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).

• Reusable building blocks in biological systems.

  PMID 30958230 · PMC6303794 · Journal of the Royal Society, Interface · 2018 · 8 claims · 4 setups

  Has reproduction · 82

  Biological systems can be decomposed into phenotypic building blocks (PBBs) via k-maximally reusable decompositions (k-MRD) that maximize average reusability across conditions.

  tissues conditions randomized est-based mirna randomization

• Disease-aging network reveals significant roles of aging genes in connecting genetic diseases.

  PMID 19779549 · PMC2739292 · PLoS computational biology · 2009 · 8 claims · 8 setups

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  Human disease genes are much closer to aging genes in the PPI network than expected by chance

  protein-protein randomized dan aging network degree-conserved closeness

• A mechanistic model captures the emergence and implications of non-genetic heterogeneity and reversible drug resistance in ER+ breast cancer cells.

  PMID 34316714 · PMC8271219 · NAR cancer · 2021 · 7 claims · 8 setups

  Has reproduction · 85

  EMT and tamoxifen-resistance (TamR) regulatory axes can drive one another, enabling non-genetic heterogeneity via six co-existing phenotypes (ES, ER, HS, HR, MS, MR)

  gene same randomized publicly racipe stochastic randomized

• Bias of selection on human copy-number variants.

  PMID 16482228 · PMC1366494 · PLoS genetics · 2006 · 8 claims · 8 setups

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  Human CNVs are significantly overrepresented near telomeres and centromeres and enriched in simple tandem repeats relative to the genome as a whole

  genome human-mouse cnv-encompassed inbred comparative randomization molecular

• Evolutionary distance estimation and fidelity of pair wise sequence alignment.

  PMID 15840174 · PMC1087827 · BMC bioinformatics · 2005 · 8 claims · 8 setups

  Full-text index only

  Evolutionary distance estimation is relatively unaffected by alignment error as long as 50% or more of homologous sites remain identical between sequences

  simulated simulated sequence indel

• Network properties of complex human disease genes identified through genome-wide association studies.

  PMID 19956617 · PMC2779513 · PloS one · 2009 · 7 claims · 6 setups

  Full-text index only

  Complex disease genes are significantly less central (lower degree/closeness, higher eccentricity) in the human interactome than essential and monogenic disease genes, occupying an intermediate niche between monogenic disease genes and non-disease genes

  complex interactome gene disease-sharing gene protein-protein

• Computational tradeoffs in multiplex PCR assay design for SNP genotyping.

  PMID 16042802 · PMC1190169 · BMC genomics · 2005 · 7 claims · 6 setups

  Full-text index only

  Achieving high-multiplexing/high-coverage multiplex PCR designs is subject to a computational phase transition as the SNP-pair compatibility probability crosses a critical threshold

  simulated real chromosome randomly simulation multiplex coverage-vs-n

• OptiType: precision HLA typing from next-generation sequencing data.

  PMID 25143287 · PMC4441069 · Bioinformatics (Oxford, England) · 2014 · 8 claims · 8 setups

  Has reproduction · 95

  OptiType, an ILP-based HLA genotyping algorithm, produces accurate four-digit HLA-I predictions from NGS data not enriched for the HLA cluster.

  colorectal lymphoblastic hapmap genomes rna-seq low-coverage exome