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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Has reproduction · 75
Revealing the critical state and identifying individualized dynamic network biomarker for type 2 diabetes through advanced analysis methods on individual basis.
PMID 39890881 · PMC11785715 · Scientific reports · 2025 · 8 claims · 5 setups
sJSD, NIG, and TNFE methods can detect critical states/tipping points before disease deterioration using only a single sample
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The evolutionary dynamics of a rapidly mutating virus within and between hosts: the case of hepatitis C virus.
PMID 19911046 · PMC2768904 · PLoS computational biology · 2009 · 8 claims · 3 setups
The replication rate of the strain that initiates an infection has a strong effect on the fitness of the infection at the between-host level, even though the virus evolves rapidly within the host.
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Has reproduction · 77
spotter: a single-nucleotide resolution stochastic simulation model of supercoiling-mediated transcription and translation in prokaryotes.
PMID 37602419 · PMC10516669 · Nucleic acids research · 2023 · 8 claims · 4 setups
spotter is the first simulation model to integrate transcription, DNA supercoiling, and translation simultaneously in a single stochastic framework for prokaryotes.
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Has reproduction · 67
Assembly of Macromolecular Complexes in the Whole-Cell Model of a Minimal Cell.
PMID 41427637 · PMC12794154 · The journal of physical chemistry. B · 2026 · 8 claims · 6 setups
The assembly of 21 unique macromolecular complexes (20 plus a reduced ribosome biogenesis model) was incorporated into the existing whole-cell kinetic model of Syn3A.
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Has reproduction · 50
MoDLE: high-performance stochastic modeling of DNA loop extrusion interactions.
PMID 36451166 · PMC9710047 · Genome biology · 2022 · 7 claims · 6 setups
MoDLE is a high-performance stochastic model that simulates DNA-DNA contacts from loop extrusion genome-wide in minutes using less than 1 GB of RAM
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Accuracy of predicting the genetic risk of disease using a genome-wide approach.
PMID 18852893 · PMC2561058 · PloS one · 2008 · 8 claims · 4 setups
Deterministic equations can predict the accuracy (r_gĝ) of genome-wide genetic risk/value prediction for continuous, dichotomous, and case-control study designs.
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Antigenic diversity, transmission mechanisms, and the evolution of pathogens.
PMID 19847288 · PMC2759524 · PLoS computational biology · 2009 · 8 claims · 3 setups
Three distinct infection types (A, B, C) emerge as maxima in the pathogen fitness landscape, each with characteristic within-host dynamics, contact network structure, and transmission mode
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Has reproduction · 85
A mechanistic model captures the emergence and implications of non-genetic heterogeneity and reversible drug resistance in ER+ breast cancer cells.
PMID 34316714 · PMC8271219 · NAR cancer · 2021 · 7 claims · 8 setups
EMT and tamoxifen-resistance (TamR) regulatory axes can drive one another, enabling non-genetic heterogeneity via six co-existing phenotypes (ES, ER, HS, HR, MS, MR)
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Has reproduction · 84
A scalable, open-source implementation of a large-scale mechanistic model for single cell proliferation and death signaling.
PMID 35729113 · PMC9213456 · Nature communications · 2022 · 7 claims · 5 setups
Developed a python-based, scalable model creation and simulation pipeline that converts structured text files into an SBML-standard model and is high-performance/cloud-computing ready.
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Has reproduction · 100
Computational modeling demonstrates that glioblastoma cells can survive spatial environmental challenges through exploratory adaptation.
PMID 31836713 · PMC6911112 · Nature communications · 2019 · 8 claims · 6 setups
Stochastic exploration of the gene-regulatory network structure confers enhanced adaptive capacity, enabling GBM cells to converge to new target phenotypes in novel environments.
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Has reproduction · 53
spliceJAC: transition genes and state-specific gene regulation from single-cell transcriptome data.
PMID 36321549 · PMC9627675 · Molecular systems biology · 2022 · 8 claims · 6 setups
spliceJAC quantifies multivariate mRNA splicing from unspliced/spliced count matrices to construct cell state-specific gene-gene (Jacobian) interaction matrices.
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Has reproduction · 83
SIRE 2.0: a novel method for estimating polygenic host effects underlying infectious disease transmission, and analytical expressions for prediction accuracies.
PMID 40169992 · PMC11963337 · Genetics, selection, evolution : GSE · 2025 · 8 claims · 2 setups
SIRE 2.0 is a novel Bayesian methodology and software tool for estimating polygenic contributions (variance components and additive genetic effects) to host susceptibility, infectivity and recoverability from temporal epidemic data using pedigree/genomic relationship matrices.
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Duplication count distributions in DNA sequences.
PMID 19256873 · PMC3121164 · Physical review. E, Statistical, nonlinear, and soft matter physics · 2008 · 8 claims · 8 setups
Duplication count distributions N(c) for complex 40-mers show power-law-like decay for c roughly 3 to 50 (or higher) across human, C. elegans, A. thaliana, and D. melanogaster genomes.