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 25

System / cell line: structures ✕ Assay: type ✕ Clear

GLIDA: GPCR--ligand database for chemical genomics drug discovery--database and tools update.

PMID 17986454 · PMC2238933 · Nucleic acids research · 2008 · 7 claims · 5 setups

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GLIDA is a public relational database integrating biological information on GPCRs with chemical information on their ligands and their binding interactions.

ligand gpcr glida principal sequence gene
MutDB: update on development of tools for the biochemical analysis of genetic variation.

PMID 17827212 · PMC2238958 · Nucleic acids research · 2008 · 7 claims · 5 setups

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MutDB integrates dbSNP and Swiss-Prot genetic variation data with protein structural information, functional disruption prediction scores, and clinical phenotype links (OMIM, dbGAP)

proteins mutdb nonsynonymous genes sequence web functional
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
Double-strand breaks in the myotonic dystrophy type 1 and the fragile X syndrome triplet repeat sequences induce different types of mutations in DNA flanking sequences in Escherichia coli.

PMID 17012280 · PMC1636463 · Nucleic acids research · 2006 · 7 claims · 5 setups

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DSBs induced at the TRS/vector junction (EcoRV site) generate numerous mutagenic events in flanking sequences, whereas DSBs within the repeat tract (EcoRI site) produce no such mutants

coli plasmids plasmid white plasmid sequencing non-b
Using structural bioinformatics to investigate the impact of non synonymous SNPs and disease mutations: scope and limitations.

PMID 19758473 · PMC2745591 · BMC bioinformatics · 2009 · 8 claims · 8 setups

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None of 39 tested structural properties can be used as a sole classification criterion to separate neutral SNPs from disease mutations.

ensembl swissprot same structural foldx side
Early cAMP signaling orchestrates single-cell synchronicity throughout Dictyostelium development.

PMID 41792273 · PMC13096493 · Communications biology · 2026 · 7 claims · 6 setups

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cAMP-pulse signaling during early development induces transcriptome synchronicity at the single-cell level and morphological synchronicity at the multicellular level; its absence compromises synchronicity despite continued development.

discoideum single-cell scrna-seq dissecting
Dissecting the homeodomain MAT locus and engineering novel tripolar and bipolar mating systems in Cryptococcus amylolentus.

PMID 41841731 · PMC13059729 · mBio · 2026 · 8 claims · 8 setups

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A CRISPR-Cas9 gene editing system was developed and optimized for C. amylolentus

amylolentus diploid sxi1 mating scanning flow
AICellType: a large language model-based platform for accurate cell type annotation.

PMID 42001469 · PMC13092268 · Briefings in bioinformatics · 2026 · 8 claims · 8 setups

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Claude 3.5 Sonnet achieved the best overall performance among 79 benchmarked LLMs for cell type annotation, balancing accuracy, robustness, speed, and cost-efficiency

single-cell immune pbmc in-house llm-based scrna-seq spatial
An efficient method for the prediction of deleterious multiple-point mutations in the secondary structure of RNAs using suboptimal folding solutions.

PMID 18445289 · PMC2386494 · BMC bioinformatics · 2008 · 8 claims · 6 setups

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Using RNAsubopt suboptimal solutions computed once for the wild-type sequence, specific multiple-point mutations likely to cause conformational rearrangement can be selected without brute-force enumeration.

example hepatitis minimum suboptimal multiple-point
Cruciform extrusion propensity of human translocation-mediating palindromic AT-rich repeats.

PMID 17264116 · PMC1851657 · Nucleic acids research · 2007 · 8 claims · 4 setups

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Cruciform extrusion propensity of PATRRs depends on both length and central symmetry of the repeat.

plasmids same single-stranded patrr-containing cruciform endonuclease secondary
Prediction by graph theoretic measures of structural effects in proteins arising from non-synonymous single nucleotide polymorphisms.

PMID 18654622 · PMC2447880 · PLoS computational biology · 2008 · 8 claims · 5 setups

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Bongo identifies mutations causing local and global structural effects with a remarkably low false positive rate

p53 1bpi mutations disease-associated graph correlation structural
scDock: streamlining drug discovery targeting cell-cell communication via scRNA-seq analysis and molecular docking.

PMID 41769845 · PMC12996892 · Bioinformatics (Oxford, England) · 2026 · 8 claims · 5 setups

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scDock is an integrated pipeline connecting scRNA-seq processing, cell-cell communication inference, and molecular docking-based drug discovery through a single configuration file

diabetic kidney ppia glimepiride-ppia scrna-seq cell-cell type
Ultra-precision deconvolution of spatial transcriptomics decodes immune heterogeneity and fate-defining programs in tissues.

PMID 41862467 · PMC13168514 · Nature communications · 2026 · 8 claims · 8 setups

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UCASpatial is a novel deconvolution algorithm that uses Shannon entropy-based gene weighting combined with weighted non-negative least squares to estimate cell-type composition from spatial transcriptomics data

simulated colorectal hippocampus ear simulated runtime spatial
Finding the needle in the haystack: why high-throughput screening is good for your health.

PMID 12100740 · PMC138735 · Breast cancer research : BCR · 2002 · 8 claims · 8 setups

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HTS is essential for finding lead compounds, especially for novel targets whose active-site structure is unknown

raf-1 mitotic mutant tumor biochemical cell-based conformational
Disruption of the EGFR E884-R958 ion pair conserved in the human kinome differentially alters signaling and inhibitor sensitivity.

PMID 19015641 · PMC2633425 · Oncogene · 2009 · 8 claims · 8 setups

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E884K works in concert with L858R in-cis, in a dominant fashion, to differentially alter EGFR downstream signaling and inhibitor sensitivity in an inhibitor-specific manner

cos-7 kinase japanese western cellular mts
Gene prediction in eukaryotes with a generalized hidden Markov model that uses hints from external sources.

PMID 16469098 · PMC1409804 · BMC bioinformatics · 2006 · 7 claims · 3 setups

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AUGUSTUS+ extends the AUGUSTUS GHMM by combining intrinsic sequence information with extrinsic hints via an extended emission alphabet, so the GHMM jointly models the DNA sequence, gene structure, and hint collection.

chromosome genomic training ghmm-based sequence parameter
Mutations in the formin gene INF2 cause focal segmental glomerulosclerosis.

PMID 20023659 · PMC2980844 · Nature genetics · 2010 · 8 claims · 8 setups

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Mutations in INF2, a formin family actin-regulating protein, cause autosomal dominant focal segmental glomerulosclerosis (FSGS)

families genes individuals kidney genome-wide sanger resequencing
Unraveling the Causal Linkages of RBP7 and SCGB3A1 on Pelvic Organ Prolapse: Multifaceted Insights From Genome-Wide Mendelian Randomization, Single-Cell RNA Analysis, and Network Pharmacology.

PMID 41497737 · PMC12765987 · BioMed research international · 2026 · 8 claims · 7 setups

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High RBP7 expression causally increases POP risk

vaginal gwas rbp7 key single-cell mendelian protein-protein
Cell neighborhood topology directs rare cell population identification.

PMID 41912521 · PMC13199379 · Nature communications · 2026 · 8 claims · 8 setups

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RareQ is a framework that quantifies neighborhood connectivity (Q), a cell-specific measure of kNN-graph cliquishness, to detect rare cell populations from single-cell and spatial omics data

downsampled pbmc brain simulated scrna-seq cite-seq single-cell
DAVID Knowledgebase: a gene-centered database integrating heterogeneous gene annotation resources to facilitate high-throughput gene functional analysis.

PMID 17980028 · PMC2186358 · BMC bioinformatics · 2007 · 7 claims · 3 setups

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The DAVID Gene Concept, a single-linkage algorithm, merges gene clusters from Entrez Gene, UniRef100, and PIR-NREF100 that share protein IDs and species into unified DAVID gene clusters, improving cross-referencing between NCBI and UniProt systems

members entire usp8 sequence annotation

Experiments

GLIDA: GPCR--ligand database for chemical genomics drug discovery--database and tools update.

MutDB: update on development of tools for the biochemical analysis of genetic variation.

Opportunities and challenges in synthetic oligosaccharide and glycoconjugate research.

Double-strand breaks in the myotonic dystrophy type 1 and the fragile X syndrome triplet repeat sequences induce different types of mutations in DNA flanking sequences in Escherichia coli.

Using structural bioinformatics to investigate the impact of non synonymous SNPs and disease mutations: scope and limitations.

Early cAMP signaling orchestrates single-cell synchronicity throughout Dictyostelium development.

Dissecting the homeodomain MAT locus and engineering novel tripolar and bipolar mating systems in Cryptococcus amylolentus.

AICellType: a large language model-based platform for accurate cell type annotation.

An efficient method for the prediction of deleterious multiple-point mutations in the secondary structure of RNAs using suboptimal folding solutions.

Cruciform extrusion propensity of human translocation-mediating palindromic AT-rich repeats.

Prediction by graph theoretic measures of structural effects in proteins arising from non-synonymous single nucleotide polymorphisms.

scDock: streamlining drug discovery targeting cell-cell communication via scRNA-seq analysis and molecular docking.

Ultra-precision deconvolution of spatial transcriptomics decodes immune heterogeneity and fate-defining programs in tissues.

Finding the needle in the haystack: why high-throughput screening is good for your health.

Disruption of the EGFR E884-R958 ion pair conserved in the human kinome differentially alters signaling and inhibitor sensitivity.

Gene prediction in eukaryotes with a generalized hidden Markov model that uses hints from external sources.

Mutations in the formin gene INF2 cause focal segmental glomerulosclerosis.

Unraveling the Causal Linkages of RBP7 and SCGB3A1 on Pelvic Organ Prolapse: Multifaceted Insights From Genome-Wide Mendelian Randomization, Single-Cell RNA Analysis, and Network Pharmacology.

Cell neighborhood topology directs rare cell population identification.

DAVID Knowledgebase: a gene-centered database integrating heterogeneous gene annotation resources to facilitate high-throughput gene functional analysis.