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).

• Targeting the epigenome and the integrated stress response to normalize colorectal cancer subclonal plasticity and progression.

  PMID 41963303 · PMC13181133 · Cell death & disease · 2026 · 8 claims · 8 setups

  Has reproduction · 68

  The integrated stress response (ISR) induces CRC cell plasticity, subclonal diversity, and tumor progression in stress-surviving cells

  ht29-derived ht29 nod rna-seq faire-qpcr chip-seq

• An archaeal histone-like protein regulates gene expression in response to salt stress.

  PMID 34883507 · PMC8682779 · Nucleic acids research · 2021 · 8 claims · 4 setups

  Has reproduction · 94

  HpyA is important for maintaining wild-type growth rate under reduced salinity

  hbt growth phase chip-seq

• Transcriptomics, regulatory syntax, and enhancer identification in mesoderm-induced ESCs at single-cell resolution.

  PMID 35977485 · PMC9644345 · Cell reports · 2022 · 8 claims · 8 setups

  Has reproduction · 63

  Bmp4 treatment instructs ESCs to downregulate pluripotency genes and upregulate genes associated with formative pluripotency and fate specification

  escs naive facs-isolated freshly bulk atac-seq chip-seq

• Dioxin-elicited decrease in cobalamin redirects propionyl-CoA metabolism to the β-oxidation-like pathway resulting in acrylyl-CoA conjugate buildup.

  PMID 35931118 · PMC9418907 · The Journal of biological chemistry · 2022 · 8 claims · 8 setups

  Has reproduction · 73

  TCDD dose-dependently decreases cobalamin (Cbl) levels, compromising MUT activity and redirecting propionyl-CoA metabolism from the canonical Cbl-dependent carboxylation pathway to the alternate Cbl-independent β-oxidation-like pathway.

  liver hepatic intestinal serum targeted untargeted chip-seq

• In vitro identification and in silico utilization of interspecies sequence similarities using GeneChip technology.

  PMID 15871745 · PMC1156887 · BMC genomics · 2005 · 7 claims · 6 setups

  Full-text index only

  Only 14±2% of canine transcripts were detected by U133A probe sets versus 49±6% of human transcripts when hybridized to the same chip

  canine tissues hg-u133a probes microarray sequence ortholog

• Differential analysis for high density tiling microarray data.

  PMID 17892592 · PMC2231405 · BMC bioinformatics · 2007 · 8 claims · 6 setups

  Full-text index only

  gSAM, a generalized extension of Significance Analysis of Microarrays (SAM), uses a piece-wise function to segment genome-wide differential response by protein-coding vs non-coding regions and by 5' vs 3' vs intra-genic bias within genes, rather than treating a gene as an atomic unit.

  hl60 profiling chip-on-chip

• Exploration of the omics evidence landscape: adding qualitative labels to predicted protein-protein interactions.

  PMID 17880677 · PMC2375035 · Genome biology · 2007 · 7 claims · 8 setups

  Full-text index only

  Combining pairs of omics evidence types into two-dimensional 'evidence landscapes' allows regions to be identified that specifically and purely predict either physical or metabolic protein interactions

  saccharomyces correlated chip-chip gene

• Downregulation of death-associated protein kinase 1 (DAPK1) in chronic lymphocytic leukemia.

  PMID 17540169 · PMC4647864 · Cell · 2007 · 8 claims · 13 setups

  Full-text index only

  DAPK1 promoter is epigenetically silenced by DNA methylation in almost all sporadic CLL cases

  cd19+ leukemia raji jurkat quantitative cobra chromatin

• High-density SNP genotyping to define beta-globin locus haplotypes.

  PMID 18829352 · PMC4251776 · Blood cells, molecules & diseases · 2009 · 8 claims · 5 setups

  Full-text index only

  RFLP analysis lacks sufficient site density/coverage to accurately reflect the genomic complexity of the β-locus

  genomic rflp subset rflp high-density haploview

• Surface-enhanced laser desorption/ionization time-of-flight proteomic profiling of breast carcinomas identifies clinicopathologically relevant groups of patients similar to previously defined clusters from cDNA expression.

  PMID 18510725 · PMC2481497 · Breast cancer research : BCR · 2008 · 7 claims · 7 setups

  Full-text index only

  Unsupervised hierarchical clustering of 130 SELDI-TOF peaks yielded six peak clusters and five distinct groups of breast cancer patients.

  lysates breast microarrays imac-preseparated seldi-tof pilot immunohistochemistry

• Characterization of the human DYRK1A promoter and its regulation by the transcription factor E2F1.

  PMID 18366763 · PMC2292204 · BMC molecular biology · 2008 · 8 claims · 8 setups

  Full-text index only

  Transcription start sites of human DYRK1A are distributed over an 800 bp region within an unmethylated CpG island

  pc3 saos2 resting phoenix 5'-race-pcr rt-pcr chip-seq

• An integrative genomic and epigenomic approach for the study of transcriptional regulation.

  PMID 18365023 · PMC2266992 · PloS one · 2008 · 8 claims · 7 setups

  Full-text index only

  Integrative analysis combining gene expression, DNA methylation, and H3K9 acetylation data reveals hundreds of additional differentially expressed genes missed by gene expression arrays alone

  aml computational help chip-chip gene

• Genome sequence, comparative analysis, and population genetics of the domestic horse.

  PMID 19892987 · PMC3785132 · Science (New York, N.Y.) · 2009 · 8 claims · 7 setups

  Full-text index only

  Produced a high-quality draft genome assembly of the domestic horse (EquCab2.0)

  single horse eight twelve genome fish chip-on-chip

• Characterizing natural variation using next-generation sequencing technologies.

  PMID 19801172 · PMC3994700 · Trends in genetics : TIG · 2009 · 8 claims · 8 setups

  Full-text index only

  Next-generation sequencing enables complete, genome-wide surveys of genetic variation at unprecedented resolution, overcoming limitations of genotyping panels and microarrays.

  pichia individuals saccharomyces individual whole-genome partial comparative

• Endogenous retroviruses mediate transcriptional rewiring in response to oncogenic signaling in colorectal cancer.

  PMID 39018396 · PMC466953 · Science advances · 2024 · 8 claims · 8 setups

  Full-text index only

  Primate-specific ERVs are a rich source of enhancers displaying cancer-specific activity across multiple tumor types

  cancer hct116 tcga colorectal atac-seq chip-seq bulk

• Sequence and chemical specificity define the functional landscape of intrinsically disordered regions.

  PMID 41688823 · PMC12904797 · Nature cell biology · 2026 · 8 claims · 8 setups

  Full-text index only

  IDR function depends on two distinct but related properties: sequence specificity (motifs) and chemical specificity (distributed multivalent chemistry)

  cerevisiae orthologous abf1 fus1-163 plasmid anti-flag proteome-wide

• Microbial genomics: from sequence to function.

  PMID 10998380 · PMC2627950 · Emerging infectious diseases · 2000 · 8 claims · 4 setups

  Full-text index only

  Whole-genome shotgun sequencing (sequencing and assembly of random genome fragments), first demonstrated with Haemophilus influenzae in 1995, is now the method of choice for sequencing most genomes, including the human genome.

  yeast bacteria microbial high-throughput microarray ribosomal

• The lords of the genomes.

  PMID 15461811 · PMC545592 · Genome biology · 2004 · 8 claims · 8 setups

  Full-text index only

  Functionally active clusters of transcription-factor binding sites are evolutionarily conserved between Drosophila species, whereas inactive clusters are not, even when sequence identity alone cannot distinguish them

  drosophila cdna-derived saccharomyces acid reporter-gene enhancer chromatin

• The UCSC Genome Browser Database: 2008 update.

  PMID 18086701 · PMC2238835 · Nucleic acids research · 2008 · 8 claims · 8 setups

  Full-text index only

  The UCSC Genome Browser Database (GBD) provides integrated sequence and annotation data for a large collection of vertebrate and model organism genomes.

  zebrafish yale vertebrate non-human sage expression snp

• Ensembl 2008.

  PMID 18000006 · PMC2238821 · Nucleic acids research · 2008 · 8 claims · 6 setups

  Full-text index only

  The Ensembl regulatory build integrates multiple genome-wide functional genomics datasets to automatically annotate regulatory regions and assign putative functions across the genome.

  embryonic amniota multi-species individuals automated chip-chip comparative