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).

• Genome wide identification of recessive cancer genes by combinatorial mutation analysis.

  PMID 18846217 · PMC2557123 · PloS one · 2008 · 7 claims · 4 setups

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  A combinatorial mutation analysis identified 154 candidate recessive cancer genes (pRecessiveCancer<1.5x10-7, FDR=0.39)

  refseq tp53 tumor 154-gene est paired array

• Exploring microproteins from various model organisms using the mip-mining database.

  PMID 37919660 · PMC10623795 · BMC genomics · 2023 · 5 claims · 4 setups

  Has reproduction · 85

  Mip-mining is a database of 336 curated RNA-seq datasets from 8626 samples across nine species, built specifically to explore microprotein functions under stress and disease conditions

  nine cerevisiae thaliana bulk transcriptome growth

• Mining expressed sequence tags identifies cancer markers of clinical interest.

  PMID 17078886 · PMC1635568 · BMC bioinformatics · 2006 · 8 claims · 6 setups

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  An EST-mining approach (Fisher Exact Test on tumor vs. non-tumor library hit counts) identifies differentially expressed transcripts with an estimated false discovery rate below 22% when human and mouse screens are combined.

  dbest cancer gene est human-mouse leave-one-out

• SysPIMP: the web-based systematical platform for identifying human disease-related mutated sequences from mass spectrometry.

  PMID 19036792 · PMC2686442 · Nucleic acids research · 2009 · 8 claims · 7 setups

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  SysPIMP is a web-based platform integrating disease mutation databases with X!Tandem and BLAST to identify disease-related mutated proteins from MS results

  omim pmd swissprot msipi database sequence tandem

• BABELOMICS: a systems biology perspective in the functional annotation of genome-scale experiments.

  PMID 16845052 · PMC1538844 · Nucleic acids research · 2006 · 8 claims · 8 setups

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  Babelomics is presented as an updated, complete suite of web tools for functional analysis of genome-scale experiments with new and improved modules

  pre-selected pre-tabulated genes ranked kegg expression text-mining

• MALDI profiling of human lung cancer subtypes.

  PMID 19890392 · PMC2767501 · PloS one · 2009 · 8 claims · 8 setups

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  PIMAC/MALDI-TOF peptide profiles combined with classification models can distinguish normal lung from tumor and differentiate NSCLC histological subtypes

  lung tryptic peak ffpe maldi-tof parallel stepwise

• TM4SF10 gene sequencing in XLMR patients identifies common polymorphisms but no disease-associated mutation.

  PMID 15345028 · PMC517934 · BMC medical genetics · 2004 · 8 claims · 4 setups

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  No disease-associated mutations were found in TM4SF10 in 16 XLMR patients from 14 families with linkage to the TM4SF10 locus.

  genomic dog sage pcr northern sage

• Towards precise classification of cancers based on robust gene functional expression profiles.

  PMID 15774002 · PMC1274255 · BMC bioinformatics · 2005 · 6 claims · 7 setups

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  Functional expression profiles (FEPs) achieve comparable or better classification performance than conventional gene expression profiles (GEPs) across four public microarray datasets

  nci60 lymphoma fep go-annotated cdna recursive hypergeometric

• Whole genome association mapping by incompatibilities and local perfect phylogenies.

  PMID 17042942 · PMC1624851 · BMC bioinformatics · 2006 · 8 claims · 8 setups

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  Blossoc scores the perfect phylogenetic tree spanning the largest compatible region around each marker as a decision tree for case/control status to detect association

  coalescent-simulated artificial empirical same perfect-phylogeny hapminer haplotype

• Advanced Methods for Analyzing in-Situ Observations of Magnetic Reconnection.

  PMID 39234211 · PMC11369046 · Space science reviews · 2024 · 7 claims · 8 setups

  Has reproduction

  Collisionless magnetic reconnection in geospace has multi-scale structure: MHD regions (ions and electrons frozen-in), ion diffusion regions (ions demagnetized, electrons magnetized), and electron diffusion regions (both demagnetized, magnetic topology changes).

  solar multi-mission single mms maximum global mining

• FatiGO +: a functional profiling tool for genomic data. Integration of functional annotation, regulatory motifs and interaction data with microarray experiments.

  PMID 17478504 · PMC1933151 · Nucleic acids research · 2007 · 8 claims · 8 setups

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  FatiGO+ is a web-based tool for functional profiling of genome-scale experiments that integrates functional annotation, regulatory motifs and interaction data

  user-supplied gene predicted interactome gene kegg transcription