XIAOBO contact ZHOU
Affiliation: The Methodist Hospital
- A novel cell segmentation method and cell phase identification using Markov modelXiaobo Zhou
The Methodist Hospital Research Institute, Weill Medical College, Cornell University, Houston, TX 77030, USA
IEEE Trans Inf Technol Biomed 13:152-7. 2009..Using the context information of time-lapse data, the phases of cell nuclei are identified accurately via a Markov model. Experimental results show that the proposed system is effective for nuclei segmentation and phase identification...
- Drug inhibition profile prediction for NFκB pathway in multiple myelomaHuiming Peng
Department of Radiology, The Methodist Hospital Research Institute and Weill Cornell Medical College, Houston, Texas, United States of America
PLoS ONE 6:e14750. 2011....
- Prediction of S-glutathionylation sites based on protein sequencesChenglei Sun
Institute of Systems Biology, Shanghai University, Shanghai, China
PLoS ONE 8:e55512. 2013..879 in 5-fold cross-validation, which demonstrates the predictive power of our proposed method. The datasets used in this work are available at http://csb.shu.edu.cn/SGDB...
- Reversible jump MCMC approach for peak identification for stroke SELDI mass spectrometry using mixture modelYuan Wang
Center for Biotechnology and Informatics, The Methodist Hospital Research Institute, and Department of Radiology, The Methodist Hospital, Weill Cornell Medical College, Houston, TX 77030, USA
Bioinformatics 24:i407-13. 2008....
- Pattern-selection based power analysis and discrimination of low- and high-grade myelodysplastic syndromes study using SNP arraysXiaorong Yang
Department of Radiology, The Methodist Hospital Research Institute, Weill Medical College, Cornell University, Center for Biotechnology and Informatics, Houston, Texas, United States of America
PLoS ONE 4:e5054. 2009....
- Computer-assisted lip diagnosis on Traditional Chinese Medicine using multi-class support vector machinesFufeng Li
Laboratory of Information Access and Synthesis of TCM Four Diagnosis, Shanghai University of Traditional Chinese Medicine, Shanghai, 201203, China
BMC Complement Altern Med 12:127. 2012..In this paper, we design a computer-assisted classification model to provide an automatic and quantitative approach for the diagnosis of TCM based on the lip images...
- Multi-scale agent-based brain cancer modeling and prediction of TKI treatment response: incorporating EGFR signaling pathway and angiogenesisXiaoqiang Sun
Department of Radiology, The Methodist Hospital Research Institute, Weil Cornell Medical College, Houston, TX 77030, USA
BMC Bioinformatics 13:218. 2012....
- A computational model for compressed sensing RNAi cellular screeningHua Tan
Department of Radiology, The Methodist Hospital Research Institute, Weill Medical College of Cornell University, Houston, TX 77030, USA
BMC Bioinformatics 13:337. 2012..The traditional RNAi screening scheme, in which one siRNA is designed to knockdown one specific mRNA target, needs a large library of siRNAs and turns out to be time-consuming and expensive...
- Cancer bioinformatics: detection of chromatin states, SNP-containing motifs, and functional enrichment modulesXiaobo Zhou
Center for Bioinformatics and Systems Biology, Wake Forest University School of Medicine, Winston Salem, NC 27103, USA
Chin J Cancer 32:153-4. 2013....
- A system mathematical model of a cell-cell communication network in amyotrophic lateral sclerosisHongwei Shao
Methodist Hospital Research Institute, 6670 Bertner Avenue, Houston, USA
Mol Biosyst 9:398-406. 2013..In the future, if we combine the side effects of different therapies, this model can be used to optimize the therapeutic strategies so that they can effectively improve survival rates and quality of life for patients with ALS...
- Developing a multiscale, multi-resolution agent-based brain tumor model by graphics processing unitsLe Zhang
Department of Mathematical Sciences, Michigan Technological University, Houghton, MI 49931, USA
Theor Biol Med Model 8:46. 2011..Therefore, the new model has great potential for simulating and predicting real-time GBM progression, if real experimental data are incorporated...
- Genomic profiling of plasmablastic lymphoma using array comparative genomic hybridization (aCGH): revealing significant overlapping genomic lesions with diffuse large B-cell lymphomaChung Che Chang
Department of Pathology, The Methodist Hospital and The Methodist Hospital Research Institute, Houston TX, USA
J Hematol Oncol 2:47. 2009..The goal of the current study was to evaluate the genetic similarities and differences among PL, DLBCL (AIDS-related and non AIDS-related) and PCM using array-based comparative genomic hybridization...
- An information-flow-based model with dissipation, saturation and direction for active pathway inferenceXianwen Ren
Academy of Mathematics and Systems Science, Chinese Academy of Sciences, 100190, Beijing, China
BMC Syst Biol 4:72. 2010..Previous methods design different heuristics but do not describe explicitly the behaviours of the information flow...
- Semi-supervised drug-protein interaction prediction from heterogeneous biological spacesZheng Xia
Bioinformatics and Bioengineering Program, The Methodist Hospital Research Institute, Weill Medical College, Cornell University, Houston, TX 77030, USA
BMC Syst Biol 4:S6. 2010..Furthermore, our semi-supervised learning method integrates known drug-protein interaction network information as well as chemical structure and genomic sequence data...
- Integrative analysis of next generation sequencing for small non-coding RNAs and transcriptional regulation in Myelodysplastic SyndromesDominik Beck
Bioengineering and Bioinformatics Program, Department of Pathology, The Methodist Hospital Research Institute, Weill Cornell Medical College, Houston, TX, 77030, USA
BMC Med Genomics 4:19. 2011..Little is known about small regulatory RNAs and how they contribute to pathogenesis, progression and transcriptome changes in MDS...
- Transcriptional profiling reveals developmental relationship and distinct biological functions of CD16+ and CD16- monocyte subsetsPetronela Ancuta
CRCHUM, Universite de Montreal, INSERM Unit 743, Montreal, Quebec, Canada
BMC Genomics 10:403. 2009..CD16+ Mo produce pro-inflammatory cytokines and are expanded in certain inflammatory conditions including sepsis and HIV infection...
- High content image analysis for human H4 neuroglioma cells exposed to CuO nanoparticlesFuhai Li
The Center for Biomedical Informatics, The Methodist Hospital Research Institute, Weill Cornell Medical College, Houston, TX 77030, USA
BMC Biotechnol 7:66. 2007..This system has been proved to be an essential tool in our study...
- NSMAP: a method for spliced isoforms identification and quantification from RNA-SeqZheng Xia
Department of Radiology, The Methodist Hospital Research Institute, Houston, TX 77030, USA
BMC Bioinformatics 12:162. 2011..Novel study on isoform inference and estimation purely from RNA-Seq without annotation information is desirable...
- Using iterative cluster merging with improved gap statistics to perform online phenotype discovery in the context of high-throughput RNAi screensZheng Yin
Center for Bioinformatics, The Methodist Hospital Research Institute and Weill Cornell College of Medicine, 6565 Fannin Street, Houston, TX 77030, USA
BMC Bioinformatics 9:264. 2008..Arbitrarily extracted information causes biased analysis, while combining the complete existing datasets with each new image is intractable in high-throughput screens...
- A semi-supervised learning approach to predict synthetic genetic interactions by combining functional and topological properties of functional gene networkZhu Hong You
Intelligent Computing Lab, Institute of Intelligent Machine, Chinese Academy of Science, P O Box 1130, Hefei, Anhui 230031, China
BMC Bioinformatics 11:343. 2010..Therefore, an accurate computational approach to predict genetic interaction is highly desirable, and such methods have the potential of alleviating the bottleneck on experiment design...
- Conditional random pattern model for copy number aberration detectionFuhai Li
Center for Bioengineering and Informatics, Department of Radiology, The Methodist Hospital Research Institute, Weill Cornell Medical College, Houston, TX 77030, USA
BMC Bioinformatics 11:200. 2010..Thus, more sophisticated statistical models are needed to make the CNAs detection, using the low SNR signals, more robust and reliable...
- Predicting enzyme targets for cancer drugs by profiling human metabolic reactions in NCI-60 cell linesLimin Li
Center for Biotechnology and Informatics, The Methodist Hospital Research Institute and Department of Radiology, The Methodist Hospital, Weill Cornell Medical College, Houston, TX 77030, USA
BMC Bioinformatics 11:501. 2010..Drugs can influence the whole metabolic system by targeting enzymes which catalyze metabolic reactions. The existence of interactions between drugs and metabolic reactions suggests a potential way to discover drug targets...
- Identification of biomarkers for risk stratification of cardiovascular events using genetic algorithm with recursive local floating searchXiaobo Zhou
Center for Biotechnology and Informatics, The Methodist Hospital Research Institute and Cornell University, Houston, TX 77030, USA
Proteomics 9:2286-94. 2009..The method has been applied to SELDI/MALDI MS datasets to discover an optimized panel of protein biomarkers to distinguish disease from control...