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).
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Proteomic approaches to cancer biomarkers.
PMID 19931265 · PMC2873613 · Gastroenterology · 2010 · 8 claims · 8 setups
Combining abundant-protein depletion, offline fractionation, and subproteome (e.g., glycoproteome) enrichment with 2D LC-MS/MS increases the dynamic range and depth of blood proteome analysis for biomarker discovery.
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Has reproduction · 67
Therapeutic Stress-Induced Remodeling of Transposable Elements and TE-Gene Chimeras in KYSE150 Esophageal Squamous Cell Carcinoma Cells.
PMID 42074115 · PMC13116134 · International journal of molecular sciences · 2026 · 8 claims · 8 setups
Combined 125I radiation and carfilzomib treatment causes structured, non-random remodeling of the TE transcriptome in KYSE150 ESCC cells.
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Novel approaches for identifying target antigens of autoreactive human B and T cells.
PMID 19763575 · PMC2845891 · Seminars in immunopathology · 2009 · 8 claims · 8 setups
CD8+ T cells infiltrating MS brain and IM muscle tissue show clonal expansions consistent with antigen-driven selection
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Lost in the world of functional genomics, systems biology, and translational research: is there life after the Milstein award?
PMID 17681845 · PMC1994668 · Cytokine & growth factor reviews · 2007 · 8 claims · 8 setups
Genomic and proteomic approaches provide a comprehensive view of virus-host interactions and advance understanding of innate immunity and interferon/cytokine signaling
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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
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.
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High-resolution, high-throughput HLA genotyping by next-generation sequencing.
PMID 19845894 · PMC4205125 · Tissue antigens · 2009 · 7 claims · 5 setups
Clonal 454 sequencing reads (>250 nt) are long enough to span HLA exons and set phase of linked polymorphisms, resolving ambiguities inherent to Sanger-based heterozygote sequencing.
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Has reproduction · 64
GeMI: interactive interface for transformer-based Genomic Metadata Integration.
PMID 35657113 · PMC9216561 · Database : the journal of biological databases and curation · 2022 · 8 claims · 5 setups
GeMI is a web tool that uses a fine-tuned GPT2 model to extract 15 structured key-value attributes from free-text GEO sample metadata.
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Has reproduction · 63
Clustering and machine learning-based integration identify cancer associated fibroblasts genes' signature in head and neck squamous cell carcinoma.
PMID 37065499 · PMC10098459 · Frontiers in genetics · 2023 · 8 claims · 8 setups
Clustering of 31 CAFs genes across 868 HNSCC samples identifies two distinct molecular patterns (C1, C2) with different survival outcomes
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Has reproduction · 84
A scalable, open-source implementation of a large-scale mechanistic model for single cell proliferation and death signaling.
PMID 35729113 · PMC9213456 · Nature communications · 2022 · 7 claims · 5 setups
Developed a python-based, scalable model creation and simulation pipeline that converts structured text files into an SBML-standard model and is high-performance/cloud-computing ready.
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PubMatrix: a tool for multiplex literature mining.
PMID 14667255 · PMC317283 · BMC bioinformatics · 2003 · 8 claims · 3 setups
PubMatrix is a web-based CGI tool that queries PubMed with two lists of terms (search terms vs modifier terms) and returns a matrix of pairwise co-occurrence frequency counts
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Systems biology and the host response to viral infection.
PMID 18066032 · PMC7097743 · Nature biotechnology · 2007 · 8 claims · 8 setups
Systems biology integration of 'omics data (transcriptomics, proteomics, genomics) with computational modeling is needed to fully understand virus-host interactions and identify novel antiviral targets
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Expression genomics in breast cancer research: microarrays at the crossroads of biology and medicine.
PMID 17397520 · PMC1868923 · Breast cancer research : BCR · 2007 · 8 claims · 8 setups
Genome-wide expression microarray studies reveal transcriptional networks/signatures that explain breast cancer biological and clinical heterogeneity
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Has reproduction · 99
Systematic benchmarking of tools for CpG methylation detection from nanopore sequencing.
PMID 34103501 · PMC8187371 · Nature communications · 2021 · 7 claims · 4 setups
Nanopore methylation detection tools exhibit a tradeoff between false positives and false negatives and high dispersion relative to expected per-site methylation frequencies.
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Has reproduction · 85
Systematic Analysis of Long Non-Coding RNA Genes in Nonalcoholic Fatty Liver Disease.
PMID 35893239 · PMC9332188 · Non-coding RNA · 2022 · 6 claims · 5 setups
Many lncRNAs, like protein-coding genes, are differentially expressed in NAFLD patients compared to healthy normal-weight and obese individuals.
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The genomic analysis of lactic acidosis and acidosis response in human cancers.
PMID 19057672 · PMC2585811 · PLoS genetics · 2008 · 8 claims · 8 setups
Lactic acidosis and hypoxia induce largely distinct gene expression programs in HMECs, with lactic acidosis producing a much larger and more dramatic response