A5009471000- Genomics and Phylogenetic Studies
- RNA and protein synthesis mechanisms
- Genomics and Chromatin Dynamics
- DNA Repair Mechanisms
- Bacterial Genetics and Biotechnology
- RNA modifications and cancer
- Machine Learning in Bioinformatics
- Microbial Metabolic Engineering and Bioproduction
- Gut microbiota and health
- Cancer-related molecular mechanisms research
- CRISPR and Genetic Engineering
- RNA Research and Splicing
- Probiotics and Fermented Foods
- Bioinformatics and Genomic Networks
- Bacteriophages and microbial interactions
- Adaptive Dynamic Programming Control
- Invertebrate Immune Response Mechanisms
- Molecular Biology Techniques and Applications
- Mollusks and Parasites Studies
- Insect Utilization and Effects
- Neurobiology and Insect Physiology Research
- Single-cell and spatial transcriptomics
- Cytomegalovirus and herpesvirus research
- Diabetes, Cardiovascular Risks, and Lipoproteins
- Antibiotic Resistance in Bacteria
Tianjin University
2014-2025
Sichuan Cancer Hospital
2025
University of Electronic Science and Technology of China
2025
Chalmers University of Technology
2021-2024
Nankai University
2024
Tongji University
2023
National Institute for Radiological Protection
2023
Southern Medical University
2023
South China Agricultural University
2014-2022
Sichuan University of Science and Engineering
2022
Protein post-translational modifications (PTMs) at the lysine residue, such as methylation, acetylation, and ubiquitination, are diverse, abundant, dynamic. They play a key role in regulation of diverse cellular physiology. Here we report discovery new type PTM, malonylation (Kmal). Kmal was initially detected by mass spectrometry protein sequence-database searching. The modification comprehensively validated Western blot, tandem MS, high-performance liquid chromatography synthetic peptides,...
The combination of high-density transposon-mediated mutagenesis and high-throughput sequencing has led to significant advancements in research on essential genes, resulting a dramatic increase the number identified prokaryotic genes under diverse conditions revised essential-gene concept that includes all genomic elements, rather than focusing protein-coding only. DEG 10, new release Database Essential Genes (available at http://www.essentialgene.org), been developed accommodate these...
Abstract Essential genes refer to that are required by an organism survive under specific conditions. Studies of the minimal-gene-set for bacteria have elucidated fundamental cellular processes sustain life. The past five years seen a significant progress in identifying human essential genes, primarily due successful use CRISPR/Cas9 various types cells. DEG 15, new release Database Genes (www.essentialgene.org), has provided major advancements, compared 10. Specifically, number eukaryotic...
Despite of the progress in identifying many Lys acetylation (Kac) proteins, Kac substrates for Kac-regulatory enzymes remain largely unknown, presenting a major knowledge gap biology. Here we identified and quantified 4623 sites 1800 proteins <i>SIRT1</i><sup>+/+</sup> <i>SIRT1</i><sup>−/−</sup> MEF cells, representing first study to reveal an enzyme-regulated subproteome largest acetylome reported date from single study. Four hundred eighty-five were enhanced by more than 100% after...
Replication of chromosomes is one the central events in cell cycle. Chromosome replication begins at specific sites, called origins (oriCs), for all three domains life. However, still remain unknown a considerably large number bacterial and archaeal genomes completely sequenced so far. The availability increasing complete has created challenges opportunities identification their oriCs silico, as well vivo. Based on Z-curve theory, we have developed web-based system Ori-Finder to predict with...
Transcription-regulating long non-coding RNAs (lncRNAs) have the potential to control site-specific gene expression of thousands targets. Previously, we showed that Evf2, first described ultraconserved lncRNA, increases association transcriptional activators (DLX homeodomain proteins) key DNA enhancers, but represses expression. In this report, mass spectrometry shows Evf2/DLX1 ribonucleoprotein (RNP) contains SWI/SNF related chromatin-remodelers, Brahma 1 (BRG1, SMARCA4) and...
DoriC, a database of replication origins, was initially created to present the bacterial oriCs predicted by Ori-Finder or determined experiments in 2007. DoriC 5.0, an updated oriC regions both and archaeal genomes, published 2013 Nucleic Acids Research issue. Now, latest release 10, large-scale update origins prokaryotic genomes including chromosomes plasmids, has been presented with completely redesigned user interface, which is freely available at http://tubic.org/doric/...
Abstract Recent studies have shown that probiotic supplementation has beneficial effects on bone metabolism. In a randomized controlled trial (RCT) we demonstrated of Lactobacillus reuteri ATCC PTA 6475 reduced loss in older women with low mineral density. To investigate the mechanisms underlying effect L. metabolism, 20 highest changes (good responders) and lowest (poor tibia total volumetric BMD after one-year were selected from our previous RCT. current study characterized gut microbiome...
Abstract The replication of DNA is a complex biological process that essential for life. Bacterial initiated at genomic loci referred to as origins (oriCs). Integrating the Z-curve method, DnaA box distribution, and comparative analysis, we developed web server predict bacterial oriCs in 2008 called Ori-Finder, which helpful clarify characteristics oriCs. hundreds sequenced genomes have been annotated genome reports using Ori-Finder predicted results deposited DoriC, manually curated...
The National Genomics Data Center (NGDC), which is a part of the China for Bioinformation (CNCB), offers comprehensive suite database resources to support global scientific community. Amidst unprecedented accumulation multi-omics data, CNCB-NGDC committed continually evolving and updating its core through big data archiving, integrative analysis value-added curation. Over past year, has expanded collaborations with international databases established new subcenters focusing on biodiversity,...
DNA single-strand break repair (SSBR) is important for maintaining genome stability and homeostasis. The current SSBR model derived from an in vitro-reconstituted reaction suggests that the complex mediated by X-ray cross-complementing protein 1 (XRCC1) assembled sequentially at site of damage. In this study, we provide biochemical data to demonstrate two preformed XRCC1 complexes exist cycling HeLa cells. One contains known enzymes are SSBR, including ligase 3 (DNL3), polynucleotide kinase...
Essential genes are thought to be critical for the survival of organisms under certain circumstances, and natural selection acting on essential is expected stricter than nonessential ones. Up now, have been identified in approximately thirty bacterial by experimental methods. In this paper, we performed a comprehensive comparison between genomes 23 species based Ka/Ks ratio, found that more evolutionarily conserved most bacteria examined. Furthermore, also analyzed conservation functional...
DNA replication is one of the most basic processes in all three domains cellular life. With advent post-genomic era, increasing number complete archaeal genomes has created an opportunity for exploration molecular mechanisms initiating by vivo experiments as well silico analysis. However, location origins (oriCs) many sequenced remains unknown. We present a web-based tool Ori-Finder 2 to predict oriCs automatically, based on integrated method comprising analysis base composition asymmetry...
Previously constructed classifiers in predicting eukaryotic essential genes integrated a variety of features including experimental ones. If we can obtain satisfactory prediction using only nucleotide (sequence) information, it would be more promising. Three groups recently identified human cancer cell lines wet experiments and provided wonderful opportunity to accomplish our idea. Here improved the Z curve method into λ-interval form denote composition association information used construct...
Abstract The molecular basis of how temperature affects cell metabolism has been a long-standing question in biology, where the main obstacles are lack high-quality data and methods to associate effects on function individual proteins as well combine them at systems level. Here we develop apply Bayesian modeling approach resolve genome scale metabolic models (GEM). minimizes uncertainties enzymatic thermal parameters greatly improves predictive strength GEMs. resulting constrained yeast GEM...
Radiotherapy is a prevalent treatment modality for thoracic tumors; however, it can lead to radiation-induced lung injury (RILI), which currently lacks effective interventions. ACT001, prodrug of micheliolide, has demonstrated promising clinical application potential, yet its impact on RILI requires further validation. This study aims investigate the radioprotective effects ACT001 and elucidate underlying mechanism. Sprague-Dawley rats were utilized induce following 20 Gy X-ray chest...
ObjectivesTo determine the genome sequence of Acinetobacter baumannii strain MDR-TJ and characterize mechanisms multidrug resistance in this strain.