A5102869887- Bioinformatics and Genomic Networks
- Genomics and Phylogenetic Studies
- Gene expression and cancer classification
- Reproductive System and Pregnancy
- Genomics and Chromatin Dynamics
- Physiological and biochemical adaptations
- Prenatal Screening and Diagnostics
- Reproductive Physiology in Livestock
- Genetic Mapping and Diversity in Plants and Animals
- Neuroendocrine regulation and behavior
- Congenital heart defects research
- RNA and protein synthesis mechanisms
- Receptor Mechanisms and Signaling
- Fungal and yeast genetics research
- Evolution and Genetic Dynamics
- Molecular Biology Techniques and Applications
- Chromosomal and Genetic Variations
- Cancer Genomics and Diagnostics
- Genomic variations and chromosomal abnormalities
- Chemical Synthesis and Analysis
- RNA modifications and cancer
- Diabetes Treatment and Management
- Genetic diversity and population structure
- Microbial Metabolic Engineering and Bioproduction
- Fish biology, ecology, and behavior
Sinotech Genomics (China)
2024-2025
Fudan University
2011-2024
Zhongshan Hospital
2021
State Key Laboratory of Genetic Engineering
2013-2017
Zero to Three
2009
Zhejiang University
2006
DIVERGE is a software system for phylogeny-based analyses of protein family evolution and functional divergence. It provides suite statistical tools selection prioritization the amino acid sites that are responsible divergence gene family. The synergistic efforts other methods have convincingly demonstrated pattern rate change at particular site may contain insightful information about underlying following duplication. These predicted be used as candidates further experiments. We now...
Abstract RNA secondary structure may influence many cellular processes, including processing, stability, localization, and translation. Single-nucleotide variations (SNVs) that alter structure, referred to as riboSNitches, are potentially causative of human diseases, especially in untranslated regions (UTRs) noncoding RNAs (ncRNAs). The functions somatic mutations act riboSNitches cancer development remain poorly understood. In this study, we developed a computational pipeline called SNIPER...
TATA box, the core promoter element, exists in a broad range of eukaryotes, and expression TATA-containing genes usually responds to various environmental stresses. Hence, evolution TATA-box duplicate may provide some clues for interrelationship among stress, differentiation, gene preservation. In present study, we observed that box is significantly overrepresented compared with singletons human, worm, Arabidopsis, yeast genomes. We then conducted an extensive functional genomic analysis...
Thanks to the microarray technology, our understanding of transcriptome evolution at genome level has been considerably advanced in past decade. Yet, further investigation was challenged by several technical limitations this technology. Recent innovation next-generation sequencing, particularly invention RNA-seq shed insightful lights on resolving problem. Though a number statistical and computational methods have developed analyze data, analytical framework specifically designed for...
// Zhan Zhou 1, 4, * , Yangyun Zou Gangbiao Liu 1 Jingqi Jingcheng Wu 4 Shimin Zhao 2 Zhixi Su and Xun Gu 3, Ministry of Education Key Laboratory Contemporary Anthropology, School Life Sciences, Fudan University, Shanghai, China State Genetic Engineering, Collaborative Innovation Center Genetics Development, 3 Department Genetics, Development Cell Biology, Program Bioinformatics Computational Iowa Ames, Iowa, USA College Pharmaceutical Zhejiang Hangzhou, These authors have contributed...
Abstract Genetical genomics, a novel approach combining microarray technology and quantitative genetic analysis, aims to identify the expression trait loci (eQTLs), which may regulate genome‐wide pattern. In this article, we have studied yeast genomic eQTL data investigate how regulation of ancestral gene has diverged since duplication. Our findings are as follows: (i) Duplicate genes higher heritability for than single‐copy genes, but little difference in their epistasis directional effect....
Gene duplication and subsequent functional divergence especially expression have been widely considered as main sources for evolutionary innovations. Many studies evidenced that genetic regulatory network evolved rapidly shortly after gene duplication, thus leading to accelerated diversification. However, little is known whether epigenetic factors mediated the evolution of regulation since duplication. In this study, we conducted detailed analyses on yeast histone modification (HM), major...
Abstract Background: Window of implantation (WOI) displacement was known as one endometrial origin leading to embryo failure, especially for repeated failure (RIF). A accurately prediction tool receptivity (ER) is extraordinary needed precisely guide the successful implantation. We aimed establish an RNA-seq based test (rsERT) using transcriptomic biomarkers, and evaluate benefit personalized transfer (pET) guided by this in patients with Methods: Two-phase strategy including establishment...
RNA sequencing (RNA-Seq) technology provides the detailed transcriptomic information for a biological sample. Using RNA-Seq data of six organs from nine vertebrate species, we identified number organ-specifically expressed or repressed orthologous genes whose expression patterns are mostly conserved across species. Our analyses show following results: (i) About 80% these have chordate more ancient origin and than half them legacy one multiple rounds large-scale gene duplication events. (ii)...
Abstract Side effects from targeted drugs remain a serious concern. One reason is the nonselective binding of drug to unintended proteins such as its paralogs, which are highly homologous in sequences and have similar structures drug-binding pockets. To identify targetable differences between we analyzed two types (type-I type-II) functional divergence paralogs known target protein receptor family G-protein coupled receptors (GPCRs) at amino acid level. Paralogous glucagon-like subfamily,...
The independent origins of multiple electric organs (EOs) fish are fascinating examples convergent evolution. However, comparative transcriptomics different lineages scarce. In this study, we found that the gene expression EOs and skeletal muscles from three (Mormyroidea, Siluriformes, Gymnotiformes) tended to cluster together based on species origin, irrespective organ which they derived. A pairwise comparison differentially expressed genes (DEGs) revealed no less than half shared DEGs...
Though pleiotropy, which refers to the phenomenon of a gene affecting multiple traits, has long played central role in genetics, development, and evolution, estimation number pleiotropy components remains hard mission accomplish. In this paper, we report newly developed software package, Genepleio, estimate effective from phylogenetic analysis protein sequences. Since can be interpreted as minimum gene, it is used play reference for many empirical measures. This work would facilitate our...
ABSTRACT Traditionally, preimplantation genetic testing (PGT) for in vitro fertilization (IVF) requires invasive trophectoderm (TE) biopsy, which might be detrimental to the embryo. Recently proposed non-invasive PGT (ni-PGT) utilizing cell-free DNA from spent embryo culture medium (SCM) also faces serious challenges accuracy, especially monogenic diseases (niPGT-M), due trace content, maternal cell contamination, and high Allele Drop-Out (ADO) rates. In this study, an improved linear...
Abstract Although gene/genome duplications in the early stage of vertebrates have been thought to provide major resources raw genetic materials for evolutionary innovations, it is unclear whether they continuously contribute evolution morphological complexity during course vertebrate evolution, such as from two heart chambers (fishes) four (mammals and birds). We addressed this issue by our RNA‐Seq experiments combined with published data, using 13 one invertebrate (sea squirt, an outgroup)....
Abstract Side effects from targeted drugs is a serious concern. One reason the nonselective binding of drug to unintended proteins such as its paralogs, which are highly homologous in sequences and exhibit similar structures drug-binding pockets. In this study, we analyzed amino acid residues with type-II functional divergence, i.e., sites that conserved sequence constraints but differ physicochemical properties between identify targetable differences two paralogs. We paralogous protein...
ABSTRACT Human genes exhibit different effects on fitness in cancer and normal cells. Here, we present an evolutionary approach to measure the selection pressure human genes, using well-known ratio of nonsynonymous synonymous substitution rate both genomes ( C N /C S ) populations p /p ). A new mutation-profile-based method that adopts sample-specific mutation profiles instead conventional models was developed. We found cancer-specific is quite from at species population levels. Both...