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).

Publications 1.3k Datasets 392.5k Experiments 32

System / cell line: mutations ✕ Assay: computational ✕ Clear

Cancer-specific high-throughput annotation of somatic mutations: computational prediction of driver missense mutations.

PMID 19654296 · PMC2763410 · Cancer research · 2009 · 7 claims · 7 setups

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CHASM, a Random Forest-based computational method, was developed to identify and prioritize missense mutations likely to be functional drivers of tumor cell proliferation.

missense same synthetic tp53 random support principal
Computational analysis of splicing errors and mutations in human transcripts.

PMID 18194514 · PMC2234086 · BMC genomics · 2008 · 8 claims · 4 setups

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Retained introns are significantly shorter than constitutively spliced introns

refseq genes intron exon computational splice prediction
Institutional Profile: The University of California Pharmacogenomics Center: at the interface of genomics, biological mechanisms and drug therapy.

PMID 19842929 · PMC2923222 · Pharmacogenomics · 2009 · 8 claims · 8 setups

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Approximately 15-20% of nonsynonymous variants in membrane transporters exhibit reduced function

abc hek293 expressing sophie computational transporter transport
Emergence of recombinant forms of HIV: dynamics and scaling.

PMID 17967052 · PMC2041978 · PLoS computational biology · 2007 · 7 claims · 5 setups

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A detailed mathematical model incorporating multiple cell infections and recombination quantitatively captures experimental observations of recombinant HIV emergence dynamics in vitro

cd4+ scid-hu splenocytes computational single-round replication-competent proviral
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
Predicting positive p53 cancer rescue regions using Most Informative Positive (MIP) active learning.

PMID 19756158 · PMC2742196 · PLoS computational biology · 2009 · 8 claims · 4 setups

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MIP active learning is a novel active learning method that preferentially seeks informative Positive (functionally active) examples rather than only maximizing classifier accuracy.

engineered p53 computational yeast-based regional homology
Nonclassic congenital lipoid adrenal hyperplasia: a new disorder of the steroidogenic acute regulatory protein with very late presentation and normal male genitalia.

PMID 16968793 · PMC1865081 · The Journal of clinical endocrinology and metabolism · 2006 · 8 claims · 7 setups

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Homozygous StAR missense mutations Val187Met and Arg188Cys cause a novel, milder form of lipoid CAH ('non-classic lipoid CAH') presenting at 2-4 years of age rather than in infancy

blood cos-1 bacteria mitochondria sequencing cell-based recombinant
Computational disease gene identification: a concert of methods prioritizes type 2 diabetes and obesity candidate genes.

PMID 16757574 · PMC1475747 · Nucleic acids research · 2006 · 6 claims · 8 setups

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Applying seven independent computational disease-gene prioritization methods in concert to 9556 positional candidate genes identifies a prioritized set of likely T2D and obesity candidate genes

pubmed genes same randomly geneseeker evoc disease
Reduced secretion of fibulin 5 in age-related macular degeneration and cutis laxa.

PMID 16652333 · PMC1828612 · Human mutation · 2006 · 7 claims · 6 setups

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FBLN5 missense mutations are associated with ARMD in a European (UK/Dutch) cohort, confirming prior US findings

armd dutch fibulin pef6-ssflag mutation computational site-directed
InSite: a computational method for identifying protein-protein interaction binding sites on a proteome-wide scale.

PMID 17868464 · PMC2375030 · Genome biology · 2007 · 8 claims · 8 setups

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InSite predicts protein-pair-specific binding motifs ('Motif M on protein A binds to protein B') by integrating heterogeneous PPI and motif-motif interaction evidence within a Bayesian network trained by EM

saccharomyces homo bank computational yeast tandem
Mutations in the formin gene INF2 cause focal segmental glomerulosclerosis.

PMID 20023659 · PMC2980844 · Nature genetics · 2010 · 8 claims · 8 setups

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Mutations in INF2, a formin family actin-regulating protein, cause autosomal dominant focal segmental glomerulosclerosis (FSGS)

families genes individuals kidney genome-wide sanger resequencing
The mitochondrial genome, a growing interest inside an organelle.

PMID 18488415 · PMC2526360 · International journal of nanomedicine · 2008 · 8 claims · 8 setups

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mtDNA mutations are causally linked to a wide range of mitochondrial diseases, aging, and chronic degenerative diseases

post-mitotic mtdna homozygous high-fat southern rflp-pcr dhplc
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
A restricted spectrum of NRAS mutations causes Noonan syndrome.

PMID 19966803 · PMC3118669 · Nature genetics · 2010 · 8 claims · 6 setups

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Germline NRAS mutations (T50I, G60E) cause a subset of Noonan syndrome cases via enhanced MAPK activation

cohort cos-7 recombinant nras mutation western ras
Biased exon/intron distribution of cryptic and de novo 3' splice sites.

PMID 16141195 · PMC1197134 · Nucleic acids research · 2005 · 7 claims · 5 setups

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Cryptic 3'ss (from 3'YAG consensus mutations) are significantly more frequent in exons than in introns

disease authentic hek293t nuclear literature shapiro-senapathy splicing
ABO exon and intron analysis in individuals with the AweakB phenotype reveals a novel O1v-A2 hybrid allele that causes four missense mutations in the A transferase.

PMID 14617382 · PMC305365 · BMC genetics · 2003 · 8 claims · 7 setups

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A novel O1v-A2 hybrid allele, containing four missense mutations, causes the A weak B phenotype in five individuals of African descent

genomic red computational abo sequencing blood
Genomics: applications in mechanism elucidation.

PMID 19166886 · PMC2698023 · Advanced drug delivery reviews · 2009 · 8 claims · 8 setups

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Genomic tools require no a priori knowledge of a compound's mode of action and can reveal biological pathways (metabolism, distribution, off-target effects) in addition to the precise mechanism of action.

extract panel saccharomyces inbred affinity cytotoxicity genome-wide
Core signaling pathways in human pancreatic cancers revealed by global genomic analyses.

PMID 18772397 · PMC2848990 · Science (New York, N.Y.) · 2008 · 8 claims · 6 setups

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Pancreatic cancers contain an average of 63 genetic alterations, the majority of which are point mutations

pancreatic computational targeted prevalence snp
Rise of the machines.

PMID 18670625 · PMC2467494 · PLoS genetics · 2008 · 8 claims · 4 setups

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New short-read sequencing platforms (Illumina Genome Analyzer, 454 FLX, ABI SOLiD) enable rapid, scalable whole-genome resequencing that was previously restricted to dedicated sequencing centers using Sanger methods.

bacillus independent subtilis whole-genome read
Probing the cancer genome.

PMID 18492227 · PMC2441462 · Genome biology · 2008 · 8 claims · 8 setups

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Combined Sanger and 454 pyrosequencing of MCF-7 BAC clones identified 157 PCR-confirmed translocation breakpoint junctions, including 10 in-frame junctions confirmed at the transcript level

mcf-7 tumor lung oral sanger solexa gistic

Experiments

Cancer-specific high-throughput annotation of somatic mutations: computational prediction of driver missense mutations.

Computational analysis of splicing errors and mutations in human transcripts.

Institutional Profile: The University of California Pharmacogenomics Center: at the interface of genomics, biological mechanisms and drug therapy.

Emergence of recombinant forms of HIV: dynamics and scaling.

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

Predicting positive p53 cancer rescue regions using Most Informative Positive (MIP) active learning.

Nonclassic congenital lipoid adrenal hyperplasia: a new disorder of the steroidogenic acute regulatory protein with very late presentation and normal male genitalia.

Computational disease gene identification: a concert of methods prioritizes type 2 diabetes and obesity candidate genes.

Reduced secretion of fibulin 5 in age-related macular degeneration and cutis laxa.

InSite: a computational method for identifying protein-protein interaction binding sites on a proteome-wide scale.

Mutations in the formin gene INF2 cause focal segmental glomerulosclerosis.

The mitochondrial genome, a growing interest inside an organelle.

Patterns of somatic mutation in human cancer genomes.

A restricted spectrum of NRAS mutations causes Noonan syndrome.

Biased exon/intron distribution of cryptic and de novo 3' splice sites.

ABO exon and intron analysis in individuals with the AweakB phenotype reveals a novel O1v-A2 hybrid allele that causes four missense mutations in the A transferase.

Genomics: applications in mechanism elucidation.

Core signaling pathways in human pancreatic cancers revealed by global genomic analyses.

Rise of the machines.

Probing the cancer genome.