Bioinformatic software uses the available information on various identified transcriptional activator or repressorbinding sequences, and scans the 5. Lempicki, systematic and integrative analysis of large gene lists using david bioinformatics resources, nature protocols, vol. The program and supplementary materials are available at. Raine computational methods for subtyping of tumors and their appplications for deciphering tumor heterogeneity shihua zhang statistically supported identification of tumor subtypes. Genomics and molecular structure, function and evolution regular papers. Cancerrelated variations and conrresponding annotations can be queried through the webinterface using. Fa zhang, zhipeng cai, pavel skums, shihua zhang this book constitutes the proceedings of the 14th international conference on bioinformatics research and applications, isbra 2018, held in beijing, china, in june 2018. The main focus of the zhang lab is to develop bioinformatics approaches to predict the threedimensional structures of. See the complete profile on linkedin and discover yutings. Bioinformatics and data science shihua zhangs lab at cas. This book constitutes the proceedings of the 14th international conference on bioinformatics research and applications, isbra 2018, held in beijing, china, in june 2018.
Applied microarray data analysis using r and sas software exploration of the underlying biological mechanisms of disease is useful. About cookies, including instructions on how to turn off cookies if you wish to do so. Welcome to shihua zhang s lab bioinformatics and data science. Association between the tumour necrosis factor308ga polymorphism and chronic obstructive pulmonary disease. Wenwen min, juan liu, fei luo, and shihua zhang b292 construction of signaling networks with incomplete rnai data qiyao wang, yaunfang ren, mahmudul hasan, ahmet ay, and tamer. Shihua zhang, academy of mathematics and systems science, chinese academy of sciences.
Here, the authors develop music, a computational pipeline. 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. List of researchers and developers in bioinformatics omicx. 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. We would like to show you a description here but the site wont allow us. Shihua zhang chinese academy of sciences, beijing cas.
State key laboratory of software engineering, school of computer, wuhan university, wuhan, china. In this study, we proposed an edgegroup sparse pca espca model by incorporating the group structure from a prior gene network into the pca framework for dimension reduction and feature interpretation. Department of electronic engineering, heilongjiang institute of technology, harbin. Specifically, it considers an ensemble of finite mixture models combined with a local false discovery rate fdr for analyzing chipseq data comparing two samples. Shihua zhang is an associate professor of the academy of mathematics and. Predictionbased taxonomic software tools for shotgun metagenomic analysis. Proceedings ieee xplore proceedings online program. An improved greengenes taxonomy with explicit ranks for ecological and evolutionary analyses of bacteria and archaea. View xia zhang s profile on linkedin, the worlds largest professional community.
Edgegroup sparse pca for networkguided high dimensional. Efficient methods for identifying mutated driver pathways in. Discovery of multidimensional modules by integrative analysis of. This volume covers a wide variety of state of the art cancerrelated methods and tools for data analysis and interpretation. Medical research council institute of genetics and molecular medicine. Singlecell crispr screening combines pooled crispr screening with scrnaseq analysis to expand the resolution power of genetic screening. We developed molbiolib to address the need for adaptable nextgeneration sequencing analysis tools. Modelbased understanding of singlecell crispr screening.
One of the main focuses of our lab is to develop computational methods to predict 3dimensional structure of protein molecules from amino acid sequence, and to deduce the biological functions based on the sequencetostructuretofunction paradigm. Bioinformatics oxford academic journals oxford university press. Zhang zhang, beijing institute of genomics, chinese academy of sciences. Zhang editors basics of bioinformatics lecture notes of the graduate summer school on bioinformatics of china 123. Mixture model my biosoftware bioinformatics softwares blog. College of bioinformatics science and technology, harbin medical university. We have implemented the method as a matlab software package, which is available from the supplementary. Senior bioinformatics software engineer agilent technologies. The interests of our lab are within i bioinformatics and computational biology relating to genomics, epigenetics, and network biology, and ii data science relating to machine learning, optimization and statistical models and algorithms. Shihua zhang academy of mathematics and systems science, chinese academy of sciences xianghong zhou. Matrix integrative analysis mia of multiple genomic data. Lecture notes in bioinformatics 10847 subseries of lecture notes in computer science. Mathematical and computational approaches in highthroughput.
Association between the tumour necrosis factor308ga. Sign up for your own profile on github, the best place to host code, manage projects, and build software alongside 40 million developers. We have implemented the method as a matlab software package, which is available from the supplementary data. Principal component analysis pca has been widely used to deal with highdimensional gene expression data. Inferring protein interactions from experimental data by. A novel computational framework for simultaneous integration of multiple types of genomic data to identify micrornagene regulatory modules. Plos computational biology, bmc genomics, bmc bioinformatics, ieee tsp, ieeeacm tcbb and so. Integrative analysis for identifying joint modular patterns of gene. Sign up bioinformatics 2018 edgegroup sparse pca for networkguided high dimensional data analysis. Organization committees 14th international symposium. Bmc bioinformatics is part of the bmc series which publishes subjectspecific journals focused on the needs of individual research communities across all. Shihua zhang, guangdong sky dragon printing ink group co.
Itasser as zhang server and quark were ranked as the top two servers in th communitywide casp experiment for automated protein 3d structure prediction. One of the main challenges when analyzing scrnaseq data is the presence of zeros or dropout events, which may mislead downstream analyses. This list of sequence alignment software is a compilation of software tools and web portals used in pairwise sequence alignment and multiple sequence alignment. The 8th international conference on systems biology isb 2014, organized by chinese academy of sciences and qingdao university was coheld with and the 4th translational bioinformatics conference tbc 2014, in qingdao, china, october 2427, 2014. See structural alignment software for structural alignment of proteins. Bioinformatics software an overview sciencedirect topics. A novel computational framework for simultaneous integration of. Taxonomy my biosoftware bioinformatics softwares blog. Networkregularized sparse logistic regression models for. Itasser server for protein structure and function prediction. By continuing to browse this site you agree to us using cookies as described in about cookies remove maintenance message. The use of general descriptive names, registered names. View yuting tsengs profile on linkedin, the worlds largest professional community. Shihua zhang is board member at guangdong sky dragon printing ink group co ltd.
Singlecell rnasequencing scrnaseq is a recent breakthrough technology, which paves the way for measuring rna levels at single cell resolution to study precise biological functions. Fa zhang ict, china shihua zhang amss, china zhipeng cai gsu, usa pavel skums gsu, usa. Please indicate in your cover letter if this applies to your manuscript. School of software, dalian university of technology, china. Zhang was awarded the ten thousand talent program for young topnotch talent. Request pdf bioinformatics techniques in microarray research. Lecture notes in computer science 10847, springer 2018, isbn 9783319949673.
Bioinformatics, cancer research, plos computational biology, bmc genomics, bmc bioinformatics. Shihua zhang is the author of jian ming han yi ci dian 0. Bioinformatics research and applications 14th international symposium, isbra 2018, beijing, china, june 811, 2018, proceedings. Determining structure and function of protein molecules is a cornerstone of modern biology and medicine. The discovery of mutated driver pathways in cancer. Current bioinformatics aims to publish all the latest and outstanding developments in bioinformatics. Dime differential identification using mixtures ensemble is an ensemble of methods for differential analysis. Genomics and molecular structure, function and evolution. National center for mathematics and interdisciplinary sciences. Comparison of computational methods for imputing single. Chapters were designed to attract a broad readership, ranging from active researchers in computational biology and bioinformatics developers, clinical oncologists, and anticancer drug developers wishing to rationalize their search for new compounds.