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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Has reproduction · 58
Comprehensive analysis of peroxisome proliferator-activated receptors to predict the drug resistance, immune microenvironment, and prognosis in stomach adenocarcinomas.
PMID 38529307 · PMC10962337 · PeerJ · 2024 · 8 claims · 8 setups
PPARA, PPARD and PPARG are more abnormally expressed in STAD samples and cell lines compared to most of 32 cancer types in TCGA
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Has reproduction · 66
RNAseq analysis of the parasitic nematode Strongyloides stercoralis reveals divergent regulation of canonical dauer pathways.
PMID 23145190 · PMC3493385 · PLoS neglected tropical diseases · 2012 · 8 claims · 8 setups
S. stercoralis possesses homologs of nearly all C. elegans dauer genes, but with significant differences in protein structure, developmental regulation, and gene family expansion.
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Has reproduction · 85
COVID-19 lung disease shares driver AT2 cytopathic features with Idiopathic pulmonary fibrosis.
PMID 35870428 · PMC9297827 · EBioMedicine · 2022 · 8 claims · 8 setups
COVID-19 lung disease resembles IPF at a fundamental level, recapitulating ViP/IPF gene expression patterns, an IL15-centric cytokine storm, and AT2 cytopathic changes (injury, DNA damage, transient progenitor-state arrest, senescence/SASP).
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Has reproduction · 80
Differential analysis of RNA structure probing experiments at nucleotide resolution: uncovering regulatory functions of RNA structure.
PMID 35869080 · PMC9307511 · Nature communications · 2022 · 7 claims · 4 setups
DiffScan is a computational framework combining a Normalization module and a Scan module to identify SVRs at nucleotide resolution from SP data.
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Understanding incidental findings in the context of genetics and genomics.
PMID 18547195 · PMC2581745 · The Journal of law, medicine & ethics : a journal of the American Society of Law, Medicine & Ethics · 2008 · 8 claims · 3 setups
No consensus exists on researchers' responsibilities to disclose individual genetic/genomic research results to participants.
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Has reproduction · 48
Bioinformatics Analysis of the Characteristics and Correlation of m6A Methylation in Breast Cancer Progression.
PMID 35655723 · PMC9148239 · Contrast media & molecular imaging · 2022 · 8 claims · 8 setups
Breast cancer samples can be classified into 4 m6A subtypes (quiescent, m6A methylation, protein-binding, mixed) based on Z-score median of Set1 (writer+reader) and Set2 (eraser) gene expression
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Comparative genomic analysis reveals a novel mitochondrial isoform of human rTS protein and unusual phylogenetic distribution of the rTS gene.
PMID 16162288 · PMC1261261 · BMC genomics · 2005 · 8 claims · 5 setups
A novel rTS protein isoform, rTSγ, exists with a 27-residue longer N-terminus generated from an alternative upstream start codon relative to rTSβ.
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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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Has reproduction · 85
Exploring microproteins from various model organisms using the mip-mining database.
PMID 37919660 · PMC10623795 · BMC genomics · 2023 · 5 claims · 4 setups
Mip-mining is a database of 336 curated RNA-seq datasets from 8626 samples across nine species, built specifically to explore microprotein functions under stress and disease conditions
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Has reproduction · 66
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
Differentially expressed genes in MDD patients are enriched in immune response, inflammatory response, neurodegeneration, and cerebellar atrophy pathways.
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Comparative genomics and understanding of microbial biology.
PMID 10998382 · PMC2627966 · Emerging infectious diseases · 2000 · 8 claims · 7 setups
GC content varies widely among prokaryotic genomes (29% in B. burgdorferi to 68% in M. tuberculosis) and shapes codon usage and amino acid composition.
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Emerging genomic and proteomic evidence on relationships among the animal, plant and fungal kingdoms.
PMID 15629046 · PMC5172449 · Genomics, proteomics & bioinformatics · 2004 · 8 claims · 7 setups
Sequence-based molecular phylogenies widely support a sister relationship between animals and fungi, grouped as the Opisthokonta
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Has reproduction · 71
Protein structure quality assessment based on the distance profiles of consecutive backbone Cα atoms.
PMID 24555103 · PMC3892923 · F1000Research · 2013 · 8 claims · 8 setups
The distance between consecutive backbone Cα atoms in high-quality structures is normally distributed with mean 3.8 Å and standard deviation 0.04 Å, justifying a reference state in which all consecutive Cα atoms are 3.8 Å apart.
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A new family of giardial cysteine-rich non-VSP protein genes and a novel cyst protein.
PMID 17183673 · PMC1762436 · PloS one · 2006 · 8 claims · 7 setups
HCNCp is a novel invariant (non-variant) cyst protein belonging to a new family of high-cysteine membrane proteins (HCMp) abundant in the Giardia genome
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Multilocus analysis of SNP and metabolic data within a given pathway.
PMID 16412218 · PMC1382210 · BMC genomics · 2006 · 8 claims · 7 setups
The combinatorial partitioning method (CPM) with optimal thresholds can identify SNPs associated with quantitative metabolite levels rather than only categorical traits.
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Comparative sequence analysis of leucine-rich repeats (LRRs) within vertebrate toll-like receptors.
PMID 17517123 · PMC1899181 · BMC genomics · 2007 · 8 claims · 4 setups
A new method combining known LRR structures, multiple sequence alignment, and secondary structure prediction identifies and aligns LRRs in TLRs more accurately than PFAM/InterPro/SMART
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Genome-wide analysis of the H3K4 histone demethylase RBP2 reveals a transcriptional program controlling differentiation.
PMID 18722178 · PMC3003864 · Molecular cell · 2008 · 7 claims · 8 setups
RBP2 target promoters separate into two functionally distinct classes: differentiation-independent genes (mitochondrial function, RNA/DNA metabolism) and differentiation-dependent genes (cell cycle)
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Gene structure and mutant alleles of PCDH15: nonsyndromic deafness DFNB23 and type 1 Usher syndrome.
PMID 18719945 · PMC2716558 · Human genetics · 2008 · 8 claims · 6 setups
PCDH15 has an updated gene structure with four additional exons beyond the previously reported 35, producing isoforms in four classes with three alternative cytoplasmic domains (CD1, CD2, CD3).
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Managing incidental findings in human subjects research: analysis and recommendations.
PMID 18547191 · PMC2575242 · The Journal of law, medicine & ethics : a journal of the American Society of Law, Medicine & Ethics · 2008 · 8 claims · 5 setups
Little guidance currently exists on managing research IFs, and no consensus exists on the best approach across genetic/genomic and imaging research domains.
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An integrative approach to reveal driver gene fusions from paired-end sequencing data in cancer.
PMID 19881495 · PMC3086882 · Nature biotechnology · 2009 · 8 claims · 8 setups
A 'concept signature' (ConSig) score algorithm ranks genes by association with molecular concepts characteristic of fusion or mutation cancer genes, nominating biologically important fusions from large candidate sets.