Volume B · since 2013
bioRxiv
Biology before peer review: genomics, neuroscience and ecology as the work happens.
Biology Preprints
Newest strong work in bioRxiv
Volume B · since 2013
Biology before peer review: genomics, neuroscience and ecology as the work happens.
Biology Preprints
Newest strong work in bioRxiv
Yuqiao Liu, Siyu Yi, Hengchuang Yin, Wei Ju
Single-cell RNA sequencing profiles cellular heterogeneity at atlas scale, making automated annotation essential. However, target datasets often contain novel cell types missing from incomplete references. We present scOLAR, an ontology-guided open-set framework that learns prototypes over the Cell Ontology and uses…
Yanick Aqua Stong Tangan, G Takop Nchanji, Marcel Nyuylam Moyeh, Teke Mary Efeti + 15 more
Hookworm disease, primarily caused by Necator americanus, affects about 472 million people worldwide and contributes substantially to global disease burden, yet no approved vaccine is currently available. The clinical failure of Na-ASP-2 protein due to IgE-mediated hypersensitivity highlights the need for safe…
Negin Rahimzadeh, Samuel Morabito, Saniya Khullar, Zechuan Shi + 2 more
Interindividual heterogeneity in Alzheimer’s disease (AD) remains poorly understood, as disparate single-cell studies leave it unclear whether findings reflect shared architecture or dataset-specific idiosyncrasies. Here, we present panAD, a transcriptomic atlas of >3 million nuclei from 791 individuals across 13…
Jalaja Madhusudhanan, Anton Parinov, Charles Fieseler, Manuel Zimmer
Behavior arises from the interplay between spontaneous brain dynamics and sensory-driven responses, yet how spontaneous neural activity shapes variability in decision-making remains unclear. We leverage the tractable C. elegans nervous system to address this question. During oxygen avoidance, we observe binary…
Jahnavi Bhaskaran, Elizabeth Ing-Simmons, Irina Balaguer Balsells, Sara Di Persio + 11 more
Gametogenesis, the production of oocytes and sperm, ensures the faithful transmission of genetic material to the next generation. In males, spermatogenesis occurs within the testis, where germ cells progress through a highly ordered developmental programme in close association with supporting somatic cells. Defects in…
Brett Kiyota, Chaehyeon Lee, Haoyang Yao, Nozomu Yachie
The rapid expansion of single-cell genomic datasets has led to the compilation of biological resources comprising hundreds of millions of cells across tissues, developmental stages, and disease states. This has underscored the need for scalable and interpretable data representations that preserve the complex…
Ziyi Wang, Ken Chen, Jinzhuang Dou
Small insertions and deletions (Indels) provide critical information for cancer genomics and clonal evolution, yet their detection from single-cell sequencing (SCS) such as scRNA-seq and scATAC-seq remains challenging due to sparse coverage, alignment artifacts, and RNA editing. Here, we present Monopogen-Indel, a…
Henrique Reis Aguiar, Matthias H. Hennig
Predictive coding is a powerful normative framework for understanding cortical computation, but it is still an open question how biologically plausible networks with local plasticity support predictive inference and representation learning. In this work we show that a recurrent excitatory-inhibitory circuit with purely…
Margarita Gutova, Eric Ma, Heini N. Natri, Sean Sepulveda + 14 more
Pediatric and adult brain tumors, including glioblastoma, astrocytoma, ependymoma, and medulloblastoma, remain associated with poor prognosis despite advances in surgery, radiation, and chemotherapy. Therapeutic resistance, tumor heterogeneity, and treatment-related toxicity highlight the need for clinically relevant…
Xingzhi Niu, Deepali Kundnani, Mikaela Dicome, Luis Tafoya + 4 more
Clinical response to immune checkpoint blockade (ICB) remains variable. We performed a reference-wide screen to identify immune-cell populations in the tumor microenvironment (TME) associated with benefit across treatment modalities and tumor types. We analyzed pretreatment bulk tumor RNA-seq to identify RNA-abundance…
Florian Köhler, Anna Delgado-Tejedor, Maik Zehnsdorf, Marisol Salgado Albarran + 5 more
Short-read sequencing-based single-cell transcriptomics represents the current gold standard for studying cellular transcriptomes but remains limited in its ability to resolve full-length transcript isoforms and splicing patterns. Long-read single-cell and single-nucleus RNA sequencing (LR sc/snRNA-seq) enables the…
Patricia Lamirande, Mia Brunetti, Terry Easlick, Fatemeh Beigmohammadi + 1 more
Mechanistic mathematical models have been used extensively to provide a deeper understanding of biological mechanisms, including unveiling the regulation of tumour growth and its response to various treatments. However, given the breadth of biological regulatory mechanisms, these models are frequently large and thus…
Rafal Czapiewski, Michael Chiang, James Ding, Catherine Naughton + 3 more
Cell-to-cell transcriptional heterogeneity, or noise, is an intrinsic property of the transcriptome with implications for development, disease progression, and aging. Bulk RNA-seq masks this variability by averaging gene expression across cells, whereas single-cell RNA sequencing (scRNA-seq) resolves it. Nevertheless…
Yee-Chen Liu, Andrew Kelly, Robyn Esterbauer, Wen Shi Lee + 3 more
Avian influenza A viruses pose a persistent zoonotic threat to humans owing to their expanding host range and high case fatality rates. In particular, viruses from the 2.3.4.4b clade of the H5 subtype have now been detected in over 60 mammalian species, raising serious pandemic concerns. Understanding immune…
Junghwa Seo, Emma Buck, Bryan Machani, Oscar Murillo + 6 more
Current vaccines for respiratory viruses are primarily administered intramuscularly. Messenger RNA-lipid nanoparticle (LNP)-based intramuscular vaccination for respiratory coronaviruses induces strong systemic IgG antibody responses; they do not consistently elicit IgA in the upper and lower respiratory tracts. Using a…
Corey Keith Goldman
Peptide cancer vaccines can elicit antigen-specific immunity, but peripheral immunogenicity often does not translate into durable tumor control. We analyzed transcriptomic profiles across three public human peptide-vaccine cohorts: C1/GSE278476, a MUC1 plus Poly-ICLC PBMC RNA-seq cohort with ordered anti-MUC1 IgG…
Jaedong Hwang, Sujaya Neupane, Mehrdad Jazayeri, Ila Fiete
Flexible behavior requires generalizable memory and learning. For example, we rapidly learn to commute in new cities by reusing our knowledge of Euclidean two-dimensional space and structures like roundabouts and subway systems without forgetting how to get to a favorite restaurant back home. Yet we lack a detailed…
HS Ji, KR Kang, JA Kim, YH Kwon + 4 more
Bacille Calmette–Guérin (BCG) remains the only licensed tuberculosis (TB) vaccine, yet its protective efficacy against adult pulmonary TB is limited. To overcome this, we evaluated a novel recombinant Mycobacterium smegmatis (rMs) booster vaccine expressing Ag85B and ESAT-6 via the pMyong2 vector, combined with…
Ioanna Pandi, Spyridon Chavlis, Hatem Oraby, Mostafa A. Nashaat + 3 more
Adaptive behavior requires updating responses when contingencies change while preserving prior associations and the capacity to learn a new. How this trade-off is resolved remains unknown. Here, we combined in vivo imaging of apical tuft spines in the secondary motor cortex (M2) with biologically constrained network…
Jieyu Zheng, Rogério Guimarães, Zeynep Turan, Anwesha Das + 4 more
Rapid learning, memory, and generalization are often attributed to circuits of the neocortex and hippocampus, but their specific role remains unclear. To examine these cognitive abilities together in individual mice, we observed mice navigating the Manhattan Maze, a reconfigurable 3D labyrinth. Naïve wildtype mice…