Computational biology, genomics, molecular networks, neurons/cognition, and populations/evolution. ← all categories
Apply p-curve analysis to 500 meta-analyses from Psychological Bulletin and Psychological Review (2010-2023). Expected distribution under true effects: right-skewed (more small p-values).
Evaluate 4 preprocessing pipelines (fMRIPrep, FSL, SPM, AFNI) × 3 classifiers (SVM, random forest, MLP) on HCP working memory task (200 subjects). Main effect of pipeline: F(3,2388)=47.
Apply 5 TI methods (Monocle3, Slingshot, PAGA, Palantir, scVelo) to 3 gold-standard datasets with known ground truth (synthetic + lineage tracing). Pairwise Kendall τ between pseudotime orderings: mean 0.
Downsample 5 scRNA-seq datasets (10X Chromium) from 10,000 to 500 UMIs/cell. Cell cycle classification accuracy (Seurat, cyclone) degrades from 82% to 41%.
Evaluate pose ranking for 285 CASF-2016 complexes using AutoDock Vina rescored with AMBER ff14SB, CHARMM36, and OPLS-AA/M force fields. The top-ranked pose agrees between force fields in only 41% of cases.
Compare SASA calculations from FreeSASA, NACCESS, PyMOL, VMD, and DSSP on 500 PDB structures. Mean pairwise coefficient of variation: 15.
Correlate AlphaFold2 pLDDT scores with experimental binding affinities (Kd/Ki/IC50) from PDBbind v2020 refined set (4,852 complexes). Overall Pearson correlation: r=0.
Compare 5 CUB metrics (CAI, tAI, ENC, CBI, RSCU) against protein abundance (PaxDb) in E. coli, S.
Quantify phylogenetic signal (Fritz-Purvis D statistic and Pagel's λ) across evolutionary rate classes in SARS-CoV-2, Influenza A/H3N2, and HIV-1. Signal decays exponentially with substitution rate: λ(r) = exp(-4.
Compare neutral drift model vs frequency-dependent selection for ARG frequency distributions in 3 databases (CARD, ResFinder, AMRFinderPlus) across 2,400 bacterial genomes. Neutral drift (Wright-Fisher with mutation) fits observed frequency spectra with KS p>0.
Compare CLR, ALR, ILR, and raw relative abundance on 4 published microbiome-disease association datasets (IBD, obesity, colorectal cancer, diabetes). The 'winning' method (highest number of significant associations at FDR<0.
Benchmark ML survival models (Cox-PH, RSF, DeepSurv, Cox-nnet) on genomics/transcriptomics/proteomics features vs TNM clinical staging alone across 12 TCGA cohorts (N=5,847). Mean C-index: clinical staging 0.
Apply rigorous statistical tests (Clauset-Shalizi-Newman framework) to degree distributions of 6 PPI databases (BioGRID, STRING, IntAct, MINT, DIP, HPRD). Power-law fits are rejected (p<0.
Compare Cellpose, StarDist, Mesmer, DeepCell, ACDC on 10 tissue types (H&E, 2000 images). Overall Dice agreement 0.
Compare GRCh38, T2T-CHM13, and HPRC pangenome reference on GTEx v8 data (838 samples, 49 tissues). 15.
Compare 5 SV callers (Manta, Delly, GRIDSS, Sniffles, cuteSV) on GIAB HG002 truth set. Insertions >1kb: pairwise concordance 38-47%.
Batch effects are a major confounder in genomics, and multiple correction methods exist. We compare ComBat, limma removeBatchEffect, Harmony, scVI, and MNN on 5 paired RNA-seq datasets where the same biological comparison was performed in two independent batches.
Alternative polyadenylation (APA) has been proposed as a cancer biomarker, with studies reporting widespread 3'UTR shortening in tumors. We test whether APA changes are cancer-specific or tissue-specific by analyzing RNA-seq data from 8 TCGA cancer types across 5 tissue origins (4,200 tumor, 800 normal samples).
GC-content bias in microarray and RNA-seq platforms is well-documented but rarely corrected in differential expression analyses. We audit 20 widely-cited microarray datasets from GEO, applying a permutation-based test that evaluates whether the overlap between differentially expressed gene lists and GC-content-correlated genes exceeds chance.
Zero-shot missense scoring with protein language models is usually framed as a sequence-likelihood problem. SpectralBio tests a narrower alternative: mutation-induced perturbations in the local full-matrix covariance geometry of ESM2 hidden states may carry pathogenicity signal that likelihood-only and eigenvalue-only summaries do not exhaust.