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).

• CorGen--measuring and generating long-range correlations for DNA sequence analysis.

  PMID 16845099 · PMC1538783 · Nucleic acids research · 2006 · 8 claims · 3 setups

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  CorGen is a web server that measures long-range correlations in DNA sequences and generates random sequences with the same (or user-specified) correlation and composition parameters

  chromosome query synthetic long-range sequence

• CIRCprimerXL: Convenient and High-Throughput PCR Primer Design for Circular RNA Quantification.

  PMID 36304334 · PMC9580850 · Frontiers in bioinformatics · 2022 · 8 claims · 5 setups

  Has reproduction · 88

  CIRCprimerXL is a high-throughput, user-friendly circRNA RT-qPCR primer design pipeline available as both a web tool and a standalone Nextflow/Docker pipeline

  synthetic sw480 circrnas rt-qpcr circrna primer

• Threshold-dominated regulation hides genetic variation in gene expression networks.

  PMID 18062810 · PMC2238762 · BMC systems biology · 2007 · 8 claims · 2 setups

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  Threshold robustness (insensitivity of a singular/regulating variable's equilibrium value to parameter perturbations, except threshold changes) increases with increasing response function steepness and is present even under Michaelis-Menten conditions, not just in the step-function limit.

  three-gene illustrative numerical analytical

• 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

• Stability analysis of mixtures of mutagenetic trees.

  PMID 18366778 · PMC2335279 · BMC bioinformatics · 2008 · 7 claims · 5 setups

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  Mutagenetic trees mixture models capture multiple alternative pathways of ordered accumulation of genetic events (e.g., HIV resistance mutations, cancer chromosomal aberrations).

  simulated hiv-1 hiv timed simulation genotypic mutagenetic

• 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

• Viroporin potential of the lentivirus lytic peptide (LLP) domains of the HIV-1 gp41 protein.

  PMID 18028545 · PMC2211469 · Virology journal · 2007 · 8 claims · 4 setups

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  Synthetic peptides corresponding to LLP-1, LLP-2, and LLP-3 domains partition into POPC:POPG lipid membranes and adopt amphipathic α-helical secondary structure

  hiv-1 synthetic nbd 90%popc wimley-white circular tryptophan

• Cancer-specific high-throughput annotation of somatic mutations: computational prediction of driver missense mutations.

  PMID 19654296 · PMC2763410 · Cancer research · 2009 · 7 claims · 7 setups

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  CHASM, a Random Forest-based computational method, was developed to identify and prioritize missense mutations likely to be functional drivers of tumor cell proliferation.

  missense same synthetic tp53 random support principal

• Net positive charge of HIV-1 CRF01_AE V3 sequence regulates viral sensitivity to humoral immunity.

  PMID 18787705 · PMC2527523 · PloS one · 2008 · 8 claims · 5 setups

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  Reduction in V3's net positive charge makes V3 less variable due to limited positive selection

  hiv-1 recombinant plasma gp120 sequence single-round v3-peptide-based

• Identification of functional SNPs in the 5-prime flanking sequences of human genes.

  PMID 15717931 · PMC550646 · BMC genomics · 2005 · 6 claims · 5 setups

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  7 of 10 candidate SNPs tested by EMSA showed reproducible allele-specific differences in TF-DNA complex binding/stability

  flanking synthetic genomic cloned comparative electrophoretic rflp

• Calibration-free NGS quantitation of mutations below 0.01% VAF.

  PMID 34675197 · PMC8531361 · Nature communications · 2021 · 8 claims · 6 setups

  Has reproduction · 96

  QBDA (Quantitative Blocker Displacement Amplification) integrates UMI molecular barcoding with BDA variant enrichment to enable calibration-free VAF quantitation

  h37rv repository healthy same single-plex 10-plex 22-plex

• Early life-stage thermal resilience is determined by climate-linked regulatory variation.

  PMID 41505517 · PMC12799179 · Proceedings of the National Academy of Sciences of the United States of America · 2026 · 8 claims · 8 setups

  Has reproduction · 64

  Embryonic heat tolerance in D. melanogaster is determined by climate-linked regulatory genetic variation at loci on chromosomes 2R and X

  melanogaster simulated synthetic wild-collected heat-shock pool-seq drift-only

• Genomic profiling of microRNA and messenger RNA reveals deregulated microRNA expression in prostate cancer.

  PMID 18676839 · PMC2597340 · Cancer research · 2008 · 8 claims · 7 setups

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  MicroRNA processing components (Dicer, DGCR8) and microRNA host genes (MCM7, C9orf5) are significantly up-regulated in prostate tumors versus non-tumor tissue

  prostate subset lncap 22rv1 microrna quantitative western

• Hit selection with false discovery rate control in genome-scale RNAi screens.

  PMID 18628291 · PMC2504311 · Nucleic acids research · 2008 · 8 claims · 3 setups

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  A Bayesian FDR-controlling methodology for hit selection in genome-scale RNAi HTS is proposed, using a direct posterior probability approach analogous to Newton et al.

  hela hepatitis simulated genome-scale simulation

• Rapid identification of PAX2/5/8 direct downstream targets in the otic vesicle by combinatorial use of bioinformatics tools.

  PMID 18828907 · PMC2760872 · Genome biology · 2008 · 8 claims · 8 setups

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  A combinatorial bioinformatics pipeline (evolutionary double filtering comparative genomics, GXD/ZFIN database queries, MEDLINE text mining) can rapidly and specifically identify PAX2/5/8 direct downstream targets in the otic vesicle

  genome candidate gxd medline evolutionary gene expression

• Generative and integrative modeling for transcriptomics with formalin fixed paraffin embedded material.

  PMID 41029822 · PMC12486589 · Journal of translational medicine · 2025 · 8 claims · 6 setups

  Has reproduction · 67

  The negative binomial distribution best fits fRNA-seq transcript counts, with little evidence supporting zero-inflated extensions

  compendium ffpe simulated frna-seq statistical bulk integrity

• RiboTaxa: combined approaches for rRNA genes taxonomic resolution down to the species level from metagenomics data revealing novelties.

  PMID 36159175 · PMC9492272 · NAR genomics and bioinformatics · 2022 · 8 claims · 6 setups

  Has reproduction · 66

  RiboTaxa, combining BBTools, FastQC, SortMeRNA, MetaRib, EMIRGE, VSEARCH, BBMap and QIIME 2's Sklearn classifier, was built as a pipeline for SSU rRNA-based taxonomic profiling of metagenomics data.

  microbial reconstructed synthetic real shotgun ssu full-length

• MoDLE: high-performance stochastic modeling of DNA loop extrusion interactions.

  PMID 36451166 · PMC9710047 · Genome biology · 2022 · 8 claims · 6 setups

  Has reproduction · 50

  MoDLE is a high-performance stochastic model/software for simulating DNA-DNA contacts generated by loop extrusion genome-wide

  h1-hesc five synthetic chip-seq stochastic molecular

• Accurate chromatin marks peak calling with Omnipeak.

  PMID 41521664 · PMC12784980 · Nucleic acids research · 2026 · 8 claims · 6 setups

  Has reproduction · 77

  Omnipeak is a universal unsupervised peak-calling algorithm based on a constrained three-state hidden Markov model (zero, noise, signal states)

  gm12878 roadmap abf immgen chip-seq ultra-low-input atac-seq