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).

• 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

• TM4SF10 gene sequencing in XLMR patients identifies common polymorphisms but no disease-associated mutation.

  PMID 15345028 · PMC517934 · BMC medical genetics · 2004 · 8 claims · 4 setups

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  No disease-associated mutations were found in TM4SF10 in 16 XLMR patients from 14 families with linkage to the TM4SF10 locus.

  genomic dog sage pcr northern sage

• GeneSeer: a sage for gene names and genomic resources.

  PMID 16176584 · PMC1266031 · BMC genomics · 2005 · 7 claims · 4 setups

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  GeneSeer aggregates gene name synonyms from GenBank, FlyBase, ExPASy, HUGO, ENSEMBL, UCSC and Gene Ontology into a name-translation database that maps any familiar name to a reference (SOFAR) identifier.

  sofar clusters rnai gene blast sequence shrna

• Expoldb: expression linked polymorphism database with inbuilt tools for analysis of expression and simple repeats.

  PMID 17038195 · PMC1618849 · BMC genomics · 2006 · 8 claims · 6 setups

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  EXPOLDB is a novel database integrating human gene expression variability data (including monozygotic twin comparisons) with (TG/CA)n repeat polymorphism information

  blood genomic genes housekeeping microarray repeat est-based

• Molecular phylogeny of the antiangiogenic and neurotrophic serpin, pigment epithelium derived factor in vertebrates.

  PMID 17020603 · PMC1609119 · BMC genomics · 2006 · 8 claims · 8 setups

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  A single PEDF gene is present in all examined vertebrate species but is absent from invertebrates (D. melanogaster, C. elegans, C. intestinalis)

  vertebrate cdna pedf complete genomic rt-pcr phylogenetic

• Molecular and clinical analyses of 84 patients with tuberous sclerosis complex.

  PMID 16981987 · PMC1592085 · BMC medical genetics · 2006 · 8 claims · 6 setups

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  Mutations were identified in 64 of 84 (76%) TSC probands, comprising 9 TSC1 and 55 TSC2 mutations

  genomic pcr-amplified tsc healthy dhplc direct pcr

• ATM variants and cancer risk in breast cancer patients from Southern Finland.

  PMID 16914028 · PMC1592307 · BMC cancer · 2006 · 8 claims · 6 setups

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  Neither 5557G>A nor ivs38-8T>C, nor any haplotype containing them, was significantly associated with breast cancer risk in any patient group

  familial brca1 same genotype genotyping denaturing direct

• CEAS: cis-regulatory element annotation system.

  PMID 16845068 · PMC1538818 · Nucleic acids research · 2006 · 7 claims · 5 setups

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  CEAS is the first web server to streamline genome-scale ChIP-chip downstream analyses for biologists without strong bioinformatics support

  genome genomic chip-chip repeat-masked conservation

• Comparison of RNA-Seq by poly (A) capture, ribosomal RNA depletion, and DNA microarray for expression profiling.

  PMID 24888378 · PMC4070569 · BMC genomics · 2014 · 8 claims · 8 setups

  Has reproduction · 77

  Ribo-Zero-Seq removes rRNA with efficiency comparable to poly(A)-based mRNA-Seq in both FF and FFPE RNA, whereas DSN-Seq leaves significantly more rRNA and shows greater variation.

  fresh-frozen ffpe breast unc microarray mrna-seq ribo-zero-seq

• Intragenic deletion in the LARGE gene causes Walker-Warburg syndrome.

  PMID 17436019 · PMC1914248 · Human genetics · 2007 · 7 claims · 8 setups

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  A homozygous 63.1-kb intragenic deletion in LARGE (exons 9-10) causes Walker-Warburg syndrome in a consanguineous Saudi family

  genomic family skeletal blood microsatellite direct multiplex

• Structural and functional divergence of two fish aquaporin-1 water channels following teleost-specific gene duplication.

  PMID 18811940 · PMC2564943 · BMC evolutionary biology · 2008 · 8 claims · 8 setups

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  Teleosts, unlike tetrapods, possess two closely linked paralogous AQP1 genes, aqp1a and aqp1b (formerly AQP1o), arising from a teleost-specific duplication of an ancestral AQP1 gene

  aqp1-like pufferfish tissues xenopus phylogenetic genomic rt-pcr

• Five novel mutations of the FRMD7 gene in Chinese families with X-linked infantile nystagmus.

  PMID 18431453 · PMC2324116 · Molecular vision · 2008 · 7 claims · 5 setups

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  Five novel FRMD7 mutations were identified in five of seven Chinese families with X-linked infantile nystagmus.

  genomic affected patients linkage direct snp

• Mutation analysis of the MSMB gene in familial prostate cancer.

  PMID 19997100 · PMC2816656 · British journal of cancer · 2010 · 8 claims · 5 setups

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  No deleterious mutations were found in the MSMB coding region in 192 familial prostate cancer cases

  germline blood 161-nt genotype sanger taqman transcription

• Fibrinogen Yecheon: congenital dysfibrinogenemia with gamma methionine-310 to threonine substitution.

  PMID 19949684 · PMC2775876 · Journal of Korean medical science · 2009 · 7 claims · 6 setups

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  A novel de novo heterozygous FGG mutation (c.1007T>C) causing γ Met310Thr substitution was identified in a Korean patient, named 'fibrinogen Yecheon'

  plasma coagulation fibrinogen pcr

• 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

• Inference of RNA polymerase II transcription dynamics from chromatin immunoprecipitation time course data.

  PMID 24830797 · PMC4022483 · PLoS computational biology · 2014 · 8 claims · 8 setups

  Has reproduction · 75

  A convolved Gaussian process model of pol-II occupancy across gene segments captures the transcription wave and yields estimates of transcription speed and promoter-proximal pol-II activity.

  mcf7 promoter gene signals pol-ii clustering transcription

• Transcriptome assemblies for two drug-type cannabis chemotypes by long-read RNA sequencing.

  PMID 41968651 · PMC13071343 · The plant genome · 2026 · 8 claims · 7 setups

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  PacBio Iso-Seq transcriptome assemblies were generated for two contrasting drug-type cannabis chemotypes (THC-dominant and CBD-dominant)

  cannabis same pacbio short-read functional

• Chromosome-level genome assembly of agar-producing red seaweed Gracilaria vermiculophylla.

  PMID 41629338 · PMC12966425 · Scientific data · 2026 · 8 claims · 8 setups

  Has reproduction · 91

  Assembled the first chromosome-level genome of G. vermiculophylla: 77.5 Mb, 22 pseudochromosomes, contig N50 2.61 Mb, scaffold N50 3.16 Mb

  vermiculophylla assembled predicted genome short-read nanopore hi-c

• Introduction of in vitro transcribed ENO1 mRNA into neuroblastoma cells induces cell death.

  PMID 16359544 · PMC1327688 · BMC cancer · 2005 · 8 claims · 6 setups

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  ENO1 has tumour suppressor activity

  sk-n-as neuroblastoma genomic growth tunel real-time

• A mutation in GJA8 (p.P88Q) is associated with "balloon-like" cataract with Y-sutural opacities in a family of Indian origin.

  PMID 18587493 · PMC2435161 · Molecular vision · 2008 · 6 claims · 4 setups

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  A heterozygous c.262C>A mutation in GJA8 (connexin 50), causing p.P88Q, is associated with a novel 'balloon-like' cataract phenotype with prominent Y-sutural opacities in an Indian family.

  lens family genomic clinical family pcr