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 29

System / cell line: coli ✕ Assay: acid ✕ Clear

Exploring microproteins from various model organisms using the mip-mining database.

PMID 37919660 · PMC10623795 · BMC genomics · 2023 · 5 claims · 4 setups

Has reproduction · 85

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

nine cerevisiae thaliana bulk transcriptome growth
Versatile and open software for comparing large genomes.

PMID 14759262 · PMC395750 · Genome biology · 2004 · 8 claims · 8 setups

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MUMmer 3.0 efficiently handles comparisons of large eukaryotic genomes at varying evolutionary distances

escherichia chromosome drosophila anopheles suffix-tree whole-genome protein-level
Searching for interpretable rules for disease mutations: a simulated annealing bump hunting strategy.

PMID 16984653 · PMC1618409 · BMC bioinformatics · 2006 · 8 claims · 6 setups

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The proposed feature set outperforms existing published feature sets for predicting effects of amino acid substitutions

coli bacteriophage lac proteins svm simulated pearson
Genetic diversity among five T4-like bacteriophages.

PMID 16716236 · PMC1524935 · Virology journal · 2006 · 8 claims · 8 setups

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A core set of 82 conserved genes (T4-like genes) is present in all five genomes analyzed, clustered in large collinear blocks.

bacteriophages five conserved aeh1 genome orf trna
A focused antibody library for selecting scFvs expressed at high levels in the cytoplasm.

PMID 18034894 · PMC2241821 · BMC biotechnology · 2007 · 7 claims · 7 setups

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A human scFv library was built on the single scFv13R4 framework with CDR3 loops diversified to mimic natural human CDR3 amino-acid distributions.

coli hela filamentous scfv gfp sds-page fluorescence
L-Arabinose Alters the E. coli Transcriptome to Favor Biofilm Growth and Enhances Survival During Fluoroquinolone Stress.

PMID 40732174 · PMC12299780 · Microorganisms · 2025 · 8 claims · 6 setups

Has reproduction · 74

L-arabinose increases planktonic growth rate but reduces total growth of E. coli at both 28°C and 37°C

coli growth crystal colony
Towards the identification of essential genes using targeted genome sequencing and comparative analysis.

PMID 17052348 · PMC1624830 · BMC genomics · 2006 · 8 claims · 8 setups

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Phyletic retention (ortholog presence across organisms) is the single most predictive feature of gene essentiality in both E. coli and S. cerevisiae.

coli cerevisiae comparative machine single-gene
Opportunities and challenges in synthetic oligosaccharide and glycoconjugate research.

PMID 20161474 · PMC2794050 · Nature chemistry · 2009 · 8 claims · 7 setups

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A parallel combinatorial one-pot multi-step protecting-group procedure (Lewis acid catalyzed, up to seven steps) can transform tetra-O-TMS glucopyranosides into differentially protected monosaccharide building blocks without intermittent work-up/purification

library database oligovalent b-cells glycan bioinformatics one-pot
The commonly-used DNA probe for diffusely-adherent Escherichia coli cross-reacts with a subset of enteroaggregative E. coli.

PMID 20025771 · PMC2803494 · BMC microbiology · 2009 · 7 claims · 5 setups

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The daaC probe cross-hybridizes with a specific subset of EAEC strains, namely those carrying the aafA gene (AAF/II fimbriae)

coli hep-2 pslm862 eaec colony hep-2 pcr
Interspecies diversity of the occludin sequence: cDNA cloning of human, mouse, dog, and rat-kangaroo homologues.

PMID 8601611 · PMC2120780 · The Journal of cell biology · 1996 · 8 claims · 7 setups

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Full-length cDNAs encoding occludin were cloned and sequenced from rat-kangaroo (potoroo), human, mouse, and dog

ptk2 t84 escherichia computational expression immunofluorescence immunoblotting
Evolution of variants of yeast site-specific recombinase Flp that utilize native genomic sequences as recombination target sites.

PMID 17003057 · PMC1635253 · Nucleic acids research · 2006 · 8 claims · 8 setups

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Stepwise directed evolution using chimeric FLRT (FRT/genomic hybrid) intermediate sites can generate Flp variants capable of recombining native genomic FRT-like sequences from the human IL10 gene (FL-IL10A, FL-IL10B).

coli flp il10 flp-holliday recombination site-specific computational
Protein co-evolution, co-adaptation and interactions.

PMID 18818697 · PMC2556093 · The EMBO journal · 2008 · 8 claims · 6 setups

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The mirrortree method predicts protein-protein interactions by detecting pairs of protein families with similar phylogenetic trees (quantified as Pearson correlation of sequence similarity matrices).

nuoe intra-protein coli interacting phylogenetic correlated domain-restricted
Using DNA microarrays to study host-microbe interactions.

PMID 10998383 · PMC2627958 · Emerging infectious diseases · 2000 · 8 claims · 8 setups

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DNA microarrays can measure transcript levels and detect sequence polymorphisms for every gene simultaneously in microbial genomes

streptococcus cytomegalovirus coli mycobacterium oligonucleotide microarray gene
High incidence of human bocavirus infection in children in Spain.

PMID 17904416 · PMC7108365 · Journal of clinical virology : the official publication of the Pan American Society for Clinical Virology · 2007 · 8 claims · 6 setups

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HBoV is a significant contributor to acute lower respiratory tract infection in young children in Spain

nasopharyngeal cloned hbov-positive urine nested multiplex sanger
Polymorphism and epitope sharing between the alleles of merozoite surface protein-1 of Plasmodium falciparum among Indian isolates.

PMID 17659072 · PMC1950510 · Malaria journal · 2007 · 7 claims · 6 setups

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PfMAD20 is the predominant PfMSP-1 allelic type among Indian field isolates

falciparum escherichia coli-expressed recombinant pcr recombinant sds-page
SNAP: predict effect of non-synonymous polymorphisms on function.

PMID 17526529 · PMC1920242 · Nucleic acids research · 2007 · 7 claims · 8 setups

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SNAP, a neural network-based method using sequence-derived information, predicts whether a non-synonymous SNP is neutral or non-neutral for protein function

combined escherichia bacteriophage hiv-1 neural benchmark comparative
Comparative genomics and understanding of microbial biology.

PMID 10998382 · PMC2627966 · Emerging infectious diseases · 2000 · 8 claims · 7 setups

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GC content varies widely among prokaryotic genomes (29% in B. burgdorferi to 68% in M. tuberculosis) and shapes codon usage and amino acid composition.

completed same sequenced mycobacterium whole-genome comparative phylogenomic
Assembling a jigsaw puzzle with 20,000 parts.

PMID 12801408 · PMC193613 · Genome biology · 2003 · 8 claims · 8 setups

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Re-routing the intracellular interaction domains of receptor tyrosine kinases can redirect their signaling output, e.g. converting a growth signal into an apoptosis signal.

yeast caenorhabditis escherichia proteome-wide microarray yeast rnai
Preponderance of the oncogenic V599E and V599K mutations in B-raf kinase domain is enhanced in melanoma cutaneous/subcutaneous metastases.

PMID 15935100 · PMC1164406 · BMC cancer · 2005 · 8 claims · 4 setups

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B-raf exon 15 somatic mutations occur in 24/60 (40%) of cutaneous/subcutaneous melanoma metastases, similar to the frequency in primary melanomas

paraffin-embedded cloned same predicted pcr cloning blastx
Functional dissection of siRNA sequence by systematic DNA substitution: modified siRNA with a DNA seed arm is a powerful tool for mammalian gene silencing with significantly reduced off-target effect.

PMID 18267968 · PMC2367719 · Nucleic acids research · 2008 · 6 claims · 8 setups

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The seed arm (guide strand positions 2-8), its complementary passenger-strand sequence, the 5' end of the guide strand, and the 3' overhang of the passenger strand can be simultaneously replaced with DNA without substantial loss of gene-silencing activity.

cho-k1 e14tg2a recombinant hela dual-luciferase rt-pcr electrophoresis

Experiments

Exploring microproteins from various model organisms using the mip-mining database.

Versatile and open software for comparing large genomes.

Searching for interpretable rules for disease mutations: a simulated annealing bump hunting strategy.

Genetic diversity among five T4-like bacteriophages.

A focused antibody library for selecting scFvs expressed at high levels in the cytoplasm.

L-Arabinose Alters the E. coli Transcriptome to Favor Biofilm Growth and Enhances Survival During Fluoroquinolone Stress.

Towards the identification of essential genes using targeted genome sequencing and comparative analysis.

Opportunities and challenges in synthetic oligosaccharide and glycoconjugate research.

The commonly-used DNA probe for diffusely-adherent Escherichia coli cross-reacts with a subset of enteroaggregative E. coli.

Interspecies diversity of the occludin sequence: cDNA cloning of human, mouse, dog, and rat-kangaroo homologues.

Evolution of variants of yeast site-specific recombinase Flp that utilize native genomic sequences as recombination target sites.

Protein co-evolution, co-adaptation and interactions.

Using DNA microarrays to study host-microbe interactions.

High incidence of human bocavirus infection in children in Spain.

Polymorphism and epitope sharing between the alleles of merozoite surface protein-1 of Plasmodium falciparum among Indian isolates.

SNAP: predict effect of non-synonymous polymorphisms on function.

Comparative genomics and understanding of microbial biology.

Assembling a jigsaw puzzle with 20,000 parts.

Preponderance of the oncogenic V599E and V599K mutations in B-raf kinase domain is enhanced in melanoma cutaneous/subcutaneous metastases.

Functional dissection of siRNA sequence by systematic DNA substitution: modified siRNA with a DNA seed arm is a powerful tool for mammalian gene silencing with significantly reduced off-target effect.