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).

• CRESCENT, a comprehensive RNA-Seq expression, splicing, and coding/non-coding element network tool.

  PMID 41566196 · PMC12895761 · BMC bioinformatics · 2026 · 6 claims · 6 setups

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  CRESCENT is a Snakemake workflow performing fully automated, comprehensive RNA-Seq analysis integrating differential expression, differential alternative splicing (DAS), differential transcript usage (DTU), and GO enrichment

  arabidopsis bulk rna-seq-based rna-seq

• Analysis and comprehensive comparison of PacBio and nanopore-based RNA sequencing of the Arabidopsis transcriptome.

  PMID 32536962 · PMC7291481 · Plant methods · 2020 · 8 claims · 8 setups

  Has reproduction · 57

  ONT Pc produces higher raw data quality (higher alignment rate, lower error rate) than ONT Dc, while PacBio generates the longest reads

  arabidopsis pacbio randomly illumina pacbio nanopore

• Comparative analysis of plant genomes allows the definition of the "Phytolongins": a novel non-SNARE longin domain protein family.

  PMID 19889231 · PMC2779197 · BMC genomics · 2009 · 8 claims · 6 setups

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  A novel, plant-specific family of longin-related proteins, the 'Phytolongins', was identified in land plant genomes.

  genomes longin plant phytolongin iterative phylogenetic genomic

• Genome informatics: taming the avalanche of genomic data.

  PMID 15642109 · PMC549058 · Genome biology · 2005 · 8 claims · 7 setups

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  Ultraconserved regions (>100 bp, 100% conserved among mammals) exist in the genome and their function remains unknown

  genes arabidopsis genome vertebrate comparative conservation whole-genome

• Spontaneous symmetry breaking in genome evolution.

  PMID 18367477 · PMC2377439 · Nucleic acids research · 2008 · 6 claims · 3 setups

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  Exon size distributions in sequenced genomes follow a lognormal pattern typical of a random Kolmogoroff fractioning process

  animal homo model genome-wide alternatively computational

• Phenotypic variation meets systems biology.

  PMID 19664197 · PMC2745761 · Genome biology · 2009 · 8 claims · 8 setups

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  Cellular differentiation states are constrained by complex networks with substantial positive and negative regulation, challenging the concept of single 'master regulators'

  thp-1 arabidopsis unspecified mammalian deepcage protein-protein sequencing