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 475

System / cell line: functional ✕ Clear

HIV replication enhances production of free fatty acids, low density lipoproteins and many key proteins involved in lipid metabolism: a proteomics study.

PMID 18714345 · PMC2500163 · PloS one · 2008 · 7 claims · 4 setups

Full-text index only

HIV infection of a human T-cell line differentially regulates 18 proteins involved in lipid metabolism.

t-cell identified gel maldi-tof bioinformatics
Human QTL linkage mapping.

PMID 18668207 · PMC2761031 · Genetica · 2009 · 8 claims · 6 setups

Full-text index only

Human QTL linkage mapping remains a productive approach for complex traits despite the perception that it does not work, and will continue to be productive especially combined with RNA expression QTLs and dense SNP panels

mexican pomc gene promoter genome-wide gene expression
Analysis of expressed sequence tags from Actinidia: applications of a cross species EST database for gene discovery in the areas of flavor, health, color and ripening.

PMID 18655731 · PMC2515324 · BMC genomics · 2008 · 7 claims · 6 setups

Full-text index only

A collection of 132,577 ESTs from four Actinidia species was generated and clustered into 41,858 non-redundant clusters (18,070 TCs and 23,788 singletons)

cdna full-length tentative non-redundant est codon snp
Trans-natural antisense transcripts including noncoding RNAs in 10 species: implications for expression regulation.

PMID 18653530 · PMC2528163 · Nucleic acids research · 2008 · 8 claims · 7 setups

Full-text index only

A new computational pipeline identifies trans-SAs using ESTs (not just mRNAs) across 10 animal species, improving coverage over prior methods

est unannotated trans-sa tus computational coding hybridization
Comprehensive transcriptome study to develop molecular resources of the copepod Calanus sinicus for their potential ecological applications.

PMID 24982883 · PMC4055022 · BioMed research international · 2014 · 8 claims · 8 setups

Has reproduction · 61

Illumina RNA-Seq with Trinity de novo assembly produced a C. sinicus transcriptome of 69,751 contigs (average 928.8 bp, N50 1,127 bp) from 58.9 million reads.

calanus sinicus genomic rna-seq novo sequence
A map of human protein interactions derived from co-expression of human mRNAs and their orthologs.

PMID 18414481 · PMC2387231 · Molecular systems biology · 2008 · 8 claims · 6 setups

Full-text index only

Comparing human mRNA co-expression with co-expression of orthologous gene pairs in five other organisms identifies proteins that physically associate

genes hela proteins worm co-expression quantitative functional
Transcription network construction for large-scale microarray datasets using a high-performance computing approach.

PMID 18366618 · PMC2386070 · BMC genomics · 2008 · 8 claims · 7 setups

Full-text index only

RMT removes the random noise component of the gene expression correlation matrix by testing its eigenvalue statistics against a null hypothesis derived from a truly random correlation matrix

yeast liver eight-node microarray k-means hybrid
No evidence of a Neanderthal contribution to modern human diversity.

PMID 18304371 · PMC2374707 · Genome biology · 2008 · 8 claims · 7 setups

Full-text index only

There is no evidence of any Neanderthal contribution to modern human genetic diversity

neanderthal culture modern genomic mitochondrial nuclear gene-specific
Dissecting microregulation of a master regulatory network.

PMID 18294391 · PMC2289817 · BMC genomics · 2008 · 8 claims · 6 setups

Full-text index only

143 human miRNAs (termed p53-miRs) each contain at least one putative p53 binding site within 10 kb flanking sequence and are predicted to target at least one known gene

genome mirnas mirna-target predicted p53 mirna cross-referencing
Up regulation in gene expression of chromatin remodelling factors in cervical intraepithelial neoplasia.

PMID 18248679 · PMC2277413 · BMC genomics · 2008 · 8 claims · 4 setups

Full-text index only

Chromatin remodelling-associated genes SMARCC1, NCOR1, MRFAP1 and MORF4L2 are upregulated during progression of cervical intraepithelial neoplasia

cervical independent computational long real-time gene
The Bifidobacterium dentium Bd1 genome sequence reflects its genetic adaptation to the human oral cavity.

PMID 20041198 · PMC2788695 · PLoS genetics · 2009 · 8 claims · 8 setups

Full-text index only

The B. dentium Bd1 genome was sequenced to completion, revealing a single circular 2,636,368 bp chromosome with 2,143 predicted ORFs

dentium core whole-genome 3d-structure comparative
A novel GJA8 mutation (p.I31T) causing autosomal dominant congenital cataract in a Chinese family.

PMID 20019893 · PMC2794658 · Molecular vision · 2009 · 7 claims · 7 setups

Full-text index only

A novel missense mutation c.92T>C (p.I31T) in GJA8 causes autosomal dominant congenital nuclear cataract in this Chinese family

family genomic unrelated gja8 clinical microsatellite sequencing
SeqBuster, a bioinformatic tool for the processing and analysis of small RNAs datasets, reveals ubiquitous miRNA modifications in human embryonic cells.

PMID 20008100 · PMC2836562 · Nucleic acids research · 2010 · 8 claims · 6 setups

Full-text index only

SeqBuster is a versatile web-based and stand-alone bioinformatic toolkit for processing and analyzing large-scale small RNA deep sequencing datasets.

embryonic hesc small sequence adapter
The hemolytic and cytolytic activities of Serratia marcescens phospholipase A (PhlA) depend on lysophospholipid production by PhlA.

PMID 20003541 · PMC2800117 · BMC microbiology · 2009 · 8 claims · 8 setups

Full-text index only

S. marcescens possesses a hemolytic factor independent of ShlA, revealed because an shlAB deletion mutant loses contact hemolysis but retains hemolysis on blood agar plates.

marcescens coli his-phla sheep hemolysis contact-dependent functional
'Unknown' proteins and 'orphan' enzymes: the missing half of the engineering parts list--and how to find it.

PMID 20001958 · PMC3022307 · The Biochemical journal · 2009 · 8 claims · 8 setups

Full-text index only

Comparative genomics is the single most effective strategy for predicting functions of unknown proteins and finding genes for orphan enzymes

lactococcus lactis arabidopsis coli gene recombinant enzyme
Network properties of complex human disease genes identified through genome-wide association studies.

PMID 19956617 · PMC2779513 · PloS one · 2009 · 7 claims · 6 setups

Full-text index only

Complex disease genes are significantly less central (lower degree/closeness, higher eccentricity) in the human interactome than essential and monogenic disease genes, occupying an intermediate niche between monogenic disease genes and non-disease genes

complex interactome gene disease-sharing gene protein-protein
Quantitative proteomics analysis of maternal plasma in Down syndrome pregnancies using isobaric tagging reagent (iTRAQ).

PMID 19902006 · PMC2774473 · Journal of biomedicine & biotechnology · 2010 · 8 claims · 5 setups

Full-text index only

iTRAQ labelling combined with 4800 MALDI TOF/TOF can detect quantitative differences in the maternal plasma proteome between DS and euploid pregnancies

maternal tryptic scx-fractionated identified itraq immunodepletion strong
Inflammatory bowel disease and mutations affecting the interleukin-10 receptor.

PMID 19890111 · PMC2787406 · The New England journal of medicine · 2009 · 8 claims · 8 setups

Full-text index only

Homozygous loss-of-function mutations in IL10RA or IL10RB cause severe early-onset enterocolitis

consanguineous patients ebv-transformed pbmcs genetic-linkage single-nucleotide-polymorphism candidate-gene
MtSNPscore: a combined evidence approach for assessing cumulative impact of mitochondrial variations in disease.

PMID 19758471 · PMC2745589 · BMC bioinformatics · 2009 · 8 claims · 5 setups

Full-text index only

MtSNPscore, a weighted scoring pipeline combining literature evidence, in silico predictions, and case/control frequency, can prioritize likely pathogenic mtDNA variations

sporadic mitochondrial reported ataxia mitochondrial functional compensatory
Fibroblasts from patients with Diamond-Blackfan anaemia show abnormal expression of genes involved in protein synthesis, amino acid metabolism and cancer.

PMID 19765279 · PMC2760583 · BMC genomics · 2009 · 8 claims · 5 setups

Full-text index only

Global microarray profiling reveals 421 genes differentially expressed in DBA patient fibroblasts compared to healthy controls

dermal same fibroblasts analysis microarray quantitative rt-pcr

Experiments

HIV replication enhances production of free fatty acids, low density lipoproteins and many key proteins involved in lipid metabolism: a proteomics study.

Human QTL linkage mapping.

Analysis of expressed sequence tags from Actinidia: applications of a cross species EST database for gene discovery in the areas of flavor, health, color and ripening.

Trans-natural antisense transcripts including noncoding RNAs in 10 species: implications for expression regulation.

Comprehensive transcriptome study to develop molecular resources of the copepod Calanus sinicus for their potential ecological applications.

A map of human protein interactions derived from co-expression of human mRNAs and their orthologs.

Transcription network construction for large-scale microarray datasets using a high-performance computing approach.

No evidence of a Neanderthal contribution to modern human diversity.

Dissecting microregulation of a master regulatory network.

Up regulation in gene expression of chromatin remodelling factors in cervical intraepithelial neoplasia.

The Bifidobacterium dentium Bd1 genome sequence reflects its genetic adaptation to the human oral cavity.

A novel GJA8 mutation (p.I31T) causing autosomal dominant congenital cataract in a Chinese family.

SeqBuster, a bioinformatic tool for the processing and analysis of small RNAs datasets, reveals ubiquitous miRNA modifications in human embryonic cells.

The hemolytic and cytolytic activities of Serratia marcescens phospholipase A (PhlA) depend on lysophospholipid production by PhlA.

'Unknown' proteins and 'orphan' enzymes: the missing half of the engineering parts list--and how to find it.

Network properties of complex human disease genes identified through genome-wide association studies.

Quantitative proteomics analysis of maternal plasma in Down syndrome pregnancies using isobaric tagging reagent (iTRAQ).

Inflammatory bowel disease and mutations affecting the interleukin-10 receptor.

MtSNPscore: a combined evidence approach for assessing cumulative impact of mitochondrial variations in disease.

Fibroblasts from patients with Diamond-Blackfan anaemia show abnormal expression of genes involved in protein synthesis, amino acid metabolism and cancer.