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 16

System / cell line: tested ✕ Assay: genome ✕ Clear

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

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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

genome cos-7 promoters bioinformatic promoter-luciferase site-directed
Comparative genome and phenotypic analysis of Clostridium difficile 027 strains provides insight into the evolution of a hypervirulent bacterium.

PMID 19781061 · PMC2768977 · Genome biology · 2009 · 8 claims · 7 setups

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The 027 genomes (CD196 and R20291) contain 234 additional genes compared to strain 630, spread across at least 50 regions of genetic difference, including a phage island, transposon genes, two-component response regulators, drug resistance genes and transporters

difficile toxin whole-genome toxin paloc
Genome Alteration Print (GAP): a tool to visualize and mine complex cancer genomic profiles obtained by SNP arrays.

PMID 19903341 · PMC2810663 · Genome biology · 2009 · 7 claims · 3 setups

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GAP is a method for automatic detection of absolute segmental copy number and genotype status from SNP-array cancer genome profiles

breast snp flow karyotyping
Testing groups of genomic locations for enrichment in disease loci using linkage scan data: a method for hypothesis testing.

PMID 16848972 · PMC3525155 · Human genomics · 2006 · 8 claims · 2 setups

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A method testing enrichment of a group of genomic locations for disease loci by comparing the average NPL score of the group to a null distribution from randomly drawn groups of equal size

simulated pedigrees simulated real
HGA: de novo genome assembly method for bacterial genomes using high coverage short sequencing reads.

PMID 26945881 · PMC4779561 · BMC genomics · 2016 · 8 claims · 7 setups

Has reproduction · 58

HGA leads to significant improvement in assembly quality (N50 and corrected N50) for all 7 evaluated GAGE-B bacterial datasets using most of the 8 evaluated assemblers

bacillus mycobacterium rhodobacter vibrio novo contigs-combining re-assembly
Genome-wide identification of human functional DNA using a neutral indel model.

PMID 16410828 · PMC1326222 · PLoS computational biology · 2006 · 8 claims · 8 setups

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A neutral indel model predicting a geometric distribution of intergap segment (IGS) lengths fits human-mouse ancestral repeat (AR) alignment data excellently

chromosome human-mouse genome individual whole-genome probabilistic comparative
Ab initio identification of human microRNAs based on structure motifs.

PMID 18088431 · PMC2238772 · BMC bioinformatics · 2007 · 8 claims · 7 setups

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MiRPred predicts miRNA precursors ab initio using only predicted secondary structure motifs, ignoring nucleotide sequence

genome mirna hairpins chromosome secondary linear five-fold
A genome-wide siRNA screen reveals diverse cellular processes and pathways that mediate genome stability.

PMID 19647519 · PMC2772893 · Molecular cell · 2009 · 8 claims · 6 setups

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A genome-wide siRNA screen in HeLa cells using γH2AX as a readout identifies genes whose knockdown elevates DNA damage/genome instability

hela candidate screen genome-wide propidium sirna
Human and mouse introns are linked to the same processes and functions through each genome's most frequent non-conserved motifs.

PMID 18450818 · PMC2425492 · Nucleic acids research · 2008 · 8 claims · 5 setups

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Pyknons (recurrent, genome-specific, ≥16nt motifs with ≥30 intact intergenic/intronic copies and ≥1 exonic copy) span a substantial fraction of previously uncharacterized intronic space (7.4% human, 4.4% mouse)

pyknon computational comparative term
CAGE Basic/Analysis Databases: the CAGE resource for comprehensive promoter analysis.

PMID 16381948 · PMC1347397 · Nucleic acids research · 2006 · 6 claims · 2 setups

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CAGE Basic and Analysis Databases together form a comprehensive resource for promoter analysis using CAGE tag data from human and mouse

tested cage race
Use of suppression subtractive hybridisation to extend our knowledge of genome diversity in Campylobacter jejuni.

PMID 17470265 · PMC1868759 · BMC genomics · 2007 · 8 claims · 6 setups

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There is a clear correlation between MLST clonal complex and the distribution of metabolic genes involved in alternative terminal electron acceptor use.

jejuni ssh panel suppression blastx dot-blot
Ancient variation of the AvrPm17 gene in powdery mildew limits the effectiveness of the introgressed rye Pm17 resistance gene in wheat.

PMID 35857869 · PMC9335242 · Proceedings of the National Academy of Sciences of the United States of America · 2022 · 6 claims · 8 setups

Has reproduction · 80

AvrPm17 is encoded by a paralogous, tandemly duplicated effector gene pair located in a pericentromeric, mildew sublineage-specific effector cluster (family E003) showing signs of recurring gene conversion.

b.g parental nicotiana benthamiana qtl comparative rna-sequencing
Comparative genomic study reveals a transition from TA richness in invertebrates to GC richness in vertebrates at CpG flanking sites: an indication for context-dependent mutagenicity of methylated CpG sites.

PMID 19329065 · PMC5054122 · Genomics, proteomics & bioinformatics · 2008 · 8 claims · 8 setups

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Nucleotide preference at CpG flanking sites transitions from 5' T (invertebrates) to 5' A (vertebrates) at the invertebrate-vertebrate boundary

genomes same pufferfish elegans nucleotide genome-wide kruskal-wallis
Design factors that influence PCR amplification success of cross-species primers among 1147 mammalian primer pairs.

PMID 17029642 · PMC1635982 · BMC genomics · 2006 · 8 claims · 7 setups

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The number of index-species (IS) mismatches in a primer pair significantly reduces amplification success, with an estimated 6-8% decrease in success rate per additional mismatch.

dog hamster pcr primer pcr blast sequence
Human synthetic lethal inference as potential anti-cancer target gene detection.

PMID 20015360 · PMC2804737 · BMC systems biology · 2009 · 7 claims · 8 setups

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Targeting the synthetic lethal partner of a gene mutated in cancer selectively damages tumor cells while sparing healthy cells, offering a rationale for anti-cancer drug design

saccharomyces sapiens ihsln genes database phylogenetic gene
Analysis of the Hypoxic Response in a Mouse Cortical Collecting Duct-Derived Cell Line Suggests That Esrra Is Partially Involved in Hif1α-Mediated Hypoxia-Inducible Gene Expression in mCCD(cl1) Cells.

PMID 35806266 · PMC9267015 · International journal of molecular sciences · 2022 · 8 claims · 7 setups

Has reproduction · 76

mCCD cl1 cells mount a broad transcriptional response to 24 h hypoxia (0.2% O2), with 3086 genes differentially expressed

mccd lines bulk rt-qpcr western

Experiments

Discovery of genes activated by the mitochondrial unfolded protein response (mtUPR) and cognate promoter elements.

Comparative genome and phenotypic analysis of Clostridium difficile 027 strains provides insight into the evolution of a hypervirulent bacterium.

Genome Alteration Print (GAP): a tool to visualize and mine complex cancer genomic profiles obtained by SNP arrays.

Testing groups of genomic locations for enrichment in disease loci using linkage scan data: a method for hypothesis testing.

HGA: de novo genome assembly method for bacterial genomes using high coverage short sequencing reads.

Genome-wide identification of human functional DNA using a neutral indel model.

Ab initio identification of human microRNAs based on structure motifs.

A genome-wide siRNA screen reveals diverse cellular processes and pathways that mediate genome stability.

Human and mouse introns are linked to the same processes and functions through each genome's most frequent non-conserved motifs.

CAGE Basic/Analysis Databases: the CAGE resource for comprehensive promoter analysis.

Use of suppression subtractive hybridisation to extend our knowledge of genome diversity in Campylobacter jejuni.

Ancient variation of the AvrPm17 gene in powdery mildew limits the effectiveness of the introgressed rye Pm17 resistance gene in wheat.

Comparative genomic study reveals a transition from TA richness in invertebrates to GC richness in vertebrates at CpG flanking sites: an indication for context-dependent mutagenicity of methylated CpG sites.

Design factors that influence PCR amplification success of cross-species primers among 1147 mammalian primer pairs.

Human synthetic lethal inference as potential anti-cancer target gene detection.

Analysis of the Hypoxic Response in a Mouse Cortical Collecting Duct-Derived Cell Line Suggests That Esrra Is Partially Involved in Hif1α-Mediated Hypoxia-Inducible Gene Expression in mCCD(cl1) Cells.