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 profiling of amniotic fluid in preterm labor using two-dimensional liquid separation and mass spectrometry.
PMID 19012186 · PMC3163445 · The journal of maternal-fetal & neonatal medicine : the official journal of the European Association of Perinatal Medicine, the Federation of Asia and Oceania Perinatal Societies, the International Society of Perinatal Obstetricians · 2008 · 8 claims · 6 setups
Amniotic fluid protein composition can be analyzed by combining 2D liquid chromatography and mass spectrometry to identify differentially expressed proteins in preterm labor
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Proteomic analysis identifies MMP-9, DJ-1 and A1BG as overexpressed proteins in pancreatic juice from pancreatic ductal adenocarcinoma patients.
PMID 18706098 · PMC2528014 · BMC cancer · 2008 · 7 claims · 6 setups
MMP-9, DJ-1 and A1BG are overexpressed in pancreatic juice and tissue from PDAC patients compared with cancer-free/normal controls
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Comparative analysis of the tear protein profile in mycotic keratitis patients.
PMID 18385783 · PMC2268856 · Molecular vision · 2008 · 8 claims · 5 setups
A glutaredoxin-related protein is expressed only in the tears of fungal keratitis patients and is absent in control tears.
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Proteomics-derived cerebrospinal fluid markers of autopsy-confirmed Alzheimer's disease.
PMID 19863188 · PMC2824250 · Biomarkers : biochemical indicators of exposure, response, and susceptibility to chemicals · 2009 · 8 claims · 8 setups
2D gel electrophoresis screening of pooled postmortem CSF identified ApoA1, hemopexin (HPX), transthyretin (TTR) and PEDF as differentially abundant among AD, ND and NADD groups
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Construction of a nasopharyngeal carcinoma 2D/MS repository with Open Source XML database--Xindice.
PMID 16403238 · PMC1351203 · BMC bioinformatics · 2006 · 8 claims · 4 setups
No NPC proteome database existed prior to this work despite availability of other cancer proteome databases
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Plasma proteomics of pancreatic cancer patients by multi-dimensional liquid chromatography and two-dimensional difference gel electrophoresis (2D-DIGE): up-regulation of leucine-rich alpha-2-glycoprotein in pancreatic cancer.
PMID 17303479 · PMC7105233 · Journal of chromatography. B, Analytical technologies in the biomedical and life sciences · 2007 · 5 claims · 5 setups
Pre-fractionation of plasma with immuno-affinity depletion and anion-exchange chromatography prior to 2D-DIGE substantially increases the number of detectable protein spots compared with unfractionated plasma.
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Salivary proteomics for oral cancer biomarker discovery.
PMID 18829504 · PMC2877125 · Clinical cancer research : an official journal of the American Association for Cancer Research · 2008 · 8 claims · 5 setups
Subtractive salivary proteomics reveals proteins differentially present/expressed between OSCC patients and matched healthy controls.
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A proteomic approach for plasma biomarker discovery with iTRAQ labelling and OFFGEL fractionation.
PMID 19888438 · PMC2771280 · Journal of biomedicine & biotechnology · 2010 · 6 claims · 6 setups
iTRAQ labelling combined with OFFGEL fractionation improves proteome coverage of human plasma compared to iTRAQ alone or no iTRAQ
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Identification of novel citrullinated autoantigens of synovium in rheumatoid arthritis using a proteomic approach.
PMID 17125526 · PMC1794520 · Arthritis research & therapy · 2006 · 8 claims · 6 setups
51 citrullinated protein spots were detected in RA synovial tissue, of which 30 (58.8%) were autoantigenic (reactive with RA sera)
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Has reproduction · 59
From tides to nucleotides: Genomic signatures of adaptation to environmental heterogeneity in barnacles.
PMID 33960035 · PMC9292448 · Molecular ecology · 2021 · 7 claims · 8 setups
382 genomic regions contain SNPs whose frequencies are consistently zonated (vary with intertidal position) across all surveyed North Atlantic habitats (Maine, Rhode Island, Norway)
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In vivo pharmaco-proteomic analysis of hydroxyurea induced changes in the sickle red blood cell membrane proteome.
PMID 19914412 · PMC2818491 · Journal of proteomics · 2010 · 8 claims · 4 setups
2D-DIGE combined with tandem mass spectrometry identified 32 distinct sickle RBC membrane proteins that significantly changed in abundance after in vivo HU therapy
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DoBSeqWF: a framework for sensitive detection of individual genetic variation in pooled sequencing data.
PMID 41704565 · PMC12907731 · NAR genomics and bioinformatics · 2026 · 7 claims · 5 setups
DoBSeqWF, a Nextflow-based pipeline, processes pooled DoBSeq sequencing data through alignment, variant calling, machine-learning-based filtering, and variant pinpointing/assignment to individuals.
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Whither genomics?
PMID 11104516 · PMC138820 · Genome biology · 2000 · 8 claims · 8 setups
Genomics is both a science (understanding genome structure/evolution) and a tool (learning gene function) that collects comprehensive data on all genes, in contrast to genetics which studies a few genes controlling a phenotype
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Has reproduction · 78
A case study for large-scale human microbiome analysis using JCVI's metagenomics reports (METAREP).
PMID 22719821 · PMC3374610 · PloS one · 2012 · 8 claims · 7 setups
METAREP version 1.3.1 is an open-source, scalable tool for querying, browsing and comparing extremely large volumes of metagenomic annotations, with an extended data model, dynamic weighting, distributed searches and advanced clustering.