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).

• A negative binomial latent factor model for paired microbiome sequencing data.

  PMID 41572173 · PMC12910815 · BMC bioinformatics · 2026 · 8 claims · 2 setups

  Full-text index only

  A negative binomial model with a shared taxon-specific latent factor (JNBM) captures cross-site correlation between paired microbiome samples from two body sites.

  synthetic umicro simulation microbiome

• Projecting contact matrices in 177 geographical regions: An update and comparison with empirical data for the COVID-19 era.

  PMID 34310590 · PMC8354454 · PLoS computational biology · 2021 · 6 claims · 5 setups

  Has reproduction · 98

  Updated synthetic contact matrices extend coverage from 152 to 177 geographical locations using the most recent demographic, household, and socio-demographic data

  polymod geographical dhs age-structured bayesian synthetic rural-urban

• Glycan arrays for functional glycomics.

  PMID 12537579 · PMC151192 · Genome biology · 2002 · 6 claims · 5 setups

  Full-text index only

  Glycan arrays allow high-throughput characterization of lectin binding specificity in a single experiment, improving on material-intensive hapten inhibition assays

  synthetic biotinylated mono monosaccharides neoglycolipid carbohydrate streptavidin-biotin

• The fragile breakage versus random breakage models of chromosome evolution.

  PMID 16501665 · PMC1378107 · PLoS computational biology · 2006 · 8 claims · 6 setups

  Full-text index only

  Sankoff and Trinh's synteny block identification algorithm (ST-Synteny) is flawed, producing erroneous block identifications even in small toy examples.

  small synthetic synteny random whole-genome

• The i-motif in the bcl-2 P1 promoter forms an unexpectedly stable structure with a unique 8:5:7 loop folding pattern.

  PMID 19908860 · PMC2787777 · Journal of the American Chemical Society · 2009 · 8 claims · 6 setups

  Full-text index only

  The full-length bcl-2 C-rich promoter sequence (Py39WT) forms one major intramolecular i-motif structure with a transitional pH of 6.6

  py39wt fam 32p-labeled circular melting fret

• From single cells to whole organisms.

  PMID 16420683 · PMC1414103 · Genome biology · 2005 · 8 claims · 8 setups

  Full-text index only

  The genetic-interaction map in S. cerevisiae is roughly four times as complex as the protein-protein interaction map, and genetic interactions do not overlap with physical interactions but instead predict functional neighborhoods

  saccharomyces caenorhabditis mammalian cylindromatosis automated interference rnai

• On the analysis of glycomics mass spectrometry data via the regularized area under the ROC curve.

  PMID 18076765 · PMC2211327 · BMC bioinformatics · 2007 · 8 claims · 4 setups

  Full-text index only

  The TGDR-AUC algorithm regularizes the empirical AUC by replacing the non-differentiable 0-1 loss with a smooth sigmoid surrogate function and applies constrained threshold gradient descent regularization

  simulated serum preprocessed simulation mass high-resolution

• Assessment of algorithms for high throughput detection of genomic copy number variation in oligonucleotide microarray data.

  PMID 17910767 · PMC2148068 · BMC bioinformatics · 2007 · 8 claims · 4 setups

  Full-text index only

  Different CNV analysis software packages produce highly variable numbers and types of candidate CNVs from the same data

  normalized individuals subset same affymetrix fluorescent snp

• Opportunities and challenges in synthetic oligosaccharide and glycoconjugate research.

  PMID 20161474 · PMC2794050 · Nature chemistry · 2009 · 8 claims · 7 setups

  Full-text index only

  A parallel combinatorial one-pot multi-step protecting-group procedure (Lewis acid catalyzed, up to seven steps) can transform tetra-O-TMS glucopyranosides into differentially protected monosaccharide building blocks without intermittent work-up/purification

  library database oligovalent b-cells glycan bioinformatics one-pot

• Detecting unannotated splicing events in short-read RNA-seq with SAMI, a UMI-aware Nextflow pipeline.

  PMID 42166739 · PMC13242923 · Bioinformatics (Oxford, England) · 2026 · 8 claims · 5 setups

  Full-text index only

  SAMI is a UMI-aware, Singularity-contained Nextflow pipeline that detects splicing events diverging from transcript annotations directly from raw FASTQ files.

  seraseq simulated small processed targeted simulated computation

• Short activation domains control chromatin association of transcription factors.

  PMID 41511382 · PMC12788797 · eLife · 2026 · 8 claims · 8 setups

  Full-text index only

  Short activation domains (39-60 aa, only 5-7% of the synthetic TF) dominate the chromatin-bound fraction of a synthetic transcription factor.

  u2os synthetic single-molecule flow fluorescence

• DANST enables cell-type deconvolution in spatial transcriptomics using deep domain adversarial neural networks.

  PMID 41663685 · PMC12996496 · Communications biology · 2026 · 7 claims · 6 setups

  Full-text index only

  DANST, a deconvolution framework using deep domain adversarial neural networks, achieves superior cell-type deconvolution accuracy compared with existing methods on human and mouse benchmark datasets

  heart cortex visual brain spatial cell-type

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

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

  Full-text index only

  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

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

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

  Full-text index only

  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

• Non-negative matrix factorization and deconvolution as a dual simplex problem.

  PMID 41535969 · PMC12888666 · Genome biology · 2026 · 8 claims · 3 setups

  Full-text index only

  The NMF optimization problem can be reduced to searching for K(K-1) variables, independent of the original matrix size M×N.

  unconstrained bulk single-cell image bulk single-cell

• DeepGSEA: explainable deep gene set enrichment analysis for single-cell transcriptomic data.

  PMID 38950178 · PMC11236288 · Bioinformatics (Oxford, England) · 2024 · 8 claims · 2 setups

  Has reproduction · 40

  DeepGSEA is an explainable deep gene set enrichment analysis method built on interpretable, prototype-based neural networks.

  simulated real-world simulation scrna-seq-based

• Non-cross-linking gold nanoparticle aggregation as a detection method for single-base substitutions.

  PMID 15640441 · PMC546178 · Nucleic acids research · 2005 · 8 claims · 7 setups

  Full-text index only

  NCL aggregation of DNA-modified gold nanoparticles shows extraordinary selectivity against terminal mismatches at the free ends of surface-bound duplexes

  probe-modified probe-gnp synthetic four uv-vis ssdna pcr

• Stability analysis of mixtures of mutagenetic trees.

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

  Full-text index only

  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

• Simultaneous epigenomic profiling and regulatory activity measurement using e2MPRA.

  PMID 41535307 · PMC12913623 · Nature communications · 2026 · 8 claims · 8 setups

  Full-text index only

  e2MPRA, combining lentiviral integration-based MPRA with CUT&Tag or ATAC-seq, enables simultaneous measurement of regulatory activity, protein binding, and epigenetic modification of the same synthetic CRE sequences.

  hepg2 lentimpra atac-seq h3k27ac