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).

• Aberrant 5' splice sites in human disease genes: mutation pattern, nucleotide structure and comparison of computational tools that predict their utilization.

  PMID 17576681 · PMC1934990 · Nucleic acids research · 2007 · 8 claims · 4 setups

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  Cryptic 5'ss are best predicted by computational algorithms that accommodate nucleotide dependencies (e.g., Markov model, maximum entropy, maximum dependence decomposition) rather than by weight-matrix models

  disease mammalian compiled literature minigene computational

• Convergence of mutation and epigenetic alterations identifies common genes in cancer that predict for poor prognosis.

  PMID 18507500 · PMC2429944 · PLoS medicine · 2008 · 7 claims · 7 setups

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  At least 36 of the 189 newly mutated CAN genes are targets of promoter CpG island hypermethylation, often in both colon and breast cancer cell lines

  breast same selected hct116 expression methylation-specific rt-pcr

• Kangaroo--a pattern-matching program for biological sequences.

  PMID 12150718 · PMC119856 · BMC bioinformatics · 2002 · 7 claims · 2 setups

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  Kangaroo is a web-based regular expression pattern-matching program that searches DNA, protein, or coding-region sequences across ten organisms with no restriction on query length or complexity.

  coding regular-expression mutation

• Developing prognostic gene panel of survival time in lung adenocarcinoma patients using machine learning.

  PMID 35117753 · PMC8799101 · Translational cancer research · 2020 · 7 claims · 4 setups

  Has reproduction · 32

  A panel of 22 genetic features with Naïve Bayes can predict whether lung adenocarcinoma patient survival time is >3 years (accuracy=75%, AUC=0.81).

  tcga-luad geo bulk expression methylation

• Evaluation of NTHL1, NEIL1, NEIL2, MPG, TDG, UNG and SMUG1 genes in familial colorectal cancer predisposition.

  PMID 17029639 · PMC1624846 · BMC cancer · 2006 · 6 claims · 4 setups

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  Coding sequences and intron-exon boundaries of NTHL1, NEIL1, NEIL2, MPG, TDG, UNG and SMUG1 were screened in 94 familial CRC cases with known genes excluded

  genomic predicted archival mutation targeted functional

• Novel MEK1 mutation identified by mutational analysis of epidermal growth factor receptor signaling pathway genes in lung adenocarcinoma.

  PMID 18632602 · PMC2586155 · Cancer research · 2008 · 8 claims · 7 setups

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  A novel somatic MEK1 K57N mutation was identified in 2 of 207 primary lung adenocarcinomas

  nsclc 293t il-3-independent mutational site-directed cytokine-independence

• A spectrum of severe familial liver disorders associate with telomerase mutations.

  PMID 19936245 · PMC2775683 · PloS one · 2009 · 7 claims · 8 setups

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  Heterozygous telomerase loss-of-function mutations associate with, but are not deterministic of, a broad spectrum of hematologic and severe liver abnormalities.

  leukocyte leukocytes reconstitution liver sanger flow telomerase

• VarDetect: a nucleotide sequence variation exploratory tool.

  PMID 19091032 · PMC2638149 · BMC bioinformatics · 2008 · 8 claims · 2 setups

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  VarDetect is a stand-alone software tool that automatically detects nucleotide variation (SNPs) from fluorescence-based chromatogram traces using pre-calculated peak content ratios and artifact-handling rules.

  genomic vardetect automatic software

• The functional importance of disease-associated mutation.

  PMID 12220483 · PMC128831 · BMC bioinformatics · 2002 · 6 claims · 1 setups

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  Disease-associated mutations occur in conserved regions of genes and can be used to identify likely disease-causing mutations

  disease-associated sequence

• Patents and translational research in genomics.

  PMID 17621295 · PMC1955681 · Nature biotechnology · 2007 · 8 claims · 2 setups

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  Gene patents can impede the use of genes for research, diagnosis and treatment, thereby hindering translational genomics research

  publicly mutation patent

• Molecular epidemiology of DFNB1 deafness in France.

  PMID 15070423 · PMC385234 · BMC medical genetics · 2004 · 8 claims · 7 setups

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  35delG remains the most common pathogenic GJB2 mutation in the studied French (Languedoc Roussillon) population despite being less frequent than in other Mediterranean populations

  gjb2 dried genomic deaf dhplc pcr-mediated pcr-dhplc

• Large-scale molecular analysis of a 34 Mb interval on chromosome 6q: major refinement of the RP25 interval.

  PMID 18510646 · PMC2689154 · Annals of human genetics · 2008 · 7 claims · 5 setups

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  Direct sequencing of 43 candidate genes in 7 Spanish arRP families identified 244 sequence variants (76 novel), none pathogenic, excluding these genes as disease-causing.

  spanish rp5 population candidate direct comparative pcr

• Mutations in UPF3B, a member of the nonsense-mediated mRNA decay complex, cause syndromic and nonsyndromic mental retardation.

  PMID 17704778 · PMC2872770 · Nature genetics · 2007 · 8 claims · 6 setups

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  Mutations in UPF3B cause syndromic (Lujan-Fryns syndrome, FG syndrome) and nonsyndromic X-linked mental retardation

  probands lymphoblastoid lcls tissues gene quantitative cycloheximide

• Integrative analysis of RUNX1 downstream pathways and target genes.

  PMID 18671852 · PMC2529319 · BMC genomics · 2008 · 7 claims · 8 setups

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  Integrating gene expression profiles from three independent RUNX1 perturbation platforms (FPD-AML patient cell lines, RUNX1/CBFβ overexpression in HeLa cells, Runx1 knockout mouse embryos) identifies RUNX1-regulated genes and downstream pathways

  lymphoblastic hela runx1 aml cdna microarray affymetrix

• Patterns of somatic mutation in human cancer genomes.

  PMID 17344846 · PMC2712719 · Nature · 2007 · 8 claims · 5 setups

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  Systematic resequencing of a large gene family (protein kinases) across diverse cancers reveals a larger repertoire of cancer genes than previously anticipated

  cancers additional computational combined targeted follow-up statistical

• Frameshift mutations at mononucleotide repeats in RAD50 recombinational DNA repair gene in colorectal cancers with microsatellite instability.

  PMID 11429044 · PMC5926751 · Japanese journal of cancer research : Gann · 2001 · 6 claims · 3 setups

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  RAD50 (A)9 mononucleotide repeat is frequently frameshift-mutated in MSI-H colorectal cancer cell lines and primary tumors

  colorectal same pcr-based msi

• The continuing search for cancer-causing somatic mutations.

  PMID 17319975 · PMC1851399 · Breast cancer research : BCR · 2007 · 8 claims · 3 setups

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  A screen of 91 breast cancers uncovered 87 somatic variants spread across 16 of the 21 genes examined

  breast limited targeted gene temporal

• Constructing an APOBEC-related gene signature with predictive value in the overall survival and therapeutic sensitivity in lung adenocarcinoma.

  PMID 37954334 · PMC10637964 · Heliyon · 2023 · 8 claims · 8 setups

  Has reproduction · 88

  APOBEC family genes are aberrantly expressed across cancers, with APOBEC3B the most consistently upregulated, and APOBEC3B/APOBEC3A are markedly altered in LUAD

  tcga tcga-luad geo beas-2b bulk somatic microarray

• Mutations in the RSK2(RPS6KA3) gene cause Coffin-Lowry syndrome and nonsyndromic X-linked mental retardation.

  PMID 17100996 · PMC2714973 · Clinical genetics · 2006 · 6 claims · 6 setups

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  RSK2(RPS6KA3) mutations can present with a mild or atypical Coffin-Lowry phenotype overlapping clinically with nonsyndromic X-linked mental retardation

  blood-derived affected unaffected population mutation clinical segregation

• Ethnically diverse causes of Walker-Warburg syndrome (WWS): FCMD mutations are a more common cause of WWS outside of the Middle East.

  PMID 18752264 · PMC2577713 · Human mutation · 2008 · 8 claims · 4 setups

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  40% (16/40) of WWS families in this diverse cohort received a molecular diagnosis with mutations in POMT1, POMT2, FKRP or FCMD

  genomic pomt2 population genome-wide pcr multiplex