bioRxiv

Contrasting Effects of SARS-CoV-2 Vaccination vs. Infection on Antibody and TCR Repertoires

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URL https://www.biorxiv.org/content/10.1101/2023.09.08.556703v2.full.pdf Stage Normal Science Paradigm framing The preprint operates within the dominant paradigm of immunology, specifically focusing on adaptive immune responses mediated by B cells and T cells. It investigates the changes in antibody and T cell receptor repertoires following SARS-CoV-2 infection and vaccination. Highlights This research firmly falls within the "normal science" phase […]

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RNAtranslator: Modeling protein-conditional RNA design as sequence-to-sequence natural language translation

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URL https://www.biorxiv.org/content/10.1101/2025.03.04.641375v2.full.pdf Stage Normal Science Paradigm framing The paradigm is the use of computational methods for RNA sequence design. Highlights This preprint presents RNAtranslator, a novel computational method for designing RNA sequences that bind to specific proteins. It frames the problem as a sequence-to-sequence translation task, leveraging the power of large language models. This approach

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Identifying phage proteins that activate the bacterial innate immune system

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URL https://www.biorxiv.org/content/10.1101/2025.07.02.662641v1.full.pdf Stage Normal Science Paradigm framing The preprint operates within the dominant paradigm of molecular biology and genetics, specifically focusing on the co-evolutionary arms race between bacteria and bacteriophages. It adheres to the established understanding of bacterial immune systems and phage infection mechanisms. Highlights This preprint firmly falls within the "Normal Science" stage of

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An integrated brain-machine interface platform with thousands of channels

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URL https://www.biorxiv.org/content/10.1101/703801v4.full.pdf Stage Normal Science Paradigm framing The paradigm is Brain-Machine Interfaces (BMIs) for restoration of sensory and motor function and treatment of neurological disorders. Highlights This preprint presents incremental advancements within the existing paradigm of BMIs. It focuses on improving the scalability and bandwidth of BMIs by developing novel electrode "threads", a neurosurgical robot

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Human induced pluripotent stem cell-derived microglia with a CX3CR1-V249I genetic variant exhibit dysfunctional phenotypes and modulate neuronal growth and function

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URL https://www.biorxiv.org/content/10.1101/2025.07.01.662163v1.full.pdf Stage Normal Science Paradigm framing The preprint operates within the dominant paradigm of using human induced pluripotent stem cells (hiPSCs) and CRISPR technology to model human diseases, specifically neurodegenerative diseases, in vitro. It also adheres to the paradigm of studying microglia and their role in neuroinflammation and neurodegeneration. Highlights This research represents a

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scite: a smart citation index that displays the context of citations and classifies their intent using deep learning

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URL https://web.archive.org/web/20210325215755id_/https://www.biorxiv.org/content/biorxiv/early/2021/03/16/2021.03.15.435418.full.pdf Stage Normal Science Paradigm framing Scientometrics, Bibliometrics, and Deep Learning Highlights This preprint presents scite, a novel citation indexer that uses deep learning to classify citations based on their context within citing papers. This work falls under the normal science stage of Kuhn's paradigm cycle. The preprint operates within the existing paradigms of

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Large-scale skin metagenomics reveals extensive prevalence, coordination, and functional adaptation of skin microbiome dermotypes across body sites

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URL https://www.biorxiv.org/content/10.1101/2025.04.24.650393v2.full.pdf Stage Normal Science Paradigm framing Human Microbiome Project (HMP) Highlights This research expands upon the established paradigm of the Human Microbiome Project by focusing on in-depth characterization of the skin microbiome and introducing the novel concept of "dermotypes". While acknowledging the existing knowledge of site-specific differences in skin microbial composition, the study builds

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A Transient Increase in Cardiomyocyte Protein O-GlcNAcylation Enhances Susceptibility to Pressure Overload-Induced Cardiac Remodeling

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URL https://www.biorxiv.org/content/10.1101/2025.06.04.657956v1.full.pdf Stage Normal Science Paradigm framing The preprint operates within the dominant paradigm of metabolic memory in diabetic heart disease, specifically focusing on the role of O-GlcNAcylation. Highlights This research uses established models and methodologies to investigate a specific aspect of metabolic memory within the existing paradigm. The study builds upon prior knowledge and

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Buzzed but not elated? Effect of ethanol on cognitive judgement bias in honeybees

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URL https://www.biorxiv.org/content/10.1101/2025.06.05.658067v1.full.pdf Stage Normal Science Paradigm framing The paradigm framing of the preprint is the study of animal behavior and cognition, specifically focusing on how affective states can be measured and influenced. The dominant paradigm accepts that invertebrates, such as honeybees, can experience affective states and uses methods like Cognitive Judgement Bias (CJB) tests to

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Preprinting the COVID-19 pandemic

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URL https://www.biorxiv.org/content/10.1101/2020.05.22.111294v3.full.pdf Stage Normal Science Paradigm framing The preprint operates within the dominant paradigm of scientific communication, which traditionally involves peer-reviewed journal publications. However, it acknowledges a shift towards preprints, particularly in the context of the COVID-19 pandemic. Highlights This preprint examines the role of preprints in disseminating COVID-19 research. It analyzes preprints on bioRxiv

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