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 45

System / cell line: in-silico ✕ Assay: pairwise ✕ Clear

Mycoplasma genitalium: an efficient strategy to generate genetic variation from a minimal genome.

PMID 17784912 · PMC2169797 · Molecular microbiology · 2007 · 8 claims · 6 setups

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MG192 is highly variable among and within M. genitalium strains both in vitro and in vivo

genitalium clinical urine pairwise pcr serial
Benchmarking tools for the alignment of functional noncoding DNA.

PMID 14736341 · PMC344529 · BMC bioinformatics · 2004 · 8 claims · 4 setups

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Global alignment tools (Avid, ClustalW, Lagan, Needle, DiAlign-G) typically have higher sensitivity over entire noncoding sequences and within constrained blocks than local tools

simulated melanogaster sapiens sequence pairwise genome
Genome-wide prediction of functional gene-gene interactions inferred from patterns of genetic differentiation in mice and men.

PMID 18270580 · PMC2217631 · PloS one · 2008 · 8 claims · 6 setups

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Pairs of unlinked SNPs showing excess genetic differentiation (LD in mouse RILs, Fst in human populations) beyond what simulations/coalescent models predict by chance represent candidate functionally interacting (epistatic) gene pairs.

bxd simulated subset populations genome-wide simulation genotype-phenotype
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
Transduplication resulted in the incorporation of two protein-coding sequences into the turmoil-1 transposable element of C. elegans.

PMID 18842128 · PMC2572040 · Biology direct · 2008 · 8 claims · 6 setups

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The Turmoil-1 transposable element in C. elegans incorporated two unrelated protein-coding sequences into its inverted terminal repeats (ITRs)

turmoil-1 rrm elegans predicted pairwise maximum genome-wide
Low conservation and species-specific evolution of alternative splicing in humans and mice: comparative genomics analysis using well-annotated full-length cDNAs.

PMID 18838389 · PMC2582632 · Nucleic acids research · 2008 · 7 claims · 8 setups

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Although 86% of individual human exons are conserved in the mouse genome, only a small fraction (431/20392, ~2%) of human AS variants are perfectly conserved AS variants in mice.

genome full-length ~3x10^7 isoform whole-genome full-length polysome
Deep transcriptomics reveals cell-specific isoforms of pan-neuronal genes.

PMID 40379625 · PMC12084633 · Nature communications · 2025 · 8 claims · 5 setups

Has reproduction · 84

Pan-neuronal genes (expressed in many/all neurons) harbor highly cell-specific splice variants/isoforms restricted to single or few neuron types.

elegans short-read whole-animal rt-pcr
Emergent dynamics of underlying regulatory network links EMT and androgen receptor-dependent resistance in prostate cancer.

PMID 36851919 · PMC9957767 · Computational and structural biotechnology journal · 2023 · 8 claims · 7 setups

Has reproduction · 78

Simulations of the EMT-AR crosstalk network reveal four possible phenotypes: epithelial-sensitive (ES), epithelial-resistant (ER), mesenchymal-resistant (MR), and mesenchymal-sensitive (MS), with MS occurring rarely

gene racipe clinical tcga racipe influence principal
Improved eukaryotic detection compatible with large-scale automated analysis of metagenomes.

PMID 37032329 · PMC10084625 · Microbiome · 2023 · 8 claims · 7 setups

Has reproduction · 89

MAPQ ≥30 filtering improves precision but substantially reduces recall, especially for unrepresented/divergent eukaryotic taxa

eukdetect simulated zymobiomics read holdout mutation-rate
Leveraging human genomic information to identify nonhuman primate sequences for expression array development.

PMID 16288651 · PMC1314899 · BMC genomics · 2005 · 8 claims · 6 setups

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Human genomic DNA sequence can be leveraged to obtain 3' end sequence of NHP orthologs, which can then be used to generate NHP oligonucleotide microarrays

refseq macaca genomic rhesus exon pcr molecular
In silico and in vitro comparative analysis to select, validate and test SNPs for human identification.

PMID 18076761 · PMC2222643 · BMC genomics · 2007 · 8 claims · 7 setups

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A panel of 24 SNPs was selected and validated for human identification using 1,040 unrelated samples from three populations (Italian, Benin Gulf, Mongolian)

genomic genome pan blood snp sequence cross-species
An integrated in silico-in vitro approach for identifying therapeutic targets against osteoarthritis.

PMID 36352408 · PMC9648005 · BMC biology · 2022 · 7 claims · 5 setups

Has reproduction · 84

A signal transduction/gene regulatory network model of the articular chondrocyte was built combining knowledge-based curation and data-driven (machine learning) network inference

osteoarthritic articular chondrocyte microarray computational high-throughput
Hierarchical cell-type identifier accurately distinguishes immune-cell subtypes enabling precise profiling of tissue microenvironment with single-cell RNA-sequencing.

PMID 36681937 · PMC10025442 · Briefings in bioinformatics · 2023 · 8 claims · 8 setups

Has reproduction · 94

HiCAT is a hierarchical, marker-based cell-type identifier that uses gene set analysis (GSA) scoring with markers structured in a three-level taxonomy tree (major-type, minor-type, subset)

pbmc cord melanoma lung scrna-seq computational
Computational tradeoffs in multiplex PCR assay design for SNP genotyping.

PMID 16042802 · PMC1190169 · BMC genomics · 2005 · 7 claims · 6 setups

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Achieving high-multiplexing/high-coverage multiplex PCR designs is subject to a computational phase transition as the SNP-pair compatibility probability crosses a critical threshold

simulated real chromosome randomly simulation multiplex coverage-vs-n
Genes at human chromosome 5q31.1 regulate delayed-type hypersensitivity responses associated with Leishmania chagasi infection.

PMID 17713557 · PMC2435172 · Genes and immunity · 2007 · 7 claims · 8 setups

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SNPs in LECT2 and TGFBI show independent associations with the DTH+ phenotype, indicating two separate genes in this region control DTH+

blood family unrelated subjects snp family-based linkage
Does distance matter? Variations in alternative 3' splicing regulation.

PMID 17704130 · PMC2018619 · Nucleic acids research · 2007 · 8 claims · 7 setups

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Alternative 3' splice sites can be distinguished from constitutive splice sites by a combination of sequence/conservation properties that vary depending on the distance between the splice sites.

intronic human-mouse same comparative polypyrimidine branch
Species-Wide Phylogenomics of the Staphylococcus aureus Agr Operon Revealed Convergent Evolution of Frameshift Mutations.

PMID 35044202 · PMC8768832 · Microbiology spectrum · 2022 · 8 claims · 7 setups

Has reproduction · 79

AgrVATE, a novel kmer-based BLASTn and in silico PCR/Snippy pipeline, enables fast, standardized agr group typing and frameshift/null mutation detection from genome assemblies

aureus complete extracted agr kmer-based sheep mash
The Proteomic Code: a molecular recognition code for proteins.

PMID 17999762 · PMC2206014 · Theoretical biology & medical modelling · 2007 · 8 claims · 8 setups

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The Proteomic Code is a set of rules by which genetic information is transferred into the physico-chemical properties of amino acids, determining protein-protein interactions and folding; it is part of the redundant Genetic Code.

anti-peptide sequence exon smooth radioimmunoassay pairwise genome-wide
Evaluating the performance of commercial whole-genome marker sets for capturing common genetic variation.

PMID 17562002 · PMC1914356 · BMC genomics · 2007 · 8 claims · 5 setups

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Commercial SNP panels provide levels of coverage in a non-reference Caucasian (Estonian) population similar to those seen in the HapMap CEPH (CEU) population sample

estonian hapmap ceu snp tagsnp marker
The genomic distribution of intraspecific and interspecific sequence divergence of human segmental duplications relative to human/chimpanzee chromosomal rearrangements.

PMID 18699995 · PMC2542386 · BMC genomics · 2008 · 8 claims · 5 setups

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Some relatively recent (young) SDs accumulate in regions homologous to chromosomal inversions that occurred in the sister lineage

genome sds chimpanzee colinear comparative interspecific genomic

Experiments

Mycoplasma genitalium: an efficient strategy to generate genetic variation from a minimal genome.

Benchmarking tools for the alignment of functional noncoding DNA.

Genome-wide prediction of functional gene-gene interactions inferred from patterns of genetic differentiation in mice and men.

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

Transduplication resulted in the incorporation of two protein-coding sequences into the turmoil-1 transposable element of C. elegans.

Low conservation and species-specific evolution of alternative splicing in humans and mice: comparative genomics analysis using well-annotated full-length cDNAs.

Deep transcriptomics reveals cell-specific isoforms of pan-neuronal genes.

Emergent dynamics of underlying regulatory network links EMT and androgen receptor-dependent resistance in prostate cancer.

Improved eukaryotic detection compatible with large-scale automated analysis of metagenomes.

Leveraging human genomic information to identify nonhuman primate sequences for expression array development.

In silico and in vitro comparative analysis to select, validate and test SNPs for human identification.

An integrated in silico-in vitro approach for identifying therapeutic targets against osteoarthritis.

Hierarchical cell-type identifier accurately distinguishes immune-cell subtypes enabling precise profiling of tissue microenvironment with single-cell RNA-sequencing.

Computational tradeoffs in multiplex PCR assay design for SNP genotyping.

Genes at human chromosome 5q31.1 regulate delayed-type hypersensitivity responses associated with Leishmania chagasi infection.

Does distance matter? Variations in alternative 3' splicing regulation.

Species-Wide Phylogenomics of the Staphylococcus aureus Agr Operon Revealed Convergent Evolution of Frameshift Mutations.

The Proteomic Code: a molecular recognition code for proteins.

Evaluating the performance of commercial whole-genome marker sets for capturing common genetic variation.

The genomic distribution of intraspecific and interspecific sequence divergence of human segmental duplications relative to human/chimpanzee chromosomal rearrangements.