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).
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Comparative gene finding in chicken indicates that we are closing in on the set of multi-exonic widely expressed human genes.
PMID 15809229 · PMC1074396 · Nucleic acids research · 2005 · 8 claims · 6 setups
Comparative gene finding (SGP2) between human and chicken, followed by RT-PCR verification, adds at most ~0.2% new genes to the multi-exonic human gene catalog
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Has reproduction · 89
Comparative genomics of dairy-associated Staphylococcus aureus from selected sub-Saharan African regions reveals milk as reservoir for human-and animal-derived strains and identifies a putative animal-related clade with presumptive novel siderophore.
PMID 36046020 · PMC9421002 · Frontiers in microbiology · 2022 · 7 claims · 8 setups
Milk serves as a reservoir for both human- and animal-derived S. aureus strains in sub-Saharan Africa
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A genome-wide screen for noncoding elements important in primate evolution.
PMID 18215302 · PMC2242780 · BMC evolutionary biology · 2008 · 8 claims · 4 setups
A new likelihood ratio test (LRT) method, using nearby ancestral repeats to control for local mutation rate, can identify noncoding elements with lineage-specific accelerated substitution rates.
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Comparative genomics and experimental promoter analysis reveal functional liver-specific elements in mammalian hepatic lipase genes.
PMID 17428321 · PMC1853088 · BMC genomics · 2007 · 8 claims · 7 setups
Cis-regulatory elements responsible for liver-specific HL expression are conserved among mammalian HL genes
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Genome comparison without alignment using shortest unique substrings.
PMID 15910684 · PMC1166540 · BMC bioinformatics · 2005 · 8 claims · 8 setups
A number of sequence comparison tasks, including detection of unique genomic regions, can be accomplished efficiently without an alignment step using shortest unique substrings.
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Inverse symmetry in complete genomes and whole-genome inverse duplication.
PMID 19898631 · PMC2771390 · PloS one · 2009 · 8 claims · 5 setups
Reverse and complement symmetries are essentially absent in genomic sequences at all scales.
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Comprehensive genomic analysis reveals clinically relevant molecular distinctions between thymic carcinomas and thymomas.
PMID 19861435 · PMC2783876 · Clinical cancer research : an official journal of the American Association for Cancer Research · 2009 · 7 claims · 7 setups
Comprehensive genomic analysis shows thymic carcinomas are molecularly distinct from thymomas
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Systems biology and the host response to viral infection.
PMID 18066032 · PMC7097743 · Nature biotechnology · 2007 · 8 claims · 8 setups
Systems biology integration of 'omics data (transcriptomics, proteomics, genomics) with computational modeling is needed to fully understand virus-host interactions and identify novel antiviral targets
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Eurasian and African mitochondrial DNA influences in the Saudi Arabian population.
PMID 17331239 · PMC1810519 · BMC evolutionary biology · 2007 · 8 claims · 4 setups
The majority (85%) of Saudi Arab mtDNA lineages have a western Asia (Eurasian) provenance
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The Bifidobacterium dentium Bd1 genome sequence reflects its genetic adaptation to the human oral cavity.
PMID 20041198 · PMC2788695 · PLoS genetics · 2009 · 8 claims · 8 setups
The B. dentium Bd1 genome was sequenced to completion, revealing a single circular 2,636,368 bp chromosome with 2,143 predicted ORFs
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Nucleotide-resolution analysis of structural variants using BreakSeq and a breakpoint library.
PMID 20037582 · PMC2951730 · Nature biotechnology · 2010 · 8 claims · 7 setups
A standardized, non-redundant library of 1,889 breakpoint-resolved SVs was assembled from eight published surveys
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Has reproduction · 91
Genomic Description of 'Candidatus Abyssubacteria,' a Novel Subsurface Lineage Within the Candidate Phylum Hydrogenedentes.
PMID 30210471 · PMC6121073 · Frontiers in microbiology · 2018 · 8 claims · 7 setups
SURF_5 and SURF_17 are the first full genomes of a novel bacterial lineage, 'Candidatus Abyssubacteria,' within the candidate phylum Hydrogenedentes
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Tracing the origin of functional and conserved domains in the human proteome: implications for protein evolution at the modular level.
PMID 17090320 · PMC1654190 · BMC evolutionary biology · 2006 · 8 claims · 5 setups
HHpred (HMM-HMM comparison) detects remote homologs in the human proteome with higher sensitivity than hmmpfam (HMMER), giving 10% more functional domain coverage and 20% higher residue coverage against Pfam-A families.
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Has reproduction · 30
Minimal metabolic pathway structure is consistent with associated biomolecular interactions.
PMID 24987116 · PMC4299494 · Molecular systems biology · 2014 · 8 claims · 8 setups
MinSpan, a mixed-integer linear optimization algorithm, computes the shortest, linearly independent pathways (sparsest basis of the null space of the stoichiometric matrix S) for genome-scale metabolic networks, which convex approaches (extreme pathways, elementary flux modes) cannot do at genome scale.
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The integrated world of functional genomics.
PMID 12537543 · PMC151279 · Genome biology · 2003 · 8 claims · 8 setups
Integrating chromatin immunoprecipitation (promoter-binding) data with expression data reveals the yeast cell-cycle transcriptional regulatory network, including network motifs such as autoregulation, multi-component loops, and feedforward loops.