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).

Publications 1.3k Datasets 392.5k Experiments 60

System / cell line: types ✕ Assay: identification ✕ Clear

In vitro identification and in silico utilization of interspecies sequence similarities using GeneChip technology.

PMID 15871745 · PMC1156887 · BMC genomics · 2005 · 7 claims · 6 setups

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Only 14±2% of canine transcripts were detected by U133A probe sets versus 49±6% of human transcripts when hybridized to the same chip

canine tissues hg-u133a probes microarray sequence ortholog
Sequencing the regulatory genome.

PMID 18598374 · PMC2481419 · Genome biology · 2008 · 8 claims · 8 setups

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Nuclear-lamina-associated domains (LADs) define chromatin regions with distinct transcriptional characteristics (fewer, lower-expressed genes, low RNA Pol II occupancy, H3K27me3-enriched borders)

interphase nine beta-globin drosophila nuclear digital chip
CircleBase V2: an eccDNA annotation platform across cancers and species.

PMID 41273082 · PMC12807720 · Nucleic acids research · 2026 · 8 claims · 7 setups

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CircleBase V2 provides a 12-fold increase in human eccDNA data, comprising over 3.8 million entries from >300 cell types/tissues

raw eccdna tissues cancer circle-seq motif gene
Cell-type annotation with accurate unseen cell-type identification using multiple references.

PMID 37379341 · PMC10335708 · PLoS computational biology · 2023 · 8 claims · 4 setups

Has reproduction · 68

mtANN integrates multiple reference datasets and eight gene selection methods via ensemble learning (multiple deep classification models + majority voting) to improve cell-type annotation accuracy

pbmc pancreas covid-19 scrna-seq
CanCellCap: robust cancer cell capture across tissue types on single-cell RNA-seq data by multi-domain learning.

PMID 40739511 · PMC12312500 · BMC biology · 2025 · 8 claims · 7 setups

Has reproduction · 42

CanCellCap identifies cancer cells in scRNA-seq data across 13 tissue types, 23 cancer types, and 7 sequencing platforms with 0.977 average accuracy

cancer testing sequencing unseen scrna-seq spatial
Large-scale identification and characterization of alternative splicing variants of human gene transcripts using 56,419 completely sequenced and manually annotated full-length cDNAs.

PMID 16914452 · PMC1557807 · Nucleic acids research · 2006 · 8 claims · 8 setups

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Analysis of 56,419 full-length cDNAs identified 6877 alternative splicing genes encoding 18,297 alternative splicing variants made of 37,670 exons.

full-length deduced alternative panel cdna-to-genome manual motif
Toward stem cell systems biology: from molecules to networks and landscapes.

PMID 19329576 · PMC2738746 · Cold Spring Harbor symposia on quantitative biology · 2008 · 7 claims · 6 setups

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Stem-cell-fate specification is an extremely complex process regulated by multiple mutually interacting molecular mechanisms with numerous regulatory feedback loops.

stem embryonic promyelocytic genome-wide serial chip-chip
Systems spatiotemporal dynamics of traumatic brain injury at single-cell resolution reveals humanin as a therapeutic target.

PMID 35951114 · PMC9372016 · Cellular and molecular life sciences : CMLS · 2022 · 8 claims · 8 setups

Has reproduction · 98

Coordinated gene expression patterns across cell types are disrupted and re-organized by mTBI with distinct regional, cellular, and temporal (24-h vs 7-day) specificity.

hippocampus frontal peripheral cell-type single-cell svm-based ligand-receptor
Integration with the human genome of peptide sequences obtained by high-throughput mass spectrometry.

PMID 15642101 · PMC549070 · Genome biology · 2005 · 8 claims · 4 setups

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PeptideAtlas, a public database integrating MS/MS-derived peptide identifications with the human genome, was built as an expandable resource for proteomic data.

subset drosophila ensembl lc-ms icat peptide-to-genome
Evidence for a preferential targeting of 3'-UTRs by cis-encoded natural antisense transcripts.

PMID 16204454 · PMC1243798 · Nucleic acids research · 2005 · 8 claims · 4 setups

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Cis-encoded natural antisense RNAs show striking preferential complementarity to 3′-UTRs of their target genes in human and mouse genomes

human-mouse model genome-wide comparative computational
Multimodal-based analysis of single-cell ATAC-seq data enables highly accurate delineation of clinically relevant tumor cell subpopulations.

PMID 41530870 · PMC12888741 · Genome medicine · 2026 · 8 claims · 8 setups

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MAAS integrates chromatin accessibility, CNVs, and SNVs from scATAC-seq data to identify functional tumor cell subpopulations

tumor pediatric b-cell glioblastoma scatac-seq bulk gene
Endothelial PDGF Signaling Dysregulation Impairs Testicular Interstitial Homeostasis in Diabetes.

PMID 41643060 · PMC13073339 · Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026 · 8 claims · 7 setups

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Testicular endothelial cells (TECs) function as a central signaling hub coordinating intercellular communication within the human testicular interstitium

testicular testis leydig diabetic single-cell integrative cell-cell
Identification and validation of lymphangiogenesis-related genes for predicting acute myeloid leukemia prognosis: insights from bulk RNA sequencing and single-cell RNA sequencing analyses.

PMID 41772327 · PMC12979290 · Clinical and experimental medicine · 2026 · 7 claims · 8 setups

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A 6-LYMRG risk model (ANGPT1, HGF, MAPK8, PCNA, TBL1XR1, TLR4) is the optimal prognostic signature for AML

gse142698 tcga-laml tcga-laml1 gse116256 differential univariate kaplan-meier
Population genomics: diversity and virulence in the Neisseria.

PMID 18822386 · PMC2612085 · Current opinion in microbiology · 2008 · 8 claims · 8 setups

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Horizontal genetic exchange (recombination) plays a central role in shaping bacterial speciation and population structure in Neisseria

neisseria meningitidis meningococcal multi-locus microarray genome
Pan-Cancer Single-Cell RNA Sequencing Analysis Refines Multi-Origin Monocyte and Macrophage Lineages.

PMID 41231218 · PMC12865363 · Cancer immunology research · 2026 · 6 claims · 8 setups

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TAMs arise from two distinct origins: C1QC+ TAMs likely derive from resident tissue macrophages, while SPP1+ TAMs and ISG15+ TAMs likely originate from circulating monocytes.

myeloid melanoma monocyte-to-macrophage coad-read scrna-seq differential developmental
Systematic annotation of orphan RNAs reveals blood-accessible molecular barcodes of cancer identity and cancer-emergent oncogenic drivers.

PMID 41579861 · PMC12923976 · Cell reports. Medicine · 2026 · 8 claims · 8 setups

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oncRNA binary presence-absence patterns constitute digital molecular barcodes that capture cancer type and subtype identity

tcga exrna cptac mda-mb-231 small machine atac-seq
Sex-Based Differences in Cell Types and Gene Expression within the Anterior Cruciate Ligament.

PMID 41587266 · PMC13011956 · The Journal of bone and joint surgery. American volume · 2026 · 8 claims · 5 setups

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ACL tissue is heterogeneous, containing 5 major cell types: fibroblasts, pericytes, endothelial cells, macrophages, and T cells.

acl differentially study flow single-cell immunofluorescence
scCNMF: an integrated analysis model for paired single-cell RNA sequencing and assay for transposase-accessible chromatin sequencing data leveraging cell similarity and cis-regulatory potential.

PMID 41800139 · PMC12962131 · PeerJ · 2026 · 7 claims · 2 setups

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scCNMF is an NMF-based model for vertical integration of paired scRNA-seq and scATAC-seq data that jointly incorporates a cell similarity matrix and a cis-regulatory potential (CRP) matrix

publicly 10x paired
CellMap: precision mapping of cellular landscape in spatial transcriptomics.

PMID 41505103 · PMC12781899 · Nucleic acids research · 2026 · 7 claims · 3 setups

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CellMap combines co-linearity of seed genes, a random forest model, and the linear assignment algorithm to achieve optimal assignment of single cells to spatial spots

platforms single-cell expression computational scrna-seq spatial
PredTAD: A machine learning framework that models 3D chromatin organization alterations leading to oncogene dysregulation in breast cancer cell lines.

PMID 34093998 · PMC8142020 · Computational and structural biotechnology journal · 2021 · 6 claims · 8 setups

Has reproduction · 77

PredTAD, a Gradient Boosting Machine model using epigenomic and genomic ChIP-seq-derived features plus neighboring-bin information, classifies 10 kb genomic bins as TAD boundary or non-boundary

mcf10a t47d mcf7 tcga hi-c chip-seq atac-seq

Experiments

In vitro identification and in silico utilization of interspecies sequence similarities using GeneChip technology.

Sequencing the regulatory genome.

CircleBase V2: an eccDNA annotation platform across cancers and species.

Cell-type annotation with accurate unseen cell-type identification using multiple references.

CanCellCap: robust cancer cell capture across tissue types on single-cell RNA-seq data by multi-domain learning.

Large-scale identification and characterization of alternative splicing variants of human gene transcripts using 56,419 completely sequenced and manually annotated full-length cDNAs.

Toward stem cell systems biology: from molecules to networks and landscapes.

Systems spatiotemporal dynamics of traumatic brain injury at single-cell resolution reveals humanin as a therapeutic target.

Integration with the human genome of peptide sequences obtained by high-throughput mass spectrometry.

Evidence for a preferential targeting of 3'-UTRs by cis-encoded natural antisense transcripts.

Multimodal-based analysis of single-cell ATAC-seq data enables highly accurate delineation of clinically relevant tumor cell subpopulations.

Endothelial PDGF Signaling Dysregulation Impairs Testicular Interstitial Homeostasis in Diabetes.

Identification and validation of lymphangiogenesis-related genes for predicting acute myeloid leukemia prognosis: insights from bulk RNA sequencing and single-cell RNA sequencing analyses.

Population genomics: diversity and virulence in the Neisseria.

Pan-Cancer Single-Cell RNA Sequencing Analysis Refines Multi-Origin Monocyte and Macrophage Lineages.

Systematic annotation of orphan RNAs reveals blood-accessible molecular barcodes of cancer identity and cancer-emergent oncogenic drivers.

Sex-Based Differences in Cell Types and Gene Expression within the Anterior Cruciate Ligament.

scCNMF: an integrated analysis model for paired single-cell RNA sequencing and assay for transposase-accessible chromatin sequencing data leveraging cell similarity and cis-regulatory potential.

CellMap: precision mapping of cellular landscape in spatial transcriptomics.

PredTAD: A machine learning framework that models 3D chromatin organization alterations leading to oncogene dysregulation in breast cancer cell lines.