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).

• Specific Marker Gene Analysis for Primary Central Nervous System Lymphoma Based on Methylation Difference and Development of Detection Primers.

  PMID 41097902 · PMC12528802 · Brain and behavior · 2025 · 6 claims · 6 setups

  Has reproduction · 62

  RHEB promoter hypermethylation is a PCNSL-specific biomarker distinguishing PCNSL from other CNS diseases.

  datasets cns tcga gdc 450k rrbs roc

• Digital sorting of complex tissues for cell type-specific gene expression profiles.

  PMID 23497278 · PMC3626856 · BMC bioinformatics · 2013 · 8 claims · 8 setups

  Has reproduction · 85

  The Digital Sorting Algorithm (DSA) deconvolves mixed tissue expression into cell type-specific profiles using only marker genes, without requiring prior knowledge of cell type frequencies or in vitro pure-cell profiles.

  liver im-9 immune deconvolved microarray simulation roc

• 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

  Full-text index only

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

  pooled saliva shotgun two-dimensional elisa

• Landscape of allele-specific transcription factor binding in the human genome.

  PMID 33980847 · PMC8115691 · Nature communications · 2021 · 8 claims · 6 setups

  Has reproduction · 82

  A novel statistical framework (ADASTRA) calls allele-specific TF binding from existing ChIP-Seq alignments by jointly correcting for background allelic dosage (BAD, from aneuploidy/CNVs) and reference mapping bias.

  gtrd k562 mcf7 types chip-seq variant bayesian

• Detecting DNA modifications from SMRT sequencing data by modeling sequence context dependence of polymerase kinetic.

  PMID 23516341 · PMC3597545 · PLoS computational biology · 2013 · 8 claims · 7 setups

  Has reproduction · 44

  Local sequence context strongly determines position-specific polymerase kinetic rate: roughly 80% of IPD variation is explained by a 10 bp context (7 bases upstream, 2 bases downstream of the incorporation site), saturating at 7 bases upstream.

  plasmid coli wild-type artificial smrt read-mixing distributional

• A response to Yu et al. "A forward-backward fragment assembling algorithm for the identification of genomic amplification and deletion breakpoints using high-density single nucleotide polymorphism (SNP) array", BMC Bioinformatics 2007, 8: 145.

  PMID 17939873 · PMC2222656 · BMC bioinformatics · 2007 · 8 claims · 4 setups

  Full-text index only

  Yu et al.'s original comparison ran RJaCGH's MCMC sampler for a severely insufficient number of iterations (50 burn-in, 500 total)

  simulated same mcmc-based direct original

• Discovery and identification of potential biomarkers of papillary thyroid carcinoma.

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

  Full-text index only

  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

• Evaluating Distribution and Prognostic Value of New Tumor-Infiltrating Lymphocytes in HCC Based on a scRNA-Seq Study With CIBERSORTx.

  PMID 33043022 · PMC7527443 · Frontiers in medicine · 2020 · 5 claims · 6 setups

  Has reproduction · 78

  CIBERSORTx can combine scRNA-seq-derived signatures with bulk HCC transcriptomes to estimate proportions of 11 TIL subsets and infer cell-type-specific gene expression.

  hcc tcga geo single-cell bulk microarray

• Constructing eRNA-mediated gene regulatory networks to explore the genetic basis of muscle and fat-relevant traits in pigs.

  PMID 38594607 · PMC11003151 · Genetics, selection, evolution : GSE · 2024 · 8 claims · 8 setups

  Has reproduction · 100

  H3K27ac ChIP-seq and RNA-seq were used to construct eRNA expression profiles across multiple tissues in Enshi Black (ES) and Duroc pigs, revealing tissue-level eRNA regulatory landscapes

  longissimus muscle snps pig h3k27ac strand-specific starr-seq

• Single-Cell Transcriptome Analysis Revealed Heterogeneity and Identified Novel Therapeutic Targets for Breast Cancer Subtypes.

  PMID 37190091 · PMC10137100 · Cells · 2023 · 8 claims · 8 setups

  Has reproduction · 54

  Single-cell transcriptomic analysis of EPCAM+Lin- epithelial cells identified unique gene signatures/markers that distinguish ER+, HER2+, ER+HER2+, and TNBC molecular subtypes

  breast epcam+cd45-cd8a-cd4-cd19-cd3e cancer identified single-cell differential crispr-cas9

• BRCA1 and BRCA2 mutation predictions using the BOADICEA and BRCAPRO models and penetrance estimation in high-risk French-Canadian families.

  PMID 16417652 · PMC1413985 · Breast cancer research : BCR · 2006 · 8 claims · 7 setups

  Full-text index only

  BOADICEA predicts accurately the number of BRCA1 and BRCA2 mutations across family groups and discriminates well between carriers and noncarriers

  french-canadian families brca1-positive same targeted full-length multiplex

• CARAT: a novel method for allelic detection of DNA copy number changes using high density oligonucleotide arrays.

  PMID 16504045 · PMC1402331 · BMC bioinformatics · 2006 · 8 claims · 5 setups

  Full-text index only

  CARAT is a novel algorithm that uses SNP probe intensity and genotype-based allelic dosage response in a regression framework to estimate allele-specific copy number genome-wide.

  normal genomic sk-br-3 cancer snp quantitative allele-specific

• Pre-operative urinary cathepsin D is associated with survival in patients with renal cell carcinoma.

  PMID 19789534 · PMC2768081 · British journal of cancer · 2009 · 8 claims · 7 setups

  Full-text index only

  Cathepsin D, identified via comparative 2D PAGE of conditioned media from RCC cell lines vs normal renal cultures, is a candidate secreted biomarker of RCC

  htb49 excised conditioned urine page maldi western

• 5-methylcytosine RNA modification regulators-based patterns and features of immune microenvironment in acute myeloid leukemia.

  PMID 38277218 · PMC10911375 · Aging · 2024 · 8 claims · 8 setups

  Has reproduction · 93

  Most of the 17 m5C regulators are differentially expressed between AML and normal samples and correlate with AML prognosis.

  aml bulk mutation copy

• Exploring the prognostic and diagnostic value of lactylation-related genes in sepsis.

  PMID 39367086 · PMC11452377 · Scientific reports · 2024 · 8 claims · 7 setups

  Has reproduction · 73

  Intersecting sepsis-associated differentially expressed genes with a curated list of 332 lactylation genes yields 55 sepsis-related lactylation genes.

  peripheral overlapping geo pbmcs bulk kegg protein-protein

• Adaptive discriminant function analysis and reranking of MS/MS database search results for improved peptide identification in shotgun proteomics.

  PMID 18788775 · PMC3744223 · Journal of proteome research · 2008 · 7 claims · 4 setups

  Full-text index only

  PeptideProphet's fixed LDA coefficients for combining search scores (Xcorr', ΔCn, SpRank) may not be optimal under all search/instrument conditions.

  trypsin-digested mix serum same shotgun sequest lc-ms

• Network-assisted protein identification and data interpretation in shotgun proteomics.

  PMID 19690572 · PMC2736651 · Molecular systems biology · 2009 · 7 claims · 7 setups

  Full-text index only

  Confidently identified proteins in a sample form tightly connected sub-networks in the protein interaction network, with significantly higher clustering coefficients than random or topology-matched random sub-networks.

  yeast organs mammary organ shotgun clique-enrichment microarray

• Severe COVID-19 Shares a Common Neutrophil Activation Signature with Other Acute Inflammatory States.

  PMID 35269470 · PMC8909161 · Cells · 2022 · 7 claims · 7 setups

  Has reproduction · 88

  COVID-19 and HLH share immunological pathways, yielding 237 common up-regulated DEGs dominated by cytokine/chemokine signaling and neutrophil-mediated immune responses.

  peripheral leukocytes plasma degs bulk single-cell plasma

• Machine learning-based identification of biomarkers and drugs in immunologically cold and hot pancreatic adenocarcinomas.

  PMID 39152432 · PMC11328457 · Journal of translational medicine · 2024 · 7 claims · 8 setups

  Has reproduction · 42

  PAAD tumors can be consensus-clustered into immunologically hot and cold subtypes based on CIBERSORT-derived immune cell fractions, with significantly different survival outcomes.

  paad degs bulk consensus tumor

• Prediction-based approaches to characterize bidirectional promoters in the mammalian genome.

  PMID 18366609 · PMC2386062 · BMC genomics · 2008 · 8 claims · 7 setups

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  The mapping algorithm identified 5,647 candidate bidirectional promoter regions in the mouse genome, similar in number to those previously found in human.

  genome seven genes computational cage comparative