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).

• Analysis of virulence factors of Helicobacter pylori isolated from a Vietnamese population.

  PMID 19698173 · PMC2739534 · BMC microbiology · 2009 · 8 claims · 5 setups

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  Three distinct deletion patterns (39-bp, 18-bp, no deletion) exist upstream of the cagA EPIYA repeat region (pre-EPIYA region), providing a novel genotyping marker.

  pylori gastric pcr sequence comparative

• Cancer-specific high-throughput annotation of somatic mutations: computational prediction of driver missense mutations.

  PMID 19654296 · PMC2763410 · Cancer research · 2009 · 7 claims · 7 setups

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  CHASM, a Random Forest-based computational method, was developed to identify and prioritize missense mutations likely to be functional drivers of tumor cell proliferation.

  missense same synthetic tp53 random support principal

• Local combinational variables: an approach used in DNA-binding helix-turn-helix motif prediction with sequence information.

  PMID 19651875 · PMC2761287 · Nucleic acids research · 2009 · 8 claims · 7 setups

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  The LCV approach predicts HTH motifs with 93.29% accuracy, 93.93% sensitivity and 92.66% specificity using only primary sequence information

  quintessentialset-88 hth same newly lcs svm traditional

• Proteomic-based identification of maternal proteins in mature mouse oocytes.

  PMID 19646285 · PMC2730056 · BMC genomics · 2009 · 8 claims · 6 setups

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  625 different proteins were identified from 2700 zona pellucida-free mature mouse MII oocytes, the largest oocyte proteome catalog to date

  mature mii identified tissues sds-page acid gene

• Complex genetic diseases: controversy over the Croesus code.

  PMID 11532206 · PMC138948 · Genome biology · 2001 · 8 claims · 3 setups

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  The common disease/common variant hypothesis is predicted by population genetic theory (founder population dynamics, mutation-drift-selection balance) and supported by empirical examples such as APOE*E4.

  chromosome northern disease large-scale genome-wide database

• pSTIING: a 'systems' approach towards integrating signalling pathways, interaction and transcriptional regulatory networks in inflammation and cancer.

  PMID 16381926 · PMC1347407 · Nucleic acids research · 2006 · 8 claims · 3 setups

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  pSTIING is a publicly accessible web-based knowledgebase integrating protein-protein, protein-lipid, protein-small molecule interactions, transcriptional regulatory associations, ligand-receptor-cell type information, and signal transduction modules, with a focus on inflammation, cell migration and cancer.

  model gene molecular sequence clustering literature

• Mitochondrial DNA aberrations of bone marrow cells from patients with aplastic anemia.

  PMID 19119453 · PMC2610644 · Journal of Korean medical science · 2008 · 7 claims · 3 setups

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  Bone marrow cells from AA patients show significantly more mtDNA aberrations (mean=25.6) than healthy controls (mean=12.8)

  bone buccal mtdna direct sequence

• Bioinformatics analysis of the locus for enterocyte effacement provides novel insights into type-III secretion.

  PMID 15757514 · PMC1084347 · BMC microbiology · 2005 · 8 claims · 7 setups

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  PSI-BLAST identified several novel homologies between LEE-encoded and Ysc-Yop-associated proteins

  lee-encoded escc sepq escd psi-blast blastp domain

• Using multiple alignments to improve seeded local alignment algorithms.

  PMID 16100379 · PMC1185574 · Nucleic acids research · 2005 · 8 claims · 2 setups

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  Using information implicit in a multiple alignment to dynamically build a spaced-seed index weighted toward promising regions increases sensitivity of local alignment search compared to indexing a sequence alone

  alignment query leave-one-species-out seeded

• CEBS--Chemical Effects in Biological Systems: a public data repository integrating study design and toxicity data with microarray and proteomics data.

  PMID 17962311 · PMC2238989 · Nucleic acids research · 2008 · 8 claims · 5 setups

  Full-text index only

  CEBS is a public repository that integrates study design, timeline, clinical chemistry and histopathology data with microarray and proteomics data

  subcellular laboratory cebs microarray gel clinical

• Ensembl's 10th year.

  PMID 19906699 · PMC2808936 · Nucleic acids research · 2010 · 8 claims · 8 setups

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  Ensembl provides comprehensive gene annotation and integrated genomic resources (variation, regulation, comparative genomics) across a growing set of chordate genomes

  anole western genome cd4+ whole-genome gene cross-database

• MutScreener: primer design tool for PCR-direct sequencing.

  PMID 16845093 · PMC1538803 · Nucleic acids research · 2006 · 8 claims · 4 setups

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  MutScreener is a web-based application that automates PCR-direct sequencing assay design by annotating gene structure and designing PCR and sequencing primers.

  sim4 cdna gene comparative sequence pcr

• Expanding the clinical spectrum of COL2A1 related disorders by a mass like phenotype.

  PMID 35296718 · PMC8927422 · Scientific reports · 2022 · 8 claims · 8 setups

  Has reproduction · 84

  Four FBN1-negative patients from three families with a MASS-like phenotype carry likely pathogenic or uncertain-significance missense variants in the propeptide-coding regions of COL2A1

  blood-derived four patients col2a1 targeted clinical transthoracic

• Viral Diagnostics in Plants Using Next Generation Sequencing: Computational Analysis in Practice.

  PMID 29123534 · PMC5662881 · Frontiers in plant science · 2017 · 8 claims · 8 setups

  Has reproduction · 100

  NGS/RNA-seq enables unbiased, hypothesis-free detection of multiple known and emergent plant viruses, unlike RT-PCR which only detects one or a few known viruses per test.

  garlic pepper pear grapevine rna-seq mrna-seq transcriptome

• Expansion of the SOS regulon of Vibrio cholerae through extensive transcriptome analysis and experimental validation.

  PMID 29783948 · PMC5963079 · BMC genomics · 2018 · 8 claims · 8 setups

  Has reproduction · 85

  Whole transcriptome sequencing with extensive TSS mapping identified 3078 transcription start sites and 629 ncRNAs in V. cholerae N16961

  cholerae lexa identified directional end rt-pcr

• Genomic Description of 'Candidatus Abyssubacteria,' a Novel Subsurface Lineage Within the Candidate Phylum Hydrogenedentes.

  PMID 30210471 · PMC6121073 · Frontiers in microbiology · 2018 · 8 claims · 7 setups

  Has reproduction · 91

  SURF_5 and SURF_17 are the first full genomes of a novel bacterial lineage, 'Candidatus Abyssubacteria,' within the candidate phylum Hydrogenedentes

  deep co-assembled surf_17 surf_5 whole-genome novo 16s

• COVID-19 lung disease shares driver AT2 cytopathic features with Idiopathic pulmonary fibrosis.

  PMID 35870428 · PMC9297827 · EBioMedicine · 2022 · 8 claims · 8 setups

  Has reproduction · 85

  COVID-19 lung disease resembles IPF at a fundamental level, recapitulating ViP/IPF gene expression patterns, an IL15-centric cytokine storm, and AT2 cytopathic changes (injury, DNA damage, transient progenitor-state arrest, senescence/SASP).

  lung covid-19 interaction pre-clinical composite single-cell kaplan-meier

• Identification and verification of diagnostic biomarkers in recurrent pregnancy loss via machine learning algorithm and WGCNA.

  PMID 37691920 · PMC10485775 · Frontiers in immunology · 2023 · 8 claims · 8 setups

  Has reproduction · 55

  352 DEGs (198 up-regulated, 154 down-regulated) were identified between RPL and control endometrial samples

  endometrial degs hub decidua microarray wgcna machine

• Macrophages on the run: Exercise balances macrophage polarization for improved health.

  PMID 39476967 · PMC11585839 · Molecular metabolism · 2024 · 8 claims · 7 setups

  Has reproduction · 81

  Immediate/acute exercise triggers an M1 (pro-inflammatory) macrophage polarization surge.

  gene affymetrix pooled muscle meta-analysis stepminer gene

• Dynamics and regulation of mitotic chromatin accessibility bookmarking at single-cell resolution.

  PMID 36696508 · PMC9876548 · Science advances · 2023 · 7 claims · 8 setups

  Has reproduction · 50

  Chromatin accessibility continually decreases from mitotic entry until metaphase, then gradually increases as chromosomes segregate.

  l02 tissues hepatoma scatac-seq immunofluorescence atac-see