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).

• Integrative analysis of transcriptomic data reveals a predictive gene signature for chemoradiotherapy response in rectal cancer.

  PMID 41550766 · PMC12803930 · iScience · 2026 · 8 claims · 8 setups

  Has reproduction · 50

  A 186-gene signature predictive of nCRT response was derived from integrating six GEO transcriptomic datasets using machine learning.

  pre-treatment combined larc 186-gene differential machine molecular

• Analysis of Tumor-Infiltrating T-Cell Transcriptomes Reveal a Unique Genetic Signature across Different Types of Cancer.

  PMID 36232369 · PMC9569723 · International journal of molecular sciences · 2022 · 8 claims · 8 setups

  Has reproduction · 87

  Common genes shared across five cancer types differ from those found in nonmalignant tissue-resident T-cells for each subset (CD4-T, CD8-T, Treg)

  breast lung colorectal melanoma single-cell gene reactome

• Combining evidence of preferential gene-tissue relationships from multiple sources.

  PMID 23950964 · PMC3741196 · PloS one · 2013 · 8 claims · 8 setups

  Has reproduction · 53

  A high-level integration approach combining three methods across four human microarray datasets, merged by consensus voting and a rule-based inner/total score, predicts preferentially expressed genes while reducing method- and study-specific bias.

  normal four microarray genes microarray computational bayes

• CoMoDis: composite motif discovery in mammalian genomes.

  PMID 17130158 · PMC1702496 · Nucleic acids research · 2007 · 7 claims · 4 setups

  Full-text index only

  CoMoDis is a new bioinformatics tool that streamlines computational identification of novel regulatory modules starting from a single seed motif

  ncbi35 gata-1 gene imr90 computational microarray seed-motif-anchored

• BAC to the future! or oligonucleotides: a perspective for micro array comparative genomic hybridization (array CGH).

  PMID 16439806 · PMC1356528 · Nucleic acids research · 2006 · 8 claims · 7 setups

  Full-text index only

  oaCGH, not BAC CGH arrays, is the platform that will prevail in the future

  genomic lung genetics bt474 array exon

• LMPD: LIPID MAPS proteome database.

  PMID 16381922 · PMC1347484 · Nucleic acids research · 2006 · 8 claims · 5 setups

  Full-text index only

  LMPD is an object-relational database of lipid-associated protein sequences and annotations, publicly available from the LIPID MAPS Consortium website.

  uniprot kegg in-house oracle9i kegg database enzyme

• OptiType: precision HLA typing from next-generation sequencing data.

  PMID 25143287 · PMC4441069 · Bioinformatics (Oxford, England) · 2014 · 8 claims · 8 setups

  Has reproduction · 95

  OptiType, an ILP-based HLA genotyping algorithm, produces accurate four-digit HLA-I predictions from NGS data not enriched for the HLA cluster.

  colorectal lymphoblastic hapmap genomes rna-seq low-coverage exome

• Validation of pooled genotyping on the Affymetrix 500 k and SNP6.0 genotyping platforms using the polynomial-based probe-specific correction.

  PMID 20003400 · PMC2806376 · BMC genetics · 2009 · 7 claims · 4 setups

  Full-text index only

  Pooled genotyping on the Affymetrix 500k platform using PPC yields highly accurate allele frequency estimates (correlation 0.988) comparable to or better than the 10k/100k platforms.

  case hapmap snp individual allele

• Delineation of a gene network underlying the pulmonary response to oxidative stress in asthma.

  PMID 19730131 · PMC3328512 · Journal of investigative medicine : the official publication of the American Federation for Clinical Research · 2009 · 8 claims · 6 setups

  Full-text index only

  Integration of multiple public microarray datasets via a four-way Venn diagram identifies genes commonly expressed in asthma- and cigarette smoke-exposed lung

  respiratory lung a549 gene affymetrix network

• Alpseq: an open-source workflow to turbocharge nanobody discovery with high-throughput sequencing.

  PMID 41631412 · PMC12885427 · mAbs · 2026 · 8 claims · 8 setups

  Full-text index only

  alpseq is an open-source, end-to-end workflow combining a PCR-free sequencing library prep protocol with a Nextflow pre-processing pipeline and an R-based analysis/reporting module for nanobody NGS data.

  nanobody raw hanke candidate pcr-free bioinformatic comparison