Biology subjects

Tan, H.-Y.

Publications and source records attributed to Tan, H.-Y..

3 recordsLinked to original sources

bioRxiv2026

MCseg: AI agent-guided workflow search for no-code cell segmentation and transcript attribution in spatial transcriptomics

Cell-level analysis of high-resolution spatial transcriptomics depends on accurate segmentation and transcript assignment, yet current workflows often trade transcript capture for boundary purity and can require substantial image-analysis expertise. We developed MCseg, a downloadable no-code platform whose fixed segmentation engine was derived by an AI-agent-guided search in which an AI agent iteratively proposed and evaluated combinations of image-processing and segmentation operations against Xenium-derived cell boundaries. In a lung adenocarcinoma development set, fixed-parameter MCseg increased mean panoptic quality from 0.432 to 0.472 relative to an Optuna-tuned two-diameter Cellpose baseline, while a reference-guided calibration analysis reached 0.554. In an independent expert-annotated colorectal cancer region, MCseg showed higher lineage recall and micro-F1 than the StarDist-based ENACT workflow among cells covered by both methods. Across 15 colorectal cancer regions, MCseg increased neighborhood expression discordance and reduced lineage-exclusive co-expression relative to Space Ranger at similar UMI density. The fixed workflow also transferred to fresh-frozen breast cancer without tissue-specific architecture search, illustrating an agent-guided route to reproducible, locally deployable cell-level spatial transcriptomic analysis.

bioinformatics↗

bioRxiv2024

Tracing neurodiverse disruptions underlying emotional episodic memory to diagnosis-specific network of emotional regulation in psychiatric disorders

BackgroundAffective symptoms are a prevalent psychopathological feature in various psychiatric disorders. However, the underlying neurobiological mechanisms are complex and not yet fully understood. MethodsWe used normative modelling to establish a reference for neurofunctional activation of functional magnetic resonance imaging based on an emotional episodic memory task, which is frequently used to study affective symptoms in psychiatric disorders. This normative reference was derived from a large dataset of healthy individuals (n = 409), and used to evaluate individualized functional alterations by calculating deviations from this reference in a clinical dataset of 328 participants, which included 168 healthy controls and patients with major depressive disorder (MDD, n = 56), bipolar disorder (BD, n = 31), and schizophrenia (SZ, n = 73). The neurofunctional deviations were mapped to emotional networks with specific emotional functions and used to predict affective symptoms in different mental disorders. The microscale cellular signatures underlying macroscale variations were identified using imaging transcriptomic analysis, and associated with affective symptoms. ResultsWe observed distinct patterns of cross-scale neural alterations linked to affective symptoms in three psychiatric disorders. Macroscale neural dysfunctions in distinct disorders were embedded into non-overlapping emotional networks and significantly associated with affective symptoms. The oligodendrocytes may mediate the network-specific impairments, and microglia for MDD, astrocytes for BD, and excitatory neurons for SZ as replicable cell-type correlates of affective symptoms. ConclusionsThese findings have potential implications for the understanding of unique neuropathological patterns of affective symptoms in distinct psychiatric disorders and improving individualized treatment response.

neuroscience↗

bioRxiv2020

SSB facilitates fork substrate discrimination by PriA

PriA is a member of the SuperFamily 2 helicase family. Its role in vivo is to reload the primosome onto stalled replication forks resulting in the restart of the previously stalled DNA replication process. SSB is known to play key roles in mediating activities at replication forks and it is known to bind to PriA. To gain mechanistic insight into the PriA-SSB interaction, a coupled spectrophotometric assay was utilized to characterize the ATPase activity of PriA in vitro in the presence of fork substrates. The results demonstrate that SSB enhances the ability of PriA to discriminate between fork substrates 140-fold. This is due to a significant increase in the catalytic efficiency of the helicase induced by DNA-bound SSB. This interaction is species-specific as bacteriophage gene 32 protein cannot substitute for the E.coli protein. SSB, while enhancing the activity of PriA on its preferred fork, both decreases the affinity of the helicase for other forks and decreases catalytic efficiency. Central to the stimulation afforded by SSB is the unique ability of PriA to bind with high affinity to the 3-OH placed at the end of the nascent leading strand at the fork. When both the 3-OH and SSB are present, the maximum effect is observed. This ensures that PriA will only load onto the correct fork, in the right orientation, thereby ensuring that replication restart is directed to only the template lagging strand.

biochemistry↗