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 1.3k

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Transcription-terminating mutation in telethonin causing autosomal recessive muscular dystrophy type 2G in a European patient.

PMID 18948002 · PMC2592511 · Neuromuscular disorders : NMD · 2008 · 7 claims · 7 setups

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The patient carries a homozygous Trp25X (TGG→TGA) mutation in TCAP causing premature termination of translation/transcription and complete telethonin deficiency.

pelvis skeletal muscle genomic muscle histology electron
Aggregation propensity of the human proteome.

PMID 18927604 · PMC2557143 · PLoS computational biology · 2008 · 8 claims · 7 setups

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Long proteins have, on average, less intense/pronounced aggregation peaks than short proteins

proteome non-membrane proteins membrane sequence-based correlation statistical
Differential protein expression in human corneal endothelial cells cultured from young and older donors.

PMID 18852868 · PMC2565687 · Molecular vision · 2008 · 8 claims · 5 setups

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Cultured HCEC protein profiles show age-related differences between young and older donors

corneal 2-d trypsin-digested confluent 2-d gel maldi-tof
Breast cancer proteomics reveals correlation between estrogen receptor status and differential phosphorylation of PGRMC1.

PMID 18922159 · PMC2614521 · Breast cancer research : BCR · 2008 · 8 claims · 5 setups

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PGRMC1 protein spots are differentially abundant between ER-negative and ER-positive breast tumors, with two of three spots more abundant in ER-negative tumors

sections pooled mcf7 paraffin-embedded 2d-page shrimp viability
Metabolic syndrome: from epidemiology to systems biology.

PMID 18852695 · PMC2829312 · Nature reviews. Genetics · 2008 · 8 claims · 8 setups

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MetSyn component traits (obesity, insulin resistance, dyslipidaemia, hypertension) exhibit causal interactions and common etiologies rather than being independent conditions

populations rats adipose four genome-wide linkage gene
The genome of the simian and human malaria parasite Plasmodium knowlesi.

PMID 18843368 · PMC2656934 · Nature · 2008 · 8 claims · 7 setups

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The P. knowlesi (H strain) nuclear genome was sequenced and assembled: 23.5 Mb across 14 chromosomes with 5,188 predicted protein-encoding genes.

knowlesi predicted type whole-genome comparative pfam
Malaria research in the post-genomic era.

PMID 18843360 · PMC2705782 · Nature · 2008 · 8 claims · 7 setups

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Genome-dependent methods can partially substitute for forward genetic approaches that are unavailable or limited in malaria parasites.

falciparum plasmodium malaria hela comparative two-hybrid proteomics
Versatile online-offline engine for automated acquisition of high-resolution tandem mass spectra.

PMID 18841935 · PMC2716176 · Analytical chemistry · 2008 · 7 claims · 6 setups

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An integrated hardware/software online-offline platform (TriVersa NanoMate + 12T LTQ FT Ultra + AUTOMATION WAREHOUSE) automates collection of high-resolution MS/MS data for polypeptides >3 kDa that cannot be acquired online on a chromatographic timescale

acid-extracted hela online offline
Improving the specificity of exon prediction using comparative genomics.

PMID 18831778 · PMC2559877 · BMC genomics · 2008 · 8 claims · 6 setups

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A log-odds ratio scoring method based on codon conservation across human-mouse/human-dog alignments and adjacent-codon dependency can classify putative exons as coding vs non-coding.

human-mouse human-dog genome simulated comparative single-genome simulated
SIGMA2: a system for the integrative genomic multi-dimensional analysis of cancer genomes, epigenomes, and transcriptomes.

PMID 18840289 · PMC2571113 · BMC bioinformatics · 2008 · 8 claims · 6 setups

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SIGMA2 is a Java-based software system that integrates and visualizes genomic, epigenomic, and transcriptomic cancer data.

single hcc2218 nsclc array gene multi-omics
Differential membrane proteomics using 18O-labeling to identify biomarkers for cholangiocarcinoma.

PMID 18839982 · PMC3204659 · Journal of proteome research · 2008 · 7 claims · 4 setups

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Golgi membrane protein 1 (GOLM1/GP73), Annexin IV, and Eps8 are validated candidate biomarkers for cholangiocarcinoma

membrane bile 18o-labeling sds-page western
Pol II promoter prediction using characteristic 4-mer motifs: a machine learning approach.

PMID 18834544 · PMC2575220 · BMC bioinformatics · 2008 · 8 claims · 8 setups

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128 discriminating 4-mer motifs combined with an SVM (RBF kernel, LIBSVM) can distinguish promoter from non-promoter DNA sequences

plant drosophila promoter same 4-mer tata blast
Direct evidence of extensive diversity of HIV-1 in Kinshasa by 1960.

PMID 18833279 · PMC3682493 · Nature · 2008 · 7 claims · 8 setups

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Recovered and characterized HIV-1 sequences (DRC60) from a 1960 Bouin's-fixed paraffin-embedded lymph node biopsy from Léopoldville, Belgian Congo

archival hiv-1-positive cdna concatenated rt-pcr quantitative pcr
G-quadruplexes: the beginning and end of UTRs.

PMID 18832370 · PMC2577360 · Nucleic acids research · 2008 · 8 claims · 5 setups

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UTRs show significant strand asymmetry with C-PQS more common than G-PQS, consistent with general depletion of G-quadruplex-forming RNA

genome 5'-utr simulated protein-coding computational high-resolution utr
Evaluating the performance of Affymetrix SNP Array 6.0 platform with 400 Japanese individuals.

PMID 18803882 · PMC2566316 · BMC genomics · 2008 · 8 claims · 5 setups

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About 20% of the 909,622 SNPs on the SNP Array 6.0 are monomorphic in the Japanese population

genomic japanese reference snp concentration agarose
Adaptive discriminant function analysis and reranking of MS/MS database search results for improved peptide identification in shotgun proteomics.

PMID 18788775 · PMC3744223 · Journal of proteome research · 2008 · 7 claims · 4 setups

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PeptideProphet's fixed LDA coefficients for combining search scores (Xcorr', ΔCn, SpRank) may not be optimal under all search/instrument conditions.

trypsin-digested mix serum same shotgun sequest lc-ms
High fidelity of whole-genome amplified DNA on high-density single nucleotide polymorphism arrays.

PMID 18786630 · PMC2659594 · Genomics · 2008 · 8 claims · 7 setups

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WGA product performs well on the Affymetrix 250K SNP array compared to genomic DNA, especially with the BRLMM calling algorithm.

genomic whole-genome same call snp technical genotype
Mitochondrial dysregulation of osteoarthritic human articular chondrocytes analyzed by proteomics: a decrease in mitochondrial superoxide dismutase points to a redox imbalance.

PMID 18784066 · PMC2713027 · Molecular & cellular proteomics : MCP · 2009 · 7 claims · 5 setups

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A mitochondria-enriched 2-D DIGE plus MALDI-TOF/TOF proteomics workflow can define a characteristic mitochondrial protein profile of OA chondrocytes.

articular chondrocytes 2-d real western
Developmental and genetic regulation of human surfactant protein B in vivo.

PMID 18776725 · PMC2765709 · Neonatology · 2009 · 8 claims · 7 setups

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Pro-SP-B peptides are more common in developmentally less mature humans (amniotic fluid, neonatal tracheal aspirates) than in adults

amniotic tracheal bronchoalveolar simultaneous immunoblotting reducing gene
Lymphocytes from patients with type 1 diabetes display a distinct profile of chromatin histone H3 lysine 9 dimethylation: an epigenetic study in diabetes.

PMID 18776137 · PMC2584123 · Diabetes · 2008 · 6 claims · 7 setups

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Lymphocytes (but not monocytes) from type 1 diabetic patients show a distinct subset of genes with significantly increased H3K9me2 compared with healthy controls.

blood pooled gene chip-chip conventional quantitative

Experiments

Transcription-terminating mutation in telethonin causing autosomal recessive muscular dystrophy type 2G in a European patient.

Aggregation propensity of the human proteome.

Differential protein expression in human corneal endothelial cells cultured from young and older donors.

Breast cancer proteomics reveals correlation between estrogen receptor status and differential phosphorylation of PGRMC1.

Metabolic syndrome: from epidemiology to systems biology.

The genome of the simian and human malaria parasite Plasmodium knowlesi.

Malaria research in the post-genomic era.

Versatile online-offline engine for automated acquisition of high-resolution tandem mass spectra.

Improving the specificity of exon prediction using comparative genomics.

SIGMA2: a system for the integrative genomic multi-dimensional analysis of cancer genomes, epigenomes, and transcriptomes.

Differential membrane proteomics using 18O-labeling to identify biomarkers for cholangiocarcinoma.

Pol II promoter prediction using characteristic 4-mer motifs: a machine learning approach.

Direct evidence of extensive diversity of HIV-1 in Kinshasa by 1960.

G-quadruplexes: the beginning and end of UTRs.

Evaluating the performance of Affymetrix SNP Array 6.0 platform with 400 Japanese individuals.

Adaptive discriminant function analysis and reranking of MS/MS database search results for improved peptide identification in shotgun proteomics.

High fidelity of whole-genome amplified DNA on high-density single nucleotide polymorphism arrays.

Mitochondrial dysregulation of osteoarthritic human articular chondrocytes analyzed by proteomics: a decrease in mitochondrial superoxide dismutase points to a redox imbalance.

Developmental and genetic regulation of human surfactant protein B in vivo.

Lymphocytes from patients with type 1 diabetes display a distinct profile of chromatin histone H3 lysine 9 dimethylation: an epigenetic study in diabetes.