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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RAId_DbS: mass-spectrometry based peptide identification web server with knowledge integration.
PMID 18954448 · PMC2605478 · BMC genomics · 2008 · 7 claims · 4 setups
Constructed enhanced protein databases integrating annotated SAPs, PTMs, and disease associations for 17 organisms.
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Prediction of missed cleavage sites in tryptic peptides aids protein identification in proteomics.
PMID 17203985 · PMC2664920 · Journal of proteome research · 2007 · 8 claims · 4 setups
An information-theoretic log-likelihood scoring method can predict experimentally observed missed cleavage sites from amino acid sequence alone with up to 90% accuracy.
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Satellog: a database for the identification and prioritization of satellite repeats in disease association studies.
PMID 15949044 · PMC1181805 · BMC bioinformatics · 2005 · 7 claims · 6 setups
Satellog is a database cataloging all pure 1-16 unit satellite repeats in the human genome with supplementary polymorphism, gene-location, and expression data for prioritizing repeats in disease-association studies.
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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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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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Proteomic analysis of human aqueous humor using multidimensional protein identification technology.
PMID 20019884 · PMC2793904 · Molecular vision · 2009 · 8 claims · 4 setups
Albumin/IgG depletion combined with MudPIT (2D-LC-MS/MS) enables high-confidence, extensive characterization of the human AH proteome
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Interactome networks: the state of the science.
PMID 16515723 · PMC1431712 · Genome biology · 2006 · 8 claims · 8 setups
Spastin interacts with CHMP1B, an ESCRT-III-associated protein, supporting a role for spastin in intracellular membrane trafficking relevant to hereditary spastic paraplegia
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Genes implicated in multiple sclerosis pathogenesis from consilience of genotyping and expression profiles in relapse and remission.
PMID 18366677 · PMC2324081 · BMC medical genetics · 2008 · 8 claims · 7 setups
Distinct sets of dysregulated genes are found in peripheral blood during the relapse phase versus the remission phase of RRMS
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Anopheles gambiae genome reannotation through synthesis of ab initio and comparative gene prediction algorithms.
PMID 16569258 · PMC1557760 · Genome biology · 2006 · 8 claims · 7 setups
An exon-gene-union (EGU) algorithm followed by an open-reading-frame-selection algorithm can synthesize ab initio (GENSCAN, GeneMark, SNAP) and comparative (Ensembl/Genewise) predictions into a single, more complete CDS set
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Gap-free telomere-to-telomere haplotype assembly of the tomato hind (Cephalopholis sonnerati).
PMID 39578472 · PMC11584678 · Scientific data · 2024 · 8 claims · 8 setups
Two T2T gap-free haplotype assemblies of C. sonnerati (YSFRI_Csonn_HA_1.0 and YSFRI_Csonn_HB_1.0) were successfully generated, each spanning 24 chromosomes with no gaps.