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).
-
Has reproduction · 85
Digital sorting of complex tissues for cell type-specific gene expression profiles.
PMID 23497278 · PMC3626856 · BMC bioinformatics · 2013 · 8 claims · 8 setups
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.
-
Has reproduction · 90
Cell Specific eQTL Analysis without Sorting Cells.
PMID 25955312 · PMC4425538 · PLoS genetics · 2015 · 5 claims · 3 setups
A genome-environment interaction meta-analysis on whole blood can predict neutrophil- and lymphocyte-specific cis-eQTLs without sorting cells.
-
Has reproduction · 50
Estimating and Correcting for Off-Target Cellular Contamination in Brain Cell Type Specific RNA-Seq Data.
PMID 33746712 · PMC7966716 · Frontiers in molecular neuroscience · 2021 · 6 claims · 7 setups
A computational method using high-quality scRNA-seq reference data can estimate per-sample, per-cell-type off-target contamination coefficients in sctRNA-seq datasets.
-
Has reproduction · 95
Single-cell transcriptomics and chromatin accessibility profiling elucidate the kidney-protective mechanism of mineralocorticoid receptor antagonists.
PMID 37906287 · PMC10760974 · The Journal of clinical investigation · 2024 · 8 claims · 7 setups
Mineralocorticoid (DOCA) effects are established through open chromatin and target gene expression primarily in principal and connecting tubule cells, and to a lesser extent in distal convoluted tubule (DCT2) cells.
-
Has reproduction · 71
Utilizing the codon adaptation index to evaluate the susceptibility to HIV-1 and SARS-CoV-2 related coronaviruses in possible target cells in humans.
PMID 36760235 · PMC9905242 · Frontiers in cellular and infection microbiology · 2022 · 7 claims · 8 setups
CAI is positively correlated with translational efficiency, supporting its use as a proxy for viral mRNA translation in cell types.
-
Full-text index only
Human Proteinpedia: a unified discovery resource for proteomics research.
PMID 18948298 · PMC2686511 · Nucleic acids research · 2009 · 8 claims · 8 setups
Human Proteinpedia is a community portal using a distributed annotation system (DAS) to share both published and unpublished human proteomic data
-
Has reproduction · 59
Cell-Type-Specific Gene Modules Related to the Regional Homogeneity of Spontaneous Brain Activity and Their Associations With Common Brain Disorders.
PMID 33958982 · PMC8093778 · Frontiers in neuroscience · 2021 · 7 claims · 8 setups
Fourteen gene modules were consistently associated with ReHo across three independent fMRI datasets.
-
Has reproduction · 42
Machine learning-based identification of biomarkers and drugs in immunologically cold and hot pancreatic adenocarcinomas.
PMID 39152432 · PMC11328457 · Journal of translational medicine · 2024 · 7 claims · 8 setups
PAAD tumors can be consensus-clustered into immunologically hot and cold subtypes based on CIBERSORT-derived immune cell fractions, with significantly different survival outcomes.
-
Has reproduction · 78
Evaluating Distribution and Prognostic Value of New Tumor-Infiltrating Lymphocytes in HCC Based on a scRNA-Seq Study With CIBERSORTx.
PMID 33043022 · PMC7527443 · Frontiers in medicine · 2020 · 5 claims · 6 setups
CIBERSORTx can combine scRNA-seq-derived signatures with bulk HCC transcriptomes to estimate proportions of 11 TIL subsets and infer cell-type-specific gene expression.
-
Has reproduction · 93
5-methylcytosine RNA modification regulators-based patterns and features of immune microenvironment in acute myeloid leukemia.
PMID 38277218 · PMC10911375 · Aging · 2024 · 8 claims · 8 setups
Most of the 17 m5C regulators are differentially expressed between AML and normal samples and correlate with AML prognosis.
-
Full-text index only
BioGPS: an extensible and customizable portal for querying and organizing gene annotation resources.
PMID 19919682 · PMC3091323 · Genome biology · 2009 · 8 claims · 4 setups
BioGPS aggregates distributed, third-party gene annotation resources into a single customizable portal for human, mouse, and rat genes.
-
Has reproduction
Mapping the Development of Human Spermatogenesis Using Transcriptomics-Based Data: A Scoping Review.
PMID 39000031 · PMC11241379 · International journal of molecular sciences · 2024 · 8 claims · 8 setups
scRNA-seq of human testis reveals major transcriptional modifications occurring around 11 years of age, marking a transition toward the adult cellular state
-
Has reproduction · 83
Integrative transcriptomic and machine learning framework reveals candidate genes and potential mechanisms of aflatoxin B1 exposure in breast cancer.
PMID 41688730 · PMC12982753 · Scientific reports · 2026 · 7 claims · 8 setups
Twenty-two genes lie at the intersection of AFB1-predicted targets and breast cancer-associated co-expression modules/DEGs
-
Full-text index only
Neuroscience in the era of functional genomics and systems biology.
PMID 19829370 · PMC3645852 · Nature · 2009 · 8 claims · 7 setups
Omics/discovery-based approaches do not eschew hypotheses but elevate hypothesis testing to high-throughput hypothesis generation and prioritization.
-
Has reproduction
Trans-ethnic association study of blood pressure determinants in over 750,000 individuals.
PMID 30578418 · PMC6365102 · Nature genetics · 2019 · 8 claims · 8 setups
Discovery and replication GWAS of SBP, DBP and pulse pressure in up to 776,078 individuals identified 208 novel common blood pressure SNPs and 53 rare variants.
-
Has reproduction · 73
Exploring the prognostic and diagnostic value of lactylation-related genes in sepsis.
PMID 39367086 · PMC11452377 · Scientific reports · 2024 · 8 claims · 7 setups
Intersecting sepsis-associated differentially expressed genes with a curated list of 332 lactylation genes yields 55 sepsis-related lactylation genes.
-
Full-text index only
Combining transcriptional profiling and genetic linkage analysis to uncover gene networks operating in hematopoietic stem cells and their progeny.
PMID 18560825 · PMC2493868 · Immunogenetics · 2008 · 8 claims · 8 setups
Neither transcriptional profiling alone nor genetic linkage analysis alone has been an effective approach to identify genes or gene networks that specify stemness or initiate differentiation/lineage specification.
-
Has reproduction · 50
Spatial transcriptomics demonstrates the role of CD4 T cells in effector CD8 T cell differentiation during chronic viral infection.
PMID 36450262 · PMC9792173 · Cell reports · 2022 · 7 claims · 7 setups
Following transient CD4 depletion, IL-21-producing Tfh cells do repopulate but are outnumbered by immunomodulatory CD4 T cells (Tregs, Th17), and IL-21+ frequency remains low within activated CD4 T cells.
-
Has reproduction · 67
HArmonized single-cell RNA-seq Cell type Assisted Deconvolution (HASCAD).
PMID 37907883 · PMC10619225 · BMC medical genomics · 2023 · 6 claims · 5 setups
HASCAD, a DNN-based cell composition deconvolution model, predicts the fractions of up to 15 immune cell types from bulk RNA-seq.
-
Has reproduction · 95
Itaconate and derivatives reduce interferon responses and inflammation in influenza A virus infection.
PMID 35025971 · PMC8846506 · PLoS pathogens · 2022 · 8 claims · 8 setups
Acod1 expression and itaconate synthesis are induced in mouse lung during IAV infection and correlate with inflammation and disease severity