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).

• Microbial genomics: from sequence to function.

  PMID 10998380 · PMC2627950 · Emerging infectious diseases · 2000 · 8 claims · 4 setups

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  Whole-genome shotgun sequencing (sequencing and assembly of random genome fragments), first demonstrated with Haemophilus influenzae in 1995, is now the method of choice for sequencing most genomes, including the human genome.

  yeast bacteria microbial high-throughput microarray ribosomal

• Identification of serum biomarkers for colon cancer by proteomic analysis.

  PMID 16755300 · PMC2361335 · British journal of cancer · 2006 · 8 claims · 8 setups

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  Complement C3a des-arg, α1-antitrypsin and transferrin were identified as serum proteins with diagnostic potential for CRC.

  serum pooled seldi seldi-tof seldi artificial

• Proteomic identification of non-Gal antibody targets after pig-to-primate cardiac xenotransplantation.

  PMID 18957049 · PMC2586876 · Xenotransplantation · 2008 · 8 claims · 6 setups

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  Non-Gal antibody response after cardiac xenotransplantation is directed to a diverse set of stress response, inflammation-related, cytoskeletal and metabolic pig EC antigens, with several immunodominant targets remaining undefined

  gt-ko spots explanted flow western nanolc

• Trans-natural antisense transcripts including noncoding RNAs in 10 species: implications for expression regulation.

  PMID 18653530 · PMC2528163 · Nucleic acids research · 2008 · 8 claims · 7 setups

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  A new computational pipeline identifies trans-SAs using ESTs (not just mRNAs) across 10 animal species, improving coverage over prior methods

  est unannotated trans-sa tus computational coding hybridization

• Genomic view of the evolution of the complement system.

  PMID 16896831 · PMC2480602 · Immunogenetics · 2006 · 8 claims · 6 setups

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  Bony fish and higher vertebrates share practically the same set of complement genes, indicating most complement gene duplications occurred by the teleost/mammalian divergence (~500 MYA)

  chicken complement sponge shark comparative phylogenetic reverse

• Meeting highlights: beyond the genome 2000: the 18th International Congress of Biochemistry and Molecular Biology.

  PMID 11119309 · PMC2448388 · Yeast (Chichester, England) · 2000 · 8 claims · 8 setups

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  Celera sequenced a human genome to ~45-fold coverage from one donor and used high-quality sequence stretches to define ~6 million SNPs

  homo saccharomyces nicotiana arabidopsis whole-genome oligonucleotide molecular

• Comparative genomics of multidrug resistance in Acinetobacter baumannii.

  PMID 16415984 · PMC1326220 · PLoS genetics · 2006 · 7 claims · 5 setups

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  A. baumannii strain AYE contains an 86-kb genomic resistance island (AbaR1) clustering 45 of its 52 resistance genes, the largest resistance island described to date

  baumannii resistance clinical whole-genome comparative sequence

• From endosymbiont to host-controlled organelle: the hijacking of mitochondrial protein synthesis and metabolism.

  PMID 17983265 · PMC2062474 · PLoS computational biology · 2007 · 8 claims · 7 setups

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  There has been a large turnover of the mitochondrial proteome during evolution: cell envelope synthesis proteins virtually disappeared, and replication, transcription, cell division, transport, regulation, and signal transduction proteins were replaced by eukaryotic proteins

  alpha-proteobacterial reclinomonas reconstructed yeast comparative phylogenomic cog

• Biomarker discovery in neurodegenerative diseases: a proteomic approach.

  PMID 18938247 · PMC2939006 · Neurobiology of disease · 2009 · 6 claims · 8 setups

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  Proteomic profiling of CSF and plasma can identify candidate protein biomarkers that distinguish AD patients from controls with high sensitivity and specificity

  csf plasma brain 2-dge lc-ms seldi-tof-ms

• 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

• Genomic analysis of the TRIM family reveals two groups of genes with distinct evolutionary properties.

  PMID 18673550 · PMC2533329 · BMC evolutionary biology · 2008 · 8 claims · 6 setups

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  The human TRIM family is split into two groups (group 1 and group 2) that differ in domain structure, genomic organization, and evolutionary properties.

  redundant mammalian genomic vertebrates blast pattern-hit tblastn

• Exploring the immunome: A brave new world for human vaccine development.

  PMID 20009527 · PMC2919815 · Human vaccines · 2009 · 7 claims · 7 setups

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  Screening the Mtb proteome in silico for epitopes ('fishing for antigens using epitopes as bait') revealed a remarkable diversity of human immune responses to Mtb proteins without an ascribed function, suggesting human immune response to Mtb is omnivorous rather than focused on single immunodominant proteins.

  mycobacterium subjects francisella autologous epitope-mapping response epitope