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).

Publications 1.3k Datasets 392.5k Experiments 15

System / cell line: regions ✕ Assay: regional ✕ Clear

Predicting positive p53 cancer rescue regions using Most Informative Positive (MIP) active learning.

PMID 19756158 · PMC2742196 · PLoS computational biology · 2009 · 8 claims · 4 setups

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MIP active learning is a novel active learning method that preferentially seeks informative Positive (functionally active) examples rather than only maximizing classifier accuracy.

engineered p53 computational yeast-based regional homology
A third approach to gene prediction suggests thousands of additional human transcribed regions.

PMID 16543943 · PMC1391917 · PLoS computational biology · 2006 · 8 claims · 7 setups

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A third basic concept for gene prediction exists, based on detecting strand-specific 'transcription footprints' (mutational and selectional biases) rather than gene structure or sequence similarity.

genome 4.4-mb known nucleotide repeat polyadenylation
Cell-Type-Specific Gene Modules Related to the Regional Homogeneity of Spontaneous Brain Activity and Their Associations With Common Brain Disorders.

PMID 33958982 · PMC8093778 · Frontiers in neuroscience · 2021 · 7 claims · 8 setups

Has reproduction · 59

Fourteen gene modules were consistently associated with ReHo across three independent fMRI datasets.

healthy six ahba neurons resting-state microarray wgcna
A transcriptomic atlas of Aedes aegypti reveals detailed functional organization of major body parts and gut regional specializations in sugar-fed and blood-fed adult females.

PMID 35471187 · PMC9113746 · eLife · 2022 · 8 claims · 5 setups

Has reproduction · 73

Created Aegypti-Atlas, an online RNAseq resource covering Ae. aegypti body parts, gut regions, and a blood meal digestion time course

dissected five anterior midguts rnaseq rt-qpcr
SNP@Evolution: a hierarchical database of positive selection on the human genome.

PMID 19732458 · PMC2755008 · BMC evolutionary biology · 2009 · 7 claims · 6 setups

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SNP@Evolution is a hierarchical database integrating HET, FST, and iHS from HapMap Phase II and III to identify genome-wide positive selection signals

hapmap autosomes simulated sliding snp sliding haplotype-based
FGFR3 protein expression and its relationship to mutation status and prognostic variables in bladder cancer.

PMID 17668422 · PMC2443273 · The Journal of pathology · 2007 · 8 claims · 4 setups

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FGFR3 mutations occur in 42% of primary urothelial carcinomas and are significantly associated with low tumour grade and stage

urothelial tumour direct manual immunohistochemistry
Spns1-dependent endocardial lysosomal function drives valve morphogenesis through Notch1-signaling.

PMID 39720516 · PMC11667069 · iScience · 2024 · 7 claims · 8 setups

Has reproduction · 78

Autophagosomal, autolysosomal, and lysosomal vesicles significantly accumulate in the atrioventricular canal (AVC) and outflow tract (OFT)/bulboventricular regions and their developing valves during zebrafish heart development.

β-actin2 tgki cmv tgbac light-sheet lysotracker lysosome
Genomic divergences among cattle, dog and human estimated from large-scale alignments of genomic sequences.

PMID 16759380 · PMC1525190 · BMC genomics · 2006 · 8 claims · 6 setups

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Overall pairwise genomic divergences among cattle, dog and human are relatively constant (0.32–0.37 change/site)

orthologous random cattle aligned three-way pairwise bac
Genome sequence, comparative analysis, and population genetics of the domestic horse.

PMID 19892987 · PMC3785132 · Science (New York, N.Y.) · 2009 · 8 claims · 7 setups

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Produced a high-quality draft genome assembly of the domestic horse (EquCab2.0)

single horse eight twelve genome fish chip-on-chip
Neuroscience in the era of functional genomics and systems biology.

PMID 19829370 · PMC3645852 · Nature · 2009 · 8 claims · 7 setups

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Omics/discovery-based approaches do not eschew hypotheses but elevate hypothesis testing to high-throughput hypothesis generation and prioritization.

developing hippocampus bac-transgenic fetal situ gene bac-transgenic
Multimodal techniques for diagnosis and prognosis of Alzheimer's disease.

PMID 19829371 · PMC2810658 · Nature · 2009 · 8 claims · 8 setups

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AD pathology accumulates for approximately 10-15 years in a preclinical phase before synaptic and neuronal loss manifest as cognitive decline

subjects csf peripheral amyloid structural functional
ADZE: a rarefaction approach for counting alleles private to combinations of populations.

PMID 18779233 · PMC2732282 · Bioinformatics (Oxford, England) · 2008 · 6 claims · 2 setups

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A generalized rarefaction-based statistic can estimate the sample size-corrected number of distinct alleles private to any combination of populations, generalizing Kalinowski's (2004) private allelic richness to groups of populations.

populations simulated microsatellite computational
Motif discovery in promoters of genes co-localized and co-expressed during myeloid cells differentiation.

PMID 19059999 · PMC2632922 · Nucleic acids research · 2009 · 6 claims · 8 setups

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A novel multi-step computational method (built on approximate pattern enumeration, binomial over-representation scoring with FDR correction, and k-medoids clustering) can identify over-represented motifs in a selected set of promoters relative to a background promoter set.

myeloid reference selected genome-localized microarray promoter k-medoids
Ancient gene duplicates in Gossypium (cotton) exhibit near-complete expression divergence.

PMID 24558256 · PMC3971588 · Genome biology and evolution · 2014 · 8 claims · 8 setups

Has reproduction · 50

Nearly all (99.4%) ancient paralog pairs in Gossypium raimondii are differentially expressed in at least one of three tissues (petal, leaf, seed), indicating massive, near-complete expression-level divergence.

gossypium transcripts uq-normalized differentially comparative coding bulk
Integrative bioinformatics and artificial intelligence analyses of transcriptomics data identified genes associated with major depressive disorders including NRG1.

PMID 37583471 · PMC10423927 · Neurobiology of stress · 2023 · 7 claims · 5 setups

Has reproduction · 66

Differentially expressed genes in MDD patients are enriched in immune response, inflammatory response, neurodegeneration, and cerebellar atrophy pathways.

blood transcriptomic postmortem saliva gsea machine differential

Experiments

Predicting positive p53 cancer rescue regions using Most Informative Positive (MIP) active learning.

A third approach to gene prediction suggests thousands of additional human transcribed regions.

Cell-Type-Specific Gene Modules Related to the Regional Homogeneity of Spontaneous Brain Activity and Their Associations With Common Brain Disorders.

A transcriptomic atlas of Aedes aegypti reveals detailed functional organization of major body parts and gut regional specializations in sugar-fed and blood-fed adult females.

SNP@Evolution: a hierarchical database of positive selection on the human genome.

FGFR3 protein expression and its relationship to mutation status and prognostic variables in bladder cancer.

Spns1-dependent endocardial lysosomal function drives valve morphogenesis through Notch1-signaling.

Genomic divergences among cattle, dog and human estimated from large-scale alignments of genomic sequences.

Genome sequence, comparative analysis, and population genetics of the domestic horse.

Neuroscience in the era of functional genomics and systems biology.

Multimodal techniques for diagnosis and prognosis of Alzheimer's disease.

ADZE: a rarefaction approach for counting alleles private to combinations of populations.

Motif discovery in promoters of genes co-localized and co-expressed during myeloid cells differentiation.

Ancient gene duplicates in Gossypium (cotton) exhibit near-complete expression divergence.

Integrative bioinformatics and artificial intelligence analyses of transcriptomics data identified genes associated with major depressive disorders including NRG1.