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).

• Single-Cell Mitochondrial Lineage Tracing Decodes Fate Decision and Spatial Clonal Architecture in Human Hematopoietic Organoids.

  PMID 41560697 · PMC13042525 · Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026 · 8 claims · 8 setups

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  Mitochondrial somatic mutations from scRNA-seq can be repurposed as endogenous genetic barcodes for lineage tracing in hPSC-derived organoids.

  hpsc hemo larry-barcoded pdgfrα+ scrna-seq mitochondrial cospar

• A lack of parasitic reduction in the obligate parasitic green alga Helicosporidium.

  PMID 24809511 · PMC4014436 · PLoS genetics · 2014 · 8 claims · 8 setups

  Has reproduction · 30

  The Helicosporidium nuclear genome is small and compact (~2.5-fold smaller than Chlorella and Coccomyxa) yet shows almost no evidence of functional/metabolic reduction.

  helicosporidium ten whole-genome transcriptome gene

• Integrative miRNA-mRNA Network and Molecular Dynamics-Based Identification of Therapeutic Candidates for Paroxysmal Nocturnal Hemoglobinuria.

  PMID 41599741 · PMC12845513 · Pharmaceuticals (Basel, Switzerland) · 2026 · 8 claims · 8 setups

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  A PIGA-knockout (PIGA-KO) THP-1 cell model was successfully established using CRISPR/Cas9 RNP technology as a PNH model

  thp-1 literature-validated pnh cxcl8 crispr rt-qpcr bulk

• Substantial unannotated noncoding transcripts in tumors may transcriptionally regulate cancer-related genes.

  PMID 41606598 · PMC12924361 · BMC biology · 2026 · 8 claims · 8 setups

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  Many unannotated genes and transcripts (MSTRG/UNTs) are pervasively generated and significantly differentially expressed in cancer cell lines and tissues across four tumor types (lung, liver, stomach, colon)

  cancer a549 unt bulk chip-seq computational

• Spatial transcriptome and single-cell sequencing reveal the role of nucleotide metabolism in breast cancer progression and tumor microenvironment.

  PMID 41613532 · PMC12847018 · Frontiers in oncology · 2025 · 7 claims · 8 setups

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  Tumor cells show significantly upregulated nucleotide metabolic activity, allowing stratification into NUhighepi and NUlowepi subgroups

  tcga-brca breast scrna-seq epithelial ssgsea single-cell cell-cell

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

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

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  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

• The TRIP12's intrinsically disordered region induces chromatin condensates and interferes with nuclear processes.

  PMID 41660270 · PMC12876695 · iScience · 2026 · 8 claims · 8 setups

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  TRIP12 overexpression induces dose-dependent formation of chromatin condensates enriched in heterochromatin marks

  hela u2os trip12 immunofluorescence cellular isoelectric

• pmid-41663439

  PMID 41663439 · PMC12996591 · 7 claims · 7 setups

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  Aggregating peaks from 624 high-quality bulk ATAC-seq datasets defines ~1.4 million observed consensus peaks (cPeaks) covering ~30% of the genome.

  bulk scatac-seq cnn gm12878 bulk scatac-seq deep

• pmid-41674383

  PMID 41674383 · PMC12895067 · 7 claims · 8 setups

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  HNRNPU forms extensive protein networks including an association with the mammalian SWI/SNF chromatin-remodeling complex

  ipsc-derived computational neocortical ip-ms formaldehyde alphapulldown expression-weighted

• Systems biology of gene regulation fulfills its promise.

  PMID 16719937 · PMC1779525 · Genome biology · 2006 · 8 claims · 8 setups

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  Suz12, a Polycomb Group complex component, has DNA targets identifiable by ChIP-chip and can silence large genomic regions in a cell-type-specific manner.

  unspecified embryonic five yeast chip-chip chip-pet computational

• IsomiR_Window: a system for analyzing small-RNA-seq data in an integrative and user-friendly manner.

  PMID 33522913 · PMC7852101 · BMC bioinformatics · 2021 · 7 claims · 3 setups

  Has reproduction · 78

  IsomiR Window is a novel integrated pipeline plus browser GUI that combines over ten third-party tools with a new algorithm capable of detecting all types of isomiRs (5' end, 3' end, tailings, SNP/editing, and fuzzy combinations)

  simulated basal isomir small-rna-seq mirna

• pTARGET: a web server for predicting protein subcellular localization.

  PMID 16844995 · PMC1538910 · Nucleic acids research · 2006 · 7 claims · 3 setups

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  pTARGET web server predicts nine distinct subcellular localizations in eukaryotic non-plant proteins using an algorithm based on location-specific Pfam domain occurrence patterns and amino acid composition (AAC)

  eukaryotic complete pfam amino subcellular

• Metabolomic profiling in LRRK2-related Parkinson's disease.

  PMID 19847307 · PMC2761616 · PloS one · 2009 · 7 claims · 3 setups

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  Metabolomic profiles of both idiopathic PD and LRRK2 PD are clearly separated from controls

  plasma preprocessed untargeted targeted pls-da

• Transcriptome-wide analyses of piRNA binding sites suggest distinct mechanisms regulate piRNA binding and silencing in C. elegans.

  PMID 36737102 · PMC10158993 · RNA (New York, N.Y.) · 2023 · 8 claims · 7 setups

  Has reproduction · 88

  C. elegans piRNAs preferentially bind the coding regions (CDS) of target mRNAs in vivo, rather than 3' UTRs.

  elegans clash bioinformatic iclip

• Somatic mutations in mitochondria: the chicken or the egg?

  PMID 16207343 · PMC1257449 · Arthritis research & therapy · 2005 · 6 claims · 6 setups

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  Patients with RA have a higher incidence of somatic mtDNA mutations (in MT-ND1 transcripts) in synoviocytes and synovial tissue compared with OA patients

  mutated synovial sequencing mhc expression

• Genomic approaches to the genetics of alcoholism.

  PMID 12875046 · PMC6683845 · Alcohol research & health : the journal of the National Institute on Alcohol Abuse and Alcoholism · 2002 · 8 claims · 4 setups

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  Alcoholism is a complex disease that develops from a combination of numerous genetic and environmental factors, unlike single-gene disorders such as cystic fibrosis or Huntington's disease.

  specified genomic gene genomic exon

• SelenoDB 1.0 : a database of selenoprotein genes, proteins and SECIS elements.

  PMID 18174224 · PMC2238826 · Nucleic acids research · 2008 · 6 claims · 5 setups

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  Standard genome annotation pipelines misannotate selenoprotein genes because they rely on UGA as a universal stop codon, failing to recognize its dual role as the selenocysteine-recoding codon.

  genomic cdna known sequence homology transcript

• COMUS: Clinician-Oriented locus-specific MUtation detection and deposition System.

  PMID 19958500 · PMC2788389 · BMC genomics · 2009 · 8 claims · 6 setups

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  COMUS is a bioinformatics system for detecting and depositing new mutations from patient DNA with a clinician-friendly interface

  ab1 fasta mutation hemophilia base-calling sequence known-variant

• Detection of alternative splicing: deep sequencing or deep learning?

  PMID 41520225 · PMC12790623 · Briefings in bioinformatics · 2026 · 8 claims · 8 setups

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  Sequence-based deep learning tools (AlphaGenome, SpliceAI, DeepSplice) show potential for initial hypothesis development and as additional filters in standard RNA-seq pipelines, especially when sequencing depth is limited.

  dilated dcm sequence subsampled bulk rna-seq deep

• Bases and spaces: resources on the web for accessing the draft human genome.

  PMID 11178254 · PMC138875 · Genome biology · 2000 · 8 claims · 8 setups

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  By combining currently available genomic databases and mapping resources (GenBank/Entrez, UniGene, RH maps, BAC fingerprint maps, Ensembl, NIX), it is possible to devise strategies that fully exploit the fragmentary draft human genome sequence.

  bac whole-genome draft submitted bac radiation initio