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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Proteomic solutions for analytical challenges associated with alcohol research.
PMID 23584870 · PMC3860482 · Alcohol research & health : the journal of the National Institute on Alcohol Abuse and Alcoholism · 2008 · 7 claims · 4 setups
Protein-level meta-analyses analogous to the transcriptome meta-analysis by Mulligan et al. (2006) are not yet possible because proteins lack a uniform sample preparation/analysis method and span up to 8 orders of magnitude in abundance.
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Mass spectrometry-based biomarker discovery: toward a global proteome index of individuality.
PMID 20636062 · PMC3140421 · Annual review of analytical chemistry (Palo Alto, Calif.) · 2009 · 8 claims · 4 setups
Very few large-scale longitudinal MS-based proteomics studies have been performed to establish analytical variability relative to true biological variability.
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Examination of FMR1 transcript and protein levels among 74 premutation carriers.
PMID 19927162 · PMC4122982 · Journal of human genetics · 2010 · 7 claims · 4 setups
FMR1 premutation carriers (55-199 CGG repeats) show increased FMR1 transcript levels alongside decreased FMRP levels compared to normal individuals.
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High resolution discovery and confirmation of copy number variants in 90 Yoruba Nigerians.
PMID 19900272 · PMC3091319 · Genome biology · 2009 · 7 claims · 4 setups
Custom whole-genome scan arrays (~200 bp resolution) discover CNV regions not previously reported in the literature
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A new procedure for determining the genetic basis of a physiological process in a non-model species, illustrated by cold induced angiogenesis in the carp.
PMID 19852815 · PMC2771047 · BMC genomics · 2009 · 8 claims · 5 setups
The Conditional Stepped Reciprocal Best Hit (CSRBH) approach, combining direct RBH and zebrafish-stepped RBH (SRBH), outperformed other ortholog assignment methods and attained 8,726 carp-human functional homolog relationships for 16,650 carp contigs
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Proteomic analysis of serum in lung cancer induced by 3-methylcholanthrene.
PMID 19794824 · PMC2753780 · Journal of biomedicine & biotechnology · 2009 · 7 claims · 4 setups
141 protein spots are differentially expressed between normal rat sera and MCA-induced lung cancer rat sera (82 overexpressed, 59 underexpressed)
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In Silico screening for functional candidates amongst hypothetical proteins.
PMID 19754976 · PMC2758874 · BMC bioinformatics · 2009 · 7 claims · 6 setups
An in silico selection strategy combining subcellular targeting-signal prediction with protein domain identification can enrich for true functional proteins among hypothetical proteins
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Functional restoration of BRCA2 protein by secondary BRCA2 mutations in BRCA2-mutated ovarian carcinoma.
PMID 19654294 · PMC2754824 · Cancer research · 2009 · 8 claims · 7 setups
Secondary BRCA2 mutations restore BRCA2 protein/reading frame and thereby cause acquired platinum and PARP inhibitor resistance in BRCA2-mutated ovarian carcinoma
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Has reproduction · 56
Profiling Selective Packaging of Host RNA and Viral RNA Modification in SARS-CoV-2 Viral Preparations.
PMID 35186917 · PMC8851031 · Frontiers in cell and developmental biology · 2022 · 8 claims · 3 setups
SARS-CoV-2 viral preparations show selective enrichment of specific host tRNAs, tRNA fragments, and SRP RNA compared to uninfected VeroE6 cells
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QuickSNP: an automated web server for selection of tagSNPs.
PMID 17517769 · PMC1933212 · Nucleic acids research · 2007 · 7 claims · 3 setups
QuickSNP is a freely available automated web server for selecting tagSNPs from a chromosomal region, genes within a region, or a specified gene list, with a gene-centric selection option
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Prediction of candidate primary immunodeficiency disease genes using a support vector machine learning approach.
PMID 19801557 · PMC2780952 · DNA research : an international journal for rapid publication of reports on genes and genomes · 2009 · 6 claims · 3 setups
An SVM trained on 69 binary features of known PID genes can accurately classify PID vs non-PID genes and predict novel candidate PID genes
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Identification of disease markers in human cerebrospinal fluid using lipidomic and proteomic methods.
PMID 16410651 · PMC3851111 · Disease markers · 2006 · 8 claims · 3 setups
Lipids comprise the bulk of the dry mass of the brain and serve structural, insulating, energy-storage, and signaling/inflammatory-mediator roles.
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CYCLONET--an integrated database on cell cycle regulation and carcinogenesis.
PMID 17202170 · PMC1899094 · Nucleic acids research · 2007 · 7 claims · 4 setups
Cyclonet is a web-based integrated database combining 'omics' and chemoinformatics data on mammalian cell cycle regulation in normal and pathological (cancer) states, built on a systems biology approach.
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BRENDA, AMENDA and FRENDA: the enzyme information system in 2007.
PMID 17202167 · PMC1899097 · Nucleic acids research · 2007 · 7 claims · 6 setups
BRENDA is the largest publicly available enzyme information system worldwide, manually curated from primary literature and covering all identified enzymes regardless of source.
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GenBank.
PMID 18940867 · PMC2686462 · Nucleic acids research · 2009 · 8 claims · 4 setups
GenBank is a comprehensive public database of nucleotide sequences with bibliographic and biological annotation, growing exponentially with a current doubling time of ~30 months.
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Report of the 9th HLPP Workshop October 2007, Seoul, Korea.
PMID 18683817 · PMC4601560 · Proteomics · 2008 · 8 claims · 8 setups
An integrated separating-identifying platform identified 6788 proteins (≥2 peptides, 95% confidence) in Chinese human liver samples, including 3721 new to liver and 977 hypothetical proteins
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The Universal Protein Resource (UniProt) in 2010.
PMID 19843607 · PMC2808944 · Nucleic acids research · 2010 · 8 claims · 5 setups
UniProt is a centralized, freely accessible, comprehensive knowledgebase of protein sequence and functional annotation maintained by the EBI, SIB and PIR consortium.
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Has reproduction · 91
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
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
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Has reproduction · 96
Immuno-detection by sequencing enables large-scale high-dimensional phenotyping in cells.
PMID 29921844 · PMC6008431 · Nature communications · 2018 · 8 claims · 8 setups
ID-seq combines DNA-tagged antibodies with high-throughput sequencing to enable large-scale, high-dimensional, multiplexed (phospho-)protein phenotyping in fixed cell populations across many samples in parallel.
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Has reproduction · 97
CellFishing.jl: an ultrafast and scalable cell search method for single-cell RNA sequencing.
PMID 30744683 · PMC6371477 · Genome biology · 2019 · 8 claims · 8 setups
CellFishing.jl searches prebuilt databases for cells with similar expression patterns with high accuracy and throughput using locality-sensitive hashing.