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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Phenotypic categorization of genetic skin diseases reveals new relations between phenotypes, genes and pathways.
PMID 19744994 · PMC2773259 · Bioinformatics (Oxford, England) · 2009 · 8 claims · 5 setups
560 genetic skin diseases can be decomposed into 71 elementary phenotypic features (42 dermatologic, 29 systemic) that combine to represent each disease as a point in a multidimensional phenotype space
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SUPERFAMILY--sophisticated comparative genomics, data mining, visualization and phylogeny.
PMID 19036790 · PMC2686452 · Nucleic acids research · 2009 · 7 claims · 6 setups
SUPERFAMILY provides structural, functional and evolutionary annotation for proteins from all completely sequenced genomes using SCOP-based hidden Markov models
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Has reproduction · 85
Taxonomic and functional partitioning of Chloroflexota populations under ferruginous conditions at and below the sediment-water interface.
PMID 39384533 · PMC11650866 · FEMS microbiology ecology · 2024 · 8 claims · 8 setups
Chloroflexota populations are partitioned according to alternative electron acceptors (Anaerolineae) and electron donors (Dehalococcoidia) among respiratory and fermentative metabolites at and below the sediment-water interface
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Has reproduction · 87
Machine learning reveals microbial interactions driving plastic degradation across plastisphere environments.
PMID 41657981 · PMC12876002 · Frontiers in microbiology · 2025 · 8 claims · 7 setups
Wastewater plastispheres harbor the most diverse and compositionally even microbial communities among the three habitats studied
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Has reproduction · 67
Therapeutic Stress-Induced Remodeling of Transposable Elements and TE-Gene Chimeras in KYSE150 Esophageal Squamous Cell Carcinoma Cells.
PMID 42074115 · PMC13116134 · International journal of molecular sciences · 2026 · 8 claims · 8 setups
Combined 125I radiation and carfilzomib treatment causes structured, non-random remodeling of the TE transcriptome in KYSE150 ESCC cells.
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The association of Alu repeats with the generation of potential AU-rich elements (ARE) at 3' untranslated regions.
PMID 15610565 · PMC544599 · BMC genomics · 2004 · 6 claims · 4 setups
Alu repeats are a source of AREs at 3' UTRs of human mRNA, via poly-A regions of Alu generating complementary poly-T/poly-U regions that acquire regular adenine insertions to form ARE motifs.
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Has reproduction · 48
Rbfox2 controls autoregulation in RNA-binding protein networks.
PMID 24637117 · PMC3967051 · Genes & development · 2014 · 8 claims · 8 setups
Rbfox2 cross-regulates AS-NMD events within RNA-binding protein genes to alter their expression, tuning autoregulatory splicing networks and placing Rbfox2 at a critical node of a multilayer regulatory network.
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Discovery of genes activated by the mitochondrial unfolded protein response (mtUPR) and cognate promoter elements.
PMID 17849004 · PMC1964532 · PloS one · 2007 · 8 claims · 5 setups
mtUPR responsive genes (YME1L1, MPPβ, Tim17A, NDUFB2, Endonuclease G, Thioredoxin 2, plus previously known ClpP, Cpn60/10, MtDnaJ) all contain a CHOP element in their promoters
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FatiGO +: a functional profiling tool for genomic data. Integration of functional annotation, regulatory motifs and interaction data with microarray experiments.
PMID 17478504 · PMC1933151 · Nucleic acids research · 2007 · 8 claims · 8 setups
FatiGO+ is a web-based tool for functional profiling of genome-scale experiments that integrates functional annotation, regulatory motifs and interaction data
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An analysis of human microRNA and disease associations.
PMID 18923704 · PMC2559869 · PloS one · 2008 · 8 claims · 8 setups
MicroRNAs tend to show similar dysfunctional evidence (both up- or both down-regulated) for diseases within the same disease cluster, and different dysfunctional evidence between different disease clusters.
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Tandem repeats modify the structure of human genes hosted in segmental duplications.
PMID 19954527 · PMC2812944 · Genome biology · 2009 · 8 claims · 6 setups
Around 7% of primate-specific genes located within segmental duplications contain variable internal tandem repeats (ITRs).
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A machine learning approach uncovers principles and determinants of eukaryotic ribosome pausing.
PMID 39423268 · PMC11488575 · Science advances · 2024 · 8 claims · 5 setups
An unsupervised ML pipeline using the extended isolation forest (EIF) algorithm can reliably detect ribosome pausing sites from noisy, coverage-biased RiboSeq data across expression levels
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Chimp genome: branching out.
PMID 16136102 · PMC7420934 · Nature · 2005 · 8 claims · 8 setups
The Chimpanzee Sequencing and Analysis Consortium published the initial draft chimpanzee genome sequence and compared it to the human genome.
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Inference of SARS-CoV-2 exposure biomarkers using large-scale T-cell repertoire profiling.
PMID 41680899 · PMC12903587 · Genome medicine · 2026 · 7 claims · 6 setups
A novel batch-effect correction method (log-normal gene usage modeling, Z-score normalization, and roulette-wheel resampling) allows combining AIRR-seq data from different batches and protocols.