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).

• Peptide bioinformatics: peptide classification using peptide machines.

  PMID 19065810 · PMC7122642 · Methods in molecular biology (Clifton, N.J.) · 2008 · 8 claims · 4 setups

  Full-text index only

  The bio-basis function, which converts peptides into numerical vectors using nongapped pairwise homology alignment scores against indicator peptides, can statistically quantify peptide similarity for classification.

  illustrative query generic synthetic bio-basis orthogonal hyperplane

• A modified T-test feature selection method and its application on the HapMap genotype data.

  PMID 18267305 · PMC5054219 · Genomics, proteomics & bioinformatics · 2007 · 7 claims · 4 setups

  Full-text index only

  A modified t-test ranking measure, extended to handle nominal SNP genotype data via vector transformation, can effectively rank SNPs by their discriminative capability for population classification.

  hapmap modified f-statistics informativeness

• Integromics: challenges in data integration.

  PMID 12186644 · PMC139396 · Genome biology · 2002 · 8 claims · 7 setups

  Full-text index only

  There is no simple solution to database integration in genomics/bioinformatics

  lines molecular gene monsanto high-throughput cluster-correlation microarray

• Comparing protein abundance and mRNA expression levels on a genomic scale.

  PMID 12952525 · PMC193646 · Genome biology · 2003 · 8 claims · 8 setups

  Full-text index only

  Correlations between mRNA expression and protein abundance are generally poor or limited across most studies reviewed, including in yeast and human cancers

  yeast laser-dissected serum myeloid two-dimensional seldi-tof isotope-coded

• Automatic discovery of 100-miRNA signature for cancer classification using ensemble feature selection.

  PMID 31533612 · PMC6751684 · BMC bioinformatics · 2019 · 7 claims · 8 setups

  Has reproduction · 69

  An ensemble feature selection method based on classifier consensus identifies a robust 100-miRNA signature from TCGA data.

  tcga geo 100-mirna mirna feature bibliographic

• Application of Machine Learning in Predicting Hepatic Metastasis or Primary Site in Gastroenteropancreatic Neuroendocrine Tumors.

  PMID 37887568 · PMC10605255 · Current oncology (Toronto, Ont.) · 2023 · 8 claims · 7 setups

  Has reproduction · 59

  Multi-gene random forest models classify primary tumor vs. liver metastasis samples with 100% accuracy in training/test cohorts and >90% accuracy in an independent validation cohort

  pancreatic rna-seq liver tumor bulk machine multi-label

• Supervised learning-based tagSNP selection for genome-wide disease classifications.

  PMID 18366619 · PMC2386071 · BMC genomics · 2008 · 7 claims · 2 setups

  Full-text index only

  SRFA (Supervised Recursive Feature Addition) is a novel feature selection method combining supervised learning and statistical redundancy measures for SNP selection

  micc narac snp

• In silico analysis of missense substitutions using sequence-alignment based methods.

  PMID 18951440 · PMC3431198 · Human mutation · 2008 · 8 claims · 7 setups

  Full-text index only

  Carefully validated PMSA-based computational algorithms can achieve predictive values of ~75-95% for classifying missense substitutions as pathogenic or neutral.

  clinically sequence curated deep blosum62 sift align-gvgd

• Improving melanoma classification by integrating genetic and morphologic features.

  PMID 18532874 · PMC2408611 · PLoS medicine · 2008 · 7 claims · 5 setups

  Full-text index only

  BRAF-mutant melanomas show distinct morphological features (upward migration and nesting of intraepidermal melanocytes, epidermal thickening, sharper lateral demarcation, larger/rounder/more pigmented tumor cells) compared to non-mutant melanomas

  archival same subset patients histopathological mutation quantitative

• Colorectal Cancer Prediction Based on Weighted Gene Co-Expression Network Analysis and Variational Auto-Encoder.

  PMID 32825264 · PMC7563725 · Biomolecules · 2020 · 6 claims · 7 setups

  Has reproduction · 80

  Combining WGCNA-derived hub genes with a VAE-derived 10-dimensional representation as features for an SVM classifier achieves high accuracy (0.9692) and AUC (0.9981) for colorectal cancer prediction.

  colorectal combined differentially crc microarray differential weighted

• A novel peak detection approach with chemical noise removal using short-time FFT for prOTOF MS data.

  PMID 19681055 · PMC2782493 · Proteomics · 2009 · 8 claims · 2 setups

  Full-text index only

  PDA_stFFT is a novel automatic peak detection method for prOTOF MS data that does not require a priori knowledge of protein masses

  peptide serum maldi-tof

• Scalable Prediction of Acute Myeloid Leukemia Using High-Dimensional Machine Learning and Blood Transcriptomics.

  PMID 31918046 · PMC6992905 · iScience · 2020 · 8 claims · 8 setups

  Has reproduction · 96

  Data-driven, high-dimensional ML approaches that learn multivariate signatures directly from genome-wide transcriptomic data (no prior gene selection) yield accurate and robust AML classifiers.

  peripheral pbmc datasets hg-u133 gene bulk machine

• Pharmacogenomic biomarkers.

  PMID 12364812 · PMC3850811 · Disease markers · 2002 · 8 claims · 8 setups

  Full-text index only

  Development of a pharmacogenomic biomarker requires sequential steps: laboratory identification, retrospective confirmation in clinical samples, prospective clinical trial validation, and regulatory approval before patient stratification.

  populations population tumor breast genetic array immunohistochemistry

• Emerging strategies and applications of pharmacogenomics.

  PMID 15606999 · PMC3500198 · Human genomics · 2004 · 7 claims · 7 setups

  Full-text index only

  Effective pharmacogenomics requires infrastructure including informed consent processes, accurate phenotypic data collection, high-throughput genotyping technology, and integrated information technology systems.

  subjects ethnically patients genome-wide gene case-control

• In situ origin of deep rooting lineages of mitochondrial Macrohaplogroup 'M' in India.

  PMID 16776823 · PMC1534032 · BMC genomics · 2006 · 6 claims · 5 setups

  Full-text index only

  The Indian mtDNA pool contains several deep-rooting macrohaplogroup M lineages, indicating in-situ origin of these haplogroups in South Asia, most likely India

  mtdna mitochondrial partial hvs1

• Eurasian and African mitochondrial DNA influences in the Saudi Arabian population.

  PMID 17331239 · PMC1810519 · BMC evolutionary biology · 2007 · 8 claims · 4 setups

  Full-text index only

  The majority (85%) of Saudi Arab mtDNA lineages have a western Asia (Eurasian) provenance

  saudi mtdna rflp complete

• iBRIDGE: A Data Integration Method to Identify Inflamed Tumors from Single-cell RNA-Seq Data and Differentiate Cell Type-Specific Markers of Immune-Cell Infiltration.

  PMID 37023414 · PMC10236149 · Cancer immunology research · 2023 · 8 claims · 8 setups

  Has reproduction · 94

  Malignant cells cluster by patient in scRNA-seq data while immune and stromal cells cluster by cell type, making malignant cells uniquely suited to carry patient-level inflamed/cold signal

  nsclc coad brca tcga scrna-seq bulk rna-seq

• Comparative Genomics of Borderline Oxacillin-Resistant Staphylococcus aureus Detected during a Pseudo-outbreak of Methicillin-Resistant S. aureus in a Neonatal Intensive Care Unit.

  PMID 35038924 · PMC8764539 · mBio · 2022 · 7 claims · 8 setups

  Has reproduction · 63

  Of 42 isolates flagged as MRSA by screening agar, only 9 were PBP2a- and mecA-positive true MRSA, while the remaining 33 were mecA-negative and largely met criteria for BORSA

  clinical nicu genomic maldi-tof pbp2a cefoxitin

• Timing constraints of in vivo gag mutations during primary HIV-1 subtype C infection.

  PMID 19890401 · PMC2768328 · PloS one · 2009 · 7 claims · 7 setups

  Full-text index only

  Reverse mutations to the wild type (HIV-1C consensus) in Gag appear significantly earlier than escape mutations from the wild type during primary infection

  hiv-1 same sequenced gag single-genome mhc hypermutation

• Proteome analysis enables separate clustering of normal breast, benign breast and breast cancer tissues.

  PMID 12865921 · PMC2394238 · British journal of cancer · 2003 · 6 claims · 3 setups

  Full-text index only

  Hierarchical cluster analysis of 2-DE proteome data can distinguish normal breast, benign breast, and breast cancer tissues based on protein expression profiles

  breast two-dimensional hierarchical mann-whitney