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).
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Onto-Tools: new additions and improvements in 2006.
PMID 17584796 · PMC1933142 · Nucleic acids research · 2007 · 8 claims · 3 setups
OE2GO enables functional profiling for organisms lacking public-domain annotations by allowing users to supply custom GO-format annotation files and OBO-format ontology files
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Information-based methods for predicting gene function from systematic gene knock-downs.
PMID 18959798 · PMC2596148 · BMC bioinformatics · 2008 · 8 claims · 4 setups
Information-based metrics, which incorporate a phenotype's genomic frequency, outperform non-information-based metrics for detecting gene-gene functional similarity from phenotypic knock-down profiles.
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Has reproduction · 100
The genome of the ant Tetramorium bicarinatum reveals a tandem organization of venom peptides genes allowing the prediction of their regulatory and evolutionary profiles.
PMID 38245722 · PMC10800049 · BMC genomics · 2024 · 8 claims · 8 setups
44 venom peptide genes were identified, distributed across four of the eleven chromosomes and organized in tandem repeat clusters.
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Has reproduction · 65
SPEAQeasy: a scalable pipeline for expression analysis and quantification for R/bioconductor-powered RNA-seq analyses.
PMID 33932985 · PMC8088074 · BMC bioinformatics · 2021 · 8 claims · 5 setups
SPEAQeasy is a portable, easy-to-install, Nextflow-powered RNA-seq processing pipeline that lowers the computational entry barrier for biologists/clinicians
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Has reproduction · 50
MEDUSA: A Pipeline for Sensitive Taxonomic Classification and Flexible Functional Annotation of Metagenomic Shotgun Sequences.
PMID 35330728 · PMC8940201 · Frontiers in genetics · 2022 · 7 claims · 6 setups
MEDUSA correctly identifies more species than MEGAN 6 CE, especially less abundant species.
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Has reproduction · 80
A chromosome-level genome assembly provides insights into the environmental adaptability and outbreaks of Chlorops oryzae.
PMID 36028584 · PMC9418232 · Communications biology · 2022 · 8 claims · 8 setups
A high-quality chromosome-level genome assembly of C. oryzae was generated using PacBio, Illumina, and Hi-C sequencing
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Proteomics: characterizing the cogs in the machinery of life.
PMID 14630521 · PMC1241753 · Environmental health perspectives · 2003 · 8 claims · 5 setups
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.
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Computational identification of transcriptional regulatory elements in DNA sequence.
PMID 16855295 · PMC1524905 · Nucleic acids research · 2006 · 8 claims · 3 setups
Weight matrix (PWM/PSSM) models of TF binding sites are grounded in biophysical theory of protein-DNA interactions, with position weights corresponding to log-odds contributions to binding free energy
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A cell biological perspective on genome research.
PMID 8522596 · PMC2120688 · The Journal of cell biology · 1995 · 7 claims · 7 setups
Genome sequencing represents a sixth stage in the historical progression of structural biology (comparative anatomy through crystallography), and will be similarly valuable once related to function.