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).

• Enhancing chemotherapy response prediction via matched colorectal tumor-organoid gene expression analysis and network-based biomarker selection.

  PMID 39754813 · PMC11754497 · Translational oncology · 2025 · 6 claims · 8 setups

  Has reproduction · 78

  A consensus WGCNA approach combining matched tumor-organoid and independent organoid drug-response expression data identifies gene modules and hub genes predictive of 5-FU chemotherapy response

  colorectal matched combined expression microarray rna-seq consensus

• Development of a fluorescent multiplex assay for detection of MSI-High tumors.

  PMID 15528789 · PMC3839403 · Disease markers · 2004 · 8 claims · 7 setups

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  Mononucleotide markers are the most sensitive and specific microsatellite marker type for detecting MSI-H tumors with MMR defects

  colorectal blood healthy non-msi-h microsatellite fluorescent immunohistochemistry

• Development of proteomic patterns for detecting lung cancer.

  PMID 14757945 · PMC3851077 · Disease markers · 2003 · 8 claims · 3 setups

  Full-text index only

  A decision tree classification algorithm built on three serum protein mass peaks (8122Da, 1452Da, 1610Da) can discriminate lung cancer patients from healthy controls

  serum pooled seldi-tof-ms decision reproducibility

• Detection of venous thromboembolism by proteomic serum biomarkers.

  PMID 17579716 · PMC1891085 · PloS one · 2007 · 5 claims · 8 setups

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  A neural network-based classifier built from direct MALDI-TOF MS serum protein expression profiles can diagnose VTE with sensitivity/specificity that exceeds D-dimer assays

  serum anova-selected citrated depleted direct artificial d-dimer

• An accurate method for identifying recent recombinants from unaligned sequences.

  PMID 35025988 · PMC8963311 · Bioinformatics (Oxford, England) · 2022 · 8 claims · 4 setups

  Has reproduction · 84

  A novel algorithm combining the JHMM (Zilversmit et al. 2013) mosaic representation with a distance-based triple comparison can identify recombinant sequences and their parents from unaligned, gene-length sequences without a reference panel.

  simulated dblα coalescent comparative recombinant

• 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

• Microsatellite instability and mismatch repair gene inactivation in sporadic pancreatic and colon tumours.

  PMID 10389971 · PMC2363009 · British journal of cancer · 1999 · 6 claims · 5 setups

  Full-text index only

  Microsatellite instability is common in sporadic pancreatic cancer but occurs at a uniformly low rate and is not accompanied by hMLH1/hMSH2 alterations, suggesting it does not drive pancreatic tumorigenesis.

  sporadic msi-positive tumour unstable microsatellite denaturing sequencing

• Detecting natural selection by empirical comparison to random regions of the genome.

  PMID 19783549 · PMC2778377 · Human molecular genetics · 2009 · 8 claims · 5 setups

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  Comparing candidate loci to empirically matched random genomic regions (ENCODE data) avoids the strong demographic/mutation assumptions required by theoretical neutral models and provides a robust test for selection

  ceu genomic simulated long-read snp population

• A comprehensive catalogue of somatic mutations from a human cancer genome.

  PMID 20016485 · PMC3145108 · Nature · 2010 · 8 claims · 7 setups

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  Whole-genome sequencing of COLO-829 melanoma cells and matched COLO-829BL normal cells produced the first comprehensive catalogue of somatic mutations from an individual cancer genome

  colo-829 additional whole-genome conventional pcr

• An initial characterization of the serum phosphoproteome.

  PMID 19824718 · PMC2789176 · Journal of proteome research · 2009 · 8 claims · 8 setups

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  A TiO2-based phosphopeptide enrichment method coupled with LC-MS/MS (LTQ-Orbitrap CID and LTQ-ETD) was developed and applied to characterize the serum phosphoproteome

  u266 serum lc-ms immunoprecipitation sensitivity

• TOSCA: an automated Tumor Only Somatic CAlling workflow for somatic mutation detection without matched normal samples.

  PMID 36699358 · PMC9710689 · Bioinformatics advances · 2022 · 6 claims · 2 setups

  Has reproduction · 50

  TOSCA is the first automated, open-source, end-to-end tumor-only somatic calling workflow for WES and targeted panel sequencing data.

  t-cell hcc1395 targeted whole-exome

• A proteomic analysis of IVF follicular fluid in women

  PMID 18980758 · PMC3916005 · Fertility and sterility · 2009 · 8 claims · 4 setups

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  2D-PAGE proteomic evaluation of follicular fluid can identify potential biomarkers distinguishing good versus poor IVF responders in matched patient pairs

  follicular excised clinical polyacrylamide liquid direct

• RNASEQR--a streamlined and accurate RNA-seq sequence analysis program.

  PMID 22199257 · PMC3315322 · Nucleic acids research · 2012 · 8 claims · 7 setups

  Has reproduction · 86

  RNASEQR is a new RNA-seq mapper/aligner that combines a BWT-based (Bowtie) transcriptomic/genomic alignment with hash-based BLAT local alignment in three sequential steps: transcriptome mapping, novel exon detection, and anchor-and-align novel splice junction identification.

  ccds glioblastoma experimental simulated simulated bulk quality

• Quasimonomorphic mononucleotide repeats for high-level microsatellite instability analysis.

  PMID 15528790 · PMC3888729 · Disease markers · 2004 · 8 claims · 8 setups

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  Mononucleotide repeats are more sensitive, specific, and easier to use than dinucleotide repeats for detecting MSI-H tumors

  msi-h colon hmsh6-mutated tumors pentaplex pcr dinucleotide

• Activating mutations in ALK provide a therapeutic target in neuroblastoma.

  PMID 18923525 · PMC2587486 · Nature · 2008 · 8 claims · 8 setups

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  Non-synonymous ALK kinase domain mutations occur in 8% of primary neuroblastomas, with F1174L being the most frequent

  neuroblastoma kelly fish sequencing cytokine-independence

• 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

• CpG_MI: a novel approach for identifying functional CpG islands in mammalian genomes.

  PMID 19854943 · PMC2800233 · Nucleic acids research · 2010 · 8 claims · 6 setups

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  Functional ('bona fide') CGIs show distinct average/cumulative mutual information (AMI/CMI) distributions of neighboring CpG distances compared to non-functional CGIs and random genome segments

  genome random cd4+ six average mutual chip-seq

• Sample preparation for serum/plasma profiling and biomarker identification by mass spectrometry.

  PMID 17166507 · PMC7094463 · Journal of chromatography. A · 2007 · 8 claims · 8 setups

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  Standardizing sample preparation procedures for serum/plasma profiling is critical for obtaining reliable biomarkers, since slight procedural changes can produce very different protein profiles.

  serum aqueous maldi-tof seldi-tof peak

• Logical Analysis of Data (LAD) model for the early diagnosis of acute ischemic stroke.

  PMID 18616825 · PMC2492849 · BMC medical informatics and decision making · 2008 · 7 claims · 5 setups

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  An LAD classification model built from a support-set of 3 peptide peaks can distinguish stroke patients from controls with 75% accuracy on an independent validation set

  plasma discretized seldi-tof serum logical

• PALB2 variants in hereditary and unselected Finnish prostate cancer cases.

  PMID 20003494 · PMC2806404 · Journal of negative results in biomedicine · 2009 · 8 claims · 6 setups

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  None of the detected PALB2 variants, including 1592delT, show significant association with PRCA at the population level in Finland

  blood finnish combined formalin-fixed direct additional statistical