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 81

System / cell line: predicted ✕ Assay: region ✕ Clear

Mutation screen and association studies in the diacylglycerol O-acyltransferase homolog 2 gene (DGAT2), a positional candidate gene for early onset obesity on chromosome 11q13.

PMID 17477860 · PMC1871603 · BMC genetics · 2007 · 7 claims · 5 setups

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DGAT2 is a plausible positional and functional candidate gene for obesity due to its localization at chr.11q13 (a linkage region) and its key role in triglyceride synthesis

extremely families genome sanger case-control family-based
Predicting positive p53 cancer rescue regions using Most Informative Positive (MIP) active learning.

PMID 19756158 · PMC2742196 · PLoS computational biology · 2009 · 8 claims · 4 setups

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MIP active learning is a novel active learning method that preferentially seeks informative Positive (functionally active) examples rather than only maximizing classifier accuracy.

engineered p53 computational yeast-based regional homology
Improved mutation tagging with gene identifiers applied to membrane protein stability prediction.

PMID 19758467 · PMC2745585 · BMC bioinformatics · 2009 · 8 claims · 4 setups

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MutationTagger achieves 87% F-measure for the mutation retrieval task on a benchmark dataset

pubmed uniprot five mutation gene sequence
Sequence changes in predicted promoter elements of STK11/LKB1 are unlikely to contribute to Peutz-Jeghers syndrome.

PMID 15774015 · PMC1084245 · BMC genomics · 2005 · 6 claims · 4 setups

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Integrated phylogenetic foot printing and transcription factor binding site (TFBS) prediction identified a consensus putative STK11/LKB1 promoter region between nucleotides -1090 and -1472

genomic phylogenetic direct high
Coverage of whole proteome by structural genomics observed through protein homology modeling database.

PMID 17146617 · PMC1769342 · Journal of structural and functional genomics · 2006 · 8 claims · 7 setups

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FAMSBASE, a homology-modeling database of whole-genome ORFs, currently covers about 50% of predicted ORFs (368,724 of 734,193) across 276 genomes with modeled 3D structures.

orfs predicted modeled representative homology transmembrane intrinsic
ProMiR II: a web server for the probabilistic prediction of clustered, nonclustered, conserved and nonconserved microRNAs.

PMID 16845048 · PMC1538778 · Nucleic acids research · 2006 · 6 claims · 4 setups

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ProMiR II improves on the original ProMiR by integrating free energy, G/C ratio, conservation score and entropy for more controllable miRNA prediction

genome cytomegalovirus six probabilistic 5-fold directional
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
Human CCS gene: genomic organization and exclusion as a candidate for amyotrophic lateral sclerosis (ALS).

PMID 11991808 · PMC107843 · BMC genetics · 2002 · 6 claims · 5 setups

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The genomic organization of human CCS was characterized, with the 823 bp coding region organized into 8 exons spanning 12798 bp of genomic DNA.

bac heart ccs genomic genomic rt-pcr transcription
EGASP: the human ENCODE Genome Annotation Assessment Project.

PMID 16925836 · PMC1810551 · Genome biology · 2006 · 8 claims · 6 setups

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Best-performing computational gene prediction methods correctly predict at least one transcript for close to 70% of annotated genes in the ENCODE regions.

encode computational manual rt-pcr
In silico comparative genomic analysis of GABAA receptor transcriptional regulation.

PMID 17603907 · PMC1934366 · BMC genomics · 2007 · 8 claims · 8 setups

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Previously unreported putative promoters were identified for the β2, γ1, γ3, ε, θ and π GABA A receptor subunit genes

subunit mammalian α1-β2-γ2-α6 cross-species promoter transcription
Genetic parallels in biomineralization of the calcareous sponge Sycon ciliatum and stony corals.

PMID 40922549 · PMC12419799 · eLife · 2025 · 8 claims · 8 setups

Has reproduction · 50

829 genes are overexpressed in the oscular region of increased calcite spicule formation in S. ciliatum

sycon ciliatum sponges differential go-term genome
Unraveling the role of bacteria with heritable versus non-heritable relative abundance in the gut on boar semen quality.

PMID 41199168 · PMC12590650 · Genetics, selection, evolution : GSE · 2025 · 6 claims · 7 setups

Has reproduction · 61

39 heritable and 91 non-heritable bacterial genera were identified in the boar gut based on heritability of relative abundance

fecal blood boar gut 16s snp gas
Environment and Co-occurring Native Mussel Species, but Not Host Genetics, Impact the Microbiome of a Freshwater Invasive Species (Corbicula fluminea).

PMID 35444631 · PMC9014210 · Frontiers in microbiology · 2022 · 7 claims · 7 setups

Has reproduction · 55

The gut microbiome of C. fluminea is diverse, differs with environmental conditions, and varies spatially among rivers, but is unrelated to host genetic variation

corbicula six sediment filtered 16s radseq picrust2
F-SNP: computationally predicted functional SNPs for disease association studies.

PMID 17986460 · PMC2238878 · Nucleic acids research · 2008 · 6 claims · 8 setups

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F-SNP is a database integrating functional effect predictions for SNPs from 16 bioinformatics tools/databases across four categories: splicing, transcription, translation, and post-translation

genome protein-coding genomic genome-wide non-synonymous exonic nonsense
Rapid identification of PAX2/5/8 direct downstream targets in the otic vesicle by combinatorial use of bioinformatics tools.

PMID 18828907 · PMC2760872 · Genome biology · 2008 · 8 claims · 8 setups

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A combinatorial bioinformatics pipeline (evolutionary double filtering comparative genomics, GXD/ZFIN database queries, MEDLINE text mining) can rapidly and specifically identify PAX2/5/8 direct downstream targets in the otic vesicle

genome candidate gxd medline evolutionary gene expression
A novel 154-bp deletion in the human mitochondrial DNA control region in healthy individuals.

PMID 18629826 · PMC2697596 · Human mutation · 2008 · 8 claims · 5 setups

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A novel 154-bp mtDNA control region deletion (m.16154_16307del154) was identified in a healthy family

blood-derived mtdna pcr fragment mtdna
Predicting failure rate of PCR in large genomes.

PMID 18492719 · PMC2441781 · Nucleic acids research · 2008 · 7 claims · 8 setups

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The number of predicted primer-binding sites in genomic DNA is the most important factor determining PCR failure.

genomic genome pcr combined large-scale exact-match mismatch-tolerant
Mutation analysis of the AATF gene in breast cancer families.

PMID 20025740 · PMC2806411 · BMC cancer · 2009 · 6 claims · 6 setups

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No AATF sequence alteration identified was predicted to be pathogenic or showed significant association with breast cancer risk

genomic showing aatf case conformation direct pathogenicity
The pharmacogenomics of membrane transporters project: research at the interface of genomics and transporter pharmacology.

PMID 19940846 · PMC2923224 · Clinical pharmacology and therapeutics · 2010 · 8 claims · 8 setups

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PMT identified sequence variants in 129 membrane transporter genes in the SLC and ABC superfamilies, discovering over 3100 SNPs

sophie mammalian xenopus lymphoblastoid resequencing cellular heterologous
A novel polymorphism in the 1A promoter region of the vitamin D receptor is associated with altered susceptibilty and prognosis in malignant melanoma.

PMID 15238985 · PMC2364794 · British journal of cancer · 2004 · 7 claims · 6 setups

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A novel A-1012G (adenine-guanine) polymorphism exists in the VDR exon 1a promoter region, identified by SSCP screening and sequencing

blood variant patients same sscp sanger pcr-rflp

Experiments

Mutation screen and association studies in the diacylglycerol O-acyltransferase homolog 2 gene (DGAT2), a positional candidate gene for early onset obesity on chromosome 11q13.

Predicting positive p53 cancer rescue regions using Most Informative Positive (MIP) active learning.

Improved mutation tagging with gene identifiers applied to membrane protein stability prediction.

Sequence changes in predicted promoter elements of STK11/LKB1 are unlikely to contribute to Peutz-Jeghers syndrome.

Coverage of whole proteome by structural genomics observed through protein homology modeling database.

ProMiR II: a web server for the probabilistic prediction of clustered, nonclustered, conserved and nonconserved microRNAs.

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

Human CCS gene: genomic organization and exclusion as a candidate for amyotrophic lateral sclerosis (ALS).

EGASP: the human ENCODE Genome Annotation Assessment Project.

In silico comparative genomic analysis of GABAA receptor transcriptional regulation.

Genetic parallels in biomineralization of the calcareous sponge Sycon ciliatum and stony corals.

Unraveling the role of bacteria with heritable versus non-heritable relative abundance in the gut on boar semen quality.

Environment and Co-occurring Native Mussel Species, but Not Host Genetics, Impact the Microbiome of a Freshwater Invasive Species (Corbicula fluminea).

F-SNP: computationally predicted functional SNPs for disease association studies.

Rapid identification of PAX2/5/8 direct downstream targets in the otic vesicle by combinatorial use of bioinformatics tools.

A novel 154-bp deletion in the human mitochondrial DNA control region in healthy individuals.

Predicting failure rate of PCR in large genomes.

Mutation analysis of the AATF gene in breast cancer families.

The pharmacogenomics of membrane transporters project: research at the interface of genomics and transporter pharmacology.

A novel polymorphism in the 1A promoter region of the vitamin D receptor is associated with altered susceptibilty and prognosis in malignant melanoma.