Guoqiang Yu

Bio: Guoqiang Yu is an academic researcher from Virginia Tech. The author has contributed to research in topics: Copy number analysis & Computer science. The author has an hindex of 23, co-authored 106 publications receiving 2781 citations. Previous affiliations of Guoqiang Yu include Tsinghua University & Johns Hopkins University.

A bayesian network approach to traffic flow forecasting

Abstract: A new approach based on Bayesian networks for traffic flow forecasting is proposed. In this paper, traffic flows among adjacent road links in a transportation network are modeled as a Bayesian network. The joint probability distribution between the cause nodes (data utilized for forecasting) and the effect node (data to be forecasted) in a constructed Bayesian network is described as a Gaussian mixture model (GMM) whose parameters are estimated via the competitive expectation maximization (CEM) algorithm. Finally, traffic flow forecasting is performed under the criterion of minimum mean square error (mmse). The approach departs from many existing traffic flow forecasting models in that it explicitly includes information from adjacent road links to analyze the trends of the current link statistically. Furthermore, it also encompasses the issue of traffic flow forecasting when incomplete data exist. Comprehensive experiments on urban vehicular traffic flow data of Beijing and comparisons with several other methods show that the Bayesian network is a very promising and effective approach for traffic flow modeling and forecasting, both for complete data and incomplete data

Copy number analysis indicates monoclonal origin of lethal metastatic prostate cancer

Abstract: Many studies have shown that primary prostate cancers are multifocal and are composed of multiple genetically distinct cancer cell clones. Whether or not multiclonal primary prostate cancers typically give rise to multiclonal or monoclonal prostate cancer metastases is largely unknown, although studies at single chromosomal loci are consistent with the latter case. Here we show through a high-resolution genome-wide single nucleotide polymorphism and copy number survey that most, if not all, metastatic prostate cancers have monoclonal origins and maintain a unique signature copy number pattern of the parent cancer cell while also accumulating a variable number of separate subclonally sustained changes. We find no relationship between anatomic site of metastasis and genomic copy number change pattern. Taken together with past animal and cytogenetic studies of metastasis and recent single-locus genetic data in prostate and other metastatic cancers, these data indicate that despite common genomic heterogeneity in primary cancers, most metastatic cancers arise from a single precursor cancer cell. This study establishes that genomic archeology of multiple anatomically separate metastatic cancers in individuals can be used to define the salient genomic features of a parent cancer clone of proven lethal metastatic phenotype.

Developmental heterogeneity of microglia and brain myeloid cells revealed by deep single-cell RNA sequencing

Abstract: Summary Microglia are increasingly recognized for their major contributions during brain development and neurodegenerative disease. It is currently unknown if these functions are carried out by subsets of microglia during different stages of development and adulthood or within specific brain regions. Here, we performed deep single-cell RNA sequencing (scRNA-seq) of microglia and related myeloid cells sorted from various regions of embryonic, postnatal, and adult mouse brains. We found that the majority of adult microglia with homeostatic signatures are remarkably similar in transcriptomes, regardless of brain region. By contrast, postnatal microglia represent a more heterogeneous population. We discovered that postnatal white matter-associated microglia (WAM) are strikingly different from microglia in other regions and express genes enriched in degenerative disease-associated microglia. These postnatal WAM have distinct amoeboid morphology, are metabolically active, and phagocytose newly formed oligodendrocytes. This scRNA-seq atlas will be a valuable resource for dissecting innate immune functions in health and disease. Highlights Myeloid scRNA-seq atlas across brain regions and developmental stages Limited transcriptomic heterogeneity of homeostatic microglia in the adult brain Phase-specific gene sets of proliferating microglia along cell cycle pseudotime Phagocytic postnatal white matter-associated microglia sharing DAM gene signatures

“Bioinformatics” 특집을 내면서

Abstract: BIOE 402. Medical Technology Assessment. 2 or 3 hours. Bioentrepreneur course. Assessment of medical technology in the context of commercialization. Objectives, competition, market share, funding, pricing, manufacturing, growth, and intellectual property; many issues unique to biomedical products. Course Information: 2 undergraduate hours. 3 graduate hours. Prerequisite(s): Junior standing or above and consent of the instructor.

The somatic genomic landscape of glioblastoma

Abstract: We describe the landscape of somatic genomic alterations based on multidimensional and comprehensive characterization of more than 500 glioblastoma tumors (GBMs). We identify several novel mutated genes as well as complex rearrangements of signature receptors, including EGFR and PDGFRA. TERT promoter mutations are shown to correlate with elevated mRNA expression, supporting a role in telomerase reactivation. Correlative analyses confirm that the survival advantage of the proneural subtype is conferred by the G-CIMP phenotype, and MGMT DNA methylation may be a predictive biomarker for treatment response only in classical subtype GBM. Integrative analysis of genomic and proteomic profiles challenges the notion of therapeutic inhibition of a pathway as an alternative to inhibition of the target itself. These data will facilitate the discovery of therapeutic and diagnostic target candidates, the validation of research and clinical observations and the generation of unanticipated hypotheses that can advance our molecular understanding of this lethal cancer.

Tumour evolution inferred by single-cell sequencing

Abstract: Genomic analysis provides insights into the role of copy number variation in disease, but most methods are not designed to resolve mixed populations of cells. In tumours, where genetic heterogeneity is common, very important information may be lost that would be useful for reconstructing evolutionary history. Here we show that with flow-sorted nuclei, whole genome amplification and next generation sequencing we can accurately quantify genomic copy number within an individual nucleus. We apply single-nucleus sequencing to investigate tumour population structure and evolution in two human breast cancer cases. Analysis of 100 single cells from a polygenomic tumour revealed three distinct clonal subpopulations that probably represent sequential clonal expansions. Additional analysis of 100 single cells from a monogenomic primary tumour and its liver metastasis indicated that a single clonal expansion formed the primary tumour and seeded the metastasis. In both primary tumours, we also identified an unexpectedly abundant subpopulation of genetically diverse 'pseudodiploid' cells that do not travel to the metastatic site. In contrast to gradual models of tumour progression, our data indicate that tumours grow by punctuated clonal expansions with few persistent intermediates.

Traffic Flow Prediction With Big Data: A Deep Learning Approach

Abstract: Accurate and timely traffic flow information is important for the successful deployment of intelligent transportation systems. Over the last few years, traffic data have been exploding, and we have truly entered the era of big data for transportation. Existing traffic flow prediction methods mainly use shallow traffic prediction models and are still unsatisfying for many real-world applications. This situation inspires us to rethink the traffic flow prediction problem based on deep architecture models with big traffic data. In this paper, a novel deep-learning-based traffic flow prediction method is proposed, which considers the spatial and temporal correlations inherently. A stacked autoencoder model is used to learn generic traffic flow features, and it is trained in a greedy layerwise fashion. To the best of our knowledge, this is the first time that a deep architecture model is applied using autoencoders as building blocks to represent traffic flow features for prediction. Moreover, experiments demonstrate that the proposed method for traffic flow prediction has superior performance.