The proteinprotein interaction map of helicobacter pylori. Rui zhang, phd, ms institute for health informatics. Oxford university press is a department of the university of oxford. Recent largescale investigations of proteinprotein interactions using such techniques as twohybrid systems, mass spectrometry, and protein microarrays have enriched the available protein interaction data and facilitated the construction of integrated protein.
Guangyong zheng, yaochen xu, xiujun zhang, zhiping liu, zhuo. A gene regulatory network grn represents interactions of genes inside a cell or tissue, in which vertexes and edges stand for genes and their regulatory interactions respectively. Probability and statistics are basic to bioinformatics, and this chapter begins with the fundamentals including many classical distributions including the binomial, poisson, and normal. Zhang editors basics of bioinformatics lecture notes of the graduate summer school on bioinformatics of china 123. Advancing methods for monitoring of environmental media e. In the proposed algorithm, the noisy regulations with low pairwise correlations are first removed by using mi, and the redundant regulations from indirect. Yeast as an experimental system for studying evolution. Speedup of 10x 50x was observed for simulated scalefree networks and real world protein interaction and gene coexpression networks. See the complete profile on linkedin and discover bos connections and. Inferring gene regulatory networks from gene expression. Inferring gene regulatory networks from gene expression data by path consistency algorithm based on conditional mutual informationj. Exosomal mir5a derived from human amnion mesenchymal stem.
Here, we present a software package for gene regulatory network. Zhang, xiujun, xingming zhao, kun he, le lu, yongwei cao, jingdong liu, jinkao hao, zhiping liu, and luonan chen. I am a member of technical staff mts software engineer in amd. How to promote wound healing is an urgent problem to be solved in clinical practice, and it is also the focus of longterm research by scholars worldwide. By xiujun zhang, xingming zhao, kun he, le lv, yongwei cao, jingdong liu, jinkao hao, zhiping liu and luonan chen. The migration area was calculated as % original gap area. Early diagnosis of complex diseases by molecular biomarkers. The gap area was measured and recorded and then compared to the initial gap size at 0 h by imagepro plus 6. This makes bispin and bfastgap useful additions to read mapping software. The research areas of the lab are computational genomics and bioinformatics, with a strong focus on mining and interpreting largescale genomic data ie, bigdata science. View bo zhangs profile on linkedin, the worlds largest professional community.
Chapter 2, basic statistics for bioinformatics, presents important material for the understanding and analysis of data. Keyue ding, jing zhang, kaixin zhou, yan shen, xuegong zhang, htsnper1. Biomedical named entity recognition with domain adaptation. Special issue molecular computing and bioinformatics. The biological themes of our research are centered on the genetic and epigenetic regulations of early development, including neural development and and heart development, and. Xiujun zhang phd genome institute of singapore, singapore. See the complete profile on linkedin and discover zhidongs. Xiujun zhang, keqin liu, zhiping liu, beatrice duval, jeanmichel richer, xingming zhao, jinkao hao, luonan chen. It furthers the universitys objective of excellence in research, scholarship, and education by publishing worldwide. Coeditor, journal of computational biology and bioinformatics, special issue on genome. Student in bioinformatics and systems biology 2009. His research interests include hybrid intelligent systems, neural networks, fuzzy logic, evolutionary computation, yinyang computation, granular computing, kernel machines, bioinformatics, medical informatics, computational web intelligence, data mining, and knowledge discovery. Proceedings of the 27th international conference on genome informatics. Yanqing zhang, phd, is an associate professor of computer science at the georgia state university, atlanta.
This cited by count includes citations to the following articles in scholar. Xiujun zhang, xingming zhao, kun he, le lu, yongwei cao, jingdong liu. In a position weight matrix, each row corresponds to one symbol of the alphabet, e. Reconstruction of gene regulatory networks grns, which explicitly represent the causality of developmental or regulatory process, is of utmost interest and has become a challenging computational problem for understanding the complex regulatory mechanisms in cellular systems. A betamixture quantile normalization method for correcting probe design bias in illumina infinium 450 k dna methylation data.
Key laboratory of systems biology, institute of biochemistry and cell biology, chinese academy of sciences, 320 yueyang road, shanghai, 200031, china. A position weight matrix pwm is a commonly used representation of motifs patterns in biological sequences bengal et al. Editors choice 2014, a nomination for marco ramoni distinguished paper award for translational bioinformatics 2015, and best student papers in american medical informatics association amia annual symposium 2011, medinfo 20, and amia joint summits 2014. Software licensing dme, marsmotif, marsmotifm, scpd. Marlatt vl, martyniuk cj, zhang d, xiong h, watt j, xia x, moon t, trudeau vl. Our group works in the field of computational biology and bioinformatics, applying computer science, mathematics and statistics to practical problems arising from the management and analysis of largescale biological data. The analysis of proteinprotein interactions is fundamental to the understanding of cellular organization, processes, and functions. Cmi2ni is a software for inferring gene regulatory networks from gene expression data. Inferring gene regulatory networks from gene expression data. The package is a greatly improved implementation of our previous pcacmi algorithm. Molecular computing and bioinformatics are two important interdisciplinary sciences that study molecules and computers. Biotechnology has revolutionized the whole field of life and medical science research, and has generated and continue to generate an overwhelmingly large amount of data at an alarmingly fast rate.
Given the small size samples of gene expression data, cmi2ni can not only infer the correct topology of the regulation networks but also. Growing concerns about increasing rates of antibiotic resistance call for expanded and comprehensive global monitoring. Chen zhou, shaowu zhang, fei liu, an ensemble method for reconstructing gene regulatory network with jackknife resampling and arithmetic mean fusion, international journal of data mining and bioinformatics, v. Reconstruction of gene regulatory networks grns, which explicitly represent the causality of developmental or regulatory process, is of utmost interest and has become a challenging computational problem for. Department of computational medicine and bioinformatics department of biological chemistry medical school university of. Their combined citations are counted only for the first article. Zhidong zhang director computational biology verseau. In this work, we present a novel method, namely narromi, to improve the accuracy of grn inference by combining ordinary differential equationbased recursive optimization ro and information theorybased mutual information mi. It was modified based on gistool software written by xiang zhang et al. Conditional mutual inclusive information enables accurate quantification of associations in gene regulatory networks. To display and analyse the interaction data, we developed a software platform composed of a database, a webbased graphical interface layer and. Software engineering institute, east china normal university, 3663 north zhongshan road, shanghai, 200062, china. Migration of fibroblasts was also determined by the transwell assay using an 8. Xiujun zhang, xingming zhao, kun he, le lu, yongwei cao, jingdong liu, jinkao hao, zhiping liu, luonan chen.
Bmc bioinformatics is part of the bmc series which publishes. The zhang lab computational biology and bioinformatics welcome to the zhang lab. Cancerrelated variations and conrresponding annotations can be queried through the webinterface using protein ids in the. The first verison of the software package gpufan gpubased fast analysis of networks includes methods for computing four shortest pathbased centrality metrics on nvidias cuda platform. Xiujun zhang, juan zhao, jinkao hao, xingming zhao, and luonan chen. Dec 23, 2016 software engineering institute, east china normal university, 3663 north zhongshan road, shanghai, 200062, china. Bioinformatics, volume 29, issue 1, january 20, pages 106 1. However, all existing methods of inferring grns from gene expression profiles have their strengths and. A read is counted each time someone views a publication summary such as the title, abstract, and list of authors, clicks on a figure, or views or downloads the fulltext. Homepage of zhenyu xuan cold spring harbor laboratory.
Narromi is a matlab program for inferring gene regulatory networks from gene expression data. Bibliographic content of bioinformatics, volume 29. Fan zhang computational medicine and bioinformatics. Congratulations to fei zhao for publication of jasmonatemediated wound signalling promotes plant regeneration in nature plants. Shihua zhang, daven vasishtan, min xu, maya topf, frank alber. Canprovar is designed to store and display single amino acid alterations including both germline and somatic variations in the human proteome, especially those related to the genesis or development of human cancer based on the published literatures. Machine learning in bioinformatics is an indispensable resource for computer scientists, engineers, biologists, mathematicians, researchers, clinicians, physicians, and medical informaticists. It provides a method to simulate chromatin structure and dynamics, described in plos comp biol. A fast mathematical programming procedure for simultaneous fitting of assembly components into cryoem density maps. Hy jia, y liu, xj zhang, l han, lb du, q tian, yc xu. The above lp model 8 can be solved efficiently by any lp software such as glpk. Growing concerns about increasing rates of antibiotic. Zhang lab translating omics data into biological insights. Exempted from this legal reservation are brief excerpts in connection.
Bmc bioinformatics proceedings of the 27th international. Results here, we present a software package for gene regulatory network reconstruction at a genomic level, in which gene interaction is measured by the conditional mutual information measurement using a parallel computing framework so the package is named cmip. My research interests are highperformance computing, bioinformatics, and cloud computing. Zhang research lab health informatics, data science. Bioinformatics volume 28 number 1 january 1 2012 discovery note systems biology timecourse network analysis reveals tnf. Machine learning in bioinformatics wiley series in. Molecular computing is a branch of computing that uses dna, biochemistry, and molecular biology hardware, instead of traditional siliconbased computer technologies. Guangyong zheng, yaochen xu, xiujun zhang, zhiping liu, zhuo wang, luonan chen and xinguang zhu, cmip. View zhidong zhangs profile on linkedin, the worlds largest professional community. It is a novel method using a new proposed concept of conditional mutual inclusive information cmi2 which can accurately measure direct dependences between genes.
Journal of the american chemical society 1 1, 4041, 2009. Exosomal mir5a derived from human amnion mesenchymal. It is also a valuable reference text for computer science, engineering, and biology courses at the upper undergraduate and graduate levels. Skin wound healing is a complex process involving a number of highly coordinated steps, mainly divided into inflammatory response, epithelialization and wound contraction, collagen deposition, and remodeling. Inferring gene regulatory networks from gene expression data by path consistency algorithm based on conditional mutual information. Leveraging genetic variants for rapid and robust upstream analysis of massive sequence data. Following is a list of software developed by the group for studying genome structures. Autoregulation of estrogen receptor subtypes and gene expression profiling of 17betaestradiol action in the neuroendocrine axis of male goldfish.
I am most interested in the relative roles of chance and necessity in evolution. A novel network control model for identifying personalized driver genes in cancer. This software was designed as a component of data analysis pipeline for protein biomarker discovery. Please explore our website to learn more about our people and our research. Currently, i work on amds open source deep learning library miopen. We develop and use integrative bioinformatics approaches to extract biological meanings from experimental data and generate hypotheses for experimental validation.