Zhi-Luo Deng
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View article: Genetic Regulatory Network of DNA Replication Initiation in E. coli and Its Biological Significance
Genetic Regulatory Network of DNA Replication Initiation in E. coli and Its Biological Significance Open
This review outlines the mechanisms and regulation of DNA replication in Escherichia coli within the oriC region, focusing on DnaA nucleotide state and stepwise occupation of high and lowaffinity boxes, origin DNA topology, and architectur…
View article: Metagenomic Insights into Disease-Induced Microbial Dysbiosis and Elemental Cycling Alterations in Morchella Cultivation Soils: Evidence from Two Distinct Regions
Metagenomic Insights into Disease-Induced Microbial Dysbiosis and Elemental Cycling Alterations in Morchella Cultivation Soils: Evidence from Two Distinct Regions Open
Soil-borne diseases represent a major constraint on the sustainable cultivation of morel mushrooms (Morchella spp.), yet the microbial ecological mechanisms driving disease occurrence and progression remain poorly understood. In this study…
View article: In silico genomic surveillance by CoVerage predicts and characterizes SARS-CoV-2 variants of interest.
In silico genomic surveillance by CoVerage predicts and characterizes SARS-CoV-2 variants of interest. Open
Rapidly evolving viral pathogens such as SARS-CoV-2 continuously accumulate amino acid changes, some of which affect transmissibility, virulence or improve the virus' ability to escape host immunity. Since the beginning of the SARS-CoV-2 p…
View article: Transcriptome and co-expression network analysis reveal the genetic basis of cell wall components in maize stalks
Transcriptome and co-expression network analysis reveal the genetic basis of cell wall components in maize stalks Open
View article: CAMI Benchmarking Portal: online evaluation and ranking of metagenomic software
CAMI Benchmarking Portal: online evaluation and ranking of metagenomic software Open
Finding appropriate software and parameter settings to process shotgun metagenome data is essential for meaningful metagenomic analyses. To enable objective and comprehensive benchmarking of metagenomic software, the community-led initiati…
View article: 21 Impacts of increasing soybean meal on jejunal immune challenge of nursery pigs at different ages
21 Impacts of increasing soybean meal on jejunal immune challenge of nursery pigs at different ages Open
The objective of this study was to investigate the impacts of increasing soybean meal (SBM) in feed on the jejunal immune challenge of nursery pigs at different ages after weaning. The hypothesis was that nursery pigs would be more suscept…
View article: Integrating kinetic models and BP-ANN for predicting growth and shelf-life of Listeria monocytogenes in ready-to-eat salads
Integrating kinetic models and BP-ANN for predicting growth and shelf-life of Listeria monocytogenes in ready-to-eat salads Open
View article: Detection of<i>Paracoccus yeei</i>in Spontaneous Bacterial Peritonitis using Rapid, Long Read Sequencing
Detection of<i>Paracoccus yeei</i>in Spontaneous Bacterial Peritonitis using Rapid, Long Read Sequencing Open
Ascites is a common complication in patients with decompensated liver cirrhosis. Spontaneous bacterial peritonitis (SBP) is the most frequent infection, affecting up to 30% of hospitalized patients with ascites. Multidrug-resistant bacteri…
View article: BioMaze: Benchmarking and Enhancing Large Language Models for Biological Pathway Reasoning
BioMaze: Benchmarking and Enhancing Large Language Models for Biological Pathway Reasoning Open
The applications of large language models (LLMs) in various biological domains have been explored recently, but their reasoning ability in complex biological systems, such as pathways, remains underexplored, which is crucial for predicting…
View article: Assessing computational predictions of antimicrobial resistance phenotypes from microbial genomes
Assessing computational predictions of antimicrobial resistance phenotypes from microbial genomes Open
The advent of rapid whole-genome sequencing has created new opportunities for computational prediction of antimicrobial resistance (AMR) phenotypes from genomic data. Both rule-based and machine learning (ML) approaches have been explored …
View article: In silico genomic surveillance by CoVerage predicts and characterizes SARS-CoV-2 Variants of Interest
In silico genomic surveillance by CoVerage predicts and characterizes SARS-CoV-2 Variants of Interest Open
Rapidly evolving viral pathogens such as SARS-CoV-2 continuously accumulate amino acid changes, some of which affect transmissibility, virulence or improve the virus' ability to escape host immunity. Since the beginning of the pandemic and…
View article: Assessing computational predictions of antimicrobial resistance phenotypes from microbial genomes
Assessing computational predictions of antimicrobial resistance phenotypes from microbial genomes Open
The advent of rapid whole-genome sequencing has created new opportunities for computational prediction of antimicrobial resistance (AMR) phenotypes from genomic data. Both rule-based and machine learning (ML) approaches have been explored …
View article: Engraftment of essential functions through multiple fecal microbiota transplants in chronic antibiotic-resistant pouchitis—a case study using metatranscriptomics
Engraftment of essential functions through multiple fecal microbiota transplants in chronic antibiotic-resistant pouchitis—a case study using metatranscriptomics Open
Background Ileal pouch-anal anastomosis (IPAA) is the standard of care after total proctocolectomy for ulcerative colitis (UC). Around 50% of patients will experience pouchitis, an idiopathic inflammatory condition. Antibiotics are the bac…
View article: Multi-omics analysis reveals the molecular response to heat stress in a “red tide” dinoflagellate
Multi-omics analysis reveals the molecular response to heat stress in a “red tide” dinoflagellate Open
View article: CoVerage Results
CoVerage Results Open
Datasets generated from GISAID metadata for the figures in the CoVerage manuscript. Data includes the results for the months of November 2021 to January 2021 and January 2023 to March 2023. 11_2021 11-2021_fig3_lineage_dynamics_summary_sta…
View article: CoVerage Results
CoVerage Results Open
Datasets generated from GISAID metadata for the figures in the CoVerage manuscript. Data includes the results for the months of November 2021 to January 2021 and January 2023 to March 2023. 11_2021 11-2021_fig3_lineage_dynamics_summary_sta…
View article: A platform for deep learning on (meta)genomic sequences
A platform for deep learning on (meta)genomic sequences Open
We describe deepG, a platform for the generation, interpretation, and application of deep learning models for sequence labeling, classification, and regression based on nucleotide sequences. Unlike other bioinformatic deep learning platfor…
View article: Assessment of AlphaFold structures and optimization methods for virtual screening
Assessment of AlphaFold structures and optimization methods for virtual screening Open
Recent advancements in artificial intelligence such as AlphaFold, have enabled more accurate prediction of protein three-dimensional structure from amino acid sequences. This has attracted significant attention, especially for the applicat…
View article: Multi-omics analysis reveals the molecular response to heat stress in a “red tide” dinoflagellate
Multi-omics analysis reveals the molecular response to heat stress in a “red tide” dinoflagellate Open
“Red tides” are harmful algal blooms (HABs) caused by dinoflagellate microalgae that accumulate toxins lethal to other organisms, including humans via consumption of contaminated seafood. Increasingly frequent, HABs are driven by a combina…
View article: Critical Assessment of Metagenome Interpretation: the second round of challenges
Critical Assessment of Metagenome Interpretation: the second round of challenges Open
Evaluating metagenomic software is key for optimizing metagenome interpretation and focus of the Initiative for the Critical Assessment of Metagenome Interpretation (CAMI). The CAMI II challenge engaged the community to assess methods on r…
View article: Rapid and accurate identification of ribosomal RNA sequences via deep learning
Rapid and accurate identification of ribosomal RNA sequences via deep learning Open
Advances in transcriptomic and translatomic techniques enable in-depth studies of RNA activity profiles and RNA-based regulatory mechanisms. Ribosomal RNA (rRNA) sequences are highly abundant among cellular RNA, but if the target sequences…
View article: Haploflow: strain-resolved de novo assembly of viral genomes
Haploflow: strain-resolved de novo assembly of viral genomes Open
With viral infections, multiple related viral strains are often present due to coinfection or within-host evolution. We describe Haploflow, a deBruijn graph-based assembler for de novo genome assembly of viral strains from mixed sequence s…
View article: Critical Assessment of Metagenome Interpretation - the second round of challenges
Critical Assessment of Metagenome Interpretation - the second round of challenges Open
Evaluating metagenomic software is key for optimizing metagenome interpretation and focus of the community-driven initiative for the Critical Assessment of Metagenome Interpretation (CAMI). In its second challenge, CAMI engaged the communi…
View article: Benchmarking datasets for RiboDetector paper
Benchmarking datasets for RiboDetector paper Open
The benchmarking datasets used in RiboDetector paper, including five datasets described in the material and methods part of the paper
View article: Benchmarking datasets for RiboDetector paper
Benchmarking datasets for RiboDetector paper Open
The benchmarking datasets used in RiboDetector paper, including five datasets described in the material and methods part of the paper
View article: Benchmarking datasets for RiboDetector paper
Benchmarking datasets for RiboDetector paper Open
The benchmarking datasets used in RiboDetector paper, including five datasets described in the material and methods part of the paper
View article: Haploflow: Strain-resolved<i>de novo</i>assembly of viral genomes
Haploflow: Strain-resolved<i>de novo</i>assembly of viral genomes Open
In viral infections often multiple related viral strains are present, due to coinfection or within-host evolution. We describe Haploflow, a de Bruijn graph-based assembler for de novo genome assembly of viral strains from mixed sequence sa…
View article: Evaluating assembly and variant calling software for strain-resolved analysis of large DNA viruses
Evaluating assembly and variant calling software for strain-resolved analysis of large DNA viruses Open
Infection with human cytomegalovirus (HCMV) can cause severe complications in immunocompromised individuals and congenitally infected children. Characterizing heterogeneous viral populations and their evolution by high-throughput sequencin…
View article: Evaluating assembly and variant calling software for strain-resolved analysis of large DNA-viruses
Evaluating assembly and variant calling software for strain-resolved analysis of large DNA-viruses Open
Infection with human cytomegalovirus (HCMV) can cause severe complications in immunocompromised individuals and congenitally infected children. Characterizing heterogeneous viral populations and their evolution by high-throughput sequencin…
View article: Assembly and variant calling results of strain mixtures of HCMV
Assembly and variant calling results of strain mixtures of HCMV Open
The tgz files contain the assembly contigs of 10 different assemblers and variant calling results of 6 callers on the strain mixture dataset of the HCMV virus.