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).
-
Full-text index only
Microarray-based DNA methylation profiling: technology and applications.
PMID 16428248 · PMC1345696 · Nucleic acids research · 2006 · 7 claims · 6 setups
A microarray-based method enriching unmethylated and methylated DNA fractions via methylation-sensitive restriction enzymes followed by hybridization enables high-throughput DNA methylation profiling of large genomic regions.
-
Full-text index only
Array-based profiling of reference-independent methylation status (aPRIMES) identifies frequent promoter methylation and consecutive downregulation of ZIC2 in pediatric medulloblastoma.
PMID 17344319 · PMC1874664 · Nucleic acids research · 2007 · 7 claims · 7 setups
aPRIMES is a novel array-based method that detects direct (absolute) methylation status of CGIs via competitive hybridization of McrBC-digested (methylated) versus HpaII/BstUI-digested (unmethylated) DNA from the same genome, avoiding reference-tissue and copy-number biases
-
Full-text index only
Array-based analysis of genomic DNA methylation patterns of the tumour suppressor gene p16INK4A promoter in colon carcinoma cell lines.
PMID 15860770 · PMC1087791 · Nucleic acids research · 2005 · 8 claims · 4 setups
A Geniom One-synthesized oligonucleotide microarray can determine the methylation status of individual CpG dinucleotides in parallel, combining high throughput with single-base resolution
-
Full-text index only
Methods for genome-wide analysis of DNA methylation in intestinal tumors.
PMID 19854208 · PMC2891386 · Mutation research · 2010 · 8 claims · 8 setups
Aberrant DNA methylation, including CpG island hypermethylation of tumor suppressors and genome-wide hypomethylation, is strongly linked to the origin and progression of colorectal cancer.
-
Full-text index only
Multiplex amplification enabled by selective circularization of large sets of genomic DNA fragments.
PMID 15860768 · PMC1087789 · Nucleic acids research · 2005 · 8 claims · 4 setups
Selector oligonucleotides can circularize many distinct genomic restriction fragments in one reaction, enabling parallel amplification with a single universal primer pair instead of multiple target-specific primer pairs
-
Full-text index only
Thirty years into the genomics era: tumor viruses led the way.
PMID 17940630 · PMC1994808 · The Yale journal of biology and medicine · 2006 · 8 claims · 8 setups
Restriction endonuclease-based analysis and sequencing of small tumor virus genomes (SV40, phiX174) established the technical framework later used to sequence bacterial and human genomes
-
Full-text index only
MMASS: an optimized array-based method for assessing CpG island methylation.
PMID 17041235 · PMC1635254 · Nucleic acids research · 2006 · 8 claims · 7 setups
MMASS-v2 (optimized AciI/HinP1I/HpyCH4IV/HpaII enzyme combination with McrBC digestion) offers improved sensitivity and statistical power for microarray-based CpG island methylation detection compared to MMASS-v1, MMASS-sub and the Nouzova method
-
Full-text index only
Vector algebra in the analysis of genome-wide expression data.
PMID 11897023 · PMC88809 · Genome biology · 2002 · 8 claims · 6 setups
The angle θ between expression (experiment) vectors is the geometric counterpart of the Pearson correlation coefficient r, providing a rigorous measure of similarity between profiles.
-
Full-text index only
Detection of YMDD motif mutants by oligonucleotide chips in lamivudine-untreated patients with chronic hepatitis B virus infection.
PMID 15308845 · PMC2816888 · Journal of Korean medical science · 2004 · 6 claims · 5 setups
An oligonucleotide chip was developed using probes for wild-type YMDD, M552V, and three M552I probe variants to detect HBV polymerase YMDD motif mutations
-
Full-text index only
Capturing genomic signatures of DNA sequence variation using a standard anonymous microarray platform.
PMID 17000641 · PMC1636412 · Nucleic acids research · 2006 · 8 claims · 6 setups
An anonymous SHyP oligonucleotide microarray can capture genomic signatures of DNA sequence variation from any organism, including a previously unsequenced species
-
Full-text index only
Identification of the proliferation/differentiation switch in the cellular network of multicellular organisms.
PMID 17166053 · PMC1664705 · PLoS computational biology · 2006 · 8 claims · 8 setups
Integrating interactome and transcriptome data reveals a pair of transcriptionally anticorrelated network modules (P and D) each comprising hundreds of genes, present across individuals and species.
-
Full-text index only
The mitochondrial genome, a growing interest inside an organelle.
PMID 18488415 · PMC2526360 · International journal of nanomedicine · 2008 · 8 claims · 8 setups
mtDNA mutations are causally linked to a wide range of mitochondrial diseases, aging, and chronic degenerative diseases
-
Full-text index only
High-throughput molecular analysis in lung cancer: insights into biology and potential clinical applications.
PMID 19648524 · PMC4648268 · The European respiratory journal · 2009 · 8 claims · 8 setups
High-throughput -omics technologies have revolutionised understanding of lung cancer biology and hold promise for personalised management of lung cancer
-
Full-text index only
Proposed methods for testing and selecting the ERCC external RNA controls.
PMID 16266432 · PMC1325234 · BMC genomics · 2005 · 8 claims · 5 setups
A consortium-developed, standardized set of external RNA control transcripts can be used to assess technical performance in gene expression assays (microarray and QRT-PCR)