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).

• Assessment of algorithms for high throughput detection of genomic copy number variation in oligonucleotide microarray data.

  PMID 17910767 · PMC2148068 · BMC bioinformatics · 2007 · 8 claims · 4 setups

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  Different CNV analysis software packages produce highly variable numbers and types of candidate CNVs from the same data

  normalized individuals subset same affymetrix fluorescent snp

• Metagenomic analysis of human diarrhea: viral detection and discovery.

  PMID 18398449 · PMC2290972 · PLoS pathogens · 2008 · 8 claims · 7 setups

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  Micro-mass sequencing (minimal stool input, minimal purification, ~384 reads/sample) can detect known enteric viruses in diarrhea specimens

  stool divergent extract preparations sequence-independent maximum enzyme

• The oncogene AAMDC links PI3K-AKT-mTOR signaling with metabolic reprograming in estrogen receptor-positive breast cancer.

  PMID 33772001 · PMC7998036 · Nature communications · 2021 · 8 claims · 8 setups

  Has reproduction · 85

  AAMDC is an amplified/overexpressed oncogene in a subgroup of ER-positive breast cancers (IntClust2) associated with poor prognosis

  breast luminal sum52pe t-47d immunohistochemistry fluorescence qrt-pcr

• Direct evidence of extensive diversity of HIV-1 in Kinshasa by 1960.

  PMID 18833279 · PMC3682493 · Nature · 2008 · 7 claims · 8 setups

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  Recovered and characterized HIV-1 sequences (DRC60) from a 1960 Bouin's-fixed paraffin-embedded lymph node biopsy from Léopoldville, Belgian Congo

  archival hiv-1-positive cdna concatenated rt-pcr quantitative pcr

• INI1 mutations in meningiomas at a potential hotspot in exon 9.

  PMID 11161377 · PMC2363707 · British journal of cancer · 2001 · 6 claims · 5 setups

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  A recurrent somatic INI1 mutation (G1130A, Arg377His) occurs at a hotspot in exon 9 in a subset of meningiomas.

  meningioma re-extracted sscp direct pcr

• Integration of text- and data-mining using ontologies successfully selects disease gene candidates.

  PMID 15767279 · PMC1065256 · Nucleic acids research · 2005 · 7 claims · 6 setups

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  Integrating eVOC anatomical ontology-based text-mining of PubMed abstracts with data-mining of gene expression annotation successfully selects and prioritizes candidate disease genes

  biomedical refseq training independent text-mining data-mining candidate

• Pathogenic mitochondrial DNA mutations are common in the general population.

  PMID 18674747 · PMC2495064 · American journal of human genetics · 2008 · 7 claims · 6 setups

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  At least 1 in 200 healthy humans harbors a pathogenic mtDNA mutation with potential to cause disease in offspring of female carriers

  neonatal independent m.1555a→g-positive mutation-positive high-throughput last-cycle cloning

• A proteomics grade electron transfer dissociation-enabled hybrid linear ion trap-orbitrap mass spectrometer.

  PMID 18613715 · PMC2601597 · Journal of proteome research · 2008 · 8 claims · 5 setups

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  A NCI source coupled via an added octopole and the c-trap to a QLT-orbitrap enables fast, efficient ETD reagent anion injection (4-8 ms)

  saccharomyces histone glioblastoma fluoranthene lc-ms etd anion

• Identification of deleterious non-synonymous single nucleotide polymorphisms using sequence-derived information.

  PMID 18588693 · PMC2446391 · BMC bioinformatics · 2008 · 8 claims · 5 setups

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  A decision tree built on 10 selected sequence-derived features classifies SAPs as Disease or Polymorphism with 82.6% accuracy and 0.607 MCC in cross-validation.

  sap sequence-derived humvar same decision independent greedy

• Somatically acquired JAK1 mutations in adult acute lymphoblastic leukemia.

  PMID 18362173 · PMC2292215 · The Journal of experimental medicine · 2008 · 8 claims · 8 setups

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  Somatic JAK1 mutations occur in ALL and are more prevalent among adult T-cell precursor ALL (T-ALL) than B-ALL

  genomic jak1-deficient u4c bw5147 dhplc stat1 cytokine-independent

• Meta-analysis of inter-species liver co-expression networks elucidates traits associated with common human diseases.

  PMID 20019805 · PMC2787626 · PLoS computational biology · 2009 · 8 claims · 8 setups

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  A novel semi-parametric meta-analysis method (based on a gene-centric Glass's d effect size) outperforms existing parametric and non-parametric meta-analysis methods at identifying functionally coherent gene pairs across species.

  liver simulated conserved nearly gene simulation kolmogorov-smirnov

• Variation in the E2-binding domain of HPV 16 is associated with high-grade squamous intraepithelial lesions of the cervix.

  PMID 11308254 · PMC2363853 · British journal of cancer · 2001 · 8 claims · 6 setups

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  E2 gene disruption in the analysed regions is significantly more frequent in high-grade SILs than low-grade SILs

  paraffin-embedded hpv16-positive representative cervical pcr restriction bidirectional

• Speeding disease gene discovery by sequence based candidate prioritization.

  PMID 15766383 · PMC1274252 · BMC bioinformatics · 2005 · 7 claims · 8 setups

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  Disease genes (OMIM) differ significantly from non-disease genes in sequence-based features including gene/cDNA/protein size, exon number, homolog conservation, secretion signal, 3' UTR length, CpG islands, and distance to nearest gene.

  ensembl training same hgmd comparative machine tenfold

• Minimal metabolic pathway structure is consistent with associated biomolecular interactions.

  PMID 24987116 · PMC4299494 · Molecular systems biology · 2014 · 8 claims · 8 setups

  Has reproduction · 30

  MinSpan, a mixed-integer linear optimization algorithm, computes the shortest, linearly independent pathways (sparsest basis of the null space of the stoichiometric matrix S) for genome-scale metabolic networks, which convex approaches (extreme pathways, elementary flux modes) cannot do at genome scale.

  simplified genome-scale cerevisiae coli minspan spearman comparative

• A comparative study of techniques for differential expression analysis on RNA-Seq data.

  PMID 25119138 · PMC4132098 · PloS one · 2014 · 8 claims · 8 setups

  Has reproduction · 58

  edgeR performs slightly better than DESeq and Cuffdiff2 in terms of the ability to uncover true positives.

  brain neurospheres lymphoblastoid simulation single-end paired-end rna-seq

• Cross species genomic analysis identifies a mouse model as undifferentiated pleomorphic sarcoma/malignant fibrous histiocytoma.

  PMID 19956606 · PMC2779485 · PloS one · 2009 · 8 claims · 7 setups

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  A 100-gene signature from LSL-KrasG12D;Trp53Flox/Flox mouse sarcomas (vs normal muscle) is specifically and significantly enriched in human MFH but not other soft tissue sarcoma subtypes across three independent human datasets.

  lsl-krasg12d soft combined mfh microarray gene oncogenic

• Identification of Four Potential Biomarkers Associated With Coronary Artery Disease in Non-diabetic Patients by Gene Co-expression Network Analysis.

  PMID 32714363 · PMC7344232 · Frontiers in genetics · 2020 · 6 claims · 6 setups

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  The midnight blue module and the yellow module play vital roles in the pathogenesis of CAD in non-diabetic patients

  pbmcs blood apoe genes microarray rt-qpcr elisa

• Clustering of phosphorylation site recognition motifs can be exploited to predict the targets of cyclin-dependent kinase.

  PMID 17316440 · PMC1852407 · Genome biology · 2007 · 8 claims · 6 setups

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  CDK consensus motifs are frequently clustered (closely spaced) in known CDK substrate proteins rather than uniformly distributed

  cerevisiae cycle reanalysis statistical optimal

• Two-round coamplification at lower denaturation temperature-PCR (COLD-PCR)-based sanger sequencing identifies a novel spectrum of low-level mutations in lung adenocarcinoma.

  PMID 19760750 · PMC2784016 · Human mutation · 2009 · 8 claims · 6 setups

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  Two-round fast COLD-PCR followed by Sanger sequencing detects TP53 mutations at abundances as low as ~1%, below the sensitivity of conventional Sanger sequencing (~20-25%)

  lung wild-type matched paired two-round real-time airs-rflp

• MOSAIK: a hash-based algorithm for accurate next-generation sequencing short-read mapping.

  PMID 24599324 · PMC3944147 · PloS one · 2014 · 8 claims · 8 setups

  Has reproduction · 29

  MOSAIK is the only aligner that consistently aligns reads from all major sequencing platforms (Illumina, AB SOLiD, Roche 454, Ion Torrent, Pacific Biosciences SMRT) using the same algorithmic approach.

  simulated million coli illumina short-read mapping neural-network