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 293

System / cell line: domain ✕ Clear

Helminth genomics: The implications for human health.

PMID 19855829 · PMC2757907 · PLoS neglected tropical diseases · 2009 · 8 claims · 7 setups

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More than two billion people (one-third of humanity) are infected with helminth parasites, causing major morbidity, mortality, and poverty maintenance

helminth nematode schistosoma strongyloides phylogenetic genome expressed
High resolution analysis of the human transcriptome: detection of extensive alternative splicing independent of transcriptional activity.

PMID 19804644 · PMC2768739 · BMC genetics · 2009 · 8 claims · 6 setups

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The human GWSA uses exon body and exon-exon junction probes to directly measure over 280,000 known and predicted splicing events genome-wide.

universal same lim erythrocyte genome-wide cross-platform rt-pcr
SilkDB v2.0: a platform for silkworm (Bombyx mori ) genome biology.

PMID 19793867 · PMC2808975 · Nucleic acids research · 2010 · 8 claims · 8 setups

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A new 8.5x-coverage silkworm genome assembly with N50 scaffold size of ~3.7 Mb over a 432 Mb genome represents a significant quality improvement over the prior draft.

bombyx whole-genome snp novo
Extraction of human kinase mutations from literature, databases and genotyping studies.

PMID 19758464 · PMC2745582 · BMC bioinformatics · 2009 · 7 claims · 6 setups

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A literature mining pipeline combining MutationFinder, false-positive filtering, and SVM-based classification can extract and disambiguate single-point mutation mentions from abstracts and full text

pubmed large labeled swissprot literature supervised comparative
Escape from autologous neutralizing antibodies in acute/early subtype C HIV-1 infection requires multiple pathways.

PMID 19763269 · PMC2741593 · PLoS pathogens · 2009 · 8 claims · 7 setups

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Viral escape from autologous Nab occurred repeatedly (cyclically) throughout the first two years of infection in two subtype C-infected subjects despite high-titer Nab responses.

hiv-1 longitudinal 0-month single pseudovirus single site-directed
Divide and conquer: progress in the molecular stratification of cancer.

PMID 19718393 · PMC2730607 · Yonsei medical journal · 2009 · 8 claims · 8 setups

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Cancers exhibit significant clinical, histopathologic, and molecular heterogeneity between individual patients

breast nsclc colon early-stage immunohistochemistry gene comparative
Optimization of protein solubilization for the analysis of the CD14 human monocyte membrane proteome using LC-MS/MS.

PMID 19709643 · PMC3159575 · Journal of proteomics · 2009 · 7 claims · 5 setups

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Methanol-based solubilization, alone or combined with PPS, yields significantly higher membrane protein identification/enrichment than PPS alone in monocyte membrane proteomics

bacteriorhodopsin crude immuno-affinity lc-ms sds-page shotgun facs
A novel TACSTD2 mutation identified in two Chinese brothers with gelatinous drop-like corneal dystrophy.

PMID 19693293 · PMC2728569 · Molecular vision · 2009 · 7 claims · 5 setups

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A novel in-frame 51 bp deletion (c.526_576del51) in TACSTD2, causing loss of 17 amino acids (codons 176-192), was identified as homozygous in two affected brothers with GDLD.

genomic excised left pcr pcr-restriction histopathology
Cyclic olefin homopolymer-based microfluidics for protein crystallization and in situ X-ray diffraction.

PMID 19690369 · PMC2733880 · Acta crystallographica. Section D, Biological crystallography · 2009 · 8 claims · 7 setups

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A COP-based microfluidics system (SpinX cards, 500 chambers of 320 nl each) was established for protein crystallization and in situ X-ray diffraction.

chicken bovine p53 arabidopsis microbatch situ vapour-diffusion
A novel UBIAD1 mutation identified in a Chinese family with Schnyder crystalline corneal dystrophy.

PMID 19649163 · PMC2718742 · Molecular vision · 2009 · 7 claims · 7 setups

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A novel heterozygous UBIAD1 mutation, G98S, was identified in two affected members (proband and her father) of a Chinese SCCD family.

genomic cornea corneas blood direct pcr laser
Proteomic-based identification of maternal proteins in mature mouse oocytes.

PMID 19646285 · PMC2730056 · BMC genomics · 2009 · 8 claims · 6 setups

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625 different proteins were identified from 2700 zona pellucida-free mature mouse MII oocytes, the largest oocyte proteome catalog to date

mature mii identified tissues sds-page acid gene
NOD-like receptor repertoire in the chromosome-level genome of the demosponge Dysidea avara (Schmidt, 1862).

PMID 41710890 · PMC12909245 · Frontiers in immunology · 2026 · 8 claims · 8 setups

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Dysidea avara has a chromosome-level genome assembly of 575 Mb, N50 41 Mb, 162 scaffolds, and 15 chromosomes.

dysidea avara translated nlrs long-read hi-c genome
Much ado about nothing: modeling amino acid replacement with predicted protein structures.

PMID 42036821 · PMC13171170 · Bioinformatics (Oxford, England) · 2026 · 8 claims · 7 setups

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AFSM was constructed from over 660,000 structural alignments across ~21,000 proteins (297 InterPro families), following the BLOSUM log-odds methodology.

proteins balibase pfam cath structural sequence remote
MicroRNA Enrichment and Docking-Based Evaluation of Ilomastat Targeting of MMP-2 in Esophageal Squamous Cell Carcinoma: Insights from a South African Cohort.

PMID 42158110 · PMC13181172 · Computational and structural biotechnology journal · 2026 · 7 claims · 5 setups

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The miR-29 family inhibits MMP-2 and represents a key regulatory axis in tumor invasion

paired deg mmp-2 escc bulk pathway molecular
Stress Responsive bZIP Transcription Factors ATF4 and BACH1 Cooperate With MAF-Family bZIP Protein NRL to Fine-Tune Rod Photoreceptor Gene Expression.

PMID 42246540 · PMC13249099 · Investigative ophthalmology & visual science · 2026 · 8 claims · 7 setups

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ATF4 and BACH1 are identified as bZIP protein interactors of NRL

y2hgold hek293 p28 flow-sorted yeast co-immunoprecipitation immunofluorescence
Spatial Transcriptomics of Human Decidua Identifies Molecular Signatures in Recurrent Pregnancy Loss.

PMID 41031483 · PMC13242933 · Genomics, proteomics & bioinformatics · 2026 · 7 claims · 8 setups

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The human decidua contains two coherent spatial domains, the implantation zone (IZ) and glandular-secretory zone (GZ), corresponding to the decidua compacta and spongiosa

first-trimester decidual spots dnk 10x h&e type
scXDR: drug response prediction across single-cell datasets via heterogeneous network transfer learning.

PMID 41507436 · PMC12859067 · Communications biology · 2026 · 7 claims · 7 setups

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scXDR outperforms seven methods that transfer drug response information from bulk RNA-seq to single-cell data, across all four evaluated scenarios

single-cell scrna-seq scxdr gse117872 heterogeneous benchmarking type
Short activation domains control chromatin association of transcription factors.

PMID 41511382 · PMC12788797 · eLife · 2026 · 8 claims · 8 setups

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Short activation domains (39-60 aa, only 5-7% of the synthetic TF) dominate the chromatin-bound fraction of a synthetic transcription factor.

u2os synthetic single-molecule flow fluorescence
Small molecule splicing modulators that disrupt O-GlcNAc homeostasis.

PMID 41526361 · PMC12894984 · Nature communications · 2026 · 8 claims · 7 setups

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Kinase inhibitors GSK690693 and Y-33075 act as splicing modulators that disrupt O-GlcNAc homeostasis by simultaneously downregulating both OGT and OGA

hct116 recombinant hek293t high-content western udp-glo
SGCEdb: a flexible database and web interface integrating experimental results and analysis for structural genomics focusing on Caenorhabditis elegans.

PMID 16381914 · PMC1347399 · Nucleic acids research · 2006 · 8 claims · 8 setups

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SGCEdb is a flexible, reusable database and web interface for reporting and analyzing structural genomics experiment results, focused on C. elegans

elegans expressed soluble crystallized recombinant solubility purification

Experiments

Helminth genomics: The implications for human health.

High resolution analysis of the human transcriptome: detection of extensive alternative splicing independent of transcriptional activity.

SilkDB v2.0: a platform for silkworm (Bombyx mori ) genome biology.

Extraction of human kinase mutations from literature, databases and genotyping studies.

Escape from autologous neutralizing antibodies in acute/early subtype C HIV-1 infection requires multiple pathways.

Divide and conquer: progress in the molecular stratification of cancer.

Optimization of protein solubilization for the analysis of the CD14 human monocyte membrane proteome using LC-MS/MS.

A novel TACSTD2 mutation identified in two Chinese brothers with gelatinous drop-like corneal dystrophy.

Cyclic olefin homopolymer-based microfluidics for protein crystallization and in situ X-ray diffraction.

A novel UBIAD1 mutation identified in a Chinese family with Schnyder crystalline corneal dystrophy.

Proteomic-based identification of maternal proteins in mature mouse oocytes.

NOD-like receptor repertoire in the chromosome-level genome of the demosponge Dysidea avara (Schmidt, 1862).

Much ado about nothing: modeling amino acid replacement with predicted protein structures.

MicroRNA Enrichment and Docking-Based Evaluation of Ilomastat Targeting of MMP-2 in Esophageal Squamous Cell Carcinoma: Insights from a South African Cohort.

Stress Responsive bZIP Transcription Factors ATF4 and BACH1 Cooperate With MAF-Family bZIP Protein NRL to Fine-Tune Rod Photoreceptor Gene Expression.

Spatial Transcriptomics of Human Decidua Identifies Molecular Signatures in Recurrent Pregnancy Loss.

scXDR: drug response prediction across single-cell datasets via heterogeneous network transfer learning.

Short activation domains control chromatin association of transcription factors.

Small molecule splicing modulators that disrupt O-GlcNAc homeostasis.

SGCEdb: a flexible database and web interface integrating experimental results and analysis for structural genomics focusing on Caenorhabditis elegans.