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Identification of cell cycle-related regulatory motifs using a kernel canonical correlation analysis

Identification of cell cycle-related regulatory motifs using...

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8th International Conference on Bioinformatics: Computational Biology, InCoB 2009

作者： Rhee, Je-Keun Joung, Je-Gun Chang, Jeong-Ho Fei, Zhangjun Zhang, Byoung-Tak Graduate Program in Bioinformatics Seoul National University Seoul 151-744 Korea Republic of Seoul National University Seoul 151-744 Korea Republic of Boyce Thompson Institute for Plant Research Cornell University Ithaca NY 14853 United States Konan Technology Inc. Seoul 135-080 Korea Republic of USDA Robert W. Holley Center for Agriculture and Health Ithaca NY 14853 United States School of Computer Science and Engineering Seoul National University Seoul 151-744 Korea Republic of

Background: Gene regulation is a key mechanism in higher eukaryotic cellular processes. One of the major challenges in gene regulation studies is to identify regulators affecting the expression of their target genes in specific biological processes. Despite their importance, regulators involved in diverse biological processes still remain largely unrevealed. In the present study, we propose a kernel-based approach to efficiently identify core regulatory elements involved in specific biological processes using gene expression profiles. Results: We developed a framework that can detect correlations between gene expression profiles and the upstream sequences on the basis of the kernel canonical correlation analysis (kernel CCA). Using a yeast cell cycle dataset, we demonstrated that upstream sequence patterns were closely related to gene expression profiles based on the canonical correlation scores obtained by measuring the correlation between them. Our results showed that the cell cycle-specific regulatory motifs could be found successfully based on the motif weights derived through kernel CCA. Furthermore, we identified co-regulatory motif pairs using the same framework. Conclusion: Given expression profiles, our method was able to identify regulatory motifs involved in specific biological processes. The method could be applied to the elucidation of the unknown regulatory mechanisms associated with complex gene regulatory processes. © 2012 BioMed Central Ltd .

关键词： Gene expression

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Comparison of Different Approaches to ICP Dominated Pulse Extraction

Comparison of Different Approaches to ICP Dominated Pulse Ex...

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International Conference on Bioinformatics and Biomedical Engineering (ICBBE)

作者： Peng Xu Shaozhi Wu Shadnaz Asgari Magdalena Kasprowicz Marvin Bergsneider Xiao Hu Center of Neuroinformatics School of Life Science and Technology University of Electronic Science and Technology Chengdu China Neural Systems and Dynamics Laboratory Department of Neurosurgery the David Geffen School of Medicine University of California Los Angeles USA School of Computer Science and Engineering University of Electronic Science and Technology Chengdu China Biomedical Engineering Graduate Program Henry Samueli School of Engineering and Applied Science University of California Los Angeles USA University of California Los Angeles Los Angeles CA US

Changes of ICP waveform morphology are characterized with different patients' states like hypertension, hydrocephalus and traumatic brain injury etc. Morphological clustering and analysis of ICP pulse (MOCAIP) approach is recently developed to extract ICP morphology feature, in which hierarchical clustering is used to extract the dominated pulse. In this paper, we evaluate the feasibility of using principle component analysis (PCA) and independent component analysis (ICA) to extract dominated pulse. The comparative study among clustering, PCA and ICP based approaches shows that PCA approach may be an alternative of clustering approach to extract dominated pulse in a faster fashion when dataset is of large size.

关键词： Independent component analysis Morphology Principal component analysis Biomedical engineering Feature extraction Electrocardiography Tellurium Hypertension Data mining Laboratories

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Assembly of CdSeS(ZnS) quantum dots in langmuir films with tertiary alkyl phosphine ligands

Assembly of CdSeS(ZnS) quantum dots in langmuir films with t...

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Nanotechnology - General - 214th ECS Meeting/PRiME 2008

作者： Giles, Alexander J. Pagan, J. Patel, K. Stokes, E.B. Nanoscale Science Graduate Program Department of Chemistry University of North Carolina at Charlotte 9201 University City Boulevard Charlotte NC 28223 United States Dot Metrics Technologies Charlotte Research Institute University of North Carolina at Charlotte 9201 University City Boulevard Charlotte NC 28223 United States Department of Electrical and Computer Engineering University of North Carolina at Charlotte 9201 University City Boulevard Charlotte NC 28223 United States Center for Optoelectronics and Optical Communications University of North Carolina al Charlotte 9201 University City Boulevard Charlotte NC 28223 United States

ISBN: (纸本)9781615672998

The focus of this paper is to describe studies on pre-prepared hydrophobic CdSeS(ZnS) quantum dots (QDs) at the air-water interface. Surface pressure-area (π-A) isotherms were extensively studied using QDs capped with either trioclylphosphine oxide or triethylphosphine oxide. The role of these two different ligands on monolayer behavior and thin film quality has been investigated using the Langmuir-Blodgett (LB) technique. The thin films were characterized by scanning electron microscopy (SEM), fluorescence spectroscopy, and UV-vis spectroscopy. ©The Electrochemical Society.

关键词： Cadmium compounds

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Technology as excuse for questionable ethics

Technology as excuse for questionable ethics

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作者： Mowshowitz, Abbe Department of Computer Science The City College of New York 138th Street New York NY 10031 United States PhD Program in Computer Science The City University of New York Graduate Center 365 Fifth Avenue New York NY 10016 United States

By endowing technology with the attributes of autonomous agency, human beings are ethically sidelined. Individuals are relieved of responsibility. The suggestion of being in the grip of irresistible forces provides an excuse for rejecting responsibility for oneself and others, thus creating conditions for inappropriate or antisocial behavior. It also impedes the search for solutions to pressing social problems associated with applications of technology. Failure to assign and accept responsibility for decisions to deploy "conventional" technology will inevitably impede our ability to deal with the social and ethical challenges of robotics. © Springer-Verlag London Limited 2007.

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Belief update using graphs

Belief update using graphs

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21th International Florida Artificial Intelligence Research Society Conference, FLAIRS-21

作者： Georgatos, Konstantinos Department of Mathematics and Computer Science John Jay College of Criminal Justice CUNY 445 West 59th Street New York NY 10019 United States PhD Program in Computer Science Graduate Center CUNY 365 Fifth Avenue New York NY 10016 United States

ISBN: (纸本)9781577353652

The purpose of this paper is to introduce a form of update based on the minimization of the geodesic distance on a graph. We provide a characterization of this class using set-theoretic operators and show that such operators bijectively correspond to geodesic metrics. As distance is generated by distinguishability, our framework is appropriate in contexts where distance is generated by threshold, and therefore, when measurement is erroneous. Copyright © 2008, Association for the Advancement of Artificial Intelligence (***). All rights reserved.

关键词： Geodesy

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DLM: A distributed Large Memory System using remote memory swapping over cluster nodes

DLM: A distributed Large Memory System using remote memory s...

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IEEE International Conference on Cluster Computing

作者： Hiroko Midorikawa Motoyoshi Kurokawa Ryutaro Himeno Mitsuhisa Sato Department of Computer and Information Science Seikei University Musashino Tokyo Japan Graduate School of Systems and Information Engineering University of Tsukuba Tennodai Tsukuba Ibaraki Japan Advanced Center of Computing and Communication Wako Saitama Japan Research Program for Computational Science RIKEN Wako Saitama Japan

Emerging 64 bitOSpsilas supply a huge amount of memory address space that is essential for new applications using very large data. It is expected that the memory in connected nodes can be used to store swapped pages efficiently, especially in a dedicated cluster which has a high-speed network such as 10 GbE and Infiniband. In this paper, we propose the distributed large memory system (DLM), which provides very large virtual memory by using remote memory distributed over the nodes in a cluster. The performance of DLM programs using remote memory is compared to ordinary programs using local memory. The results of STREAM, NPB and Himeno benchmarks show that the DLM achieves better performance than other remote paging schemes using a block swap device to access remote memory. In addition to performance, DLM offers the advantages of easy availability and high portability, because it is a user-level software without the need for special hardware. To obtain high performance, the DLM can tune its parameters independently from kernel swap parameters. We also found that DLMpsilas independence of kernel swapping provides more stable behavior.

关键词： Kernel Arrays Memory management Servers Bandwidth Performance evaluation Benchmark testing

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Evolving hypernetwork classifiers for microRNA expression profile analysis

Evolving hypernetwork classifiers for microRNA expression pr...

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2007 IEEE Congress on Evolutionary Computation, CEC 2007

作者： Kim, Sun Kim, Soo-Jin Zhang, Byoung-Tak Center for Bioinformatics Technology Graduate Program in Bioinformatics Seoul National University Seoul 151-742 Korea Republic of School of Computer Science and Engineering Seoul National University Seoul 151-744 Korea Republic of

ISBN: (纸本)1424413400

High-throughput microarrays inform us on different outlooks of the molecular mechanisms underlying the function of cells and organisms. While computational analysis for the microarrays show good performance, it is still difficult to infer modules of multiple co-regulated genes. Here, we present a novel classification method to identify the gene modules associated with cancers from microarray data. The proposed approach is based on 'hypernetworks', a hypergraph model consisting of vertices and weighted hyperedges. The hypernetwork model is inspired by biological networks and its learning process is suitable for identifying interacting gene modules. Applied to the analysis of microRNA (miRNA) expression profiles on multiple human cancers, the hypernetwork classifiers identified cancer-related miRNA modules. The results show that our method performs better than decision trees and naive Bayes. The biological meaning of the discovered miRNA modules has been examined by literature search. © 2007 IEEE.

关键词： Microarrays

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An information theoretic framework for eukaryotic gradient sensing 19

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20th Annual Conference on Neural Information Processing Systems, NIPS 2006

作者： Kimmel, Joseph M. Salter, Richard M. Thomas, Peter J. Computer Science Program Oberlin College Oberlin OH 44074 United States Department of Mathematics Biology and Cognitive Science Case Western Reserve University Cleveland OH 44106 United States Computational Neuroscience Graduate Program University of Chicago United States Center for Computation and Modeling United States

ISBN: (纸本)9780262195683

Chemical reaction networks by which individual cells gather and process information about their chemical environments have been dubbed "signal transduction" networks. Despite this suggestive terminology, there have been few attempts to analyze chemical signaling systems with the quantitative tools of information theory. Gradient sensing in the social amoeba Dictyostelium discoideum is a well characterized signal transduction system in which a cell estimates the direction of a source of diffusing chemoattractant molecules based on the spatiotemporal sequence of ligand-receptor binding events at the cell membrane. Using Monte Carlo techniques (MCell) we construct a simulation in which a collection of individual ligand particles undergoing Brownian diffusion in a three-dimensional volume interact with receptors on the surface of a static amoeboid cell. Adapting a method for estimation of spike train entropies described by Victor (originally due to Kozachenko and Leonenko), we estimate lower bounds on the mutual information between the transmitted signal (direction of ligand source) and the received signal (spatiotemporal pattern of receptor binding/unbinding events). Hence we provide a quantitative framework for addressing the question: how much could the cell know, and when could it know it? We show that the time course of the mutual information between the cell's surface receptors and the (unknown) gradient direction is consistent with experimentally measured cellular response times. We find that the acquisition of directional information depends strongly on the time constant at which the intracellular response is filtered.

关键词： Ligands

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Advances in Discrete Tomography and Its Applications 1

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丛书名： Applied and Numerical Harmonic Analysis

2007年

作者： Gabor T. Herman Attila Kuba

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Decision fusion of circulating markers for breast cancer detection in premenopausal women

Decision fusion of circulating markers for breast cancer det...

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7th IEEE International Conference on Bioinformatics and Bioengineering, BIBE

作者： Jesneck, Jonathan L. Mukherjee, Sayan Nolte, Loren W. Lokshin, Anna E. Marks, Jeffrey R. Lo, Joseph Department of Biomedical Engineering Department of Statistical Science Computational Biology and Bioinformatics Program Duke Advanced Imaging Labs. Institute for Genome Sciences and Policy Department of Computer Science Duke University Department of Electrical and Computer Engineering Division of Hematology/Oncology University of Pittsburgh School of Medicine University of Pittsburgh Cancer Institute Pittsburgh PA 15213 United States Department of Experimental Surgery Duke University Medical Center Medical Physics Graduate Program Duke University Durham NC 27708 United States

ISBN: (纸本)1424415098

Current mammographic screeningfor breast cancer is less effective for younger women. To complement mammography for premenopausal women, we investigated the feasibility screening test using 98 blood serum proteins. Because the data set was very noisy and contained only weak features, we used a classifier designed for noisy data: decision fusion. Decision fusion outperformed both a support vector machine (SVM) and linear regression with forward stepwise feature selection on all three two-class classification tasks: normal tissue vs. cancer, normal tissue vs. benign lesions, and benign lesions vs. cancer. Decision fusion detected cancer moderately well (AUC=0.84 on normal vs. cancer), demonstrating promise as a screening tool. Decision fusion also detected benign lesions similarly well (AUC=0.83 on normal vs. benign lesions) and was the only classifier to achieve any success in separating benign from malignant lesions (AUC=0.64 on benign vs. cancer). The classification results suggest that the assayed proteins are more indicative of a secondary effect, such as immune response, rather than specific for breast cancer. In conclusion, the decision fusion classifier demonstrated some promise in detecting breast lesions and outperformed other classifiers, especially for the very noisy classification problem of distinguishing benign from malignant lesions. ©2007 IEEE.

关键词： Tissue

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