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 281

Assay: sensitivity ✕ Clear

A genome-wide deletion mutant screen identifies pathways affected by nickel sulfate in Saccharomyces cerevisiae.

PMID 19917080 · PMC2784802 · BMC genomics · 2009 · 8 claims · 4 setups

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Genome-wide deletion screening identified 149 genes whose deletion causes NiSO4 sensitivity and 119 genes whose deletion confers NiSO4 resistance.

cerevisiae lists yeast genome-wide functional protein-protein
A genomic approach to improve prognosis and predict therapeutic response in chronic lymphocytic leukemia.

PMID 19861443 · PMC2783430 · Clinical cancer research : an official journal of the American Association for Cancer Research · 2009 · 8 claims · 8 setups

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A genomic signature derived from CLL patient leukemic cells significantly differentiates stable from progressive disease

duke nci-60 mayo spanish gene cdna igvh
Discovery and identification of potential biomarkers of papillary thyroid carcinoma.

PMID 19785722 · PMC2761863 · Molecular cancer · 2009 · 8 claims · 7 setups

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A 3-peak (m/z 9190, 6631, 8697 Da) SVM classification model discriminates PTC from non-cancer controls with high sensitivity and specificity

serum hplc-purified trypsin-digested crude seldi-tof-ms solid-phase maldi-tof-ms
Escape from autologous neutralizing antibodies in acute/early subtype C HIV-1 infection requires multiple pathways.

PMID 19763269 · PMC2741593 · PLoS pathogens · 2009 · 8 claims · 7 setups

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Viral escape from autologous Nab occurred repeatedly (cyclically) throughout the first two years of infection in two subtype C-infected subjects despite high-titer Nab responses.

hiv-1 longitudinal 0-month single pseudovirus single site-directed
Integrating complex genomic datasets and tumour cell sensitivity profiles to address a 'simple' question: which patients should get this drug?

PMID 20003409 · PMC2799438 · BMC medicine · 2009 · 8 claims · 5 setups

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A panel of 48 genomically characterized breast cancer cell lines can model patient tumour heterogeneity to identify biomarkers predicting response to PG-11047

panel breast 250-gene candidate genome growth pathway
scATD: a high-throughput and interpretable framework for single-cell cancer drug resistance prediction and biomarker identification.

PMID 40501071 · PMC12159290 · Briefings in bioinformatics · 2025 · 8 claims · 6 setups

Has reproduction · 62

scATD enables high-throughput single-cell drug sensitivity prediction for new patients without model parameter retraining via bidirectional Bi-AdaIN style transfer

panglaodb cancer geo gse137829 single-cell bulk
BOAT: Basic Oligonucleotide Alignment Tool.

PMID 19958483 · PMC2788372 · BMC genomics · 2009 · 7 claims · 3 setups

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BOAT can accurately and efficiently map sequencing reads to a reference genome while handling several substitutions and indels simultaneously

same short-read snp
Construction and use of spotted large-insert clone DNA microarrays for the detection of genomic copy number changes.

PMID 17406619 · PMC2688820 · Nature protocols · 2007 · 8 claims · 7 setups

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Combining three human-optimized DOP-PCR primers before a secondary amino-labeled PCR increases array hybridization sensitivity and reproducibility sixfold compared to the standard 6MW DOP-PCR primer

large-insert patients test genomic array-cgh manual automated
Molecular Biomarker of Drug Resistance Developed From Patient-Derived Organoids Predicts Survival of Colorectal Cancer Patients.

PMID 35425715 · PMC9004628 · Frontiers in oncology · 2022 · 8 claims · 7 setups

Has reproduction · 53

Patient-derived colorectal cancer organoids (CRCOs) can be established from surgical CRC tissue with an 82% success rate (41/50)

crc colorectal crcos crco organoid drug bulk
Enabling Single-Cell Drug Response Annotations from Bulk RNA-Seq Using SCAD.

PMID 36762572 · PMC10104628 · Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2023 · 7 claims · 7 setups

Has reproduction · 81

SCAD, a transfer learning framework integrating adversarial discriminative domain adaptation (ADDA), can infer single-cell drug sensitivities by transferring knowledge from bulk RNA-seq pharmacogenomic data (GDSC) to scRNA-seq target domains

pan-cancer pc9 451lu a375 bulk scrna-seq computational
FusionQ: a novel approach for gene fusion detection and quantification from paired-end RNA-Seq.

PMID 23768108 · PMC3691734 · BMC bioinformatics · 2013 · 8 claims · 8 setups

Has reproduction · 65

FusionQ is a novel tool that detects gene fusions, constructs chimerical transcript structures, and estimates their abundances from paired-end RNA-Seq data.

simulated four rna-seq randomly simulated paired-end read-mappability
EGASP: the human ENCODE Genome Annotation Assessment Project.

PMID 16925836 · PMC1810551 · Genome biology · 2006 · 8 claims · 6 setups

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Best-performing computational gene prediction methods correctly predict at least one transcript for close to 70% of annotated genes in the ENCODE regions.

encode computational manual rt-pcr
Ab initio identification of human microRNAs based on structure motifs.

PMID 18088431 · PMC2238772 · BMC bioinformatics · 2007 · 8 claims · 7 setups

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MiRPred predicts miRNA precursors ab initio using only predicted secondary structure motifs, ignoring nucleotide sequence

genome mirna hairpins chromosome secondary linear five-fold
Salivary proteomics for oral cancer biomarker discovery.

PMID 18829504 · PMC2877125 · Clinical cancer research : an official journal of the American Association for Cancer Research · 2008 · 8 claims · 5 setups

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Subtractive salivary proteomics reveals proteins differentially present/expressed between OSCC patients and matched healthy controls.

pooled saliva shotgun two-dimensional elisa
DiRE: identifying distant regulatory elements of co-expressed genes.

PMID 18487623 · PMC2447744 · Nucleic acids research · 2008 · 8 claims · 4 setups

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DiRE predicts distant regulatory elements by combining gene co-expression data, comparative genomics and TFBS profiles to determine TFBS-association signatures

liver myod transgenic microarray tfbs enhancer
Malaria genomics meets drug-resistance phenotyping in the field.

PMID 19664295 · PMC2745762 · Genome biology · 2009 · 8 claims · 8 setups

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Significantly longer parasite clearance times in Pailin (western Cambodia) versus Wang Pha (Thailand-Myanmar border) establish the presence of artemisinin resistance in western Cambodia.

falciparum plasmodium drug clinical high-throughput
Operon information improves gene expression estimation for cDNA microarrays.

PMID 16630355 · PMC1513396 · BMC genomics · 2006 · 7 claims · 3 setups

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A hierarchical Bayesian model that borrows expression information from other genes within the same operon improves estimation of relative transcript levels.

simulated coli simulated cdna two-color
Decision forest analysis of 61 single nucleotide polymorphisms in a case-control study of esophageal cancer; a novel method.

PMID 16026601 · PMC1637030 · BMC bioinformatics · 2005 · 8 claims · 2 setups

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DF-SNPs, a novel adaptation of the Decision Forest method, can classify esophageal cancer cases vs. controls based on SNP genotype data with high concordance, sensitivity, and specificity.

genomic snp high-throughput decision
Gene signature discovery and systematic validation across diverse clinical cohorts for TB prognosis and response to treatment.

PMID 37471455 · PMC10393163 · PLoS computational biology · 2023 · 8 claims · 7 setups

Has reproduction · 100

A network-based meta-analysis of 27 discovery cohorts identified a common 45-gene signature specific to active TB disease across studies.

blood aggregated 45-gene independent bulk network-based gene
Construction and Validation of an Immune Infiltration-Related Gene Signature for the Prediction of Prognosis and Therapeutic Response in Breast Cancer.

PMID 33986754 · PMC8110914 · Frontiers in immunology · 2021 · 7 claims · 8 setups

Has reproduction · 51

A higher immune infiltration-related risk score (IRS) indicates worse prognosis and lower sensitivity to immunotherapy in breast cancer patients

tcga candidate cancer univariate weighted lasso

Experiments

A genome-wide deletion mutant screen identifies pathways affected by nickel sulfate in Saccharomyces cerevisiae.

A genomic approach to improve prognosis and predict therapeutic response in chronic lymphocytic leukemia.

Discovery and identification of potential biomarkers of papillary thyroid carcinoma.

Escape from autologous neutralizing antibodies in acute/early subtype C HIV-1 infection requires multiple pathways.

Integrating complex genomic datasets and tumour cell sensitivity profiles to address a 'simple' question: which patients should get this drug?

scATD: a high-throughput and interpretable framework for single-cell cancer drug resistance prediction and biomarker identification.

BOAT: Basic Oligonucleotide Alignment Tool.

Construction and use of spotted large-insert clone DNA microarrays for the detection of genomic copy number changes.

Molecular Biomarker of Drug Resistance Developed From Patient-Derived Organoids Predicts Survival of Colorectal Cancer Patients.

Enabling Single-Cell Drug Response Annotations from Bulk RNA-Seq Using SCAD.

FusionQ: a novel approach for gene fusion detection and quantification from paired-end RNA-Seq.

EGASP: the human ENCODE Genome Annotation Assessment Project.

Ab initio identification of human microRNAs based on structure motifs.

Salivary proteomics for oral cancer biomarker discovery.

DiRE: identifying distant regulatory elements of co-expressed genes.

Malaria genomics meets drug-resistance phenotyping in the field.

Operon information improves gene expression estimation for cDNA microarrays.

Decision forest analysis of 61 single nucleotide polymorphisms in a case-control study of esophageal cancer; a novel method.

Gene signature discovery and systematic validation across diverse clinical cohorts for TB prognosis and response to treatment.

Construction and Validation of an Immune Infiltration-Related Gene Signature for the Prediction of Prognosis and Therapeutic Response in Breast Cancer.