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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Has reproduction · 79
Detection of Virus-Related Sequences Associated With Potential Etiologies of Hepatitis in Liver Tissue Samples From Rats, Mice, Shrews, and Bats.
PMID 34177835 · PMC8221242 · Frontiers in microbiology · 2021 · 8 claims · 6 setups
Viral metagenomics of liver tissue from rats, mice, shrews, and bats revealed a diverse set of sequences related to herpesviruses, orthomyxoviruses, anelloviruses, hepeviruses, hepadnaviruses, flaviviruses, parvoviruses, and picornaviruses
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Has reproduction · 76
Dental Plaque Microbial Resistomes of Periodontal Health and Disease and Their Changes after Scaling and Root Planing Therapy.
PMID 34287005 · PMC8386447 · mSphere · 2021 · 8 claims · 7 setups
Periodontitis significantly alters dental plaque microbial community diversity and structure compared to healthy and treated states
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Has reproduction · 75
Frequency and patterns of ribonucleotide incorporation around autonomously replicating sequences in yeast reveal the division of labor of replicative DNA polymerases.
PMID 34551434 · PMC8501979 · Nucleic acids research · 2021 · 6 claims · 4 setups
rNTP incorporation is preferentially found on the leading strand in yeast cells expressing wild-type replicative DNA polymerases
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Has reproduction · 84
Evolutionary Genomics of Sex-Related Chromosomes at the Base of the Green Lineage.
PMID 34599324 · PMC8557840 · Genome biology and evolution · 2021 · 8 claims · 6 setups
The divergence of the MT+ and MT- alleles predates speciation events within the Ostreococcus genus
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Has reproduction · 96
Calibration-free NGS quantitation of mutations below 0.01% VAF.
PMID 34675197 · PMC8531361 · Nature communications · 2021 · 8 claims · 6 setups
QBDA (Quantitative Blocker Displacement Amplification) integrates UMI molecular barcoding with BDA variant enrichment to enable calibration-free VAF quantitation
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Has reproduction · 58
Phosphorylation of ribosomal protein S6 differentially affects mRNA translation based on ORF length.
PMID 34871442 · PMC8682771 · Nucleic acids research · 2021 · 8 claims · 8 setups
RPS6 becomes progressively dephosphorylated on ribosomes as they translate along an mRNA CDS
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Has reproduction · 36
A Novel Algicidal Bacterium, Microbulbifer sp. YX04, Triggered Oxidative Damage and Autophagic Cell Death in Phaeocystis globosa, Which Causes Harmful Algal Blooms.
PMID 35019679 · PMC8754136 · Microbiology spectrum · 2022 · 8 claims · 9 setups
Microbulbifer sp. YX04 shows high algicidal activity against P. globosa, peaking at 93.2% in the declining growth phase
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Has reproduction · 71
Harnessing secretory pathway differences between HEK293 and CHO to rescue production of difficult to express proteins.
PMID 35301123 · PMC9189052 · Metabolic engineering · 2022 · 8 claims · 7 setups
Swapping expression host from CHO to HEK293 improves secreted titers for roughly one third of difficult-to-express human proteins
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Has reproduction · 50
The HCV Envelope Glycoprotein Down-Modulates NF-κB Signalling and Associates With Stimulation of the Host Endoplasmic Reticulum Stress Pathway.
PMID 35371105 · PMC8964954 · Frontiers in immunology · 2022 · 7 claims · 8 setups
HCV E1E2, and more strongly E2 alone, down-modulates HIV-1 LTR activation in 293T, TZM-bl, and Huh7 cells
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Has reproduction · 67
Satellitome Analysis and Transposable Elements Comparison in Geographically Distant Populations of Spodoptera frugiperda.
PMID 35455012 · PMC9026859 · Life (Basel, Switzerland) · 2022 · 8 claims · 5 setups
Most transposable elements are commonly shared across all eight geographically distant S. frugiperda samples, except Maverick and PIF/Harbinger elements which show divergent repeat copies
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Has reproduction · 73
A transcriptomic atlas of Aedes aegypti reveals detailed functional organization of major body parts and gut regional specializations in sugar-fed and blood-fed adult females.
PMID 35471187 · PMC9113746 · eLife · 2022 · 8 claims · 5 setups
Created Aegypti-Atlas, an online RNAseq resource covering Ae. aegypti body parts, gut regions, and a blood meal digestion time course
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Has reproduction · 61
RegulonDB 11.0: Comprehensive high-throughput datasets on transcriptional regulation in Escherichia coli K-12.
PMID 35584008 · PMC9465075 · Microbial genomics · 2022 · 8 claims · 7 setups
RegulonDB 11.0 is a radical upgrade offering access to more than 2000 high-throughput datasets on transcriptional regulation in E. coli K-12.
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Has reproduction · 81
Transcriptional regulation and chromatin architecture maintenance are decoupled functions at the Sox2 locus.
PMID 35710138 · PMC9296009 · Genes & development · 2022 · 8 claims · 7 setups
Sox2 transcriptional activation is traced almost entirely to two key transcription factor-bound regions (SRR107 and SRR111) within the SCR
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Has reproduction · 84
Main Factors Influencing the Gut Microbiota of Datong Yaks in Mixed Group.
PMID 35883324 · PMC9312300 · Animals : an open access journal from MDPI · 2022 · 7 claims · 6 setups
Gut microbial diversity (alpha and beta) differs significantly among domestic males, domestic females, and wild male Datong yaks.
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Has reproduction · 66
RiboTaxa: combined approaches for rRNA genes taxonomic resolution down to the species level from metagenomics data revealing novelties.
PMID 36159175 · PMC9492272 · NAR genomics and bioinformatics · 2022 · 8 claims · 6 setups
RiboTaxa, combining BBTools, FastQC, SortMeRNA, MetaRib, EMIRGE, VSEARCH, BBMap and QIIME 2's Sklearn classifier, was built as a pipeline for SSU rRNA-based taxonomic profiling of metagenomics data.
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Has reproduction · 99
Evaluation of taxonomic classification and profiling methods for long-read shotgun metagenomic sequencing datasets.
PMID 36513983 · PMC9749362 · BMC bioinformatics · 2022 · 8 claims · 7 setups
Long-read classifiers generally performed best among the 11 methods tested
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Has reproduction
Fast, accurate, and racially unbiased pan-cancer tumor-only variant calling with tabular machine learning.
PMID 36611079 · PMC9825621 · NPJ precision oncology · 2023 · 8 claims · 8 setups
Tree-based (XGBoost, LightGBM) and deep-learning (TabNet) tabular ML classifiers achieve state-of-the-art somatic vs germline classification in tumor-only WES samples, outperforming PureCN.
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Has reproduction · 100
Niche Modification by Sulfate-Reducing Bacteria Drives Microbial Community Assembly in Anoxic Marine Sediments.
PMID 36988509 · PMC10128000 · mBio · 2023 · 7 claims · 7 setups
SRB modify niches (e.g., pH) to affect species coexistence during organic matter degradation
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Has reproduction · 89
Improved eukaryotic detection compatible with large-scale automated analysis of metagenomes.
PMID 37032329 · PMC10084625 · Microbiome · 2023 · 8 claims · 7 setups
MAPQ ≥30 filtering improves precision but substantially reduces recall, especially for unrepresented/divergent eukaryotic taxa
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Has reproduction
αPIX Is a Trafficking Regulator that Balances Recycling and Degradation of the Epidermal Growth Factor Receptor.
PMID 26177020 · PMC4503440 · PloS one · 2015 · 8 claims · 8 setups
αPIX interacts with c-Cbl, including as endogenous proteins