Huimin Zhao

An AI-powered cloud biofoundry for autonomous biological research

The paper introduces iCloudBiofoundry, a cloud platform that autonomously designs, executes, and iteratively improves biological experiments using AI-driven workflows.

Acidic transcription factors position the genome at nuclear speckles through transcription dependent and independent mechanisms

The paper identifies acidic transcription factors that position genomic regions near nuclear speckles through both transcription-dependent and independent mechanisms.

A versatile enzymatic pathway for modification of peptide C-termini

The paper reconstitutes daptide biosynthesis in vitro to reveal enzymatic requirements and demonstrates broad substrate tolerance for modifying peptide C-termini.

MAESTRO uncovers tandem paralog dynamics as a core driver of fungal stress adaptation

MAESTRO identifies tandem paralog copy number variation as a key mechanism for stress adaptation in Pichia kudriavzevii, linking it to drug resistance and environmental tolerance.

Design of diverse, functional mitochondrial targeting sequences across eukaryotic organisms using variational autoencoder

This paper uses a variational autoencoder to design novel mitochondrial targeting sequences across eukaryotic organisms, showing they are functional and diverse.

Discovery, characterization, and application of chromosomal integration sites in the hyperthermophilic crenarchaeon Sulfolobus islandicus

This study identifies and characterizes chromosomal integration sites in Sulfolobus islandicus using CRISPR-COPIES and validates their utility for genetic manipulation.

A Generalized Platform for Artificial Intelligence-powered Autonomous Protein Engineering

This paper introduces an AI-powered platform for autonomous protein engineering that uses machine learning and biofoundry automation to rapidly improve protein function without human intervention.

Chemoenzymatic Synthesis Planning Guided by Reaction Type Score

The paper introduces RTS-CESP, a method using a reaction type score to guide chemoenzymatic synthesis planning, outperforming existing tools and validating new routes for a drug.

FoldMark: Safeguarding Protein Structure Generative Models with Distributional and Evolutionary Watermarking

This paper introduces FoldMark, a watermarking method for protein generative models that ensures biosecurity by enabling user tracing and maintaining structural quality.

Enhancing lipid production in plant cells through high-throughput genome editing and phenotyping via a scalable automated pipeline

CRISPR-COPIES: An in silico platform for discovery of neutral integration sites for CRISPR/Cas-facilitated gene integration

CRISPR-COPIES identifies neutral integration sites for CRISPR/Cas-mediated gene insertion in bacterial, fungal, and human genomes using computational methods.

Automated, self-resistance gene-guided, and high-throughput genome mining of bioactive natural products from Streptomyces

The paper introduces a high-throughput platform for discovering bioactive natural products from Streptomyces by combining computational prediction, cloning, and heterologous expression of biosynthetic gene clusters.

A landing pad system for multicopy gene integration in Issatchenkia orientalis

This paper develops a landing pad system for efficient multicopy gene integration in Issatchenkia orientalis using CRISPR-Cas9, enabling the construction of complex metabolic pathways with high integration efficiency.

Nitrogen starvation causes lipid remodeling in Rhodotorula toruloides

This study investigates lipid remodeling in Rhodotorula toruloides under nitrogen starvation, identifying phospholipid-to-storage lipid conversion and regulatory mechanisms for lipid accumulation.

An end-to-end pipeline for succinic acid production at an industrially relevant scale using Issatchenkia orientalis

This paper describes an end-to-end pipeline for cost-effective succinic acid production using Issatchenkia orientalis, achieving high titers and financial viability with reduced greenhouse gas emissions.

Proteome capacity constraints favor respiratory ATP generation

The paper shows mitochondrial respiration is more proteome-efficient than aerobic glycolysis in yeast and mammals, with flexibility arising from maintaining a fermentation-capable proteome.

Metabolic Engineering of Oleaginous Yeast Rhodotorula toruloides for Overproduction of Triacetic Acid Lactone

This paper reports the metabolic engineering of Rhodotorula toruloides to overproduce triacetic acid lactone (TAL) by enhancing acetyl-CoA flux through gene overexpression.

PlasmidMaker: a Versatile, Automated, and High Throughput End-to-End Platform for Plasmid Construction

PlasmidMaker automates high-throughput plasmid construction with error-free assembly of complex genetic sequences across multiple species.

Replication timing maintains the global epigenetic state in human cells.

This study shows that replication timing (RT) is essential for maintaining the global epigenetic state and genome compartmentalization in human cells, with RIF1 playing a central role in this process.

Preservation of Chromatin Organization after Acute Loss of CTCF in Mouse Embryonic Stem Cells

This study shows that chromatin organization remains largely intact in mouse embryonic stem cells after acute CTCF depletion, despite reduced cell growth and changes in chromatin loop interactions and cohesin occupancy.

CTCF Promotes Long-range Enhancer-promoter Interactions and Lineage-specific Gene Expression in Mammalian Cells

This study shows that CTCF depletion in mESCs weakens TAD boundaries and INs but only affects a small subset of enhancer-promoter contacts, highlighting CTCF's role in promoting long-range gene regulation.

DNA Punch Cards: Storing Data on Native DNA Sequences via Nicking

This paper introduces a DNA-based data storage method using nicks in native DNA to encode information, demonstrating proof of concept with restriction enzyme-mediated nicking and sequencing-based data reconstruction.

Evolutionary context-integrated deep sequence modeling for protein engineering

This paper introduces ECNet, a deep learning model that uses evolutionary context to predict protein variant fitness, outperforming existing methods on multiple datasets.

A comprehensive genome-scale model for Rhodosporidium toruloides IFO0880 accounting for functional genomics and phenotypic data

The paper constructs a genome-scale metabolic model for Rhodosporidium toruloides IFO0880, integrating functional genomics and phenotypic data to improve predictions of gene essentiality and metabolic capabilities.

Characterization of Cas proteins for CRISPR-Cas editing in streptomycetes

The paper evaluates alternative CRISPR-Cas systems for genome editing in streptomycetes, showing that sth1Cas9, saCas9, and fnCpf1 enable efficient genomic modifications where SpCas9 fails.