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 292

System / cell line: target ✕ Clear

Characterization of genome-wide p53-binding sites upon stress response.

PMID 18474530 · PMC2441782 · Nucleic acids research · 2008 · 7 claims · 7 setups

Full-text index only

Genome-wide ChIP-on-chip identified 1546 high-confidence p53-binding sites upon Actinomycin D treatment in U2OS cells

u2os saos-2 chip-on-chip chip-qpcr western
Network inference and network response identification: moving genome-scale data to the next level of biological discovery.

PMID 20174676 · PMC3087299 · Molecular bioSystems · 2010 · 8 claims · 8 setups

Full-text index only

Cellular response to a signal is assumed to involve only specific TRN modules (conditionally active subnetworks) rather than the entire network, providing quantitative tractability

yeast specified normal coli chip-on-chip chip-sequencing correlation-based
RExPrimer: an integrated primer designing tool increases PCR effectiveness by avoiding 3' SNP-in-primer and mis-priming from structural variation.

PMID 19958502 · PMC2788391 · BMC genomics · 2009 · 7 claims · 4 setups

Full-text index only

RExPrimer integrates local SNP, indel, pseudogene, and CNV/structural variation databases with the Primer3 core algorithm to avoid mis-priming and SNP-in-Primer effects.

genomic cyp2d6 genome pcr penta-plex sequence
Proteomic profiling in ovarian cancer.

PMID 19955909 · PMC7319026 · International journal of gynecological cancer : official journal of the International Gynecological Cancer Society · 2009 · 8 claims · 6 setups

Full-text index only

No validated or cost-efficient screening program exists for ovarian cancer; physical exam, CA125, and transvaginal ultrasound lack sufficient sensitivity/specificity for early-stage detection.

serum tumor rolling mass microarray
Skittle: a 2-dimensional genome visualization tool.

PMID 20042093 · PMC2817707 · BMC bioinformatics · 2009 · 7 claims · 6 setups

Full-text index only

Skittle is a 2D genome visualization tool combining a color-coded Nucleotide Display, a Repeat Map, a Repeat Overview, and an Alignment Cylinder to reveal genomic patterns at multiple scales

chromosome random alpha genome nucleotide repeat alignment
Exome sequencing of a multigenerational human pedigree.

PMID 20011588 · PMC2788131 · PloS one · 2009 · 8 claims · 6 setups

Full-text index only

Microarray-based exome capture combined with 454 GS FLX NGS is an efficient and reliable method to enrich for chromosomal regions of interest, validated on eight individuals from a three-generation pedigree

genomic eluted captured pcr microarray-based qpcr next-generation
Novel syntaxin 11 gene (STX11) mutation in three Argentinean patients with hemophagocytic lymphohistiocytosis.

PMID 19967551 · PMC7370861 · Journal of clinical immunology · 2010 · 8 claims · 8 setups

Full-text index only

Three unrelated Argentinean HLH patients carry an identical novel homozygous 4-bp deletion (c.581_584delTGCC; p.Leu194ProfsX2) in STX11

genomic peripheral blood fresh direct snp rt-pcr
Point mutations in GLI3 lead to misregulation of its subcellular localization.

PMID 19829694 · PMC2758996 · PloS one · 2009 · 6 claims · 8 setups

Full-text index only

The MID1-α4-PP2A complex regulates the subcellular localization and transcriptional activity of GLI3.

hela immunofluorescence real-time luciferase
MicroRNA profiling of BRCA1/2 mutation-carrying and non-mutation-carrying high-grade serous carcinomas of ovary.

PMID 19798417 · PMC2749450 · PloS one · 2009 · 7 claims · 7 setups

Full-text index only

High grade serous carcinomas with and without BRCA1/2 abnormalities show very similar miRNA expression profiles, with no clear clustering separation by BRCA1/2 status

high ovarian mir-29a mirna unsupervised significance
Transcription dynamics.

PMID 19782025 · PMC6326382 · Molecular cell · 2009 · 8 claims · 8 setups

Full-text index only

Transcription factors locate their sparse specific binding sites via a 3D scanning mechanism combining rapid nuclear diffusion with frequent, very transient (seconds-scale) nonspecific chromatin interactions.

living linker lac glucocorticoid frap single-molecule nucleosome
The potential of optical proteomic technologies to individualize prognosis and guide rational treatment for cancer patients.

PMID 19756916 · PMC2778706 · Targeted oncology · 2009 · 8 claims · 5 setups

Full-text index only

Genomic/gene expression profiling alone is insufficient to identify tumors with molecular pathway changes predictive of treatment outcome; protein-level functional assessment (activation states, PTMs, interactions) is also required

microarray ffpe models cancer immunohistochemistry fret fret-flim
Novel insights into adipogenesis from omics data.

PMID 19689276 · PMC2765082 · Current medicinal chemistry · 2009 · 8 claims · 8 setups

Full-text index only

Pparg and Cebpa are the two master transcriptional regulators governing adipogenesis

3t3-l1 embryonic multipotent nih-3t3 microarray gel non-gel-based
Recurring mutations found by sequencing an acute myeloid leukemia genome.

PMID 19657110 · PMC3201812 · The New England journal of medicine · 2009 · 8 claims · 8 setups

Full-text index only

Deep paired tumor/normal whole-genome sequencing of a cytogenetically normal AML-M1 genome identified 12 somatic coding (tier 1) mutations and 52 somatic tier 2 (conserved/regulatory) mutations.

aml-m1 tumor bone additional whole-genome snp gene-expression
Comprehensive resequence analysis of a 97 kb region of chromosome 10q11.2 containing the MSMB gene associated with prostate cancer.

PMID 19644707 · PMC2778717 · Human genetics · 2009 · 7 claims · 5 setups

Full-text index only

Resequencing of the 97-kb 10q11.2 region identified 241 novel polymorphisms not previously reported in dbSNP

genomic plco hapmap computational targeted long-range genotype
Integrating proteomic, transcriptional, and interactome data reveals hidden components of signaling and regulatory networks.

PMID 19638617 · PMC2889494 · Science signaling · 2009 · 8 claims · 6 setups

Full-text index only

Pathway reconstruction can be modeled as a prize-collecting Steiner tree problem, balancing penalties for excluding terminal nodes against costs for including edges, controlled by a parameter β.

saccharomyces phosphoproteomic expression curated
Epimutations driven by RNAi or heterochromatin evoke transient antimicrobial drug resistance in pathogenic Mucor fungi.

PMID 41628159 · PMC12863538 · PLoS biology · 2026 · 8 claims · 8 setups

Full-text index only

In M. bainieri, most (90%) FK506-resistant isolates are unstable/transient and revert to drug sensitivity without any detectable DNA mutation

mucor fk506-resistant bainieri drug sanger serial
RAPseq enables large-scale identification of RBP-RNA interactions and reveals essentials of post-transcriptional gene regulation.

PMID 41755635 · PMC12956339 · Nucleic acids research · 2026 · 7 claims · 8 setups

Full-text index only

RAPseq is a novel in vitro, antibody-free and cross-linking-free method that profiles RBP binding to native cellular RNA transcriptome-wide using recombinant Halo-tagged RBPs and affinity purification followed by sequencing.

hepg2 hur igf2bp1 ythdf1 rapseq cross-species co-rapseq
Full-length 16S rRNA nanopore sequencing enables species resolution of Fusobacterium associated with colorectal cancer.

PMID 41963777 · PMC13078227 · Gut microbes · 2026 · 8 claims · 7 setups

Full-text index only

Full-length 16S rRNA ONT sequencing combined with custom demultiplexing (nanoMux) enables robust species-level discrimination within the Fusobacterium genus

gtdb rrndb zymobiomics host-bacteria ani phylogenetic 16s
Determining the quality and complexity of next-generation sequencing data without a reference genome.

PMID 25514851 · PMC4298064 · Genome biology · 2014 · 8 claims · 8 setups

Has reproduction · 78

kPAL, an open-source alignment-free package, assesses sequencing data quality and complexity using k-mer frequency profiles and pairwise distances between them, without a reference sequence.

rna-seq genome wgs exome k-mer rna-seq read
MicroRNA Enrichment and Docking-Based Evaluation of Ilomastat Targeting of MMP-2 in Esophageal Squamous Cell Carcinoma: Insights from a South African Cohort.

PMID 42158110 · PMC13181172 · Computational and structural biotechnology journal · 2026 · 7 claims · 5 setups

Full-text index only

The miR-29 family inhibits MMP-2 and represents a key regulatory axis in tumor invasion

paired deg mmp-2 escc bulk pathway molecular

Experiments

Characterization of genome-wide p53-binding sites upon stress response.

Network inference and network response identification: moving genome-scale data to the next level of biological discovery.

RExPrimer: an integrated primer designing tool increases PCR effectiveness by avoiding 3' SNP-in-primer and mis-priming from structural variation.

Proteomic profiling in ovarian cancer.

Skittle: a 2-dimensional genome visualization tool.

Exome sequencing of a multigenerational human pedigree.

Novel syntaxin 11 gene (STX11) mutation in three Argentinean patients with hemophagocytic lymphohistiocytosis.

Point mutations in GLI3 lead to misregulation of its subcellular localization.

MicroRNA profiling of BRCA1/2 mutation-carrying and non-mutation-carrying high-grade serous carcinomas of ovary.

Transcription dynamics.

The potential of optical proteomic technologies to individualize prognosis and guide rational treatment for cancer patients.

Novel insights into adipogenesis from omics data.

Recurring mutations found by sequencing an acute myeloid leukemia genome.

Comprehensive resequence analysis of a 97 kb region of chromosome 10q11.2 containing the MSMB gene associated with prostate cancer.

Integrating proteomic, transcriptional, and interactome data reveals hidden components of signaling and regulatory networks.

Epimutations driven by RNAi or heterochromatin evoke transient antimicrobial drug resistance in pathogenic Mucor fungi.

RAPseq enables large-scale identification of RBP-RNA interactions and reveals essentials of post-transcriptional gene regulation.

Full-length 16S rRNA nanopore sequencing enables species resolution of Fusobacterium associated with colorectal cancer.

Determining the quality and complexity of next-generation sequencing data without a reference genome.

MicroRNA Enrichment and Docking-Based Evaluation of Ilomastat Targeting of MMP-2 in Esophageal Squamous Cell Carcinoma: Insights from a South African Cohort.