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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SilkDB v2.0: a platform for silkworm (Bombyx mori ) genome biology.
PMID 19793867 · PMC2808975 · Nucleic acids research · 2010 · 8 claims · 8 setups
A new 8.5x-coverage silkworm genome assembly with N50 scaffold size of ~3.7 Mb over a 432 Mb genome represents a significant quality improvement over the prior draft.
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Evolution of insect proteomes: insights into synapse organization and synaptic vesicle life cycle.
PMID 18257909 · PMC2374702 · Genome biology · 2008 · 8 claims · 3 setups
Compiled a list of 120 core presynaptic gene prototypes (PS120) and catalogued their conservation across insect proteomes.
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Activation instead of blocking mesolimbic dopaminergic reward circuitry is a preferred modality in the long term treatment of reward deficiency syndrome (RDS): a commentary.
PMID 19014506 · PMC2615745 · Theoretical biology & medical modelling · 2008 · 8 claims · 6 setups
A biphasic treatment approach—acute DA receptor blocking followed by long-term DA release/activation at the NAc—is needed to treat RDS without inducing abnormal mood or craving.
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Mass spectrometry group has mass appeal.
PMID 15598607 · PMC1247668 · Environmental health perspectives · 2004 · 7 claims · 4 setups
Mass spectrometry can identify proteins and their post-translational modifications with high specificity and sensitivity, making it central to toxicoproteomics.
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Ensembl 2005.
PMID 15608235 · PMC540092 · Nucleic acids research · 2005 · 8 claims · 4 setups
Ensembl's automatic gene build system can flexibly and reliably annotate a wide variety of genomes with limited species-specific evidence.
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The revolution of the biology of the genome.
PMID 15040884 · PMC7091781 · Cell research · 2004 · 8 claims · 6 setups
Polyploidization and gene duplication are the major mechanisms increasing eukaryotic genome size.
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Identification and characterization of insect-specific proteins by genome data analysis.
PMID 17407609 · PMC1852559 · BMC genomics · 2007 · 8 claims · 7 setups
Comparative genome analysis across five holometabolous insects and three non-insect eukaryotes (opisthokonts) identifies 154 insect-specific orthologous groups (refined to 51 proteins) and 466 eukaryote/opisthokont-core orthologous groups
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CONTRAST: a discriminative, phylogeny-free approach to multiple informant de novo gene prediction.
PMID 18096039 · PMC2246271 · Genome biology · 2007 · 8 claims · 5 setups
CONTRAST predicts exact coding region structures for 65% more human genes than the previous state-of-the-art de novo predictor (N-SCAN)
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Multiple whole genome alignments and novel biomedical applications at the VISTA portal.
PMID 17488840 · PMC1933192 · Nucleic acids research · 2007 · 8 claims · 4 setups
A novel multiple whole-genome alignment algorithm treats all genomes symmetrically, avoiding dependence on a single base/reference genome
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Retroposition and evolution of the DNA-binding motifs of YY1, YY2 and REX1.
PMID 17478514 · PMC1904287 · Nucleic acids research · 2007 · 8 claims · 5 setups
62 YY1-related sequences were identified across genomes ranging from flying insects to humans, with high zinc finger domain conservation
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The UCSC Genome Browser Database: update 2006.
PMID 16381938 · PMC1347506 · Nucleic acids research · 2006 · 8 claims · 8 setups
The UCSC Genome Browser Database (GBD) provides integrated sequence and annotation data, with web tools (Genome Browser, Table Browser, Proteome Browser, Gene Sorter, BLAT, In Silico PCR) for visualizing and querying genomes of about a dozen vertebrate species and several model organisms.
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Has reproduction · 84
Genome of the Asian longhorned beetle (Anoplophora glabripennis), a globally significant invasive species, reveals key functional and evolutionary innovations at the beetle-plant interface.
PMID 27832824 · PMC5105290 · Genome biology · 2016 · 7 claims · 7 setups
The A. glabripennis genome encodes a uniquely diverse arsenal of enzymes that degrade the main plant cell wall polysaccharide networks (cellulose, hemicellulose, pectin) and detoxify plant allelochemicals.
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Has reproduction · 80
A chromosome-level genome assembly provides insights into the environmental adaptability and outbreaks of Chlorops oryzae.
PMID 36028584 · PMC9418232 · Communications biology · 2022 · 8 claims · 8 setups
A high-quality chromosome-level genome assembly of C. oryzae was generated using PacBio, Illumina, and Hi-C sequencing
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Has reproduction · 71
A global change in RNA polymerase II pausing during the Drosophila midblastula transition.
PMID 23951546 · PMC3743134 · eLife · 2013 · 8 claims · 8 setups
Massive de novo recruitment of Pol II (and TBP) with widespread pausing occurs during the Drosophila midblastula transition, at 4007 promoters (~one third of all genes).
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Schistosoma mansoni secretes a chemokine binding protein with antiinflammatory activity.
PMID 16301741 · PMC2212990 · The Journal of experimental medicine · 2005 · 8 claims · 8 setups
S. mansoni eggs secrete a chemokine binding protein (smCKBP) that binds certain chemokines and inhibits their interaction with host chemokine receptors and biological activity
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Structural genomics and drug discovery.
PMID 17488474 · PMC3822824 · Journal of cellular and molecular medicine · 2007 · 8 claims · 8 setups
Membrane proteins represent ~70% of current drug targets but only just over 100 high-resolution structures exist for them, versus >30,000 total structures in public databases dominated by soluble proteins.