wide computational survey identifies 245 genes in mammals (264 across six species) that produce RREO events in expressed sequences
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Distribution and effects of nonsense polymorphisms in human genes.
PMID 18852891 · PMC2561068 · PloS one · 2008 · 8 claims · 8 setups
Nonsense SNPs occur at a lower density than nonsynonymous SNPs, indicating stronger purifying selection against premature stop codons than amino acid changes.
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ORFer--retrieval of protein sequences and open reading frames from GenBank and storage into relational databases or text files.
PMID 12493080 · PMC139979 · BMC bioinformatics · 2002 · 6 claims · 6 setups
ORFer retrieves protein and nucleic acid sequences and annotations from NCBI GenBank using the XML sequence format
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Comparative analysis of cancer genes in the human and chimpanzee genomes.
PMID 16438707 · PMC1382208 · BMC genomics · 2006 · 7 claims · 6 setups
All 333 examined human cancer genes have intact, highly conserved orthologs in the chimpanzee genome (99.38% protein identity).
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High accuracy mass spectrometry analysis as a tool to verify and improve gene annotation using Mycobacterium tuberculosis as an example.
PMID 18597682 · PMC2483986 · BMC genomics · 2008 · 8 claims · 5 setups
High-accuracy MS proteomics (LTQ-Orbitrap) can be used to verify and improve gene annotation by identifying peptides specific to one of two competing annotation datasets.
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Has reproduction · 61
Comprehensive transcriptome study to develop molecular resources of the copepod Calanus sinicus for their potential ecological applications.
PMID 24982883 · PMC4055022 · BioMed research international · 2014 · 8 claims · 8 setups
Illumina RNA-Seq with Trinity de novo assembly produced a C. sinicus transcriptome of 69,751 contigs (average 928.8 bp, N50 1,127 bp) from 58.9 million reads.
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Comparative genomics search for losses of long-established genes on the human lineage.
PMID 18085818 · PMC2134963 · PLoS computational biology · 2007 · 8 claims · 6 setups
A novel comparative genomics method (TransMap-based syntenic mapping of gene structures between human, mouse, and dog) can detect losses of well-established single-copy genes without relying on sequence homology to a parental gene, distinguishing them from typical duplication- or retrotransposition-derived pseudogenes.