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).

• Identification of common genetic variation that modulates alternative splicing.

  PMID 17571926 · PMC1904363 · PLoS genetics · 2007 · 7 claims · 8 setups

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  Common SNPs located close to intron-exon boundaries are associated with and causally modulate alternative splicing patterns in human genes

  ceph lcls skipped additional rt-pcr snp resequencing

• Predicting position along a looping immune response trajectory.

  PMID 30296270 · PMC6175499 · PloS one · 2018 · 8 claims · 6 setups

  Has reproduction · 98

  Looper is a computational method that automatically identifies phase-shifted gene pairs (using SAX symbolic representation) that trace loops in longitudinal expression data.

  monocytes blood pbmcs montreal microarray qrt-pcr topological

• Cross-species comparative hippocampal transcriptomics in Alzheimer's disease.

  PMID 38292167 · PMC10824791 · iScience · 2024 · 8 claims · 8 setups

  Has reproduction · 75

  The three mouse models (5xFAD, APP/PS1, hAβ-KI) share more DEGs and GOBP terms with LOAD than with EOAD patients

  hippocampus postmortem computational bulk publicly qrt-pcr

• Bone marrow ectopic expression of a non-coding RNA in childhood T-cell acute lymphoblastic leukemia with a novel t(2;11)(q11.2;p15.1) translocation.

  PMID 18947387 · PMC2579299 · Molecular cancer · 2008 · 8 claims · 8 setups

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  A novel t(2;11)(q11.2;p15.1) translocation was identified as the sole cytogenetic abnormality in a childhood T-ALL case

  bone genomic da926692 g-banding fish vectorette

• PrimerSeq: Design and visualization of RT-PCR primers for alternative splicing using RNA-seq data.

  PMID 24747190 · PMC4411361 · Genomics, proteomics & bioinformatics · 2014 · 8 claims · 3 setups

  Has reproduction · 90

  PrimerSeq is a user-friendly stand-alone software with a GUI for systematic design and visualization of RT-PCR primers for alternative splicing analysis using user-provided RNA-seq data.

  heart genome rna-seq rt-pcr

• 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

• Machine learning algorithm predicts fibrosis-related blood diagnosis markers of intervertebral disc degeneration.

  PMID 37915003 · PMC10619283 · BMC medical genomics · 2023 · 8 claims · 7 setups

  Has reproduction · 68

  CEP120 and SPDL1 were identified as diagnostic genes for IDD using a random forest model

  blood gse150408 cep120 pbmcs bulk machine single-sample

• A novel 154-bp deletion in the human mitochondrial DNA control region in healthy individuals.

  PMID 18629826 · PMC2697596 · Human mutation · 2008 · 8 claims · 5 setups

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  A novel 154-bp mtDNA control region deletion (m.16154_16307del154) was identified in a healthy family

  blood-derived mtdna pcr fragment mtdna

• The fate of the duplicated androgen receptor in fishes: a late neofunctionalization event?

  PMID 19094205 · PMC2637867 · BMC evolutionary biology · 2008 · 8 claims · 4 setups

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  AR was duplicated into two paralogs, AR-A and AR-B, during a teleost-specific whole genome duplication (WGD), after the split of Acipenseriformes but before the divergence of Osteoglossiformes.

  fish full-length tetraodon rt-pcr database molecular

• Annotation and analysis of 10,000 expressed sequence tags from developing mouse eye and adult retina.

  PMID 14519200 · PMC328454 · Genome biology · 2003 · 8 claims · 5 setups

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  Annotation of 8,633 high-quality non-mitochondrial/non-ribosomal ESTs shows 57% represent known genes and 43% are unknown or novel, with M15E having the highest proportion of novel ESTs

  embryonic high-quality unique m15e est sequence comparative

• In silico and in vivo splicing analysis of MLH1 and MSH2 missense mutations shows exon- and tissue-specific effects.

  PMID 16995940 · PMC1590028 · BMC genomics · 2006 · 8 claims · 6 setups

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  In silico ESE-prediction algorithms (ESEfinder, RescueESE, PESX) do not reliably predict actual in vivo splicing behavior of missense mutations

  hmlh1 same cos-7 hela ese splice minigene

• Novel GPR143 mutations and clinical characteristics in six Chinese families with X-linked ocular albinism.

  PMID 18978956 · PMC2576482 · Molecular vision · 2008 · 7 claims · 6 setups

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  Mutations in GPR143 were identified in each of six Chinese OA1 families, comprising five novel mutations and one previously known mutation (c.353G>A).

  genomic oa1 one gpr143 pcr heteroduplex junction-fragment

• ARSACS in the Dutch population: a frequent cause of early-onset cerebellar ataxia.

  PMID 18465152 · PMC2441586 · Neurogenetics · 2008 · 8 claims · 8 setups

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  37% (16/43) of Dutch index patients with early-onset recessive cerebellar ataxia carry SACS mutations, indicating ARSACS is far more frequent than previously estimated

  genomic identified sacs-mutation-positive alleles pcr clinical brain

• Identification of four novel cytochrome P4501B1 mutations (p.I94X, p.H279D, p.Q340H, and p.K433K) in primary congenital glaucoma patients.

  PMID 20057908 · PMC2802296 · Molecular vision · 2009 · 8 claims · 4 setups

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  Mutations in CYP1B1 are a major cause of PCG in the studied patient cohort

  genomic cyp1b1 pcg pcr missense clinical

• Genomics of Environmental Salmonella: Engaging Students in the Microbiology and Bioinformatics of Foodborne Pathogens.

  PMID 33967968 · PMC8100199 · Frontiers in microbiology · 2021 · 8 claims · 8 setups

  Has reproduction · 73

  An undergraduate CURE combining field sampling, wet-lab microbiology, and genomic bioinformatics can be used to isolate and characterize environmental S. enterica strains.

  putative enterica selected assembled endpoint genome long-read

• Mutation analysis in a German family identified a new cataract-causing allele in the CRYBB2 gene.

  PMID 17653036 · PMC2774456 · Molecular vision · 2007 · 8 claims · 4 setups

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  A novel heterozygous mutation (383A>T; D128V) in exon 5 of CRYBB2 cosegregates with congenital cataract in all three affected family members and is absent in unaffected relatives.

  genomic pcr-amplified computational pcr restriction pcr-rflp

• Resequencing PNMT in European hypertensive and normotensive individuals: no common susceptibilily variants for hypertension and purifying selection on intron 1.

  PMID 17645789 · PMC1947951 · BMC medical genetics · 2007 · 7 claims · 7 setups

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  Resequencing of PNMT found no common susceptibility variants that distinguish hypertensive from normotensive individuals

  genomic pnmt promoter pcr population haplotype

• Analysis of human sarcospan as a candidate gene for CFEOM1.

  PMID 11180757 · PMC29083 · BMC genetics · 2001 · 7 claims · 5 setups

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  Sarcospan sequence is unmutated in all six CFEOM1 families studied

  yac genomic extraocular genome pcr direct immunofluorescence

• Insulin mutation screening in 1,044 patients with diabetes: mutations in the INS gene are a common cause of neonatal diabetes but a rare cause of diabetes diagnosed in childhood or adulthood.

  PMID 18162506 · PMC7611804 · Diabetes · 2008 · 8 claims · 8 setups

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  Heterozygous INS mutations are a common cause of permanent neonatal diabetes (PNDM) diagnosed before 6 months of age

  peripheral patients mody young-onset pcr microsatellite variant

• Mutations in NYX of individuals with high myopia, but without night blindness.

  PMID 17392683 · PMC2642916 · Molecular vision · 2007 · 7 claims · 5 setups

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  Two novel NYX missense mutations (Cys48Trp and Arg191Gln) were found in unrelated males with high myopia but no night blindness.

  unrelated individuals high model direct sequencing electroretinogram