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).

• Human and mouse oligonucleotide-based array CGH.

  PMID 16361265 · PMC1316119 · Nucleic acids research · 2005 · 8 claims · 8 setups

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  Oligo array CGH detects single copy gains, multi-copy amplifications, and homozygous/heterozygous deletions as small as 100 kb

  bt474 normal gm01750 mda-mb-468 array fish

• A statistical approach for array CGH data analysis.

  PMID 15705208 · PMC549559 · BMC bioinformatics · 2005 · 8 claims · 4 setups

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  Existing model-selection criteria (AIC, BIC, and prior ad hoc penalties) are not well adapted to estimating the number of segments in array CGH data

  fibroblast simulated bt474 dissected array numerical

• HIV replication enhances production of free fatty acids, low density lipoproteins and many key proteins involved in lipid metabolism: a proteomics study.

  PMID 18714345 · PMC2500163 · PloS one · 2008 · 7 claims · 4 setups

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  HIV infection of a human T-cell line differentially regulates 18 proteins involved in lipid metabolism.

  t-cell identified gel maldi-tof bioinformatics

• Identification of direct regulatory targets of the transcription factor Sox10 based on function and conservation.

  PMID 18786246 · PMC2556353 · BMC genomics · 2008 · 6 claims · 6 setups

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  PLP, Sox10, SOD3, and Ptn are direct regulatory targets of Sox10, confirmed by chromatin immunoprecipitation binding to conserved cis-elements

  rt4d6 gst-sox10 microarray comparative real

• Sensitive detection of copy number alterations in low-pass liquid biopsy sequencing data.

  PMID 41838873 · PMC12991053 · Briefings in bioinformatics · 2026 · 8 claims · 3 setups

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  BayesCNA uses Bayesian changepoint (BCP) detection on posterior changepoint probabilities to segment the genome and reconstruct copy number profiles from low-pass liquid biopsy data.

  synthetically cell-line blood sequencing low-pass

• Detection of chromosomal structural alterations in single cells by SNP arrays: a systematic survey of amplification bias and optimized workflow.

  PMID 18074030 · PMC2111048 · PloS one · 2007 · 8 claims · 7 setups

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  MDA-based single-cell whole-genome amplification (S-WGA) products show large variability in amplification bias, including allele dropout and preferential amplification.

  lymphoblastoid lcl cmk11-5 gel taqman oligonucleotide

• Genomic variation in myeloma: design, content, and initial application of the Bank On A Cure SNP Panel to detect associations with progression-free survival.

  PMID 18778477 · PMC2553089 · BMC medicine · 2008 · 7 claims · 7 setups

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  A custom BOAC SNP panel of 3404 SNPs in 983 genes was developed using the Affymetrix GeneChip Targeted Genotyping Platform, focused on non-synonymous coding SNPs and regulatory-region SNPs in candidate genes.

  coriell myeloma duplicate snp targeted genotyping machine

• High resolution melting for mutation scanning of TP53 exons 5-8.

  PMID 17764544 · PMC2025602 · BMC cancer · 2007 · 7 claims · 5 setups

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  HRM is an effective technique for rapid scanning of TP53 mutations that can markedly reduce required sequencing

  tp53-mutant ovarian breast high hrm dideoxy

• Proteolysis of the endothelial cell protein C receptor by neutrophil proteinase 3.

  PMID 17459006 · PMC1890847 · Journal of thrombosis and haemostasis : JTH · 2007 · 8 claims · 8 setups

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  Activated neutrophils decrease EPCR surface expression on endothelial cells over time

  ea.hy926 peripheral neutrophils recombinant flow luminol-dependent sds-page

• Glycomic approach for potential biomarkers on prostate cancer: profiling of N-linked glycans in human sera and pRNS cell lines.

  PMID 19126968 · PMC3827814 · Disease markers · 2008 · 8 claims · 5 setups

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  Glycomic profiling of N-linked glycans in serum can reveal potential biomarkers distinguishing prostate cancer patients from controls

  serum prns-1-1 n-linked maldi solid tandem

• PredTAD: A machine learning framework that models 3D chromatin organization alterations leading to oncogene dysregulation in breast cancer cell lines.

  PMID 34093998 · PMC8142020 · Computational and structural biotechnology journal · 2021 · 6 claims · 8 setups

  Has reproduction · 77

  PredTAD, a Gradient Boosting Machine model using epigenomic and genomic ChIP-seq-derived features plus neighboring-bin information, classifies 10 kb genomic bins as TAD boundary or non-boundary

  mcf10a t47d mcf7 tcga hi-c chip-seq atac-seq

• The use of laser capture microscopy in proteomics research--a review.

  PMID 15502248 · PMC3839334 · Disease markers · 2004 · 8 claims · 8 setups

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  LCM allows purification of specific, histologically defined cell populations from heterogeneous tissue for downstream proteomic analysis

  breast prostate esophageal head maldi-tof automated two-dimensional

• Genome annotation of a 1.5 Mb region of human chromosome 6q23 encompassing a quantitative trait locus for fetal hemoglobin expression in adults.

  PMID 15169551 · PMC441375 · BMC genomics · 2004 · 8 claims · 8 setups

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  A very large, previously uncharacterized gene, AHI1, containing WD40 and SH3 domains was discovered in the candidate interval

  cdna image hbs1l ahi1 rt-pcr est northern

• The specificity of the FOXL2 c.402C>G somatic mutation: a survey of solid tumors.

  PMID 19956657 · PMC2777318 · PloS one · 2009 · 6 claims · 4 setups

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  The FOXL2 c.402C>G mutation is not commonly found in a wide variety of other cancers and is likely pathognomonic for A-GCTs and closely related tumors.

  tumor ovarian kgn high sanger taqman

• Uncertainty-aware genomic deep learning with knowledge distillation.

  PMID 41523993 · PMC12779563 · NPJ artificial intelligence · 2026 · 7 claims · 6 setups

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  DEGU distills an ensemble of teacher DNNs into a single student model by jointly predicting the ensemble mean and the variability (epistemic uncertainty) across ensemble predictions.

  drosophila k562 deepstarr starr-seq starr-seq-derived lentimpra base-resolution

• An integrated in silico-in vitro approach for identifying therapeutic targets against osteoarthritis.

  PMID 36352408 · PMC9648005 · BMC biology · 2022 · 7 claims · 5 setups

  Has reproduction · 84

  A signal transduction/gene regulatory network model of the articular chondrocyte was built combining knowledge-based curation and data-driven (machine learning) network inference

  osteoarthritic articular chondrocyte microarray computational high-throughput

• Modeling nascent transcription from chromatin landscape and structure with CLASTER.

  PMID 41691282 · PMC13011747 · Genome biology · 2026 · 7 claims · 8 setups

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  CLASTER, a deep neural network combining chromatin landscape tracks and 3D contact maps, accurately predicts kilobasepair-resolution nascent RNA (EU-seq) profiles in a DNA-sequence-agnostic manner

  embryonic mescs chromatin k562 eu-seq chip-seq micro-c

• Proteome analysis enables separate clustering of normal breast, benign breast and breast cancer tissues.

  PMID 12865921 · PMC2394238 · British journal of cancer · 2003 · 6 claims · 3 setups

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  Hierarchical cluster analysis of 2-DE proteome data can distinguish normal breast, benign breast, and breast cancer tissues based on protein expression profiles

  breast two-dimensional hierarchical mann-whitney

• arrayCGHbase: an analysis platform for comparative genomic hybridization microarrays.

  PMID 15910681 · PMC1173083 · BMC bioinformatics · 2005 · 8 claims · 4 setups

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  arrayCGHbase is a MIAME-compliant, web-based database and analysis platform that stores, analyzes, interprets, compares, and visualizes arrayCGH data in a uniform format.

  hellemans boy distal cancer arraycgh

• Spatially clustered loci with multiple enhancers are frequent targets of HIV-1 integration.

  PMID 31492853 · PMC6731298 · Nature communications · 2019 · 8 claims · 8 setups

  Has reproduction · 77

  Recurrently targeted HIV-1 integration genes (RIGs) are proximal to super-enhancer (SE) genomic elements

  activated cd4+ cd3 jurkat chip-seq hiv-1 sequencing