Biology subjects

Lien, A.

Publications and source records attributed to Lien, A..

3 recordsLinked to original sources

bioRxiv2026

A long-hidden prevalent PCR artifact and its application in DNA library screening

PCR artifacts can lead to aberrant DNA products and confound result interpretation, posing significant challenges in research and diagnostics. Traditionally, it has been blamed to misannealing of primers on unintended sites. However, by sequencing, we find that most PCR byproducts and artifacts actually have both primers bound correctly but lack a middle part of the target, a phenomenon we named as PCR leaping. The leaping occurs at random positions, is independent of sequence repeats and requires a single piece template, indicating an unprecedented mechanism. It is observed with various polymerases, template qualities, GC contents, and PCR programs, thus necessitating a reset of our PCR understanding and careful consideration in future studies, for example in CRISPR editing validations. On the other hand, it provides a simple way of DNA end pairing, based on which we develop a high throughput DNA library screening method for natural product discovery at substantially reduced cost.

molecular biology↗

bioRxiv2025

Single Capture Quantitative Oblique Back-Illumination Microscopy

Quantitative oblique back-illumination microscopy (qOBM) has emerged as a powerful technique for label-free, 3D quantitative phase imaging of arbitrarily thick biological specimens. However, in its initial embodiment, qOBM requires multiple captures for phase recovery, which reduces imaging speed and increases system complexity. In this work, we present a novel advancement in qOBM: single-capture qOBM (SCqOBM) which utilizes a deep learning model to accurately reconstruct phase information from a single oblique back-illumination capture. We demonstrate that SCqOBM achieves remarkable phase imaging accuracy, closely matching the results of traditional four-capture qOBM in diverse biological samples. We first highlight the unique potential of SCqOBM for non-invasive, in-vivo imaging applications by visualizing blood flow in mouse brain and human arm. Additionally, we demonstrate single-slice (en-face) quantitative phase imaging at 2 kHz and volumetric refractive index tomography at speeds up to 10 volumes per second. SCqOBM offers transformative advantages in speed, simplicity, and system accessibility, making it highly suitable for dynamic and real-time imaging applications. Its ability to produce high-resolution, quantitative phase and refractive index images with minimal hardware complexity opens new frontiers in biomedical research and clinical diagnostics, including non-invasive hematological assessments and in-vivo tissue imaging.

bioengineering↗

bioRxiv2023

Benchmarking software tools for trimming adapters and merging next-generation sequencing data for ancient DNA

Ancient DNA is highly degraded, resulting in very short sequences. Reads generated with modern high-throughput sequencing machines are generally longer than ancient DNA molecules, therefore the reads often contain some portion of the sequencing adaptors. It is crucial to remove those adaptors, as they can interfere with downstream analysis. Furthermore, overlapping portions when DNA has been read forward and backward (paired-end) can be merged to correct sequencing errors and improve read quality. Several tools have been developed for adapter trimming and read merging, however, no one has attempted to evaluate their accuracy and evaluate their potential impact on downstream analyses. Through the simulation of sequencing data, seven commonly used tools were analyzed in their ability to reconstruct ancient DNA sequences through read merging. The analyzed tools exhibit notable differences in their abilities to correct sequence errors and identify the correct read overlap, but the most substantial difference is observed in their ability to calculate quality scores for merged bases. Selecting the most appropriate tool for a given project depends on several factors, although some tools such as fastp have some shortcomings, whereas others like leeHom outperform the other tools in most aspects. While the choice of tool did not result in a measurable difference when analyzing population genetics using principal component analysis, it is important to note that downstream analyses that rely on quality scores can be significantly impacted by the choice of tool.

bioinformatics↗