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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MitoVariome: a variome database of human mitochondrial DNA.
PMID 19958475 · PMC2788364 · BMC genomics · 2009 · 8 claims · 5 setups
MitoVariome is a web-based, integrated variome database for human mitochondrial DNA that unifies sequence variation, haplogroup, and disease annotation information not jointly available in prior databases (MITOMAP, mtDB, Mitome, MitoRes).
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AgBase: a functional genomics resource for agriculture.
PMID 16961921 · PMC1618847 · BMC genomics · 2006 · 8 claims · 7 setups
AgBase is a curated, web-accessible database providing structural and functional (GO) annotation for agricultural genomes and their pathogens.
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TassDB: a database of alternative tandem splice sites.
PMID 17142241 · PMC1669710 · Nucleic acids research · 2007 · 7 claims · 3 setups
TassDB is a relational database storing GYNGYN donor and NAGNAG acceptor tandem splice sites across eight species
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Novel gene and gene model detection using a whole genome open reading frame analysis in proteomics.
PMID 16646984 · PMC1557991 · Genome biology · 2006 · 8 claims · 4 setups
A six-frame genomic ORF translation used as an MS search database can detect novel peptides absent from standard protein databases, revealing incomplete genome annotation.
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Sequence context affects the rate of short insertions and deletions in flies and primates.
PMID 18291026 · PMC2374710 · Genome biology · 2008 · 8 claims · 6 setups
The rate of insertion or deletion of specific lengths can vary by more than 100-fold depending on the surrounding sequence context
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Polymorphic segmental duplications at 8p23.1 challenge the determination of individual defensin gene repertoires and the assembly of a contiguous human reference sequence.
PMID 15588320 · PMC544879 · BMC genomics · 2004 · 8 claims · 8 setups
The hg16 automatic assembly of the 8p23.1 DEF locus contains misassemblies caused by segmental duplications and interindividual/intraindividual genetic variation
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The HuRef Browser: a web resource for individual human genomics.
PMID 19036787 · PMC2686481 · Nucleic acids research · 2009 · 7 claims · 6 setups
The HuRef Browser is a unified web application integrating assembly, annotation, and assembly-to-assembly comparison (ATAC) views for the diploid HuRef individual human genome.
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Genomic organization and recombinational unit duplication-driven evolution of ovine and bovine T cell receptor gamma loci.
PMID 18282289 · PMC2270265 · BMC genomics · 2008 · 8 claims · 6 setups
The sheep TRG1 and TRG2 loci evolved through a series of duplication events involving either entire V-J-J-C recombinational cassettes or single V genes
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Origin and diversification of the basic helix-loop-helix gene family in metazoans: insights from comparative genomics.
PMID 17335570 · PMC1828162 · BMC evolutionary biology · 2007 · 8 claims · 4 setups
An initial diversification of bHLHs occurred in the pre-Cambrian, prior to metazoan cladogenesis
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SysPIMP: the web-based systematical platform for identifying human disease-related mutated sequences from mass spectrometry.
PMID 19036792 · PMC2686442 · Nucleic acids research · 2009 · 8 claims · 7 setups
SysPIMP is a web-based platform integrating disease mutation databases with X!Tandem and BLAST to identify disease-related mutated proteins from MS results
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Skittle: a 2-dimensional genome visualization tool.
PMID 20042093 · PMC2817707 · BMC bioinformatics · 2009 · 7 claims · 6 setups
Skittle is a 2D genome visualization tool combining a color-coded Nucleotide Display, a Repeat Map, a Repeat Overview, and an Alignment Cylinder to reveal genomic patterns at multiple scales
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Application of proteomics methods for pathogen discovery.
PMID 19751767 · PMC7119679 · Journal of virological methods · 2010 · 8 claims · 6 setups
Proteomic techniques can detect and characterize unknown infectious agents in cell culture without prior knowledge of the pathogen
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Has reproduction · 71
Prospects of telomere-to-telomere assembly in barley: Analysis of sequence gaps in the MorexV3 reference genome.
PMID 35338551 · PMC9241371 · Plant biotechnology journal · 2022 · 7 claims · 8 setups
Almost all centromeric sequences and 45S ribosomal DNA repeat arrays are absent from the MorexV3 pseudomolecules
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Genomic sequence and analysis of a vaccinia virus isolate from a patient with a smallpox vaccine-related complication.
PMID 17062162 · PMC1635044 · Virology journal · 2006 · 8 claims · 6 setups
VACV-DUKE is most similar to VACV-ACAM2000 and VACV-CLONE3, confirming it as a Dryvax-derived isolate
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Evolutionary analysis of the highly dynamic CHEK2 duplicon in anthropoids.
PMID 18831734 · PMC2566985 · BMC evolutionary biology · 2008 · 8 claims · 6 setups
CHEK2 is present as a single copy in New World monkeys, Old World monkeys, and gibbons
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The Vertebrate Genome Annotation (Vega) database.
PMID 15608237 · PMC540089 · Nucleic acids research · 2005 · 8 claims · 8 setups
Vega is a community database for browsing manual annotation of finished vertebrate genome sequences, based on an extended Ensembl-style schema.
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A mouse plasma peptide atlas as a resource for disease proteomics.
PMID 18522751 · PMC2481425 · Genome biology · 2008 · 8 claims · 6 setups
A publicly available, high-quality mouse plasma peptide/protein repository (mouse PeptideAtlas) was built from 568 LC-MS/MS runs on four reference plasma pools.