KozakExplorer: an interactive framework for genome-wide Kozak sequence analysis biorxiv.org 2026-06-26 Translation initiation signals shape gene expression across all domains of life.
A Snakemake-based bacterial whole genome comparison pipeline for multi-group clinical isolates biorxiv.org 2026-06-26 Organisms have continuously evolved in response to environmental conditions.
Recurrent Duplication of the REST-NOA1 Locus Reveals a Hotspot of Regulatory Evolution Across Even-Toed Ungulates biorxiv.org 2026-06-26 Gene duplication is a major source of evolutionary novelty, yet recurrent duplication of the same genomic locus across independent lineages remains un
SPEAK: Spatial Prompting with Expert Aligned Knowledge for Tissue Domain Identification in Spatial Transcriptomics biorxiv.org 2026-06-26 Spatially resolved transcriptomic (SRT) data requires spatial domain identification to enable tissue microenvironment-specific downstream analyses.
EpiESM-GA: Resource-Efficient Protein Foundation Model Features for Equitable B-Cell Epitope Prediction biorxiv.org 2026-06-26 Prediction of B-cell epitopes can assist in reducing costly wet-lab screening in vaccine design, diagnostics, and antibody discovery.
Defining Pseudo-Haplotype Analysis Reveals Multi-Gene Genetic Pattern Across BAF Chromatin Remodeling Complexes biorxiv.org 2026-06-26 BRG1-associated factor (BAF) is a crucial chromatin remodeling complex.
Evaluating sequence-to-function deep learning models for ancestry-stratified regulatory variant effect prediction using multi-ancestry blood eQTLs biorxiv.org 2026-06-26 Background: Sequence-to-function (S2F) deep learning models are increasingly used to prioritize non-coding regulatory variants, but their behavior acr
HALPred-B: Host-Aware Linear B-Cell Epitope Prediction: Challenges, Limitations, and Variability Across Species biorxiv.org 2026-06-26 Predicting linear B-cell epitopes is a basic immunoinformatics task that has a direct impact on vaccine design and antibody engineering.
Kente: A Graph-based Pangenomic Approach for Horizontal Gene Transfer Detection in Microbiomes biorxiv.org 2026-06-26 Motivation: Horizontal gene transfer (HGT) shapes bacterial evolution and microbial ecosystems, yet detecting HGT within microbiomes remains a challen
Acquiring Improved Protein Variants With Probabilistic Preferential Learning biorxiv.org 2026-06-26 Variant effect prediction (VEP) models can be used to select promising novel enzymes from a pool of candidates.
vDeepInsight: an injective three-dimensional voxel carrier for tabular-feature neighborhood learning biorxiv.org 2026-06-26 DeepInsight-style methods make tabular feature relationships accessible to convolutional networks by placing each feature at a fixed position on an im
Structural characterization of human endogenous retrovirus integration and strand transfer inhibition biorxiv.org 2026-06-26 Human endogenous retroviruses (hERVs) are remnants of ancestral retroviral infections that have shaped the human genome through their capacity to mobi
Exploring the large-scale properties of a protein secondary structure genotype-to-phenotype map biorxiv.org 2026-06-26 We perform a large-scale computational characterization of the map of protein primary to secondary structure using an AVR3a class protein effector dom
Interplay of Structural Heterogeneity and Active Remodeling Controls Chromatin Condensate Organization and Dynamics biorxiv.org 2026-06-26 Chromatin is an actively remodeled polymeric system whose organization emerges from the interplay of equilibrium interactions and ATP-dependent proces
Non-invasive in vivo lactate monitoring via NIR spectroscopy biorxiv.org 2026-06-26 We present a non-invasive approach for continuous monitoring of lactate dynamics in-vivo using near-infrared (NIR) spectroscopy.
A Chromatin Biology Assessment of AlphaFold3 biorxiv.org 2026-06-26 Biomolecular structure prediction tools such as AlphaFold have achieved remarkable success in predicting structures of single proteins and multiprotei
Ecological drivers of social complexity: the role of predation risk and nesting resource in group-living cichlid biorxiv.org 2026-06-26 Understanding how social complexity responds to environmental variation remains a longstanding challenge in evolutionary biology.
The Vertebrate Genomes Project Phase I: A global reference genome resource biorxiv.org 2026-06-26 The Vertebrate Genomes Project (VGP) aims to produce complete and near-error-free reference genomes for all [~]70,000 extant vertebrate species.
Aposematic signals are dynamic over time in bioluminescent ostracods biorxiv.org 2026-06-26 Colour and contrast are commonly deployed in anti-predator signals like aposematism or deimatism.
Cardiolipin modulation of MmpL3 in mycobacteria biorxiv.org 2026-06-26 The complex cell envelope of mycobacteria is characterized by the presence of a unique outer membrane (OM) rich in mycolic acids (MAs).
Conjugation dynamics and persistence of a carbapenem resistance gene blaOXA-72 from Acinetobacter pittii to Acinetobacter baumannii biorxiv.org 2026-06-26 Carbapenem-resistant Acinetobacter (CRA) has been associated with increased morbidity and mortality in clinical settings.
MYC and RNA Polymerase II Binding Near Transcriptional End Sites Regulate the Expression of Functionally-Related Genes biorxiv.org 2026-06-26 MYC oncoprotein binding at promoters and enhancers influences RNA polymerase II (RNAPII)-driven gene expression.
TDP-43 subtypes shape transcriptomic signatures in Alzheimer's disease biorxiv.org 2026-06-26 TAR DNA-binding protein 43 (TDP-43) pathology frequently co-occurs with Tau neurofibrillary tangles (NFTs) and amyloid {beta} plaques in Alzheimer's d
Ferroptosis is a Physiologic Vulnerability of Iron-Recycling Macrophages biorxiv.org 2026-06-26 Iron deficiency anemia affects one-third of the global human population.
RNAPII and NER stall loop extrusion at UV lesions, shaping the 3D genome during repair biorxiv.org 2026-06-26 The three-dimensional (3D) genome architecture is highly elastic, adapting to nuclear processes such as transcription and the DNA damage response (Dek
Learning Perturbation Effects Through Contrastive Alignment of Multimodal Biological Embeddings biorxiv.org 2026-06-26 Multimodal single cell perturbation screens offer a scalable approach for characterizing the effects of genetic and chemical interventions on cellular
Microglia-Specific Molecular Magnetic Resonance Imaging Probe Enables Noninvasive Separation of Parkinsonian Mice from Controls biorxiv.org 2026-06-26 Neuroinflammation mediated by reactive microgliosis is a central driver of Parkinsons disease (PD) pathogenesis.
Spatially mediated interactions shape founder-cell fitness and community assembly in multi-species soil bacteria biorxiv.org 2026-06-26 Microbial communities spontaneously colonize pristine environments, yet how species growth kinetics and individual cell variation shape community asse
Predictable induction responses of gut prophages biorxiv.org 2026-06-26 Temperate bacteriophages are dominant members of the human gut microbiome that can infect and lyse their bacterial hosts or integrate as prophages.
Plasmid-encoded anatoxin biosynthesis in benthic cyanobacteria biorxiv.org 2026-06-26 Anatoxin-producing cyanobacteria pose growing ecological and public health risks, yet the genomic organization of anatoxin biosynthesis remains poorly