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 · 75
The formation of avian montane diversity across barriers and along elevational gradients.
PMID 35022441 · PMC8755808 · Nature communications · 2022 · 8 claims · 8 setups
Genetic differentiation is generally greater across the oceanic barrier separating Buru and Seram than across the lowland barrier separating New Guinea mountain ranges.
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Has reproduction · 60
Deconvolution of the hematopoietic stem cell microenvironment reveals a high degree of specialization and conservation.
PMID 35494238 · PMC9046238 · iScience · 2022 · 8 claims · 6 setups
A customized bootstrapping/random-forest divide-and-conquer clustering pipeline integrating three scRNA-seq datasets robustly resolves cell states despite high cell-to-cell similarity within compartments
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Has reproduction · 83
Accurate prediction of metagenome-assembled genome completeness by MAGISTA, a random forest model built on alignment-free intra-bin statistics.
PMID 35248155 · PMC8898458 · Environmental microbiome · 2022 · 7 claims · 7 setups
MAGISTA, a random forest model built on alignment-free intra-bin distance-distribution statistics, can estimate MAG completeness and purity without relying on reference marker genes.
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Has reproduction · 81
Comparing the utility of in vivo transposon mutagenesis approaches in yeast species to infer gene essentiality.
PMID 32681306 · PMC7599172 · Current genetics · 2020 · 7 claims · 7 setups
A Random Forest machine-learning approach can predict gene essentiality from in vivo transposon insertion data across multiple yeast species and transposon systems
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Has reproduction · 68
Machine learning algorithm predicts fibrosis-related blood diagnosis markers of intervertebral disc degeneration.
PMID 37915003 · PMC10619283 · BMC medical genomics · 2023 · 7 claims · 7 setups
CEP120 and SPDL1 are fibrosis-related diagnostic genes for IDD, identified via a random forest model from 29 differentially expressed fibrosis-related genes
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Has reproduction · 89
Gut-derived Lactobacillus from exceptional responders mitigates chemoradiotherapy-induced intestinal injury through methionine-driven epigenetic modulation.
PMID 40469520 · PMC12130557 · iMeta · 2025 · 8 claims · 8 setups
High pretreatment gut abundance of Lactobacillus (and Bifidobacterium) is strongly associated with the absence of ACRIII in rectal cancer patients undergoing neoadjuvant chemoradiotherapy.
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Has reproduction · 64
Environmental Drivers of Genetic Divergence in Two Corals From the Florida Keys.
PMID 40589611 · PMC12206660 · Evolutionary applications · 2025 · 8 claims · 8 setups
Temperature was not the most important driver of coral genetic divergence in the Florida Keys; depth and water chemistry were more important
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Has reproduction · 78
GenTB: A user-friendly genome-based predictor for tuberculosis resistance powered by machine learning.
PMID 34461978 · PMC8407037 · Genome medicine · 2021 · 8 claims · 6 setups
GenTB is a free, open, web-based application offering two ML predictors (Random Forest and WDNN) that predict resistance to 13 and 10 anti-TB drugs, respectively.
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Genome microevolution of chikungunya viruses causing the Indian Ocean outbreak.
PMID 16700631 · PMC1463904 · PLoS medicine · 2006 · 8 claims · 6 setups
The Indian Ocean outbreak was initiated by a strain related to East African CHIKV isolates, which subsequently evolved via a traceable microevolution history
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Cancer-specific high-throughput annotation of somatic mutations: computational prediction of driver missense mutations.
PMID 19654296 · PMC2763410 · Cancer research · 2009 · 7 claims · 7 setups
CHASM, a Random Forest-based computational method, was developed to identify and prioritize missense mutations likely to be functional drivers of tumor cell proliferation.
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Has reproduction · 83
Macrel: antimicrobial peptide screening in genomes and metagenomes.
PMID 33384902 · PMC7751412 · PeerJ · 2020 · 8 claims · 8 setups
Macrel is an end-to-end pipeline that predicts high-quality AMP candidates from peptides, contigs, or reads of (meta)genomes
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Has reproduction · 77
Electroacupuncture reshapes the microbial co-occurrence networks related to the behavioral and psychological symptoms of dementia in Alzheimer's disease.
PMID 41676443 · PMC12806058 · iMetaOmics · 2025 · 6 claims · 7 setups
Electroacupuncture reshapes microbial co-occurrence network topology and drives keystone species in AD-related BPSD, with R. gnavus emerging as a likely keystone species post-intervention.
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Has reproduction · 55
Natural clines and human management impact the genetic structure of Algerian honey bee populations.
PMID 38114899 · PMC10729559 · Genetics, selection, evolution : GSE · 2023 · 7 claims · 8 setups
No significant admixture from European subspecies was detected in Algerian honey bees, suggesting large-scale queen imports have not occurred in Algeria.
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Genetic variation at hair length candidate genes in elephants and the extinct woolly mammoth.
PMID 19747392 · PMC2754481 · BMC evolutionary biology · 2009 · 8 claims · 5 setups
The coding sequence of FGF5 is not the critical determinant of hair length differences among elephantids, including the woolly mammoth.
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The VIZIER project: preparedness against pathogenic RNA viruses.
PMID 18083241 · PMC7114271 · Antiviral research · 2008 · 8 claims · 6 setups
Almost all newly emerging human pathogenic viruses are RNA viruses, largely because their error-prone RNA-dependent RNA polymerases and zoonotic reservoirs allow rapid adaptation to new hosts.
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Has reproduction · 44
A Reference DNA Barcode Library for UK Fungi associated with Bark and Ambrosia Beetles.
PMID 41022899 · PMC12480477 · Scientific data · 2025 · 6 claims · 6 setups
A reference DNA barcode library of fungi associated with over 1000 UK bark and ambrosia beetles (25 native Scolytinae species) was generated, yielding 5274 identified fungal OTUs.
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Has reproduction
Unlocking the microbial studies through computational approaches: how far have we reached?
PMID 36920617 · PMC10016191 · Environmental science and pollution research international · 2023 · 8 claims · 8 setups
Metagenomics enables culture-independent study of microbial communities directly from their natural environments, bypassing the need for clonal isolation.
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Has reproduction · 63
Comparative Genomics of Borderline Oxacillin-Resistant Staphylococcus aureus Detected during a Pseudo-outbreak of Methicillin-Resistant S. aureus in a Neonatal Intensive Care Unit.
PMID 35038924 · PMC8764539 · mBio · 2022 · 7 claims · 8 setups
Of 42 isolates flagged as MRSA by screening agar, only 9 were PBP2a- and mecA-positive true MRSA, while the remaining 33 were mecA-negative and largely met criteria for BORSA
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Has reproduction · 73
Exploring the prognostic and diagnostic value of lactylation-related genes in sepsis.
PMID 39367086 · PMC11452377 · Scientific reports · 2024 · 8 claims · 7 setups
Intersecting sepsis-associated differentially expressed genes with a curated list of 332 lactylation genes yields 55 sepsis-related lactylation genes.