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 31

System / cell line: independent ✕ Assay: identification ✕ Clear

Identification of common genetic variation that modulates alternative splicing.

PMID 17571926 · PMC1904363 · PLoS genetics · 2007 · 7 claims · 8 setups

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Common SNPs located close to intron-exon boundaries are associated with and causally modulate alternative splicing patterns in human genes

ceph lcls skipped additional rt-pcr snp resequencing
Recurrent RNA edits in human preimplantation potentially enhance maternal mRNA clearance.

PMID 36543858 · PMC9772385 · Communications biology · 2022 · 8 claims · 7 setups

Has reproduction · 100

Compiled the largest human embryonic A-to-I editome to date from 2071 RNA-seq transcriptomes and identified thousands of per-stage Recurrent Embryonic Edits (REEs, present in ≥50% of samples per stage)

preimplantation single uniparental embryos rna-seq paired gene
Computer-aided identification of polymorphism sets diagnostic for groups of bacterial and viral genetic variants.

PMID 17672919 · PMC1973086 · BMC bioinformatics · 2007 · 6 claims · 8 setups

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The Not-N algorithm, incorporated into the Minimum SNPs program, identifies small marker sets diagnostic for user-defined subgroups of genetic variants with 0% false negatives

hcv campylobacter yersinia clostridium snp comparative cgh
Molecular Classification Models for Triple Negative Breast Cancer Subtype Using Machine Learning.

PMID 34575658 · PMC8472680 · Journal of personalized medicine · 2021 · 6 claims · 4 setups

Has reproduction · 86

A training gene set of 719 unique upregulated DEGs (subtype-specific) can be used to build ML models that classify TNBC into BLIA, BLIS, MES, and LAR subtypes.

known tnbc unique unknown gene machine term
Proteomic and phospho-proteomic profile of human platelets in basal, resting state: insights into integrin signaling.

PMID 19859549 · PMC2762604 · PloS one · 2009 · 8 claims · 8 setups

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A comprehensive platelet proteome of 1507 unique proteins was identified from ten independent human platelet samples, the most comprehensive platelet proteome assembled to date

platelets platelet anti-coagulated lc-ms phospho-proteomic membrane
Rise of the machines.

PMID 18670625 · PMC2467494 · PLoS genetics · 2008 · 8 claims · 4 setups

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New short-read sequencing platforms (Illumina Genome Analyzer, 454 FLX, ABI SOLiD) enable rapid, scalable whole-genome resequencing that was previously restricted to dedicated sequencing centers using Sanger methods.

bacillus independent subtilis whole-genome read
Somatically acquired JAK1 mutations in adult acute lymphoblastic leukemia.

PMID 18362173 · PMC2292215 · The Journal of experimental medicine · 2008 · 8 claims · 8 setups

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Somatic JAK1 mutations occur in ALL and are more prevalent among adult T-cell precursor ALL (T-ALL) than B-ALL

genomic jak1-deficient u4c bw5147 dhplc stat1 cytokine-independent
2D-DIGE proteomic characterization of head and neck squamous cell carcinoma.

PMID 19861202 · PMC2847880 · Otolaryngology--head and neck surgery : official journal of American Academy of Otolaryngology-Head and Neck Surgery · 2009 · 8 claims · 4 setups

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Cornulin is downregulated in HNSCC relative to normal adjacent tissue and represents a novel biomarker in HNSCC.

hnscc excised independent identified 2d-dige lc-ms immunohistochemistry
Association of p53 gene mutations with short survival in pancreatic adenocarcinoma.

PMID 7730141 · PMC5920762 · Japanese journal of cancer research : Gann · 1995 · 8 claims · 4 setups

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p53 gene mutations were detected in 16 of 37 (43%) pancreatic adenocarcinomas by SSCP and direct sequencing

pancreatic single-strand direct univariate
Variation in the E2-binding domain of HPV 16 is associated with high-grade squamous intraepithelial lesions of the cervix.

PMID 11308254 · PMC2363853 · British journal of cancer · 2001 · 8 claims · 6 setups

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E2 gene disruption in the analysed regions is significantly more frequent in high-grade SILs than low-grade SILs

paraffin-embedded hpv16-positive representative cervical pcr restriction bidirectional
INI1 mutations in meningiomas at a potential hotspot in exon 9.

PMID 11161377 · PMC2363707 · British journal of cancer · 2001 · 6 claims · 5 setups

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A recurrent somatic INI1 mutation (G1130A, Arg377His) occurs at a hotspot in exon 9 in a subset of meningiomas.

meningioma re-extracted sscp direct pcr
Polymorphism at the C-reactive protein locus influences gene expression and predisposes to systemic lupus erythematosus.

PMID 14645206 · PMC3707088 · Human molecular genetics · 2004 · 8 claims · 5 setups

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The minor (rare) allele of CRP SNP 'CRP 4' is associated/linked with development of SLE in family-based transmission studies.

crp simplex same serum direct family-based linkage
Analysis of the human Alu Ye lineage.

PMID 15725352 · PMC554112 · BMC evolutionary biology · 2005 · 8 claims · 6 setups

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Two new Alu subfamilies, Ye4 and Ye6, were discovered, complementing the previously described Ye5 subfamily.

draft genomic non-human geographically blast sequence pcr
An investigation of polymorphisms in the 17q11.2-12 CC chemokine gene cluster for association with multiple sclerosis in Australians.

PMID 16872505 · PMC1550395 · BMC medical genetics · 2006 · 7 claims · 7 setups

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Marginally significant (uncorrected) transmission distortion was found for four SNPs after stratification by HLA-DRB1*1501 status, disease course, or gender.

pooled australian independent trio pool snapshot snplex
Meta-analysis of inter-species liver co-expression networks elucidates traits associated with common human diseases.

PMID 20019805 · PMC2787626 · PLoS computational biology · 2009 · 8 claims · 8 setups

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A novel semi-parametric meta-analysis method (based on a gene-centric Glass's d effect size) outperforms existing parametric and non-parametric meta-analysis methods at identifying functionally coherent gene pairs across species.

liver simulated conserved nearly gene simulation kolmogorov-smirnov
Sequences of complete human cytomegalovirus genomes from infected cell cultures and clinical specimens.

PMID 19906940 · PMC2885759 · The Journal of general virology · 2010 · 8 claims · 5 setups

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Both PCR sequencing and IGA sequencing (via de novo assembly guiding reference-dependent assembly plus PCR finishing) can successfully generate complete HCMV genome sequences from infected cell cultures and clinical specimens

hcmv six pcr illumina reference-dependent
Single-cell protein activity analysis reveals aberrant myogenesis and IGF2-PI3K pathway dependencies in MYOD1-mutant rhabdomyosarcoma.

PMID 41758938 · PMC12947870 · Science advances · 2026 · 8 claims · 8 setups

Has reproduction · 84

MYOD1 L122R-mutant SRMS tumors contain three coexisting, conserved cell states (progenitor, transition, differentiated) reflecting aberrant myogenic differentiation

patient-derived tumor single paired single-nucleus infercnv aracne-ap
Enthoprotin: a novel clathrin-associated protein identified through subcellular proteomics.

PMID 12213833 · PMC2173151 · The Journal of cell biology · 2002 · 8 claims · 8 setups

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Subcellular proteomics of purified CCVs identifies enthoprotin (encoded by KIAA0171), a novel ENTH domain-containing protein not previously detected at the protein level.

brain cos-7 hek-293 clathrin subcellular western ccv
Recent segmental and gene duplications in the mouse genome.

PMID 12914656 · PMC193640 · Genome biology · 2003 · 8 claims · 8 setups

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33.6 Mb (1.2%) of the February 2003 mouse genome assembly (2,695 Mb) is involved in recent segmental duplications

genome gene ensembl-annotated chromosome pairwise gene blat
Proteomic analysis of nipple aspirate fluid from women with early-stage breast cancer using isotope-coded affinity tags and tandem mass spectrometry reveals differential expression of vitamin D binding protein.

PMID 16542425 · PMC1431555 · BMC cancer · 2006 · 8 claims · 5 setups

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ICAT tandem MS can identify and quantify differences in specific protein expression between NAF from tumor-bearing and disease-free breasts

paired icat-labeled spectra naf icat sds-page liquid

Experiments

Identification of common genetic variation that modulates alternative splicing.

Recurrent RNA edits in human preimplantation potentially enhance maternal mRNA clearance.

Computer-aided identification of polymorphism sets diagnostic for groups of bacterial and viral genetic variants.

Molecular Classification Models for Triple Negative Breast Cancer Subtype Using Machine Learning.

Proteomic and phospho-proteomic profile of human platelets in basal, resting state: insights into integrin signaling.

Rise of the machines.

Somatically acquired JAK1 mutations in adult acute lymphoblastic leukemia.

2D-DIGE proteomic characterization of head and neck squamous cell carcinoma.

Association of p53 gene mutations with short survival in pancreatic adenocarcinoma.

Variation in the E2-binding domain of HPV 16 is associated with high-grade squamous intraepithelial lesions of the cervix.

INI1 mutations in meningiomas at a potential hotspot in exon 9.

Polymorphism at the C-reactive protein locus influences gene expression and predisposes to systemic lupus erythematosus.

Analysis of the human Alu Ye lineage.

An investigation of polymorphisms in the 17q11.2-12 CC chemokine gene cluster for association with multiple sclerosis in Australians.

Meta-analysis of inter-species liver co-expression networks elucidates traits associated with common human diseases.

Sequences of complete human cytomegalovirus genomes from infected cell cultures and clinical specimens.

Single-cell protein activity analysis reveals aberrant myogenesis and IGF2-PI3K pathway dependencies in MYOD1-mutant rhabdomyosarcoma.

Enthoprotin: a novel clathrin-associated protein identified through subcellular proteomics.

Recent segmental and gene duplications in the mouse genome.

Proteomic analysis of nipple aspirate fluid from women with early-stage breast cancer using isotope-coded affinity tags and tandem mass spectrometry reveals differential expression of vitamin D binding protein.