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 99

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Systematic identification of pseudogenes through whole genome expression evidence profiling.

PMID 16945953 · PMC1636364 · Nucleic acids research · 2006 · 8 claims · 8 setups

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Developed a novel bioinformatics method that identifies pseudogenes by profiling whole-genome transcript and protein expression evidence

genome ensembl vega celera spliced protein-to-genome pseudogene
Comprehensive splice-site analysis using comparative genomics.

PMID 16914448 · PMC1557818 · Nucleic acids research · 2006 · 8 claims · 6 setups

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Over half a million splice sites were collected from five species (H. sapiens, M. musculus, D. melanogaster, C. elegans, A. thaliana) and classified into four main subtypes: U2-type GT-AG and GC-AG, and U12-type GT-AG and AT-AC.

refseq u2-type genes comparative information phylogenetic
Comparison of characteristics and function of translation termination signals between and within prokaryotic and eukaryotic organisms.

PMID 16614446 · PMC1435984 · Nucleic acids research · 2006 · 8 claims · 5 setups

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A core termination signal of 4 nt (stop codon plus the following nucleotide) is preferred across most prokaryotic and eukaryotic genomes

orf coli rabbit cos-7 bioinformatic codon prokaryotic
Optimality driven nearest centroid classification from genomic data.

PMID 17912341 · PMC1991588 · PloS one · 2007 · 7 claims · 5 setups

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A theoretical result determines the subset of features of a given size that minimizes the misclassification rate for a nearest-centroid (LDA) classifier, based on equation (4).

artificial simulated previously-published simulated simulation clinical
Subarachnoid hemorrhage: tests of association with apolipoprotein E and elastin genes.

PMID 17672902 · PMC1950089 · BMC medical genetics · 2007 · 8 claims · 6 setups

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The major APOE haplotype (Hap1) is significantly associated with SAH

caucasian same genomic snp rflp genome
Motif discovery in promoters of genes co-localized and co-expressed during myeloid cells differentiation.

PMID 19059999 · PMC2632922 · Nucleic acids research · 2009 · 6 claims · 8 setups

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A novel multi-step computational method (built on approximate pattern enumeration, binomial over-representation scoring with FDR correction, and k-medoids clustering) can identify over-represented motifs in a selected set of promoters relative to a background promoter set.

myeloid reference selected genome-localized microarray promoter k-medoids
Aggregation propensity of the human proteome.

PMID 18927604 · PMC2557143 · PLoS computational biology · 2008 · 8 claims · 7 setups

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Long proteins have, on average, less intense/pronounced aggregation peaks than short proteins

proteome non-membrane proteins membrane sequence-based correlation statistical
Exhaustive prediction of disease susceptibility to coding base changes in the human genome.

PMID 18793467 · PMC2537574 · BMC bioinformatics · 2008 · 8 claims · 7 setups

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Inter-species conservation is the strongest single predictor of disease-associated coding mutations among the factors tested.

hgmd refseq aligned svm svm reciprocal inter-species
Genomic variation in myeloma: design, content, and initial application of the Bank On A Cure SNP Panel to detect associations with progression-free survival.

PMID 18778477 · PMC2553089 · BMC medicine · 2008 · 7 claims · 7 setups

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A custom BOAC SNP panel of 3404 SNPs in 983 genes was developed using the Affymetrix GeneChip Targeted Genotyping Platform, focused on non-synonymous coding SNPs and regulatory-region SNPs in candidate genes.

coriell myeloma duplicate snp targeted genotyping machine
PRESTO: rapid calculation of order statistic distributions and multiple-testing adjusted P-values via permutation for one and two-stage genetic association studies.

PMID 18620604 · PMC2483288 · BMC bioinformatics · 2008 · 8 claims · 4 setups

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PRESTO is an order of magnitude faster than other existing permutation testing software for genetic association studies.

case-control same wtccc genome-wide benchmark stratified
A comparative study of techniques for differential expression analysis on RNA-Seq data.

PMID 25119138 · PMC4132098 · PloS one · 2014 · 8 claims · 8 setups

Has reproduction · 58

edgeR performs slightly better than DESeq and Cuffdiff2 in terms of the ability to uncover true positives.

brain neurospheres lymphoblastoid simulation single-end paired-end rna-seq
A global view of protein expression in human cells, tissues, and organs.

PMID 20029370 · PMC2824494 · Molecular systems biology · 2009 · 7 claims · 6 setups

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A high fraction (>65%) of proteins is expressed in most human cells and tissues, while very few proteins (<2%) are detected in any single cell type.

normal computational hepatocytes same immunohistochemistry immunofluorescence unsupervised
Ultra high throughput sequencing excludes MDH1 as candidate gene for RP28-linked retinitis pigmentosa.

PMID 20011630 · PMC2790479 · Molecular vision · 2009 · 8 claims · 5 setups

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MDH1 is not the causative gene for RP28-linked autosomal recessive retinitis pigmentosa

genomic lr-pcr uhts v-4 long-range ultra sanger
Needles in the haystack: identifying individuals present in pooled genomic data.

PMID 19798441 · PMC2747273 · PLoS genetics · 2009 · 8 claims · 7 setups

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The distribution of T for null samples (individuals not in F or G) deviates strongly from the assumed standard normal, in both location and width.

cgems hapmap genetic-distance within-population snp-count
Swarm intelligence based wavelet coefficient feature selection for mass spectral classification: an application to proteomics data.

PMID 19733729 · PMC2748225 · Analytica chimica acta · 2009 · 8 claims · 4 setups

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ACA-based wavelet coefficient feature selection can achieve up to 100% classification accuracy on training, validating, and independent testing sets using only 5 selected features.

blood baseline-corrected 953-dimensional training seldi-tof wavelet ant
Clustering by neurocognition for fine mapping of the schizophrenia susceptibility loci on chromosome 6p.

PMID 19694819 · PMC4286260 · Genes, brain, and behavior · 2009 · 6 claims · 6 setups

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A family-based clustering strategy using neurocognitive test scores (CPT, WCST) can identify more homogeneous subgroups of schizophrenia families for genetic association analysis

multiplex affected subjects cluster-specific family-based continuous wisconsin
Teasing apart the joint effect of demography and natural selection in the birth of a contact zone.

PMID 36093739 · PMC9828440 · The New phytologist · 2022 · 8 claims · 8 setups

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Natural selection contributed to the establishment and maintenance of the Scandinavian contact zone between the NFE and CSE genetic clusters.

picea swedish subsets exome principal umap
Single-cell analysis of signalling and transcriptional responses to type I interferons.

PMID 41896367 · PMC13172048 · EMBO reports · 2026 · 7 claims · 6 setups

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Different immune cell types show cell-type-specific patterns of STAT phosphorylation and gene expression changes in response to type I IFN

freshly pbmcs mass rt-qpcr bulk
Single-cell lineage tracing identifies hemogenic endothelial cells in the adult mouse bone marrow.

PMID 42043300 · PMC13120821 · eLife · 2026 · 8 claims · 8 setups

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Adult bone marrow-resident Cdh5/VE-Cadherin+ endothelial cells produce hematopoietic cell progeny both in vitro and in vivo.

bone lin sorted lethally flow confocal sorted-cell
Integrating single-cell and bulk transcriptomes identifies B cell features associated with neoadjuvant chemoradiotherapy sensitivity in rectal cancer.

PMID 41484196 · PMC12800305 · Scientific reports · 2026 · 8 claims · 8 setups

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A B cell subpopulation co-expressing HLA-DRB5, HLA-DQA2, HLA-DQB1, CD74, and ACTG1 is significantly associated with favorable nCRT response in rectal cancer

larc scrna-seq scissor+ single-cell bulk pseudotime

Experiments

Systematic identification of pseudogenes through whole genome expression evidence profiling.

Comprehensive splice-site analysis using comparative genomics.

Comparison of characteristics and function of translation termination signals between and within prokaryotic and eukaryotic organisms.

Optimality driven nearest centroid classification from genomic data.

Subarachnoid hemorrhage: tests of association with apolipoprotein E and elastin genes.

Motif discovery in promoters of genes co-localized and co-expressed during myeloid cells differentiation.

Aggregation propensity of the human proteome.

Exhaustive prediction of disease susceptibility to coding base changes in the human genome.

Genomic variation in myeloma: design, content, and initial application of the Bank On A Cure SNP Panel to detect associations with progression-free survival.

PRESTO: rapid calculation of order statistic distributions and multiple-testing adjusted P-values via permutation for one and two-stage genetic association studies.

A comparative study of techniques for differential expression analysis on RNA-Seq data.

A global view of protein expression in human cells, tissues, and organs.

Ultra high throughput sequencing excludes MDH1 as candidate gene for RP28-linked retinitis pigmentosa.

Needles in the haystack: identifying individuals present in pooled genomic data.

Swarm intelligence based wavelet coefficient feature selection for mass spectral classification: an application to proteomics data.

Clustering by neurocognition for fine mapping of the schizophrenia susceptibility loci on chromosome 6p.

Teasing apart the joint effect of demography and natural selection in the birth of a contact zone.

Single-cell analysis of signalling and transcriptional responses to type I interferons.

Single-cell lineage tracing identifies hemogenic endothelial cells in the adult mouse bone marrow.

Integrating single-cell and bulk transcriptomes identifies B cell features associated with neoadjuvant chemoradiotherapy sensitivity in rectal cancer.