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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A statistical change point model approach for the detection of DNA copy number variations in array CGH data.
PMID 19875853 · PMC4154476 · IEEE/ACM transactions on computational biology and bioinformatics · 2009 · 7 claims · 4 setups
A novel mean and variance change point model (MVCM) is proposed to detect CNVs/breakpoints in aCGH data.
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Predicting failure rate of PCR in large genomes.
PMID 18492719 · PMC2441781 · Nucleic acids research · 2008 · 7 claims · 8 setups
The number of predicted primer-binding sites in genomic DNA is the most important factor determining PCR failure.
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An oncogenomics-based in vivo RNAi screen identifies tumor suppressors in liver cancer.
PMID 19012953 · PMC2990916 · Cell · 2008 · 7 claims · 8 setups
shRNA pools targeting genes recurrently deleted in human HCC accelerate hepatocarcinogenesis in vivo, whereas randomly selected shRNA pools do not.
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Screening large-scale association study data: exploiting interactions using random forests.
PMID 15588316 · PMC545646 · BMC genetics · 2004 · 7 claims · 3 setups
Random forest importance measure significantly outperforms the Fisher Exact test as a screening tool when risk SNPs interact.
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Expansion of the Bactericidal/Permeability Increasing-like (BPI-like) protein locus in cattle.
PMID 17362520 · PMC1839098 · BMC genomics · 2007 · 8 claims · 8 setups
The bovine BPI-like locus spans 470 kbp and contains 14 contiguous genes (13 intact + 1 pseudogene); 9 are orthologous to human/mouse BPI-like genes and 4 (named BSP30A, BSP30B, BSP30C, BSP30D) arose through cattle-specific duplication of the PSP gene
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The fragile breakage versus random breakage models of chromosome evolution.
PMID 16501665 · PMC1378107 · PLoS computational biology · 2006 · 8 claims · 6 setups
Sankoff and Trinh's synteny block identification algorithm (ST-Synteny) is flawed, producing erroneous block identifications even in small toy examples.
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Complete genome sequence and comparative analysis of the wild-type commensal Escherichia coli strain SE11 isolated from a healthy adult.
PMID 18931093 · PMC2608844 · DNA research : an international journal for rapid publication of reports on genes and genomes · 2008 · 8 claims · 6 setups
The SE11 genome comprises a 4.8 Mb chromosome encoding 4679 protein-coding genes and six plasmids encoding 323 protein-coding genes
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Functional copy-number alterations in cancer.
PMID 18784837 · PMC2527508 · PloS one · 2008 · 8 claims · 3 setups
RAE is a comprehensive computational framework that robustly maps chromosomal alterations in tumor samples and statistically assesses their functional importance in cancer.
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Has reproduction · 65
High-throughput sequencing SELEX for the determination of DNA-binding protein specificities in vitro.
PMID 35776646 · PMC9243297 · STAR protocols · 2022 · 8 claims · 8 setups
HT-SELEX enables unbiased, in vitro determination of preferred DNA target motifs for DNA-binding proteins by iterative selection and PCR amplification of bound oligonucleotides
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Disease-aging network reveals significant roles of aging genes in connecting genetic diseases.
PMID 19779549 · PMC2739292 · PLoS computational biology · 2009 · 8 claims · 8 setups
Human disease genes are much closer to aging genes in the PPI network than expected by chance
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Has reproduction
Predicting favorable landing pads for targeted integrations in Chinese hamster ovary cell lines by learning stability characteristics from random transgene integrations.
PMID 33304461 · PMC7710658 · Computational and structural biotechnology journal · 2020 · 7 claims · 6 setups
Expression stability in CHO cell lines is controlled at three levels: choice of integration site, integrity/concatemerization pattern of the transgene, and stress-related cellular processes.
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Ab initio identification of human microRNAs based on structure motifs.
PMID 18088431 · PMC2238772 · BMC bioinformatics · 2007 · 8 claims · 7 setups
MiRPred predicts miRNA precursors ab initio using only predicted secondary structure motifs, ignoring nucleotide sequence
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Construction and use of spotted large-insert clone DNA microarrays for the detection of genomic copy number changes.
PMID 17406619 · PMC2688820 · Nature protocols · 2007 · 8 claims · 7 setups
Combining three human-optimized DOP-PCR primers before a secondary amino-labeled PCR increases array hybridization sensitivity and reproducibility sixfold compared to the standard 6MW DOP-PCR primer
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Has reproduction · 94
Topological signatures in regulatory network enable phenotypic heterogeneity in small cell lung cancer.
PMID 33729159 · PMC8012062 · eLife · 2021 · 7 claims · 6 setups
Discrete (Boolean/Ising) and continuous (RACIPE) simulations of the SCLC regulatory network yield similar multistable phenotypic distributions, with four dominant steady states (X1-X4) that map onto experimentally observed SCLC molecular subtypes.
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Optimal step length EM algorithm (OSLEM) for the estimation of haplotype frequency and its application in lipoprotein lipase genotyping.
PMID 12529185 · PMC149347 · BMC bioinformatics · 2003 · 5 claims · 4 setups
OSLEM (Optimal Step Length EM), which approximates an optimal step length via a fixed-point search (D_N = D_{N-1} + λ(D_preN - D_{N-1})), runs about twice as fast as standard EM while producing the same haplotype frequency estimates.
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Computational tradeoffs in multiplex PCR assay design for SNP genotyping.
PMID 16042802 · PMC1190169 · BMC genomics · 2005 · 7 claims · 6 setups
Achieving high-multiplexing/high-coverage multiplex PCR designs is subject to a computational phase transition as the SNP-pair compatibility probability crosses a critical threshold
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Evaluation of two methods for computational HLA haplotypes inference using a real dataset.
PMID 18230173 · PMC2268655 · BMC bioinformatics · 2008 · 8 claims · 5 setups
PHASE v2.1.1 had the best overall performance in both haplotype construction and frequency calculation compared to Arlequin V3.0
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Widespread dysregulation of MiRNAs by MYCN amplification and chromosomal imbalances in neuroblastoma: association of miRNA expression with survival.
PMID 19924232 · PMC2773120 · PloS one · 2009 · 8 claims · 5 setups
37 miRNAs are significantly differentially expressed between MYCN-amplified (MNA) and non-MNA neuroblastoma tumors, suggesting direct or indirect regulation by MYCN
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Compensatory mutations cause excess of antagonistic epistasis in RNA secondary structure folding.
PMID 12590655 · PMC149451 · BMC evolutionary biology · 2003 · 6 claims · 1 setups
RNA secondary structure folding shows a clear prevalence of antagonistic epistasis (β < 1) among reference sequences
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Has reproduction · 75
Sequencing of human genomes with nanopore technology.
PMID 31015479 · PMC6478738 · Nature communications · 2019 · 8 claims · 7 setups
A novel single-sample, reference panel-free, read-based phasing algorithm built on the STITCH model improves nanopore SNV calling from modest baseline levels.