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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Tandem repeats modify the structure of human genes hosted in segmental duplications.
PMID 19954527 · PMC2812944 · Genome biology · 2009 · 8 claims · 6 setups
Around 7% of primate-specific genes located within segmental duplications contain variable internal tandem repeats (ITRs).
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The i-motif in the bcl-2 P1 promoter forms an unexpectedly stable structure with a unique 8:5:7 loop folding pattern.
PMID 19908860 · PMC2787777 · Journal of the American Chemical Society · 2009 · 8 claims · 6 setups
The full-length bcl-2 C-rich promoter sequence (Py39WT) forms one major intramolecular i-motif structure with a transitional pH of 6.6
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InParanoid 7: new algorithms and tools for eukaryotic orthology analysis.
PMID 19892828 · PMC2808972 · Nucleic acids research · 2010 · 8 claims · 7 setups
InParanoid 7 expands the database by an order of magnitude to 100 species, 1.3 million proteins, and 42.7 million pairwise ortholog groups.
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Timing constraints of in vivo gag mutations during primary HIV-1 subtype C infection.
PMID 19890401 · PMC2768328 · PloS one · 2009 · 7 claims · 7 setups
Reverse mutations to the wild type (HIV-1C consensus) in Gag appear significantly earlier than escape mutations from the wild type during primary infection
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Has reproduction · 67
A consensus approach to vertebrate de novo transcriptome assembly from RNA-seq data: assembly of the duck (Anas platyrhynchos) transcriptome.
PMID 25009556 · PMC4070175 · Frontiers in genetics · 2014 · 8 claims · 8 setups
Multiple k-mer (MK) assemblies are more complete than single k-mer (SK) assemblies, showing higher reads-mapped-back-to-transcripts (RMBT) and higher CEGMA complete-gene percentages for all three tools.
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Has reproduction · 93
Elucidation of the molecular responses to waterlogging in Jatropha roots by transcriptome profiling.
PMID 25520726 · PMC4251292 · Frontiers in plant science · 2014 · 8 claims · 8 setups
24 h of waterlogging significantly alters mRNA abundance of 1968 genes in Jatropha roots (931 up, 1037 down).
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Metagenomic study of the oral microbiota by Illumina high-throughput sequencing.
PMID 19796657 · PMC3568755 · Journal of microbiological methods · 2009 · 8 claims · 6 setups
The 16S rRNA V5 hypervariable region, amplified as a short ~82-base segment, provides reliable taxonomic identification of oral bacteria against public databases like HOMD.
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In vivo phosphoproteome of human skeletal muscle revealed by phosphopeptide enrichment and HPLC-ESI-MS/MS.
PMID 19764811 · PMC2783959 · Journal of proteome research · 2009 · 8 claims · 6 setups
This is the first large-scale in vivo phosphoproteomic study of human skeletal muscle
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Evidence for limited genetic compartmentalization of HIV-1 between lung and blood.
PMID 19759830 · PMC2736399 · PloS one · 2009 · 8 claims · 7 setups
Statistical evidence of genetic compartmentalization between lung and blood HIV-1 env sequences was found in 10 of 18 subjects.
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Swarm intelligence based wavelet coefficient feature selection for mass spectral classification: an application to proteomics data.
PMID 19733729 · PMC2748225 · Analytica chimica acta · 2009 · 8 claims · 4 setups
ACA-based wavelet coefficient feature selection can achieve up to 100% classification accuracy on training, validating, and independent testing sets using only 5 selected features.
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Comparative transcriptome analysis of two pomelo accessions with different parthenocarpic ability provides insight into the molecular mechanisms of parthenocarpy in pomelo (Citrus grandis).
PMID 39135650 · PMC11317442 · Frontiers in plant science · 2024 · 6 claims · 6 setups
G pomelo exhibits significantly higher parthenocarpic ability (ovary growth, cell division, fruit setting) than S pomelo following emasculation
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Has reproduction · 86
The selection of software and database for metagenomics sequence analysis impacts the outcome of microbial profiling and pathogen detection.
PMID 37027361 · PMC10081788 · PloS one · 2023 · 7 claims · 7 setups
Obtaining an accurate species-level microbial profile using current direct-read metagenomics profiling software is still a challenging task.
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Has reproduction · 98
Uncertainty in the mating strategy of honeybees causes bias and unreliability in the estimates of genetic parameters.
PMID 38632535 · PMC11022492 · Genetics, selection, evolution : GSE · 2024 · 7 claims · 3 setups
The most precise estimates of genetic parameters and genetic trends are obtained when breeding queens are mated with drones of a single DPQ that is correctly assigned in the pedigree (SS mating).
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TassDB: a database of alternative tandem splice sites.
PMID 17142241 · PMC1669710 · Nucleic acids research · 2007 · 7 claims · 3 setups
TassDB is a relational database storing GYNGYN donor and NAGNAG acceptor tandem splice sites across eight species
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DBD--taxonomically broad transcription factor predictions: new content and functionality.
PMID 18073188 · PMC2238844 · Nucleic acids research · 2008 · 8 claims · 3 setups
DBD is a database of predicted sequence-specific DNA-binding transcription factors covering over 700 publicly available proteomes, up from 150 in the initial version.
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High-density single nucleotide polymorphism genome-wide linkage scan for susceptibility genes for diabetic nephropathy in type 1 diabetes: discordant sibpair approach.
PMID 18559660 · PMC2518505 · Diabetes · 2008 · 8 claims · 3 setups
Primary linkage finding for diabetic nephropathy is on chromosome 19q
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Emerging translational bioinformatics: knowledge-guided biomarker identification for cancer diagnostics.
PMID 19964620 · PMC5003034 · Annual International Conference of the IEEE Engineering in Medicine and Biology Society. IEEE Engineering in Medicine and Biology Society. Annual International Conference · 2009 · 8 claims · 3 setups
omniBiomarker, a web-based application, uses prior biological knowledge to identify the most biologically relevant gene ranking metric for a given clinical problem
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Prediction of candidate primary immunodeficiency disease genes using a support vector machine learning approach.
PMID 19801557 · PMC2780952 · DNA research : an international journal for rapid publication of reports on genes and genomes · 2009 · 6 claims · 3 setups
An SVM trained on 69 binary features of known PID genes can accurately classify PID vs non-PID genes and predict novel candidate PID genes
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Has reproduction · 88
Comprehensive benchmarking of large language models for RNA secondary structure prediction.
PMID 40205851 · PMC11982019 · Briefings in bioinformatics · 2025 · 7 claims · 4 setups
Existing RNA-LLMs had not previously been evaluated for secondary structure prediction in a unified, fair experimental setup with the same datasets and prediction model.
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Testing groups of genomic locations for enrichment in disease loci using linkage scan data: a method for hypothesis testing.
PMID 16848972 · PMC3525155 · Human genomics · 2006 · 8 claims · 2 setups
A method testing enrichment of a group of genomic locations for disease loci by comparing the average NPL score of the group to a null distribution from randomly drawn groups of equal size