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 18

System / cell line: using ✕ Assay: functional ✕ Clear

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
Functional coverage of the human genome by existing structures, structural genomics targets, and homology models.

PMID 16118666 · PMC1188274 · PLoS computational biology · 2005 · 8 claims · 5 setups

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Existing PDB structures provide single-domain coverage for 37% of functional classes in the human genome and complete (whole-protein) structure coverage for 25%.

genome functional registered omim comparative kendall's homology
Using random walks to identify cancer-associated modules in expression data.

PMID 24128261 · PMC4015830 · BioData mining · 2013 · 8 claims · 8 setups

Has reproduction

Walktrap-GM, a random-walk community detection algorithm adapted with stopping criteria (maximum modularity, maximum size, maximum module score), identifies modules significantly enriched with cancer genes in expression-weighted interaction networks.

hepatocellular breast sporadic geo gene differential interaction
Revealing the critical state and identifying individualized dynamic network biomarker for type 2 diabetes through advanced analysis methods on individual basis.

PMID 39890881 · PMC11785715 · Scientific reports · 2025 · 8 claims · 5 setups

Has reproduction · 75

sJSD, NIG, and TNFE methods can detect critical states/tipping points before disease deterioration using only a single sample

simulated adipose gastrocnemius dnb numerical microarray protein-protein
L1Base: from functional annotation to prediction of active LINE-1 elements.

PMID 15608246 · PMC539998 · Nucleic acids research · 2005 · 7 claims · 6 setups

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L1Base is a database of putatively active LINE-1 insertions in human, mouse and rat genomes, containing FLI-L1s (intact in both ORFs), ORF2-L1s (intact ORF2, disrupted ORF1), and FLnI-L1s (full-length, >6000 bp, non-intact)

sapiens orf1 orf fli-l1s genomic repeatmasker hmm-profile
Coverage and characteristics of the Affymetrix GeneChip Human Mapping 100K SNP set.

PMID 16680197 · PMC1456318 · PLoS genetics · 2006 · 7 claims · 7 setups

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SNPs in the Affymetrix 100K set are undersampled from coding regions (both synonymous and nonsynonymous) and oversampled from regions outside genes, relative to HapMap SNPs

genome autosomal hapmap chromosome snp chromosomal minor
Analytical code sharing practices in biomedical research.

PMID 38983240 · PMC11232620 · PeerJ. Computer science · 2024 · 8 claims · 4 setups

Has reproduction · 92

Nearly half (49.9%) of 453 examined biomedical manuscripts failed to share the analytical code used to generate their results

biomedical manuscripts journals subset bibliometric chi-square odds
Exploration of the omics evidence landscape: adding qualitative labels to predicted protein-protein interactions.

PMID 17880677 · PMC2375035 · Genome biology · 2007 · 7 claims · 8 setups

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Combining pairs of omics evidence types into two-dimensional 'evidence landscapes' allows regions to be identified that specifically and purely predict either physical or metabolic protein interactions

saccharomyces correlated chip-chip gene
Genome-wide prioritization of disease genes and identification of disease-disease associations from an integrated human functional linkage network.

PMID 19728866 · PMC2768980 · Genome biology · 2009 · 6 claims · 6 setups

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Integrating 16 genomic features (32 sub-features) via a naïve Bayes classifier produces a genome-scale FLN of 21,657 human genes and 22,388,609 weighted links that outperforms any individual data source for inferring functional linkages.

genome gene omim known naïve linkage disease-centric
A chromosome-level reference genome and pangenome for barn swallow population genomics.

PMID 36662619 · PMC10044405 · Cell reports · 2023 · 8 claims · 8 setups

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A chromosome-level, karyotype-validated reference genome (bHirRus1) was assembled using the VGP pipeline combining PacBio CLR, 10x Linked-Reads, Bionano optical maps, and Hi-C data

single barn bhirrus1 rustica genome cytogenetic reference-free
Integrated weighted gene co-expression network analysis with an application to chronic fatigue syndrome.

PMID 18986552 · PMC2625353 · BMC systems biology · 2008 · 8 claims · 6 setups

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Integrated WGCNA (IWGCNA), which adds genetic marker-based causality testing to standard WGCNA, can identify a disease-related module and its causal drivers

cfs most candidate second microarray snp weighted
Genome-Wide Survey and Development of the First Microsatellite Markers Database (AnCorDB) in Anemone coronaria L.

PMID 35328546 · PMC8949970 · International journal of molecular sciences · 2022 · 8 claims · 8 setups

Has reproduction · 55

Generated the first draft genome assembly of A. coronaria by Illumina sequencing a haploid androgenetic plant

haploid mistral assembled masked whole-genome k-mer genome-wide
Genome-wide in silico identification and analysis of cis natural antisense transcripts (cis-NATs) in ten species.

PMID 16849434 · PMC1524920 · Nucleic acids research · 2006 · 8 claims · 7 setups

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A fast integrative in silico pipeline combining UniGene mRNA/EST mapping to GoldenPath genomes with CDS, poly(A) signal, poly(A) tail and splicing site evidence can reliably identify cis-NATs genome-wide across multiple species

est gene worm fly blat-based transcription comparative
Separating selection from mutation in antibody language models.

PMID 41944291 · PMC13056363 · eLife · 2026 · 8 claims · 6 setups

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Masked antibody language models such as AbLang2 are biased by nucleotide-level mutation processes (germline memorization, codon table, SHM rate variation)

single nine antibody reconstructed masked-site correlation functional
Inferring combinatorial regulation of transcription in silico.

PMID 15647509 · PMC546154 · Nucleic acids research · 2005 · 8 claims · 5 setups

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Combining Cluster-Buster (TFBS cluster prediction) with GOSSIP (rigorous GO enrichment statistics with multiple-testing/FDR correction) predicts biological functions controlled by combinatorial transcription factor action, without prior knowledge of factor targets

upstream monocytes same tfbs microarray permutation
Alternative splicing dynamics during human cardiac development in vivo and in vitro.

PMID 41483812 · PMC12925949 · Stem cell reports · 2026 · 8 claims · 8 setups

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iPSC-CMs globally resemble prenatal cardiac cells at both the transcriptional and splicing levels

ipsc-cms heart bulk ipsc-cm immunofluorescence single-cell bulk
Biocomputing enters its adolescence.

PMID 15960815 · PMC1175967 · Genome biology · 2005 · 8 claims · 8 setups

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A 'match augmentation' algorithm efficiently matches structural motifs by prioritizing functionally significant residues, enabling function prediction between evolutionarily unrelated proteins

bank antibody-antigen yeast genome protein-protein empirical integrative
Pancreatic tumours: molecular pathways implicated in ductal cancer are involved in ampullary but not in exocrine nonductal or endocrine tumorigenesis.

PMID 11161385 · PMC2363700 · British journal of cancer · 2001 · 8 claims · 6 setups

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PDC shows frequent alterations of K-ras, p53, p16 and DPC4, confirming these as the core molecular fingerprint of ductal cancer

pancreatic same tumor pet sscp methylation-specific microsatellite

Experiments

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

Functional coverage of the human genome by existing structures, structural genomics targets, and homology models.

Using random walks to identify cancer-associated modules in expression data.

Revealing the critical state and identifying individualized dynamic network biomarker for type 2 diabetes through advanced analysis methods on individual basis.

L1Base: from functional annotation to prediction of active LINE-1 elements.

Coverage and characteristics of the Affymetrix GeneChip Human Mapping 100K SNP set.

Analytical code sharing practices in biomedical research.

Exploration of the omics evidence landscape: adding qualitative labels to predicted protein-protein interactions.

Genome-wide prioritization of disease genes and identification of disease-disease associations from an integrated human functional linkage network.

A chromosome-level reference genome and pangenome for barn swallow population genomics.

Integrated weighted gene co-expression network analysis with an application to chronic fatigue syndrome.

Genome-Wide Survey and Development of the First Microsatellite Markers Database (AnCorDB) in Anemone coronaria L.

Genome-wide in silico identification and analysis of cis natural antisense transcripts (cis-NATs) in ten species.

Separating selection from mutation in antibody language models.

Inferring combinatorial regulation of transcription in silico.

Alternative splicing dynamics during human cardiac development in vivo and in vitro.

Biocomputing enters its adolescence.

Pancreatic tumours: molecular pathways implicated in ductal cancer are involved in ampullary but not in exocrine nonductal or endocrine tumorigenesis.