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).

• Computational tradeoffs in multiplex PCR assay design for SNP genotyping.

  PMID 16042802 · PMC1190169 · BMC genomics · 2005 · 7 claims · 6 setups

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  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

  simulated real chromosome randomly simulation multiplex coverage-vs-n

• Multiplexed discovery of sequence polymorphisms using base-specific cleavage and MALDI-TOF MS.

  PMID 15731331 · PMC549577 · Nucleic acids research · 2005 · 8 claims · 7 setups

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  Multiplexed base-specific cleavage/MALDI-TOF MS (Multiplexed Comparative Sequence Analysis) enables simultaneous discovery of sequence polymorphisms across multiple target regions

  ensembl genomic simulation pcr maldi-tof

• Design and analysis issues in genome-wide somatic mutation studies of cancer.

  PMID 18692126 · PMC2820387 · Genomics · 2009 · 6 claims · 4 setups

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  Two-stage (discovery + validation) sequencing designs efficiently allocate resources and can produce highly informative candidate driver gene lists even with relatively small sample sizes.

  hypothetical panel colorectal germline simulation targeted genome-wide

• Quality control method for RNA-seq using single nucleotide polymorphism allele frequency.

  PMID 25243705 · PMC4231238 · Genes to cells : devoted to molecular & cellular mechanisms · 2014 · 8 claims · 8 setups

  Has reproduction · 50

  SNP allele frequency distributions from RNA-seq reads can detect contaminating cells whose genomic background differs from the target cells; the mode of the distribution reflects the cellular composition while its variance reflects PCR bias.

  mathematical escs pure stap simulation rna-seq contamination

• Benchmarking tools for deciphering cellular crosstalk in spatially-resolved transcriptomics.

  PMID 41952215 · PMC13174004 · Genome biology · 2026 · 8 claims · 5 setups

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  No prior systematic, quantitative benchmark exists for CCI inference methods specifically developed for spatial transcriptomics across multiple platforms

  synthetic real simulated simulation spot-purity real-data

• spliceJAC: transition genes and state-specific gene regulation from single-cell transcriptome data.

  PMID 36321549 · PMC9627675 · Molecular systems biology · 2022 · 8 claims · 8 setups

  Has reproduction · 53

  spliceJAC uses unspliced and spliced mRNA count matrices to construct cell state-specific gene-gene regulatory interaction (Jacobian) matrices from scRNA-seq data

  bistable three-gene emt circuits simulation mixed-state grn

• RNA modifications detection by comparative Nanopore direct RNA sequencing.

  PMID 34893601 · PMC8664944 · Nature communications · 2021 · 7 claims · 5 setups

  Has reproduction · 50

  Nanocompore is a model-free comparative method that uses a 2-component Gaussian mixture model (GMM) and univariate statistical tests on signal intensity/dwell time to detect RNA modifications in Nanopore direct RNA sequencing data without needing a training set

  simulated synthetic escherichia saccharomyces nanopore computational

• Differential expression analysis in single-cell and spatial RNA-seq without model assumptions.

  PMID 41980775 · PMC13198004 · Cell reports methods · 2026 · 7 claims · 4 setups

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  Common DGE analysis methods (Wilcoxon test, unweighted t-test, pseudo-bulk aggregation, SCTransform-style parametrization) rely on unnecessary simplifications and assumptions that are inconsistent with experimental data and cause false findings

  e18 simulated scrna-seq sprna-seq scrna-seq simulation count

• A Hidden Markov Model to estimate population mixture and allelic copy-numbers in cancers using Affymetrix SNP arrays.

  PMID 17996079 · PMC2206057 · BMC bioinformatics · 2007 · 8 claims · 7 setups

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  An HMM using paired germline genotype calls and tumour allelic SNP intensities can estimate allele-specific copy-numbers, distinguishing events like uniparental disomy from allelic imbalance.

  hapmap bladder prostate simulated affymetrix simulation

• nf-core/mag: a best-practice pipeline for metagenome hybrid assembly and binning.

  PMID 35118380 · PMC8808542 · NAR genomics and bioinformatics · 2022 · 8 claims · 7 setups

  Has reproduction · 100

  nf-core/mag is a Nextflow/nf-core pipeline for hybrid metagenome assembly, binning and taxonomic classification of MAGs.

  simulated assembled mags raw metagenomic novo genome

• The genomic distribution of intraspecific and interspecific sequence divergence of human segmental duplications relative to human/chimpanzee chromosomal rearrangements.

  PMID 18699995 · PMC2542386 · BMC genomics · 2008 · 8 claims · 5 setups

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  Some relatively recent (young) SDs accumulate in regions homologous to chromosomal inversions that occurred in the sister lineage

  genome sds chimpanzee colinear comparative interspecific genomic

• Detecting transcriptionally active regions using genomic tiling arrays.

  PMID 16859498 · PMC1779562 · Genome biology · 2006 · 8 claims · 4 setups

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  A non-parametric method (TranscriptionDetector) integrates single-channel p-values from multiple replicate arrays into a multi-channel p-value (MCPV) to identify transcribed probed loci without assumptions about intensity distributions.

  anopheles chromosomes simulated genomic high-density sequence-based

• Evolutionary modeling of rate shifts reveals specificity determinants in HIV-1 subtypes.

  PMID 18989394 · PMC2566816 · PLoS computational biology · 2008 · 7 claims · 4 setups

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  A novel Bayesian method, RASER, can detect site-specific evolutionary rate shifts and the lineages in which they occurred without pre-specifying candidate lineages.

  hiv-1 simulated bayesian simulation structural

• Inter-individual variation of DNA methylation and its implications for large-scale epigenome mapping.

  PMID 18413340 · PMC2425484 · Nucleic acids research · 2008 · 8 claims · 8 setups

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  CpG-rich regions (CpG islands) show low and similar methylation levels across individuals, but the sequential order of the few methylated CpGs among the many unmethylated ones varies randomly between individuals.

  cd4+ computational hep direct simulation epigraph

• A comparative study of techniques for differential expression analysis on RNA-Seq data.

  PMID 25119138 · PMC4132098 · PloS one · 2014 · 8 claims · 8 setups

  Has reproduction · 58

  edgeR performs slightly better than DESeq and Cuffdiff2 in terms of the ability to uncover true positives.

  brain neurospheres lymphoblastoid simulation single-end paired-end rna-seq

• Digital sorting of complex tissues for cell type-specific gene expression profiles.

  PMID 23497278 · PMC3626856 · BMC bioinformatics · 2013 · 8 claims · 8 setups

  Has reproduction · 85

  The Digital Sorting Algorithm (DSA) deconvolves mixed tissue expression into cell type-specific profiles using only marker genes, without requiring prior knowledge of cell type frequencies or in vitro pure-cell profiles.

  liver im-9 immune deconvolved microarray simulation roc

• Iterative pruning PCA improves resolution of highly structured populations.

  PMID 19930644 · PMC2790469 · BMC bioinformatics · 2009 · 7 claims · 7 setups

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  ipPCA is a novel algorithm that assigns individuals to subpopulations and infers the total number of subpopulations (K) present in genotypic data

  simulated hapmap cattle shriver's simulated snp comparative

• singIST: An integrative method for comparative single-cell transcriptomics between disease models and humans.

  PMID 41838773 · PMC13008255 · PLoS computational biology · 2026 · 8 claims · 7 setups

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  singIST provides explainable quantitative measures of disease model similarity to a human reference at the pathway, cell type, and gene levels

  skin ear simulated scrna-seq simulation

• Mouse-Geneformer: A deep learning model for mouse single-cell transcriptome and its cross-species utility.

  PMID 40106407 · PMC11964219 · PLoS genetics · 2025 · 7 claims · 6 setups

  Has reproduction · 95

  Mouse-Geneformer, a Transformer Encoder model pre-trained via masked-token self-supervised learning on mouse-Genecorpus-20M, was successfully constructed following the original human Geneformer architecture.

  healthy scrna-seq disease scrna-seq type perturbation

• Improved eukaryotic detection compatible with large-scale automated analysis of metagenomes.

  PMID 37032329 · PMC10084625 · Microbiome · 2023 · 8 claims · 7 setups

  Has reproduction · 89

  MAPQ ≥30 filtering improves precision but substantially reduces recall, especially for unrepresented/divergent eukaryotic taxa

  eukdetect simulated zymobiomics read holdout mutation-rate