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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CompMoby: comparative MobyDick for detection of cis-regulatory motifs.
PMID 18950538 · PMC2605473 · BMC bioinformatics · 2008 · 7 claims · 4 setups
CompMoby identifies cis-regulatory binding sites at both transcriptional and post-transcriptional levels in metazoans without prior knowledge of the trans-acting factor
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Has reproduction · 76
Bayesian prediction of microbial oxygen requirement.
PMID 26913185 · PMC4743139 · F1000Research · 2013 · 7 claims · 8 setups
A naive Bayesian classifier based on presence/absence of class-associated Pfam-A domains can distinguish three oxygen requirement classes (aerobe, anaerobe, facultative anaerobe) from genome sequence, unlike prior studies that only made pairwise distinctions.
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Has reproduction · 98
Large-scale quality assessment of prokaryotic genomes with metashot/prok-quality.
PMID 35136576 · PMC8804904 · F1000Research · 2021 · 8 claims · 6 setups
metashot/prok-quality is a container-enabled Nextflow pipeline for quality assessment and dereplication of draft prokaryotic genomes
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U7 snRNAs: a computational survey.
PMID 18267300 · PMC5054213 · Genomics, proteomics & bioinformatics · 2007 · 8 claims · 6 setups
A computational (BLAST-based) survey identified bona fide U7 snRNA genes with characteristic upstream promoter elements (PSE) across most vertebrate genomes examined, plus numerous pseudogenes.
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Expansion of the BioCyc collection of pathway/genome databases to 160 genomes.
PMID 16246909 · PMC1266070 · Nucleic acids research · 2005 · 8 claims · 6 setups
The BioCyc collection has been expanded to 160 pathway/genome databases (PGDBs) organized into three curation tiers.
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Comparative genomics of emerging human ehrlichiosis agents.
PMID 16482227 · PMC1366493 · PLoS genetics · 2006 · 8 claims · 5 setups
Ehrlichia spp. and Anaplasma spp. display a unique large expansion of immunodominant outer membrane proteins (OMP-1/P44/Msp2 family) facilitating antigenic variation
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Comprehensive genome analysis of 203 genomes provides structural genomics with new insights into protein family space.
PMID 16481312 · PMC1373602 · Nucleic acids research · 2006 · 8 claims · 7 setups
The number of protein families continues to expand steadily as more genomes are sequenced, showing no sign of saturation.
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Short-term genome evolution of Listeria monocytogenes in a non-controlled environment.
PMID 19014550 · PMC2642827 · BMC genomics · 2008 · 6 claims · 6 setups
The 2000 listeriosis outbreak was likely caused by an L. monocytogenes strain that persisted in the food processing facility for at least 12 years since 1988
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A parsimony approach to biological pathway reconstruction/inference for genomes and metagenomes.
PMID 19680427 · PMC2714467 · PLoS computational biology · 2009 · 8 claims · 6 setups
The naïve mapping approach (present if ≥1 associated function is found) leads to an inflated estimate of biological pathways and overestimates functional diversity of a sample.
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Ensembl 2007.
PMID 17148474 · PMC1761443 · Nucleic acids research · 2007 · 8 claims · 7 setups
Ensembl added 18 new chordate genomes this year, increasing total genomes available from 15 to 33, the largest yearly increase to date.
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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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Has reproduction · 100
Whole-genome sequencing of cryopreserved resources from French Large White pigs at two distinct sampling times reveals strong signatures of convergent and divergent selection between the dam and sire lines.
PMID 36864379 · PMC9979506 · Genetics, selection, evolution : GSE · 2023 · 6 claims · 8 setups
French LWD and LWS lines have lost approximately 5% of the SNPs that segregated in the 1977 ancestral population.
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Has reproduction · 76
A Deeper Insight into Evolutionary Patterns and Phylogenetic History of ASFV Epidemics in Sardinia (Italy) through Extensive Genomic Sequencing.
PMID 34696424 · PMC8539718 · Viruses · 2021 · 7 claims · 8 setups
58 new whole genomes of Sardinian ASFV isolates were sequenced, the largest ASFV whole-genome sequencing effort to date
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Has reproduction · 75
Genomic regions and candidate genes selected during the breeding of rice in Vietnam.
PMID 35899250 · PMC9309459 · Evolutionary applications · 2022 · 8 claims · 7 setups
XP-CLR and FST scans identify genomic regions with distorted allele frequency/differentiation patterns resulting from differential selective pressures between Vietnamese rice subpopulations
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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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Comparative genomics and understanding of microbial biology.
PMID 10998382 · PMC2627966 · Emerging infectious diseases · 2000 · 8 claims · 7 setups
GC content varies widely among prokaryotic genomes (29% in B. burgdorferi to 68% in M. tuberculosis) and shapes codon usage and amino acid composition.
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Comparative genomics.
PMID 14624258 · PMC261895 · PLoS biology · 2003 · 8 claims · 7 setups
Conserved DNA between species tends to encode shared functional features, while divergent DNA underlies species differences
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The post-genomic era for a select few.
PMID 14759254 · PMC395745 · Genome biology · 2004 · 8 claims · 8 setups
The Exofish comparative-genomics tool identifies protein-coding DNA segments by comparing two genome sequences and was used to compare pufferfish (Takifugu, Tetraodon) genomes with mammalian genomes, improving annotation of the human and mouse genomes.
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Chimp genome: branching out.
PMID 16136102 · PMC7420934 · Nature · 2005 · 8 claims · 8 setups
The Chimpanzee Sequencing and Analysis Consortium published the initial draft chimpanzee genome sequence and compared it to the human genome.
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The impact of low-cost, genome-wide resequencing on association studies.
PMID 16004723 · PMC3525269 · Human genomics · 2005 · 8 claims · 4 setups
The HapMap project provides more than 500,000 SNPs across three major human populations, enabling genome-wide association studies via linkage disequilibrium tagging.