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).

• A proteomic analysis of IVF follicular fluid in women

  PMID 18980758 · PMC3916005 · Fertility and sterility · 2009 · 8 claims · 4 setups

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  2D-PAGE proteomic evaluation of follicular fluid can identify potential biomarkers distinguishing good versus poor IVF responders in matched patient pairs

  follicular excised clinical polyacrylamide liquid direct

• Sys-BodyFluid: a systematical database for human body fluid proteome research.

  PMID 18978022 · PMC2686600 · Nucleic acids research · 2009 · 6 claims · 4 setups

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  Sys-BodyFluid is a web-based database integrating proteomic data from 11 human body fluids (plasma/serum, urine, cerebrospinal fluid, saliva, bronchoalveolar lavage fluid, synovial fluid, nipple aspirate fluid, tear fluid, seminal fluid, milk, amniotic fluid), containing over 10,000 proteins

  body curated proteins literature sequence cross-body-fluid

• SysZNF: the C2H2 zinc finger gene database.

  PMID 18974185 · PMC2686507 · Nucleic acids research · 2009 · 7 claims · 6 setups

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  SysZNF is a database that systematically catalogs C2H2-ZNF genes in human and mouse with physical location, gene models, expression probes, protein domains, homologs, and literature links

  user-defined hmm domain all-to-all

• "Sequencing-grade" screening for BRCA1 variants by oligo-arrays.

  PMID 18973698 · PMC2583995 · Journal of translational medicine · 2008 · 7 claims · 6 setups

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  An oligo-array platform can detect BRCA1 SNPs, insertions, and deletions of known and unknown variants, including in heterozygous conditions, with accuracy comparable to direct sequencing

  genomic pcr mcf-10a brca1 oligo-nucleotide direct pcr

• A computational screen for type I polyketide synthases in metagenomics shotgun data.

  PMID 18953415 · PMC2568958 · PloS one · 2008 · 8 claims · 6 setups

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  Combining HMM domain searches with maximum-likelihood phylogenetic trees can discriminate true PKS I sequences from evolutionarily related but functionally different enzymes (e.g., FAS I) in metagenomic data.

  predicted hmm-identified reference hmm hmm maximum-likelihood robinson-foulds

• Strong signature of natural selection within an FHIT intron implicated in prostate cancer risk.

  PMID 18953408 · PMC2568805 · PloS one · 2008 · 8 claims · 8 setups

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  Re-sequencing and genotyping across a 28.5 kb region delineates the prostate cancer risk association within FHIT intron 5 to a 15 kb LD block in European-Americans.

  european-american yoruban japanese case sanger snp linkage

• The specificity and polymorphism of the MHC class I prevents the global adaptation of HIV-1 to the monomorphic proteasome and TAP.

  PMID 18949050 · PMC2569417 · PloS one · 2008 · 6 claims · 5 setups

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  Within individual hosts, proteasome and TAP escape mutations in HIV-1 occur frequently

  hiv-1 hla-genotyped predicted bioinformatic longitudinal ancestral

• Organization of physical interactomes as uncovered by network schemas.

  PMID 18949022 · PMC2561054 · PLoS computational biology · 2008 · 7 claims · 5 setups

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  A computational procedure can systematically identify 'emergent' network schemas that are both recurrent and over-represented relative to randomized networks preserving lower-order subschema distributions

  cerevisiae sapiens uncharacterized network cross-species functional

• Genome screen to detect linkage to common susceptibility genes for intracranial and aortic aneurysms.

  PMID 18948608 · PMC2629798 · Stroke · 2009 · 8 claims · 4 setups

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  Genomewide linkage analysis in 26 multiplex IA families with AA-affected members identified LOD peaks on chromosome 11 (LOD=3.0) and chromosome 6 (LOD=2.3) using a broad IA/AA-combined phenotype

  multiplex individuals fia subjects genomewide snp medical

• Transcription-terminating mutation in telethonin causing autosomal recessive muscular dystrophy type 2G in a European patient.

  PMID 18948002 · PMC2592511 · Neuromuscular disorders : NMD · 2008 · 7 claims · 7 setups

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  The patient carries a homozygous Trp25X (TGG→TGA) mutation in TCAP causing premature termination of translation/transcription and complete telethonin deficiency.

  pelvis skeletal muscle genomic muscle histology electron

• Aggregation propensity of the human proteome.

  PMID 18927604 · PMC2557143 · PLoS computational biology · 2008 · 8 claims · 7 setups

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  Long proteins have, on average, less intense/pronounced aggregation peaks than short proteins

  proteome non-membrane proteins membrane sequence-based correlation statistical

• Differential protein expression in human corneal endothelial cells cultured from young and older donors.

  PMID 18852868 · PMC2565687 · Molecular vision · 2008 · 8 claims · 5 setups

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  Cultured HCEC protein profiles show age-related differences between young and older donors

  corneal 2-d trypsin-digested confluent 2-d gel maldi-tof

• Breast cancer proteomics reveals correlation between estrogen receptor status and differential phosphorylation of PGRMC1.

  PMID 18922159 · PMC2614521 · Breast cancer research : BCR · 2008 · 8 claims · 5 setups

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  PGRMC1 protein spots are differentially abundant between ER-negative and ER-positive breast tumors, with two of three spots more abundant in ER-negative tumors

  sections pooled mcf7 paraffin-embedded 2d-page shrimp viability

• Metabolic syndrome: from epidemiology to systems biology.

  PMID 18852695 · PMC2829312 · Nature reviews. Genetics · 2008 · 8 claims · 8 setups

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  MetSyn component traits (obesity, insulin resistance, dyslipidaemia, hypertension) exhibit causal interactions and common etiologies rather than being independent conditions

  populations rats adipose four genome-wide linkage gene

• The genome of the simian and human malaria parasite Plasmodium knowlesi.

  PMID 18843368 · PMC2656934 · Nature · 2008 · 8 claims · 7 setups

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  The P. knowlesi (H strain) nuclear genome was sequenced and assembled: 23.5 Mb across 14 chromosomes with 5,188 predicted protein-encoding genes.

  knowlesi predicted type whole-genome comparative pfam

• Malaria research in the post-genomic era.

  PMID 18843360 · PMC2705782 · Nature · 2008 · 8 claims · 7 setups

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  Genome-dependent methods can partially substitute for forward genetic approaches that are unavailable or limited in malaria parasites.

  falciparum plasmodium malaria hela comparative two-hybrid proteomics

• Versatile online-offline engine for automated acquisition of high-resolution tandem mass spectra.

  PMID 18841935 · PMC2716176 · Analytical chemistry · 2008 · 7 claims · 6 setups

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  An integrated hardware/software online-offline platform (TriVersa NanoMate + 12T LTQ FT Ultra + AUTOMATION WAREHOUSE) automates collection of high-resolution MS/MS data for polypeptides >3 kDa that cannot be acquired online on a chromatographic timescale

  acid-extracted hela online offline

• Improving the specificity of exon prediction using comparative genomics.

  PMID 18831778 · PMC2559877 · BMC genomics · 2008 · 8 claims · 6 setups

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  A log-odds ratio scoring method based on codon conservation across human-mouse/human-dog alignments and adjacent-codon dependency can classify putative exons as coding vs non-coding.

  human-mouse human-dog genome simulated comparative single-genome simulated

• SIGMA2: a system for the integrative genomic multi-dimensional analysis of cancer genomes, epigenomes, and transcriptomes.

  PMID 18840289 · PMC2571113 · BMC bioinformatics · 2008 · 8 claims · 6 setups

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  SIGMA2 is a Java-based software system that integrates and visualizes genomic, epigenomic, and transcriptomic cancer data.

  single hcc2218 nsclc array gene multi-omics

• Differential membrane proteomics using 18O-labeling to identify biomarkers for cholangiocarcinoma.

  PMID 18839982 · PMC3204659 · Journal of proteome research · 2008 · 7 claims · 4 setups

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  Golgi membrane protein 1 (GOLM1/GP73), Annexin IV, and Eps8 are validated candidate biomarkers for cholangiocarcinoma

  membrane bile 18o-labeling sds-page western