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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Inference of transcriptional regulation using gene expression data from the bovine and human genomes.
PMID 17683551 · PMC1978505 · BMC genomics · 2007 · 7 claims · 8 setups
Using human reference promoter sequences is a useful approach for studying gene expression regulation in species with limited or non-existing genomic sequence, such as cattle.
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Has reproduction · 95
A whole genome duplication drives the genome evolution of Phytophthora betacei, a closely related species to Phytophthora infestans.
PMID 34740326 · PMC8571832 · BMC genomics · 2021 · 8 claims · 7 setups
P. betacei P8084 has the largest sequenced genome in the Phytophthora genus (270 Mb)
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Nucleotide sequence analyses of the MRP1 gene in four populations suggest negative selection on its coding region.
PMID 16684361 · PMC1488846 · BMC genomics · 2006 · 8 claims · 5 setups
The coding region of MRP1 shows evidence of negative selection or recent population expansion based on nucleotide diversity statistics
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Has reproduction · 87
De Novo Transcriptome Meta-Assembly of the Mixotrophic Freshwater Microalga Euglena gracilis.
PMID 34072576 · PMC8227486 · Genes · 2021 · 7 claims · 8 setups
A new consensus transcriptome of E. gracilis was assembled by combining reads from five independent RNA-seq studies (23 samples)
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Rapid creation of BAC-based human artificial chromosome vectors by transposition with synthetic alpha-satellite arrays.
PMID 15673719 · PMC548352 · Nucleic acids research · 2005 · 8 claims · 5 setups
Presence of CENP-B box elements is required for efficient de novo centromere formation in HAC vectors
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Pathogenic mitochondrial DNA mutations are common in the general population.
PMID 18674747 · PMC2495064 · American journal of human genetics · 2008 · 7 claims · 6 setups
At least 1 in 200 healthy humans harbors a pathogenic mtDNA mutation with potential to cause disease in offspring of female carriers
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Evolution of genomic sequence inhomogeneity at mid-range scales.
PMID 19891785 · PMC2779198 · BMC genomics · 2009 · 7 claims · 3 setups
MRI regions have comparable levels of de novo mutations to control genomic sequences with average base composition.
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Has reproduction · 62
Application of alternative de novo motif recognition models for analysis of structural heterogeneity of transcription factor binding sites: a case study of FOXA2 binding sites.
PMID 34547062 · PMC8408018 · Vavilovskii zhurnal genetiki i selektsii · 2021 · 8 claims · 4 setups
MultiDeNA pipeline combines PWM, diPWM, BaMM and InMoDe models to train, evaluate, threshold, and classify ChIP-seq peaks for TFBS structural heterogeneity
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Has reproduction · 61
Comprehensive transcriptome study to develop molecular resources of the copepod Calanus sinicus for their potential ecological applications.
PMID 24982883 · PMC4055022 · BioMed research international · 2014 · 8 claims · 8 setups
Illumina RNA-Seq with Trinity de novo assembly produced a C. sinicus transcriptome of 69,751 contigs (average 928.8 bp, N50 1,127 bp) from 58.9 million reads.
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Aberrant 5' splice sites in human disease genes: mutation pattern, nucleotide structure and comparison of computational tools that predict their utilization.
PMID 17576681 · PMC1934990 · Nucleic acids research · 2007 · 8 claims · 4 setups
Cryptic 5'ss are best predicted by computational algorithms that accommodate nucleotide dependencies (e.g., Markov model, maximum entropy, maximum dependence decomposition) rather than by weight-matrix models
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Modeling genetic inheritance of copy number variations.
PMID 18832372 · PMC2588508 · Nucleic acids research · 2008 · 8 claims · 4 setups
A joint HMM framework for parents-offspring trios significantly improves CNV call rates and boundary inference accuracy compared to existing methods.
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Has reproduction · 95
Determining virus-host interactions and glycerol metabolism profiles in geographically diverse solar salterns with metagenomics.
PMID 28097058 · PMC5228507 · PeerJ · 2017 · 8 claims · 8 setups
Similar virus-host interactions and glycerol metabolism gene associations (notably dihydroxyacetone kinase with Haloquadratum/Halorubrum) exist across geographically diverse solar salterns
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DNA sequencing of a cytogenetically normal acute myeloid leukaemia genome.
PMID 18987736 · PMC2603574 · Nature · 2008 · 8 claims · 8 setups
Whole genome sequencing can identify unbiased, novel somatic mutations in a cytogenetically normal AML genome that would not have been found by candidate-gene resequencing.
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DNA methylation of cancer genome.
PMID 19960550 · PMC2940836 · Birth defects research. Part C, Embryo today : reviews · 2009 · 8 claims · 7 setups
Cancer epigenome alterations fall into two main categories: hypermethylation of tumor suppressor genes and hypomethylation of oncogenes or heterochromatin.
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Current status and the future for the genetics of type I diabetes.
PMID 19956094 · PMC2805458 · Genes and immunity · 2009 · 8 claims · 7 setups
A T1DGC genome-wide association meta-analysis of >7500 cases and >9000 controls identified 42 distinct genomic locations associated with T1D at P<10^-6.