Biology subjects

Peng, P.-H.

Publications and source records attributed to Peng, P.-H..

2 recordsLinked to original sources

bioRxiv2025

An Atlas of Extrachromosomal DNA Structures Illuminates Its Evolution and Biogenesis in Cancer

Extrachromosomal circular DNA (ecDNA) is a prevalent driver of oncogene amplification across diverse types of cancers. Leveraging single-molecule long-read sequencing and a de novo circular genome assembler, ecLego3, we charted a comprehensive atlas of ecDNA structures from longitudinal pairs of primary and recurrent glioblastoma (GBM). Our approach resolved 23 ecDNA genomes representing major oncogenes associated with GBM pathogenesis and revealed a dynamic configuration characterized by pronounced structural variation and multi-species co-existence within individual tumors. Evolutionary trajectories were shaped by hierarchical accrual of structural variants, predominated by deletions and inversions, giving rise to novel oncogene isoforms and enhancer repositioning. Such structural plasticity promotes intratumor heterogeneity and tumor fitness. Multiomic analyses at single cell resolution linked ecDNA abundance and structure to transcriptional output, uncovering non-linear scaling and synergistic co-selection among multiple ecDNA species. Comparative profiling revealed locus-dependent configuration, a contraction of ecDNA diversity upon recurrence, and convergent structural architectures across patients, implicating repeat-mediated genomic rearrangements and replication stress in ecDNA biogenesis. These findings elucidate ecDNA-driven mechanisms of tumor adaptation and highlight new molecular vulnerabilities, informing potential biomarkers and therapeutic strategies for high-grade gliomas.

cancer biology↗

bioRxiv2021

Near-Zero Phase-Lag Hyperscanning in a Novel Wireless EEG System

Hyperscanning is an emerging technology that concurrently scans the neural dynamics of multiple individuals to study interpersonal interactions. In particular, hyperscanning with wireless electroencephalography (EEG) is increasingly popular owing to its mobility and ability to decipher social interactions in natural settings at the millisecond scale. To align multiple EEG time series with sophisticated event markers in a single time domain, a precise and unified timestamp is required for stream synchronization. This study proposed a clock-synchronized method using a custom-made RJ45 cable to coordinate the sampling between wireless EEG amplifiers to prevent incorrect estimation of interbrain connectivity due to asynchronous sampling. In this method, analog-to-digital converters are driven by the same sampling clock. Additionally, two clock-synchronized amplifiers leverage additional RF channels to keep the counter of their receiving dongles updated, guaranteeing that binding event markers received by the dongle with the EEG time series have the correct timestamp. The results of two simulation experiments and one video gaming experiment revealed that the proposed method ensures synchronous sampling in a system with multiple EEG devices, achieving near-zero phase-lag and negligible amplitude difference between signals. According to all of the signal-similarity metrics, the suggested method is a promising option for wireless EEG hyperscanning and can be utilized to precisely assess the interbrain couplings underlying social-interaction behaviors.

bioengineering↗