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 21

System / cell line: tissues ✕ Assay: nucleotide ✕ Clear

Positive selection for the male functionality of a co-retroposed gene in the hominoids.

PMID 19832993 · PMC2773790 · BMC evolutionary biology · 2009 · 8 claims · 8 setups

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PIPSL is an extraordinary co-retroposed protein-coding gene that may participate in male-specific functions of humans and close relatives

african chimpanzee orangutan reconstructed population hka comparative
Interpretable prediction models for widespread m6A RNA modification across cell lines and tissues.

PMID 37995291 · PMC10697738 · Bioinformatics (Oxford, England) · 2023 · 8 claims · 8 setups

Has reproduction · 79

CLSM6A is a set of CNN-based deep learning models that predict single-nucleotide-resolution m6A RNA modification sites across eight cell lines and three tissues in H. sapiens

hct116 a549 brain hek293t miclip m6a-clip-seq m6a-seq
TEDD: a comprehensive database for translation efficiency dynamics.

PMID 41217970 · PMC12807600 · Nucleic acids research · 2026 · 8 claims · 4 setups

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TEDD integrates 1518 RNA-seq, Ribo-seq, and RNC-seq samples from 143 human projects (279 datasets) spanning 24 tissues/cell types, 74 cell lines, and 52 conditions.

tissues reference rna-seq ribo-seq rnc-seq
Variant-resolved prediction of context-specific isoform variation with a graph-based attention model.

PMID 41547351 · PMC13069856 · Cell genomics · 2026 · 8 claims · 8 setups

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Otari, an attention-based graph neural network trained on long-read transcriptomes across 30 tissues/brain regions, predicts tissue-specific differential isoform abundance

tissues genomic gtex hgmd long-read variant splice
'Genome design' model and multicellular complexity: golden middle.

PMID 17062620 · PMC1635334 · Nucleic acids research · 2006 · 8 claims · 8 setups

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Intermediately expressed human genes are the longest genes genome-wide, in both coding and intronic sequence, longer than housekeeping or tissue-specific genes.

normal genes proteins encoded oligonucleotide gene functional
pmid-41568004

PMID 41568004 · PMC12816324 · 8 claims · 8 setups

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CiTLR13 is a redundant annotation of CiTLR1 (same genomic locus, >94% sequence identity), so it is not a distinct TLR gene

ciona six lrr tlr blastp domain nucleotide
K-ras point mutation occurs in the early stage of carcinogenesis in lung cancer.

PMID 9514049 · PMC2149957 · British journal of cancer · 1998 · 6 claims · 4 setups

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K-ras codon 12 mutation is present in all carcinoma lesions examined with no intratumour heterogeneity, consistent with an early carcinogenic event

resected pcr-rflp-positive lung pcr-rflp direct selective
Mutational inactivation of mitotic checkpoint genes, hsMAD2 and hBUB1, is rare in sporadic digestive tract cancers.

PMID 10543255 · PMC5926140 · Japanese journal of cancer research : Gann · 1999 · 6 claims · 4 setups

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Mutation of the hsMAD2 gene was not observed in any of the 32 sporadic digestive tract cancers examined.

sporadic same tumor hsmad2 rt-pcr-sscp dnase direct
Decoding the interconnected splicing patterns of hepatitis B virus and host using large language and deep learning models.

PMID 41543530 · PMC12811152 · Microbial genomics · 2026 · 8 claims · 8 setups

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HBV splicing efficiency (coSI) correlates more strongly with disease progression than the overall proportion of spliced HBV RNA.

hbv same host bulk splicing splicebert
Organismal complexity, cell differentiation and gene expression: human over mouse.

PMID 17881362 · PMC2095826 · Nucleic acids research · 2007 · 8 claims · 7 setups

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Human shows a greater fraction of tissue-specific genes and a greater ratio of total expression of tissue-specific to housekeeping genes than mouse across 32 homologous tissues

human-mouse oligonucleotide exon comparative
Genome wide identification of recessive cancer genes by combinatorial mutation analysis.

PMID 18846217 · PMC2557123 · PloS one · 2008 · 7 claims · 4 setups

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A combinatorial mutation analysis identified 154 candidate recessive cancer genes (pRecessiveCancer<1.5x10-7, FDR=0.39)

refseq tp53 tumor 154-gene est paired array
Gene Expression Atlas update--a value-added database of microarray and sequencing-based functional genomics experiments.

PMID 22064864 · PMC3245177 · Nucleic acids research · 2012 · 8 claims · 5 setups

Has reproduction · 83

Gene Expression Atlas is an added-value database providing curated, re-annotated and statistically analysed gene expression data across cell types, organism parts, developmental stages, disease states and other biological/experimental conditions, derived from ArrayExpress Archive and the European Nucleotide Archive.

species microrna atlas microarray rna-seq microrna
Phylogenomic approaches to common problems encountered in the analysis of low copy repeats: the sulfotransferase 1A gene family example.

PMID 15752422 · PMC555591 · BMC evolutionary biology · 2005 · 8 claims · 8 setups

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A previously unidentified fourth human SULT1A gene (SULT1A4) exists on chromosome 16 and is transcriptionally active

genome chimpanzee sult1a3 est blast-like comparative pairwise
CircleBase V2: an eccDNA annotation platform across cancers and species.

PMID 41273082 · PMC12807720 · Nucleic acids research · 2026 · 8 claims · 7 setups

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CircleBase V2 provides a 12-fold increase in human eccDNA data, comprising over 3.8 million entries from >300 cell types/tissues

raw eccdna tissues cancer circle-seq motif gene
A gene encoding antigenic peptides of human squamous cell carcinoma recognized by cytotoxic T lymphocytes.

PMID 9449708 · PMC2212124 · The Journal of experimental medicine · 1998 · 8 claims · 8 setups

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A gene, SART-1, encoding antigenic peptides recognized by HLA-A2601-restricted CTLs was identified from human squamous cell carcinoma cells.

ke4 normal pbmcs va13 expression northern western
The absence of Mth1 inactivation and DNA polymerase kappa overexpression in rat mammary carcinomas with frequent A:T to C:G transversions.

PMID 12036445 · PMC5927037 · Japanese journal of cancer research : Gann · 2002 · 8 claims · 5 setups

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SNI (elevated spontaneous point mutation rate without microsatellite instability) is present in rat mammary carcinoma cell lines and human breast cancer cell lines

mammary same normal pcr-sscp direct quantitative
Direct evidence of extensive diversity of HIV-1 in Kinshasa by 1960.

PMID 18833279 · PMC3682493 · Nature · 2008 · 7 claims · 8 setups

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Recovered and characterized HIV-1 sequences (DRC60) from a 1960 Bouin's-fixed paraffin-embedded lymph node biopsy from Léopoldville, Belgian Congo

archival hiv-1-positive cdna concatenated rt-pcr quantitative pcr
Genotypic analysis of two hypervariable human cytomegalovirus genes.

PMID 18649324 · PMC2658010 · Journal of medical virology · 2008 · 8 claims · 8 setups

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UL146 sequences from 184 samples fall into the same 14 genotypes (G1-G14) previously defined, with no new genotypes found.

hcmv clinical pcr ul146 pcr nested molecular
Mutation of the nm23 gene, loss of heterozygosity at the nm23 locus and K-ras mutation in ovarian carcinoma: correlation with tumour progression and nm23 gene expression.

PMID 7669582 · PMC2033876 · British journal of cancer · 1995 · 8 claims · 5 setups

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A novel missense mutation (TGG→CGG, Trp133→Arg) in nm23-H2 was found in one stage III serous ovarian carcinoma

ovarian case matched same pcr-sscp subcloning loh
A big circuit model.

PMID 12940284 · PMC1316925 · Environmental health perspectives · 2003 · 8 claims · 8 setups

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In early prostate carcinogenesis, apoptosis signals are primarily suppressed rather than growth rate being increased.

prostate blood model genes microarray proteomic gene

Experiments

Positive selection for the male functionality of a co-retroposed gene in the hominoids.

Interpretable prediction models for widespread m6A RNA modification across cell lines and tissues.

TEDD: a comprehensive database for translation efficiency dynamics.

Variant-resolved prediction of context-specific isoform variation with a graph-based attention model.

'Genome design' model and multicellular complexity: golden middle.

pmid-41568004

K-ras point mutation occurs in the early stage of carcinogenesis in lung cancer.

Mutational inactivation of mitotic checkpoint genes, hsMAD2 and hBUB1, is rare in sporadic digestive tract cancers.

Decoding the interconnected splicing patterns of hepatitis B virus and host using large language and deep learning models.

Organismal complexity, cell differentiation and gene expression: human over mouse.

Genome wide identification of recessive cancer genes by combinatorial mutation analysis.

Gene Expression Atlas update--a value-added database of microarray and sequencing-based functional genomics experiments.

Phylogenomic approaches to common problems encountered in the analysis of low copy repeats: the sulfotransferase 1A gene family example.

CircleBase V2: an eccDNA annotation platform across cancers and species.

A gene encoding antigenic peptides of human squamous cell carcinoma recognized by cytotoxic T lymphocytes.

The absence of Mth1 inactivation and DNA polymerase kappa overexpression in rat mammary carcinomas with frequent A:T to C:G transversions.

Direct evidence of extensive diversity of HIV-1 in Kinshasa by 1960.

Genotypic analysis of two hypervariable human cytomegalovirus genes.

Mutation of the nm23 gene, loss of heterozygosity at the nm23 locus and K-ras mutation in ovarian carcinoma: correlation with tumour progression and nm23 gene expression.

A big circuit model.