A5031286769- Genomics and Chromatin Dynamics
- Epigenetics and DNA Methylation
- RNA modifications and cancer
- RNA and protein synthesis mechanisms
- Genomics and Phylogenetic Studies
- RNA Research and Splicing
- MicroRNA in disease regulation
- Chromosomal and Genetic Variations
- CRISPR and Genetic Engineering
- Hedgehog Signaling Pathway Studies
- Cancer-related molecular mechanisms research
- Genetics, Bioinformatics, and Biomedical Research
- FOXO transcription factor regulation
- Bioinformatics and Genomic Networks
- Renal and related cancers
- Phytochemistry and Biological Activities
- RNA Interference and Gene Delivery
- Cancer-related gene regulation
- Circular RNAs in diseases
- Gene expression and cancer classification
- Glioma Diagnosis and Treatment
- Pluripotent Stem Cells Research
- Machine Learning in Bioinformatics
- Molecular Biology Techniques and Applications
- Chromatin Remodeling and Cancer
The University of Texas at Dallas
2016-2025
The University of Texas Southwestern Medical Center
2025
Center for Systems Biology
2015-2024
Soochow University
2023
Suzhou Research Institute
2023
Guangdong University of Foreign Studies
2020-2021
Shanghai Eighth People Hospital
2013
Cold Spring Harbor Laboratory
2002-2011
Tsinghua University
2007-2011
Shanghai Drug Administration
2011
Methods for the direct detection of copy number variation (CNV) genome-wide have become effective instruments identifying genetic risk factors disease. The application next-generation sequencing platforms to studies promises improve sensitivity detect CNVs as well inversions, indels, and SNPs. New computational approaches are needed systematically these variants from genome sequence data. Existing sequence-based CNV primarily based on paired-end read mapping (PEM) reported previously by...
Dicer is an essential component of RNA interference (RNAi) pathways, which have broad functions in gene regulation and genome organization. Probing the consequences tissue-restricted loss mice indicates a critical role for during meiosis female germline. Mouse oocytes lacking arrest I with multiple disorganized spindles severe chromosome congression defects. Oogenesis early development are times significant post-transcriptional regulation, controlled mRNA storage, translation, degradation....
Identifying the downstream targets of microRNAs (miRNAs) is essential to understanding cellular regulatory networks. We devised a direct biochemical method for miRNA target discovery that combined RNA-induced silencing complex (RISC) purification with microarray analysis bound mRNAs. Because miR-124a have been analyzed, we chose it as our model. honed approach both by examining determinants stable binding between RISC and synthetic RNAs in vitro determining dependency repression...
Transcriptional factors (TFs) and many of their target genes are involved in gene regulation at the level transcription. To decipher regulatory networks (GRNs) we require a comprehensive accurate knowledge transcriptional elements. TRED (Author Webpage) was designed as resource for function studies. It collects mammalian cis- trans-regulatory elements together with experimental evidence. All were mapped on to assembled genomes. In this new release, included total 36 TF families cancer....
Abstract Background Second-generation sequencing has the potential to revolutionize genomics and impact all areas of biomedical science. New technologies will make re-sequencing widely available for such applications as identifying genome variations or interrogating oligonucleotide content a large sample ( e.g . ChIP-sequencing). The increase in speed, sensitivity availability technology brings demand advances computational perform associated analysis tasks. Solexa/Illumina 1G sequencer can...
It is now possible to perform whole-genome shotgun sequencing as well capture of specific genomic regions for extinct organisms. However, targeted resequencing large parts nuclear genomes has yet be demonstrated ancient DNA. Here we show that hybridization on microarrays can successfully recover more than a megabase target from Neandertal DNA even in the presence ~99.8% microbial Using this approach, have sequenced ~14,000 protein-coding positions inferred changed human lineage since last...
Thermoanaerobacter tengcongensis is a rod-shaped, gram-negative, anaerobic eubacterium that was isolated from freshwater hot spring in Tengchong, China. Using whole-genome-shotgun method, we sequenced its 2,689,445-bp genome an isolate, MB4 T (Genbank accession no. AE008691 ). The encodes 2588 predicted coding sequences (CDS). Among them, 1764 (68.2%) are classified according to homology other documented proteins, and the rest, 824 CDS (31.8%), functionally unknown. One of interesting...
DNA methylation stabilizes developmentally programmed gene expression states. Aberrant is associated with disease progression and a common feature of cancer genomes. Presently, few methods enable quantitative, large-scale, single-base resolution mapping states in desired regions complex mammalian genome. Here, we present an approach that combines array-based hybrid selection massively parallel bisulfite sequencing to profile genomic spanning hundreds thousands bases. This single molecule...
Epigenetic effects in mammals depend largely on heritable genomic methylation patterns. We describe a computational pattern recognition method that is used to predict the landscape of human brain DNA. This can be applied both CpG islands and non-CpG island regions. It computes propensity for an 800-bp region centered dinucleotide based specific sequence features within region. tested several classifiers classification performance, including K means clustering, linear discriminant analysis,...
Abstract Summary: We report on a major new version of the RMAP software for mapping reads from short-read sequencing technology. General improvements to accuracy and space requirements are included, along with novel functionality. Included in package tools paired-end reads, using more sophisticated use quality scores, collecting ambiguous locations bisulfite-treated reads. Availability: The applications described this note available download at http://www.cmb.usc.edu/people/andrewds/rmap...
Active transfer of a transcription factor between plant cells is required for stem cell maintenance.
Embryonic stem cells (ESCs) and induced pluripotent (iPSCs) efficiently generate all embryonic cell lineages but rarely extraembryonic types. We found that microRNA miR-34a deficiency expands the developmental potential of mouse cells, yielding both strongly inducing MuERV-L (MERVL) endogenous retroviruses, similar to what is seen with features totipotent two-cell blastomeres. restricts acquisition expanded fate in it represses MERVL expression through transcriptional regulation, at least...
Abstract Adenocarcinoma (ADC) and squamous cell carcinoma (SqCC) are the two predominant subtypes of non-small lung cancer (NSCLC) distinct in their histological, molecular clinical presentation. However, metabolic signatures specific to individual NSCLC remain unknown. Here, we perform an integrative analysis human tumour samples, patient-derived xenografts, murine model NSCLC, lines The Cancer Genome Atlas (TCGA) reveal a markedly elevated expression GLUT1 glucose transporter SqCC, which...