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).

• Vespucci: a system for building annotated databases of nascent transcripts.

  PMID 24304890 · PMC3936758 · Nucleic acids research · 2014 · 8 claims · 7 setups

  Has reproduction · 73

  Existing ChIP-seq and RNA-seq analysis platforms (e.g. Cufflinks, peak callers) are unsuited to GRO-seq because they assume spliced/exonic reads, uniform density and paired-end data, and cannot identify transcriptional units de novo across the whole genome.

  thioglycollate-elicited mcf-7 macrophages mm9 gro-seq chip-seq short-read

• Using several pair-wise informant sequences for de novo prediction of alternatively spliced transcripts.

  PMID 16925842 · PMC1810557 · Genome biology · 2006 · 8 claims · 4 setups

  Full-text index only

  MARS, an extension of the Twinscan algorithm, uses multiple pairwise informant genomes to predict human alternatively spliced transcripts de novo without expressed sequence information.

  genome tissues novo pairwise rt-pcr

• The use of whole genome amplification to study chromosomal changes in prostate cancer: insights into genome-wide signature of preneoplasia associated with cancer progression.

  PMID 16573809 · PMC1450280 · BMC genomics · 2006 · 7 claims · 8 setups

  Full-text index only

  MDA-amplified DNA does not introduce major distortion of copy number imbalance assignments compared to unamplified DNA in control CGH experiments.

  laser-capture-microdissected normal cancer fresh-frozen array gacgh laser

• Enriched domain detector: a program for detection of wide genomic enrichment domains robust against local variations.

  PMID 24782521 · PMC4066758 · Nucleic acids research · 2014 · 8 claims · 5 setups

  Has reproduction · 79

  EDD is a new algorithm that detects broad (megabase-size) enrichment domains from ChIP-seq data of widely distributed chromatin proteins such as A- and B-type lamins.

  normal dermal analysis set chip-seq chip-qpcr rna-seq

• Genome-wide analysis of KAP1 binding suggests autoregulation of KRAB-ZNFs.

  PMID 17542650 · PMC1885280 · PLoS genetics · 2007 · 8 claims · 7 setups

  Full-text index only

  H3me3K9 and H3me3K27 mark largely mutually exclusive, distinct classes of transcription factor genes: H3me3K9 at ZNF genes, H3me3K27 at homeobox genes

  ntera2 fibroblasts chip-chip chip-pcr expression

• Nitrosothiol reactivity profiling identifies S-nitrosylated proteins with unexpected stability.

  PMID 19101475 · PMC2628636 · Chemistry & biology · 2008 · 8 claims · 7 setups

  Full-text index only

  Most protein nitrosothiols are rapidly denitrosylated by physiological GSH, but a small subset show markedly reduced GSH reactivity and remain stably S-nitrosylated

  brain hemoglobin crystal send.1 biotin chemical snocap

• KEGG spider: interpretation of genomics data in the context of the global gene metabolic network.

  PMID 19094223 · PMC2646283 · Genome biology · 2008 · 8 claims · 8 setups

  Full-text index only

  KEGG spider, using a global 'pathway-free' metabolic network framework, provides deeper insight into metabolism variations than existing enrichment-based methods.

  diffuse-type liver renal anaplastic differential proteomic proteomics

• Gene-disease relationship discovery based on model-driven data integration and database view definition.

  PMID 19042916 · PMC2639000 · Bioinformatics (Oxford, England) · 2009 · 8 claims · 4 setups

  Full-text index only

  Explicit gene–disease relationships can be formulated as candidate gene definitions (e.g., co-localization, dysregulation, functional similarity) that may include intermediary orthologous or interacting genes

  acgr disease term-based database case

• CompMoby: comparative MobyDick for detection of cis-regulatory motifs.

  PMID 18950538 · PMC2605473 · BMC bioinformatics · 2008 · 7 claims · 4 setups

  Full-text index only

  CompMoby identifies cis-regulatory binding sites at both transcriptional and post-transcriptional levels in metazoans without prior knowledge of the trans-acting factor

  embryonic hela novo genome-wide

• High resolution melting analysis for rapid and sensitive EGFR and KRAS mutation detection in formalin fixed paraffin embedded biopsies.

  PMID 18495026 · PMC2408599 · BMC cancer · 2008 · 8 claims · 4 setups

  Full-text index only

  HRM correctly identified all 73 EGFR-mutation-positive FFPE samples previously found by sequencing, giving 100% sensitivity and 90% specificity

  ffpe single high direct hrm

• Bayesian transcriptome assembly.

  PMID 25367074 · PMC4397945 · Genome biology · 2014 · 8 claims · 8 setups

  Has reproduction · 68

  Bayesembler, a probabilistic transcriptome assembler built on a Bayesian model of the RNA sequencing process with Gibbs sampling over expressed candidates, abundances and read assignments, is introduced.

  k562 embryonic dendritic rna-seq simulated paired-end long-read

• Exploration of RNA-binding proteins identified RPS27 as a potential regulator associated with Kaposi's sarcoma development.

  PMID 40016701 · PMC11866810 · BMC cancer · 2025 · 6 claims · 8 setups

  Full-text index only

  48 RBP genes are differentially expressed in KS tissue (3 upregulated: PCBP3, L1TD1, PEG10; 45 downregulated, mostly ribosomal protein genes including RPS27)

  matched lesion huvecs rna-sequencing rna-seq irip-seq

• MrHAMER yields highly accurate single molecule viral sequences enabling analysis of intra-host evolution.

  PMID 33849057 · PMC8266615 · Nucleic acids research · 2021 · 8 claims · 7 setups

  Full-text index only

  MrHAMER yields >1000s of viral genomes per sample at 99.9% accuracy

  psg3.1 transcribed double-stranded mrhamer transcription reverse mrhamer

• Seasonal Dynamics Are the Major Driver of Microbial Diversity and Composition in Intensive Freshwater Aquaculture.

  PMID 34248892 · PMC8264503 · Frontiers in microbiology · 2021 · 7 claims · 6 setups

  Full-text index only

  Natural seasonality is the primary driver of aquatic bacterial community structure in the fishponds and reservoir

  pond filtered phytoplankton common 16s photosynthetic inorganic

• MobiCT: a UMI-based circulating tumor DNA analysis pipeline.

  PMID 41503160 · PMC12770973 · NAR genomics and bioinformatics · 2026 · 7 claims · 7 setups

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  MobiCT is a Nextflow/nf-core UMI-based ctDNA pipeline (deduplication, alignment, variant calling with VarDict, annotation with VEP) achieving sensitivity, precision, and F1-score around 90% after comprehensive filtering.

  cfdna same tumor horizon targeted droplet ngs

• Decoding of superimposed traces produced by direct sequencing of heterozygous indels.

  PMID 18654614 · PMC2429969 · PLoS computational biology · 2008 · 7 claims · 3 setups

  Full-text index only

  A dynamic programming method (implemented as web app Indelligent) can decode superimposed allelic sequences from a single mixed trace, using only the observed string of ambiguous peak calls, without a reference sequence or reverse trace.

  genomic artificial simulated direct computational comparative

• YANA - a software tool for analyzing flux modes, gene-expression and enzyme activities.

  PMID 15929789 · PMC1175843 · BMC bioinformatics · 2005 · 7 claims · 3 setups

  Full-text index only

  YANA integrates METATOOL to provide a graphical, platform-independent front-end for editing, calculating, visualizing, and comparing elementary flux modes, with SBML support.

  redox elementary flux evolutionary

• Differentiating Drosophila female germ cells initiate Polycomb silencing by regulating PRC2-interacting proteins.

  PMID 32773039 · PMC7438113 · eLife · 2020 · 8 claims · 2 setups

  Has reproduction · 87

  Germline stem cells (GSCs) have a non-canonical PRC2 distribution and lack silenced chromatin, resembling early embryonic progenitors

  drosophila facs-purified hsgfp chipseq

• spliceJAC: transition genes and state-specific gene regulation from single-cell transcriptome data.

  PMID 36321549 · PMC9627675 · Molecular systems biology · 2022 · 8 claims · 8 setups

  Has reproduction · 53

  spliceJAC uses unspliced and spliced mRNA count matrices to construct cell state-specific gene-gene regulatory interaction (Jacobian) matrices from scRNA-seq data

  bistable three-gene emt circuits simulation mixed-state grn

• WASP: a versatile, web-accessible single cell RNA-Seq processing platform.

  PMID 33736596 · PMC7977290 · BMC genomics · 2021 · 7 claims · 7 setups

  Has reproduction · 59

  WASP is a software platform for processing Drop-Seq-based scRNA-seq data generated with ddSEQ or 10x protocols, combining a Snakemake pre-processing pipeline with an R Shiny post-processing application.

  specified generic scrna-seq read reference