Tao Liu

Rational Design of 5' UTRs for Optimized mRNA Expression and Cost-Effective, Rapid Analysis of Capped mRNA

This paper designs a 5' UTR that enables rapid, cost-effective analysis of mRNA capping efficiency and poly(A) tail length without probes or biotin.

Improved surfactant-assisted one-pot sample preparation for robust convenient single cell proteomics

This paper introduces an improved single-cell proteomics method, iSOP-MS, which enhances robustness and convenience for quantitative analysis by using a low-volume 384-well plate and optimized enzyme mixtures.

Detection of Melanoma Using Deep Serum Proteome Profiling and Machine Learning

This study detects melanoma using serum proteome profiling and machine learning, identifying eight protein biomarkers with high diagnostic accuracy.

MYST acetyltransferases are a targetable therapeutic vulnerability in SETBP1-mutant leukemia

This study identifies MYST acetyltransferases as therapeutic targets in SETBP1-mutant leukemia, showing that MYST inhibitors reduce target gene expression and improve survival in mouse models.

Long-read RNA-seq atlas of novel microglia isoforms elucidates disease-associated genetic regulation of splicing

The paper presents a long-read RNA-seq atlas of microglia isoforms, identifying novel isoforms and their associations with genetic risk loci in Alzheimer's and Parkinson's disease.

Robust collection and processing for label-free single voxel proteomics

This paper introduces a method for label-free single voxel proteomics using wcSOP, enabling spatial resolution of protein expression in tissue samples.

Myalgic Encephalomyelitis/Chronic Fatigue Syndrome and fibromyalgia are indistinguishable by their cerebrospinal fluid proteomes

The paper compares cerebrospinal fluid proteomes of ME/CFS patients with and without fibromyalgia, finding no significant differences, suggesting they may not be distinct conditions.

RealSeq2: a software integrated with UMI identification, error correction, and methylation modifications storing

RealSeq2 is a preprocessing software for high-throughput sequencing data that includes UMI identification, error correction, and methylation data storage, supporting co-detection of ultra-low frequency mutations and methylation sites.

High-throughput and high-efficiency sample preparation for single-cell proteomics using a nested nanowell chip

This paper introduces a nested nanowell chip to improve single-cell proteomics throughput and robustness, demonstrating the ability to quantify ~1500 proteins from ~100 cells with low abundance variation.

Zfp36l1 and Zfp36l2 balances proliferation and differentiation in the developing retina

This study shows that Zfp36l1 and Zfp36l2 regulate retinal development by balancing proliferation and differentiation, with their loss causing reduced proliferation and increased differentiation in the retina.

High-quality de novo genome assembly of Kappaphycus alvarezii based on both PacBio and HiSeq sequencing

The paper reports a high-quality draft genome of Kappaphycus alvarezii using PacBio and HiSeq sequencing, providing resources for genomic and genetic studies.

HMMRATAC: a Hidden Markov ModeleR for ATAC-seq

HMMRATAC is a semi-supervised machine learning tool for ATAC-seq that improves accessible region prediction by incorporating nucleosome positioning information.

Rapidly Assessing the Quality of Targeted Proteomics Experiments Through Monitoring Stable-isotope Labeled Standards

Q4SRM is a software tool that rapidly assesses the quality of targeted proteomics experiments by monitoring stable-isotope labeled standards.

Feasibility of constructing multi-dimensional genomic maps of juvenile idiopathic arthritis

This study demonstrates the feasibility of creating multi-dimensional genomic maps for juvenile idiopathic arthritis using limited patient samples and identifies epigenetic and genetic features associated with the disease.

Characterization of mannitol metabolism genes in Saccharina explains its key role in mannitol biosynthesis and evolutionary significance in Laminariales

The paper characterizes mannitol metabolism genes in Saccharina japonica, revealing their role in mannitol biosynthesis and evolutionary significance in Laminariales.

The brown alga Saccharina japonica features distinct vanadium-dependent bromoperoxidases and iodoperoxidases

This study identifies and characterizes vanadium-dependent bromoperoxidases and iodoperoxidases in Saccharina japonica, revealing their distinct expression patterns and enzymatic properties.

Model-based Analysis of ChIP-Seq (MACS)

MACS calls ChIP-Seq peaks by estimating tag shift from Watson/Crick strand offsets and testing enrichment against a locally adaptive Poisson background, improving specificity and binding-site resolution.