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).

Publications 1.3k Datasets 392.5k Experiments 540

System / cell line: clinical ✕ Clear

BABELOMICS: a systems biology perspective in the functional annotation of genome-scale experiments.

PMID 16845052 · PMC1538844 · Nucleic acids research · 2006 · 8 claims · 8 setups

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Babelomics is presented as an updated, complete suite of web tools for functional analysis of genome-scale experiments with new and improved modules

pre-selected pre-tabulated genes ranked kegg expression text-mining
Genomic characterization of five deletions in the LDL receptor gene in Danish Familial Hypercholesterolemic subjects.

PMID 16796766 · PMC1523332 · BMC medical genetics · 2006 · 7 claims · 5 setups

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All five LDLR deletions are flanked by Alu elements, supporting unequal homologous recombination between Alu repeats as the causative mechanism

genomic pcr-amplified ldlr blood long-range cycle diagnostic
Four genomic islands that mark post-1995 pandemic Vibrio parahaemolyticus isolates.

PMID 16672049 · PMC1464126 · BMC genomics · 2006 · 8 claims · 7 setups

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Seven genomic islands (VPaI-1 to VPaI-7, 10-81 kb) were identified in V. parahaemolyticus RIMD2210633 by aberrant GC content, presence of integrases/transposases, flanking direct repeats, and absence from related Vibrionaceae genomes.

parahaemolyticus vulnificus clinical ecori-digested bioinformatic comparative pcr
Serum diagnosis of diffuse large B-cell lymphomas and further identification of response to therapy using SELDI-TOF-MS and tree analysis patterning.

PMID 18163913 · PMC2242801 · BMC cancer · 2007 · 8 claims · 8 setups

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SELDI-TOF-MS serum proteomic patterns analyzed by decision tree classification (Biomarker Pattern Software) can discriminate DLBCL patients from healthy controls with high sensitivity and specificity.

serum seldi dlbcl pooled seldi-tof-ms proteinchip decision
Metatranscriptomics of the human oral microbiome during health and disease.

PMID 24692635 · PMC3977359 · mBio · 2014 · 8 claims · 8 setups

Has reproduction · 62

Disease-associated periodontal communities display conserved community-level metabolic gene expression profiles between patients, whereas the metabolic gene expression of individual species is highly variable between patients.

patient-matched subset health rna-seq rrna comparison metatranscriptomics
Optimality driven nearest centroid classification from genomic data.

PMID 17912341 · PMC1991588 · PloS one · 2007 · 7 claims · 5 setups

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A theoretical result determines the subset of features of a given size that minimizes the misclassification rate for a nearest-centroid (LDA) classifier, based on equation (4).

artificial simulated previously-published simulated simulation clinical
Mycoplasma genitalium: an efficient strategy to generate genetic variation from a minimal genome.

PMID 17784912 · PMC2169797 · Molecular microbiology · 2007 · 8 claims · 6 setups

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MG192 is highly variable among and within M. genitalium strains both in vitro and in vivo

genitalium clinical urine pairwise pcr serial
DNA bar coding and pyrosequencing to identify rare HIV drug resistance mutations.

PMID 17576693 · PMC1934997 · Nucleic acids research · 2007 · 6 claims · 7 setups

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DNA bar coding combined with pyrosequencing allows parallel, deep characterization of drug resistance mutations across many HIV populations in a single experiment

hiv pooled plasma pyrosequencing conventional rt-pcr
Intragenic deletion in the LARGE gene causes Walker-Warburg syndrome.

PMID 17436019 · PMC1914248 · Human genetics · 2007 · 7 claims · 8 setups

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A homozygous 63.1-kb intragenic deletion in LARGE (exons 9-10) causes Walker-Warburg syndrome in a consanguineous Saudi family

genomic family skeletal blood microsatellite direct multiplex
Expression and mutation analysis of the discoidin domain receptors 1 and 2 in non-small cell lung carcinoma.

PMID 17299390 · PMC2360060 · British journal of cancer · 2007 · 8 claims · 6 setups

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DDR1 is significantly upregulated in NSCLC tumour tissue compared with matched normal lung tissue

nsclc matched lung quantitative pcr genomic
Neuroacanthocytosis associated with a defect of the 4.1R membrane protein.

PMID 17298666 · PMC1805452 · BMC neurology · 2007 · 8 claims · 8 setups

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Four unrelated NA patients show a novel erythrocyte membrane defect: 4.1R protein deficiency

erythrocyte genomic peripheral erythrocytes sds-page non-denaturing direct
Fucosylated glycoproteins as markers of liver disease.

PMID 19126969 · PMC3827789 · Disease markers · 2008 · 8 claims · 6 setups

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Core alpha 1,6-linked fucosylation of AFP (AFP-L3) is increased in HCC and is a more specific marker of HCC than total AFP

afp pooled larger igg lectin fucose-specific immunoblot
Glycomic approach for potential biomarkers on prostate cancer: profiling of N-linked glycans in human sera and pRNS cell lines.

PMID 19126968 · PMC3827814 · Disease markers · 2008 · 8 claims · 5 setups

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Glycomic profiling of N-linked glycans in serum can reveal potential biomarkers distinguishing prostate cancer patients from controls

serum prns-1-1 n-linked maldi solid tandem
An integrated database-pipeline system for studying single nucleotide polymorphisms and diseases.

PMID 19091018 · PMC2638159 · BMC bioinformatics · 2008 · 6 claims · 5 setups

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Existing SNP/disease databases are fragmented; no combined resource widely supports gene-, SNP-, and disease-related information together

private disease uniprot snps database controlled sequence
targetTB: a target identification pipeline for Mycobacterium tuberculosis through an interactome, reactome and genome-scale structural analysis.

PMID 19099550 · PMC2651862 · BMC systems biology · 2008 · 8 claims · 8 setups

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A comprehensive in silico target identification pipeline (targetTB) integrating interactome, reactome, essentiality, sequence and structural analyses can identify high-confidence drug targets for Mtb

tuberculosis mtb protein-protein flux transposon
Short-term genome evolution of Listeria monocytogenes in a non-controlled environment.

PMID 19014550 · PMC2642827 · BMC genomics · 2008 · 6 claims · 6 setups

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The 2000 listeriosis outbreak was likely caused by an L. monocytogenes strain that persisted in the food processing facility for at least 12 years since 1988

monocytogenes additional food j774 whole-genome comparative pcr
Activation instead of blocking mesolimbic dopaminergic reward circuitry is a preferred modality in the long term treatment of reward deficiency syndrome (RDS): a commentary.

PMID 19014506 · PMC2615745 · Theoretical biology & medical modelling · 2008 · 8 claims · 6 setups

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A biphasic treatment approach—acute DA receptor blocking followed by long-term DA release/activation at the NAc—is needed to treat RDS without inducing abnormal mood or craving.

kidney alcohol-preferring obese rodents receptor dna-directed meta-analysis
Proteomic analysis of protein deposits on worn daily wear silicone hydrogel contact lenses.

PMID 18989384 · PMC2579937 · Molecular vision · 2008 · 8 claims · 4 setups

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Worn silicone hydrogel contact lenses deposit a wide array of proteins from the tear film and other sources.

deposit excised pooled worn sds-page in-gel lc-ms-ms
Novel CYP1B1 mutations in consanguineous Pakistani families with primary congenital glaucoma.

PMID 18989382 · PMC2579935 · Molecular vision · 2008 · 7 claims · 6 setups

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Missense mutations in CYP1B1 are most likely responsible for PCG in these three Pakistani families

genomic family ethnically affected genotyping two-point sanger
RNA-Seq transcriptome profiling identifies CRISPLD2 as a glucocorticoid responsive gene that modulates cytokine function in airway smooth muscle cells.

PMID 24926665 · PMC4057123 · PloS one · 2014 · 8 claims · 8 setups

Has reproduction · 87

Dexamethasone treatment (1 µM, 18 h) of primary human ASM cells differentially regulates 316 genes, including both known and previously uninvestigated glucocorticoid-responsive genes.

airway asm most single rna-seq quantitative qrt-pcr

Experiments

BABELOMICS: a systems biology perspective in the functional annotation of genome-scale experiments.

Genomic characterization of five deletions in the LDL receptor gene in Danish Familial Hypercholesterolemic subjects.

Four genomic islands that mark post-1995 pandemic Vibrio parahaemolyticus isolates.

Serum diagnosis of diffuse large B-cell lymphomas and further identification of response to therapy using SELDI-TOF-MS and tree analysis patterning.

Metatranscriptomics of the human oral microbiome during health and disease.

Optimality driven nearest centroid classification from genomic data.

Mycoplasma genitalium: an efficient strategy to generate genetic variation from a minimal genome.

DNA bar coding and pyrosequencing to identify rare HIV drug resistance mutations.

Intragenic deletion in the LARGE gene causes Walker-Warburg syndrome.

Expression and mutation analysis of the discoidin domain receptors 1 and 2 in non-small cell lung carcinoma.

Neuroacanthocytosis associated with a defect of the 4.1R membrane protein.

Fucosylated glycoproteins as markers of liver disease.

Glycomic approach for potential biomarkers on prostate cancer: profiling of N-linked glycans in human sera and pRNS cell lines.

An integrated database-pipeline system for studying single nucleotide polymorphisms and diseases.

targetTB: a target identification pipeline for Mycobacterium tuberculosis through an interactome, reactome and genome-scale structural analysis.

Short-term genome evolution of Listeria monocytogenes in a non-controlled environment.

Activation instead of blocking mesolimbic dopaminergic reward circuitry is a preferred modality in the long term treatment of reward deficiency syndrome (RDS): a commentary.

Proteomic analysis of protein deposits on worn daily wear silicone hydrogel contact lenses.

Novel CYP1B1 mutations in consanguineous Pakistani families with primary congenital glaucoma.

RNA-Seq transcriptome profiling identifies CRISPLD2 as a glucocorticoid responsive gene that modulates cytokine function in airway smooth muscle cells.