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).

• FusionQ: a novel approach for gene fusion detection and quantification from paired-end RNA-Seq.

  PMID 23768108 · PMC3691734 · BMC bioinformatics · 2013 · 8 claims · 8 setups

  Has reproduction · 65

  FusionQ is a novel tool that detects gene fusions, constructs chimerical transcript structures, and estimates their abundances from paired-end RNA-Seq data.

  simulated four rna-seq randomly simulated paired-end read-mappability

• saseR: juggling offsets unlocks RNA-seq tools for fast and scalable differential usage, aberrant splicing and expression retrieval.

  PMID 41709279 · PMC13019952 · Genome biology · 2026 · 8 claims · 5 setups

  Full-text index only

  Replacing the library-size offset with the log of the total gene count in NB-based bulk RNA-seq models (edgeR/DESeq2) lets the mean-model parameters be interpreted as transcript/exon usage, unlocking these tools for differential usage and aberrant splicing without DEXSeq-style subject-specific blocking covariates.

  simulated bulk cohort aberrant differential exon

• Accurate detection of somatic single-nucleotide variants from bulk RNA-seq data using RNA-MosaicHunter.

  PMID 41505106 · PMC12781890 · Nucleic acids research · 2026 · 6 claims · 8 setups

  Full-text index only

  RNA-MosaicHunter accurately detects sSNVs from bulk RNA-seq with high precision (94.7% in TCGA, 99.3% in cell-line mixture) in default mode

  tcga cell-line same gtex bulk whole-exome whole-genome

• maxATAC: Genome-scale transcription-factor binding prediction from ATAC-seq with deep neural networks.

  PMID 36719906 · PMC9917285 · PLoS computational biology · 2023 · 8 claims · 6 setups

  Has reproduction · 98

  maxATAC is a suite of deep neural network models enabling state-of-the-art, genome-scale TFBS prediction from ATAC-seq, with models for 127 human transcription factors

  lines hepg2 types single chip-seq omni-atac-seq atac-seq

• omnideconv: a unifying framework for using and benchmarking single-cell-informed deconvolution of bulk RNA-seq data.

  PMID 41582216 · PMC12837286 · Genome biology · 2026 · 8 claims · 6 setups

  Full-text index only

  omnideconv is an R package providing a unified interface to twelve second-generation deconvolution methods (AutoGeneS, BayesPrism, Bseq-SC, Bisque, CDseq, CIBERSORTx, CPM, DWLS, MOMF, MuSiC, SCDC, Scaden)

  blood-derived pbmc blood spleen bulk scrna-seq pseudo-bulk

• Souporcell3: robust demultiplexing for high-donor single-cell RNA-seq datasets.

  PMID 41808435 · PMC13012599 · Bioinformatics (Oxford, England) · 2026 · 8 claims · 3 setups

  Full-text index only

  Souporcell3 can robustly demultiplex pooled scRNA-seq data from up to 64 donors

  pooled scrna-seq doublet genotype-based umap-based

• RNASEQR--a streamlined and accurate RNA-seq sequence analysis program.

  PMID 22199257 · PMC3315322 · Nucleic acids research · 2012 · 8 claims · 7 setups

  Has reproduction · 86

  RNASEQR is a new RNA-seq mapper/aligner that combines a BWT-based (Bowtie) transcriptomic/genomic alignment with hash-based BLAT local alignment in three sequential steps: transcriptome mapping, novel exon detection, and anchor-and-align novel splice junction identification.

  ccds glioblastoma experimental simulated simulated bulk quality

• Genetic demultiplexing of pooled single-cell RNA-sequencing samples in cancer facilitates effective experimental design.

  PMID 34553212 · PMC8458035 · GigaScience · 2021 · 8 claims · 6 setups

  Has reproduction · 87

  Genetic variation-based demultiplexing tools can be effectively deployed on pooled scRNA-seq experimental designs in cancer tissue (HGSOC and lung adenocarcinoma) despite somatic variation.

  hgsoc lung healthy scrna-seq bulk downstream

• Leveraging RNA-seq deconvolution to improve complex in vitro model characterization.

  PMID 40701251 · PMC12391696 · The Journal of biological chemistry · 2025 · 8 claims · 6 setups

  Has reproduction · 67

  RNA-seq deconvolution can predict cell type proportions from bulk RNA-seq using scRNA-seq references, offering a useful characterization tool for CIVMs where single-cell methods are impractical

  intestine rodent duodenal neonatal bulk scrna-seq marker

• Parameter-efficient fine-tuning enables scalable transfer of regulatory sequence models to novel contexts.

  PMID 41618434 · PMC12930932 · Genome biology · 2026 · 8 claims · 7 setups

  Full-text index only

  PEFT enables accurate transfer of Borzoi to new datasets while significantly reducing GPU memory and runtime compared to joint training or full fine-tuning

  gtex encode wi-38 thp-1 bulk eqtl variant-flowfish

• Compression of structured high-throughput sequencing data.

  PMID 24260313 · PMC3832420 · PloS one · 2013 · 8 claims · 7 setups

  Has reproduction · 43

  Leveraging an explicit data schema (separate field encoding, field modeling, template compression, domain modeling) enables stronger compression of HTS alignment data than general-purpose compression of serialized bytes.

  benchmark ten rna-seq exome genome

• TiRank prioritizes phenotypic niches in tumor microenvironment for clinical biomarker discovery.

  PMID 41689080 · PMC12910759 · Genome medicine · 2026 · 7 claims · 4 setups

  Full-text index only

  TiRank is a framework that integrates scRNA-seq, ST, and bulk transcriptomes using an REO-transformation module and multitask transfer learning to align data into a unified embedding space for prioritizing clinically relevant spatial niches

  benchmark pan-cancer gastric independent scrna-seq bulk spatial

• Robust and efficient annotation of cell states through gene signature scoring.

  PMID 41708334 · PMC12951948 · Genome research · 2026 · 8 claims · 8 setups

  Full-text index only

  Established scoring methods (Seurat, SCANPY, UCell, JASMINE) fail to provide robust and comparable score distributions across diverse signatures and experimental conditions, precluding accurate unsupervised cell-state annotation.

  pbmc colorectal esophageal crc scrna-seq cross-implementation signature

• PreTSA: computationally efficient modeling of temporal and spatial gene expression patterns.

  PMID 41673899 · PMC12998178 · Genome biology · 2026 · 7 claims · 8 setups

  Full-text index only

  PreTSA dramatically reduces computational time and memory versus GAM (Monocle, TSCAN) and PseudotimeDE for identifying temporally variable genes (TVGs) while producing highly similar results

  simulated null pbmc pancreas pseudotime tvg false-positive

• Improved reconstruction of transcripts and coding sequences from RNA-seq data.

  PMID 41700087 · PMC12910111 · Nucleic acids research · 2026 · 7 claims · 3 setups

  Full-text index only

  GeMoSeq combines combinatorial enumeration of candidate transcripts, splitting heuristics, and likelihood-based (EM) quantification for transcript reconstruction from RNA-seq data

  arabidopsis nicotiana mapped rna-seq-based combined read

• iCOMIC: a graphical interface-driven bioinformatics pipeline for analyzing cancer omics data.

  PMID 35899080 · PMC9310080 · NAR genomics and bioinformatics · 2022 · 8 claims · 4 setups

  Has reproduction · 58

  iCOMIC provides a GUI-driven, Snakemake-based pipeline integrating multiple tools for DNA-Seq and RNA-Seq analysis with minimal command-line interaction.

  giab monocyte missense somatic germline rna-seq machine

• Assessment of dispersion metrics for estimating single-cell transcriptional variability.

  PMID 41770747 · PMC12970974 · PLoS computational biology · 2026 · 7 claims · 4 setups

  Full-text index only

  The variance-to-mean ratio (VMR/Fano factor) scales approximately linearly with increasing dispersion and is independent of dataset size.

  simulated manivannan lana-elola yuzwa computational scrna-seq

• BOAT: Basic Oligonucleotide Alignment Tool.

  PMID 19958483 · PMC2788372 · BMC genomics · 2009 · 7 claims · 3 setups

  Full-text index only

  BOAT can accurately and efficiently map sequencing reads to a reference genome while handling several substitutions and indels simultaneously

  same short-read snp

• Viewing RNA-seq data on the entire human genome.

  PMID 28979763 · PMC5605993 · F1000Research · 2017 · 8 claims · 3 setups

  Has reproduction · 50

  RNA-Seq Viewer is a web application that visualizes genome-wide RNA-seq expression data pulled from NCBI's SRA and GEO databases using Ideogram.js

  sra web gzip-compressed rna-seq client-side network

• Predicting enhancers in mammalian genomes using supervised hidden Markov models.

  PMID 30917778 · PMC6437899 · BMC bioinformatics · 2019 · 8 claims · 8 setups

  Has reproduction · 70

  eHMM predicts enhancers with high precision and recall comparable to state-of-the-art methods and consistently outperforms them in accuracy and resolution

  esc atac-seq chip-seq cage