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 50

System / cell line: same ✕ Assay: plus ✕ Clear

Identifying drug effects via pathway alterations using an integer linear programming optimization formulation on phosphoproteomic data.

PMID 19997482 · PMC2776985 · PLoS computational biology · 2009 · 7 claims · 4 setups

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An ILP formulation of the Boolean pathway optimization problem fits phosphoproteomic data faster and more efficiently than the previously used genetic algorithm (GA) approach.

hepg2 computational same bead-based integer comparative
Familial parkinsonism: study of original Sagamihara PARK8 (I2020T) kindred with variable clinicopathologic outcomes.

PMID 18804399 · PMC2702757 · Parkinsonism & related disorders · 2009 · 6 claims · 4 setups

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The same LRRK2 I2020T mutation can produce diverse neuropathologies (pure nigral degeneration, Lewy body pathology, or MSA-P) even when clinical presentation and PET findings are virtually identical across family members.

living post-mortem pet neuropathologic immunohistochemistry
A target enrichment method for gathering phylogenetic information from hundreds of loci: An example from the Compositae.

PMID 25202605 · PMC4103609 · Applications in plant sciences · 2014 · 8 claims · 8 setups

Has reproduction · 87

A custom sequence capture probe set (9678 baits targeting 1061 orthologous genes) was designed to enrich COS loci across the Compositae.

compositae same species helianthus targeted genome genomic
Relationship between the extent of chromosomal losses and the pattern of CpG methylation in gastric carcinomas.

PMID 16224153 · PMC2779276 · Journal of Korean medical science · 2005 · 7 claims · 4 setups

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High-level-loss (LOH-H) tumors show a tendency toward unmethylation in Maspin, CAGE, MAGE-A2, and RABGEF1 genes

microdissected same bisulfite-modified pcr microsatellite methylation-specific bisulfite
Ordinal-level phylogenomics of the arthropod class Diplopoda (millipedes) based on an analysis of 221 nuclear protein-coding loci generated using next-generation sequence analyses.

PMID 24236165 · PMC3827447 · PloS one · 2013 · 8 claims · 8 setups

Has reproduction · 82

An ordinal-level phylogeny of Diplopoda reconstructed from 221 nuclear protein-coding loci (61,641 aligned amino acid columns) differs from existing classifications in fundamental ways.

exemplar paired-end cleaned assembled transcriptome read novo
Assessing individual differences in genome-wide gene expression in human whole blood: reliability over four hours and stability over 10 months.

PMID 19653838 · PMC3819565 · Twin research and human genetics : the official journal of the International Society for Twin Studies · 2009 · 8 claims · 5 setups

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A subset of probesets (3,414) shows 4-hour test-retest reliability exceeding r=0.70 for detecting individual differences in gene expression.

blood edta reliably genome-wide twin sub-type
Mutation of the p53 gene precedes aneuploid clonal divergence in colorectal carcinoma.

PMID 7841032 · PMC2033599 · British journal of cancer · 1995 · 7 claims · 5 setups

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p53 mutation occurs as a single clonal event that precedes and may facilitate aneuploid clonal divergence in colorectal carcinoma

tumour plpd-fixed frozen pcr-sscp dideoxy restriction
Future possibilities in the prevention of breast cancer: intervention strategies in BRCA1 and BRCA2 mutation carriers.

PMID 11250722 · PMC138789 · Breast cancer research : BCR · 2000 · 8 claims · 8 setups

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BRCA1 and BRCA2 mutations confer an 80-85% lifetime risk (by age 80) of female breast cancer

normal affected women brca1 clonogenic germline mammographic
High resolution analysis of the human transcriptome: detection of extensive alternative splicing independent of transcriptional activity.

PMID 19804644 · PMC2768739 · BMC genetics · 2009 · 8 claims · 6 setups

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The human GWSA uses exon body and exon-exon junction probes to directly measure over 280,000 known and predicted splicing events genome-wide.

universal same lim erythrocyte genome-wide cross-platform rt-pcr
ABO exon and intron analysis in individuals with the AweakB phenotype reveals a novel O1v-A2 hybrid allele that causes four missense mutations in the A transferase.

PMID 14617382 · PMC305365 · BMC genetics · 2003 · 8 claims · 7 setups

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A novel O1v-A2 hybrid allele, containing four missense mutations, causes the A weak B phenotype in five individuals of African descent

genomic red computational abo sequencing blood
Homogeneous point mutation detection by quantum dot-mediated two-color fluorescence coincidence analysis.

PMID 16517937 · PMC1390686 · Nucleic acids research · 2006 · 8 claims · 6 setups

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QD-mediated two-color fluorescence coincidence detection combined with oligonucleotide ligation assay (OLA) enables separation-free, homogeneous point mutation detection.

synthetic same β-globin kras ola fluorescence photon
FGFR3 protein expression and its relationship to mutation status and prognostic variables in bladder cancer.

PMID 17668422 · PMC2443273 · The Journal of pathology · 2007 · 8 claims · 4 setups

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FGFR3 mutations occur in 42% of primary urothelial carcinomas and are significantly associated with low tumour grade and stage

urothelial tumour direct manual immunohistochemistry
Multilocus sequence typing supports the hypothesis that Ochrobactrum anthropi displays a human-associated subpopulation.

PMID 20021660 · PMC2810298 · BMC microbiology · 2009 · 8 claims · 6 setups

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A novel Multi-Locus Sequence Typing (MLST) scheme for O. anthropi was developed for the first time, based on 7 genes (3490 nucleotides) evolving mostly by neutral mutations

anthropi same candidate multi-locus pulsed-field antibiotyping
Genome sequences and great expectations.

PMID 11178275 · PMC150431 · Genome biology · 2001 · 8 claims · 3 setups

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Function is known or can be predicted for an average of 62% of proteins across 31 analyzed genomes.

complete annotated haemophilus automated benchmarking temporal
Mutation patterns of mtDNA: empirical inferences for the coding region.

PMID 18518963 · PMC2438339 · BMC evolutionary biology · 2008 · 5 claims · 3 setups

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Heteroplasmy was detected in 6.5% (3/46) of Azorean families analyzed, all caused by new point mutations with no insertions/deletions.

extended-family same direct electropherogram molecular
Experimental identification and in silico prediction of bacterivory in green algae.

PMID 33649548 · PMC8245530 · The ISME journal · 2021 · 7 claims · 6 setups

Has reproduction · 93

Five prasinophyte strains (Pterosperma cristatum NIES626, Pyramimonas parkeae CCMP726, Pyramimonas parkeae NIES254, Nephroselmis pyriformis RCC618, Dolichomastix tenuilepis CCMP3274) ingest live fluorescently labeled bacteria, detected by microscopy and/or flow cytometry

prasinophyte same green pelagibaca flow epifluorescence gene-based
Epidemiologic and evolutionary relationships between Romanian and Brazilian HIV-subtype F strains.

PMID 8903171 · PMC2626880 · Emerging infectious diseases · 1995 · 7 claims · 4 setups

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Romanian and Brazilian HIV-1 subtype F envelope C2-V3 sequences cluster into two related but distinct phylogenetic groups.

hiv-1 same brazilian phylogenetic bootstrap pruning
Information extraction from full text scientific articles: where are the keywords?

PMID 12775220 · PMC166134 · BMC bioinformatics · 2003 · 8 claims · 5 setups

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The keyword content of the five article sections (A, I, M, R, D) is heterogeneous, i.e., different sections carry different kinds of information.

corpus same articles keyword validation qualitative
Single-track sequencing for genotyping of multiple SNPs in the N-acetyltransferase 1 (NAT1) gene.

PMID 15563733 · PMC544357 · BMC biotechnology · 2004 · 8 claims · 6 setups

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A single-track sequencing (SSR) strategy on one PCR product can simultaneously address 24 genetic variants in the NAT1 gene using paired terminator tracks (A/G for coding region, A/T for 3' flanking region)

genomic nat1 same pcr single-track single
Comprehensive search for intra- and inter-specific sequence polymorphisms among coding envelope genes of retroviral origin found in the human genome: genes and pseudogenes.

PMID 16150157 · PMC1236922 · BMC genomics · 2005 · 8 claims · 5 setups

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HERV-W (envW) and HERV-FRD (envFRD) envelope genes, both specifically expressed in placenta, show strong sequence conservation with only two nonsynonymous SNPs identified across 91 individuals

genomic genotype 293t pcr-amplified pcr haplotype cell-cell

Experiments

Identifying drug effects via pathway alterations using an integer linear programming optimization formulation on phosphoproteomic data.

Familial parkinsonism: study of original Sagamihara PARK8 (I2020T) kindred with variable clinicopathologic outcomes.

A target enrichment method for gathering phylogenetic information from hundreds of loci: An example from the Compositae.

Relationship between the extent of chromosomal losses and the pattern of CpG methylation in gastric carcinomas.

Ordinal-level phylogenomics of the arthropod class Diplopoda (millipedes) based on an analysis of 221 nuclear protein-coding loci generated using next-generation sequence analyses.

Assessing individual differences in genome-wide gene expression in human whole blood: reliability over four hours and stability over 10 months.

Mutation of the p53 gene precedes aneuploid clonal divergence in colorectal carcinoma.

Future possibilities in the prevention of breast cancer: intervention strategies in BRCA1 and BRCA2 mutation carriers.

High resolution analysis of the human transcriptome: detection of extensive alternative splicing independent of transcriptional activity.

ABO exon and intron analysis in individuals with the AweakB phenotype reveals a novel O1v-A2 hybrid allele that causes four missense mutations in the A transferase.

Homogeneous point mutation detection by quantum dot-mediated two-color fluorescence coincidence analysis.

FGFR3 protein expression and its relationship to mutation status and prognostic variables in bladder cancer.

Multilocus sequence typing supports the hypothesis that Ochrobactrum anthropi displays a human-associated subpopulation.

Genome sequences and great expectations.

Mutation patterns of mtDNA: empirical inferences for the coding region.

Experimental identification and in silico prediction of bacterivory in green algae.

Epidemiologic and evolutionary relationships between Romanian and Brazilian HIV-subtype F strains.

Information extraction from full text scientific articles: where are the keywords?

Single-track sequencing for genotyping of multiple SNPs in the N-acetyltransferase 1 (NAT1) gene.

Comprehensive search for intra- and inter-specific sequence polymorphisms among coding envelope genes of retroviral origin found in the human genome: genes and pseudogenes.