Preprint Watch

Solving three core challenges in transient dynamics analysis of matrix population models

Leave a Comment / bioRxiv, Normal Science /

URL https://www.biorxiv.org/content/10.1101/2025.05.29.656837v1.full.pdf Stage Normal Science Paradigm framing The paper operates within the dominant paradigm of matrix population models in ecology and demography. Highlights This preprint presents a refinement of existing analytical tools within the established paradigm of matrix population models. It addresses specific technical challenges related to the interpretation of transient dynamics, proposing solutions like

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Cooperation Destabilizes Communities, but Competition Pays the Price

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URL https://www.biorxiv.org/content/10.1101/2023.12.26.573354v2.full.pdf Stage Normal Science Paradigm framing Community Ecology, Population Dynamics, and the paradigm of diversity-stability relationships within ecological communities. Highlights This preprint investigates a well-established problem within community ecology: the seemingly paradoxical prevalence of cooperation in natural communities despite theoretical predictions that cooperation destabilizes communities. This places the research firmly within the 'normal science'

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The MagMa Study: Quantum Magnetocardiography in Non-Ischemic Cardiomyopathy

Leave a Comment / medRxiv, Normal Science /

URL https://www.medrxiv.org/content/10.1101/2025.05.29.25328567v1.full.pdf Stage Normal Science Paradigm framing The preprint operates within the dominant paradigm of evidence-based medicine, specifically focusing on cardiology and diagnostic tools. It adheres to the established norms of clinical research, including hypothesis testing, statistical analysis, and comparison against existing gold standards. Highlights The research presented in this preprint contributes to normal science

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Biobank-scale exposome-wide risk factors in CAD and T2D: observational, predictive, and potentially causative evidence

Leave a Comment / medRxiv, Normal Science /

URL https://www.medrxiv.org/content/10.1101/2024.10.26.24316153v2.full.pdf Stage Normal Science Paradigm framing The preprint operates within the dominant paradigm of biomedicine and epidemiology, which emphasizes the interplay of genetic and environmental factors in disease development. It adheres to established research methodologies and statistical analyses commonly accepted in these fields. Highlights The study uses well-established methods like ExWAS and Mendelian Randomization,

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Deviation Error: assessing machine learning predictions for replicate measurements in genomics and beyond

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URL https://www.biorxiv.org/content/10.1101/2025.05.29.656931v1.full.pdf Stage Normal Science Paradigm framing The preprint operates within the paradigm of machine learning applied to genomics, specifically focusing on predictive modeling for replicate measurements. It accepts the established methods and assumptions of this field, such as the use of standard loss functions and the focus on minimizing prediction error. Highlights This preprint

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D1/D5 Receptor Activation Promotes Long-Term Potentiation and Synaptic Tagging/Capture in Hippocampal Area CA2

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URL https://www.biorxiv.org/content/10.1101/2025.06.01.657216v2.full.pdf Stage Normal Science Paradigm framing Long-term potentiation (LTP) as a cellular model of learning and memory Highlights This preprint investigates the effects of dopamine D1/D5 receptor activation on synaptic plasticity in the hippocampal CA2 region, an area implicated in social memory. While the broader paradigm of LTP as a correlate of learning and

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MARLOWE: Taxonomic Characterization of Unknown Samples for Forensics Using De Novo Peptide Identification

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URL https://www.biorxiv.org/content/10.1101/2024.09.30.615220v2.full.pdf Stage Normal Science Paradigm framing The preprint operates within the paradigm of forensic proteomics and metaproteomics, specifically focusing on taxonomic characterization of unknown biological samples using mass spectrometry data. Highlights This preprint presents MARLOWE, a new computational tool for taxonomic characterization using de novo peptide sequencing combined with a statistical approach. While it

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FoldMark: Safeguarding Protein Structure Generative Models with Distributional and Evolutionary Watermarking

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URL https://www.biorxiv.org/content/10.1101/2024.10.23.619960v6.full.pdf Stage Normal Science Paradigm framing The preprint operates within the dominant paradigm of protein structure prediction and design, heavily influenced by recent advancements in machine learning, particularly deep learning models like AlphaFold. It acknowledges the transformative impact of these models while addressing emerging concerns within this paradigm. Highlights This preprint presents FoldMark, a

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Synthetic Serum Markers Enable Noninvasive Monitoring of Gene Expression in Primate Brains

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URL https://www.biorxiv.org/content/10.1101/2025.06.01.657212v1.full.pdf Stage Normal Science Paradigm framing The current paradigm is the use of invasive methods, such as positron emission tomography (PET), magnetic resonance imaging (MRI) or, in some cases, electrophysiology, to monitor gene expression in the primate brain, especially long-term. Highlights The preprint presents Released Markers of Activity (RMAs) as an innovative approach for

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Non-canonical enhancers control gene expression and cell fate in human pluripotent stem cells

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URL https://www.biorxiv.org/content/10.1101/2025.06.01.657118v1.full.pdf Stage Normal Science Paradigm framing The preprint operates within the dominant paradigm of gene regulation, where enhancers play a crucial role in controlling gene expression. It specifically focuses on enhancers in human-induced pluripotent stem cells (hiPSCs). Highlights This research refines the existing understanding of enhancers by identifying a class of “non-canonical enhancers” that

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