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).

• Seeded Bayesian Networks: constructing genetic networks from microarray data.

  PMID 18601736 · PMC2474592 · BMC systems biology · 2008 · 8 claims · 4 setups

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  Seeding Bayesian Network analysis with prior networks derived from literature and/or PPI data improves recovery of known gene-gene interactions compared to BN analysis without a seed

  leukemia interactome pubmed-indexed computational microarray yeast literature

• 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

• Emerging translational bioinformatics: knowledge-guided biomarker identification for cancer diagnostics.

  PMID 19964620 · PMC5003034 · Annual International Conference of the IEEE Engineering in Medicine and Biology Society. IEEE Engineering in Medicine and Biology Society. Annual International Conference · 2009 · 8 claims · 3 setups

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  omniBiomarker, a web-based application, uses prior biological knowledge to identify the most biologically relevant gene ranking metric for a given clinical problem

  renal microarray qrt-pcr computational

• SIGMA2: a system for the integrative genomic multi-dimensional analysis of cancer genomes, epigenomes, and transcriptomes.

  PMID 18840289 · PMC2571113 · BMC bioinformatics · 2008 · 8 claims · 6 setups

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  SIGMA2 is a Java-based software system that integrates and visualizes genomic, epigenomic, and transcriptomic cancer data.

  single hcc2218 nsclc array gene multi-omics

• Microarray analysis: genome-scale hypothesis scanning.

  PMID 14551912 · PMC212694 · PLoS biology · 2003 · 8 claims · 5 setups

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  Microarrays can be used to both test and generate hypotheses, not merely to fish for candidate genes.

  drosophila yeast diffuse breast microarray integrated gene

• Predicting survival within the lung cancer histopathological hierarchy using a multi-scale genomic model of development.

  PMID 16800721 · PMC1483910 · PLoS medicine · 2006 · 8 claims · 8 setups

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  Multi-scale genomic similarities exist between four human lung cancer subtypes and the developing mouse lung, and these similarities are prognostically meaningful.

  perfused lung microarray principal wilcoxon

• Short-term genome evolution of Listeria monocytogenes in a non-controlled environment.

  PMID 19014550 · PMC2642827 · BMC genomics · 2008 · 6 claims · 6 setups

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  The 2000 listeriosis outbreak was likely caused by an L. monocytogenes strain that persisted in the food processing facility for at least 12 years since 1988

  monocytogenes additional food j774 whole-genome comparative pcr

• Graph Random Forest: A Graph Embedded Algorithm for Identifying Highly Connected Important Features.

  PMID 37509188 · PMC10377046 · Biomolecules · 2023 · 8 claims · 3 setups

  Has reproduction · 89

  Graph Random Forest (GRF) embeds graph/network information directly into the decision-tree building process by splitting on features in the k-hop neighborhood of a data-driven head-splitting node.

  scale-free non-small embryonic simulation rna-seq

• Human disease classification in the postgenomic era: a complex systems approach to human pathobiology.

  PMID 17625512 · PMC1948102 · Molecular systems biology · 2007 · 8 claims · 5 setups

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  Current syndromic disease classification lacks specificity despite historically serving clinicians well

  prostate neurodegenerative experimental genetic reverse-engineered protein-protein gene

• Proteomics: characterizing the cogs in the machinery of life.

  PMID 14630521 · PMC1241753 · Environmental health perspectives · 2003 · 8 claims · 5 setups

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  Protein expression patterns in blood serum, detected via SELDI-TOF mass spectrometry and analyzed with a genetic algorithm, can distinguish ovarian cancer patients from healthy individuals with very high sensitivity and specificity.

  blood lung hemoglobin proteins seldi-tof proteome tandem

• Comparison of RNA-Seq by poly (A) capture, ribosomal RNA depletion, and DNA microarray for expression profiling.

  PMID 24888378 · PMC4070569 · BMC genomics · 2014 · 8 claims · 8 setups

  Has reproduction · 77

  Ribo-Zero-Seq removes rRNA with efficiency comparable to poly(A)-based mRNA-Seq in both FF and FFPE RNA, whereas DSN-Seq leaves significantly more rRNA and shows greater variation.

  fresh-frozen ffpe breast unc microarray mrna-seq ribo-zero-seq

• Identifying Molecular Subtypes and 6-Gene Prognostic Signature Based on Hypoxia for Optimizing Targeted Therapies in Non-Small Cell Lung Cancer.

  PMID 35509605 · PMC9058021 · International journal of general medicine · 2022 · 8 claims · 8 setups

  Has reproduction · 59

  NSCLC samples can be classified into two molecular subtypes (C1 and C2) based on hypoxia-related gene expression via consensus clustering

  tcga-nsclc geo bulk microarray unsupervised

• Evidence of recombination in Hepatitis C Virus populations infecting a hemophiliac patient.

  PMID 19922637 · PMC2784780 · Virology journal · 2009 · 7 claims · 6 setups

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  A new intragenotypic recombinant HCV strain (1b/1a), named H23, was detected in 1 of 10 hemophiliac patients studied

  hcv 5'ncr serum maximum sequence recombination

• BioAfrica's HIV-1 proteomics resource: combining protein data with bioinformatics tools.

  PMID 15757512 · PMC555852 · Retrovirology · 2005 · 8 claims · 3 setups

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  BioAfrica's HIV-1 Proteomics Resource integrates protein structure, gene expression, post-translational modification, functional activity and protein-macromolecule interaction data with bioinformatics tools in a single website.

  hiv-1 motif sequence literature-derived

• Endemic Venezuelan equine encephalitis in northern Peru.

  PMID 15200823 · PMC3323213 · Emerging infectious diseases · 2004 · 8 claims · 8 setups

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  Four VEE complex lineages cocirculate in the Peruvian Amazon region: subtype ID (Panama genotype and Colombia/Venezuela genotype), subtype IIIC, and a newly proposed subtype IIID

  veev pe2 subtype cotton sscp pcr phylogenetic

• Functional copy-number alterations in cancer.

  PMID 18784837 · PMC2527508 · PloS one · 2008 · 8 claims · 3 setups

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  RAE is a comprehensive computational framework that robustly maps chromosomal alterations in tumor samples and statistically assesses their functional importance in cancer.

  pleomorphic hapmap large snp computational

• Molecular Classification Models for Triple Negative Breast Cancer Subtype Using Machine Learning.

  PMID 34575658 · PMC8472680 · Journal of personalized medicine · 2021 · 6 claims · 4 setups

  Has reproduction · 86

  A training gene set of 719 unique upregulated DEGs (subtype-specific) can be used to build ML models that classify TNBC into BLIA, BLIS, MES, and LAR subtypes.

  known tnbc unique unknown gene machine term

• SELDI-TOF proteomic profiling of breast carcinomas identifies clinicopathologically relevant groups of patients similar to previously defined clusters from cDNA expression.

  PMID 18644101 · PMC2481502 · Breast cancer research : BCR · 2008 · 7 claims · 3 setups

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  SELDI-TOF MS proteomic profiling of breast carcinomas identifies patient subgroups with differential co-expression of protein peaks that are analogous to gene-expression-based classifications (luminal, basal, HER2 subtypes)

  breast seldi-tof hierarchical biomarker

• Overlapping gene mutations of hepatitis B virus in a chronic hepatitis B patient with hepatitis B surface antigen loss during lamivudine therapy.

  PMID 15953865 · PMC2782199 · Journal of Korean medical science · 2005 · 7 claims · 5 setups

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  Serum HBsAg became negative after 36 months of lamivudine therapy while HBeAg and HBV DNA remained positive

  serum hbv serologic hbv pcr

• Genetic diversity of swine influenza viruses isolated from pigs during 2000 to 2005 in Thailand.

  PMID 19453423 · PMC4941901 · Influenza and other respiratory viruses · 2008 · 8 claims · 6 setups

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  Phylogenetic analysis revealed nine distinct genotypes among the 12 Thai SIVs examined.

  swine nasal infectious embryonated rt-pcr subtype-specific viral