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Human genome meeting 2016 : Houston, TX, USA. 28 February - 2 March 2016

Human genomics 2016年第1期10 Suppl 1卷 12页

作者： A. K. Srivastava Y. Wang R. Huang C. Skinner T. Thompson L. Pollard T. Wood F. Luo R. Stevenson R. Polimanti J. Gelernter X. Lin I. Y. Lim Y. Wu A. L. Teh L. Chen I. M. Aris S. E. Soh M. T. Tint J. L. MacIsaac F. Yap K. Kwek S. M. Saw M. S. Kobor M. J. Meaney K. M. Godfrey Y. S. Chong J. D. Holbrook Y. S. Lee P. D. Gluckman N. Karnani A. Kapoor D. Lee A. Chakravarti C. Maercker F. Graf M. Boutros G. Stamoulis F. Santoni P. Makrythanasis A. Letourneau M. Guipponi N. Panousis M. Garieri P. Ribaux E. Falconnet C. Borel S. E. Antonarakis S. Kumar J. Curran J. Blangero S. Chatterjee J. Akiyama D. Auer C. Berrios L. Pennacchio T. R. Donti G. Cappuccio M. Miller P. Atwal A. Kennedy A. Cardon C. Bacino L. Emrick J. Hertecant F. Baumer B. Porter M. Bainbridge P. Bonnen B. Graham R. Sutton Q. Sun S. Elsea Z. Hu P. Wang Y. Zhu J. Zhao M. Xiong David A. Bennett A. Hidalgo-Miranda S. Romero-Cordoba S. Rodriguez-Cuevas R. Rebollar-Vega E. Tagliabue M. Iorio E. D’Ippolito S. Baroni B. Kaczkowski Y. Tanaka H. Kawaji A. Sandelin R. Andersson M. Itoh T. Lassmann Y. Hayashizaki P. Carninci A. R. R. Forrest C. A. Semple E. A. Rosenthal B. Shirts L. Amendola C. Gallego M. Horike-Pyne A. Burt P. Robertson P. Beyers C. Nefcy D. Veenstra F. Hisama R. Bennett M. Dorschner D. Nickerson J. Smith K. Patterson D. Crosslin R. Nassir N. Zubair T. Harrison U. Peters G. Jarvik F. Menghi K. Inaki X. Woo P. Kumar K. Grzeda A. Malhotra H. Kim D. Ucar P. Shreckengast K. Karuturi J. Keck J. Chuang E. T. Liu B. Ji A. Tyler G. Ananda G. Carter H. Nikbakht M. Montagne M. Zeinieh A. Harutyunyan M. Mcconechy N. Jabado P. Lavigne J. Majewski J. B. Goldstein M. Overman G. Varadhachary R. Shroff R. Wolff M. Javle A. Futreal D. Fogelman L. Bravo W. Fajardo H. Gomez C. Castaneda C. Rolfo J. A. Pinto K. C. Akdemir L. Chin S. Patterson C. Statz S. Mockus S. N. Nikolaev X. I. Bonilla L. Parmentier B. King F. Bezrukov G. Kaya V. Zoete V. Seplyarskiy H. Sharpe T. McKee K. Popadin N. Basset-Seguin R. Ben Chaabene M. Andrianova C. Verdan K. Grosdemange O. Sumara M. E JCSRI Greenwood Genetic Center Greenwood USA School of Computing Clemson University Clemson USA Biochemical Genetics Laboratory Greenwood Genetic Center Greenwood USA Department Psychiatry Yale Sch Med and VA CT Healthcare Center West Haven USA Department Genetics Yale Sch Med and VA CT Healthcare Center West Haven USA Department Neurobiology Yale Sch Med and VA CT Healthcare Center West Haven USA Singapore Institute for Clinical Sciences Singapore Singapore National University of Singapore Singapore Singapore University of British Columbia Vancouver Canada KK Women’s and Children’s Hospital Singapore Singapore University of Southampton and University Hospital Southampton NHS Foundation Trust Southampton UK University of Auckland Auckland New Zealand McKusick-Nathans Institute of Genetic Medicine Johns Hopkins University School of Medicine Baltimore USA Esslingen University of Applied Sciences Esslingen Germany German Cancer Research Center Heidelberg Germany Department of Genetic Medicine and Development University of Geneva Medical School Geneva Switzerland Geneva University Hospitals-HUG Service of Genetic Medicine Geneva Switzerland GE3 Institute of Genetics and Genomics of Geneva University of Geneva Medical School Geneva Switzerland South Texas Diabetes and Obesity Institute School of Medicine University of Texas Rio-Grande Valley Edinburg USA South Texas Diabetes and Obesity Institute School of Medicine University of Texas Rio-Grande Valley Brownsville USA Institute of Genetic Medicine Johns Hopkins University Baltimore USA Genomics Division Lawrence Berkeley National Laboratory Berkeley USA Molecular and Human Genetics Baylor College of Medicine Houston USA Department of Translational Medical Sciences Federico II University Naples Italy Metabolon Inc Durham USA Section of Pediatric Neurology and Neuroscience Baylor College of Medicine Houston USA Tawam Hospital Abu Dhabi United Arab Emirates Stanford Medical School Stanford USA Sch

O1 The metabolomics approach to autism: identification of biomarkers for early detection of autism spectrum disorder A. K. Srivastava, Y. Wang, R. Huang, C. Skinner, T. Thompson, L. Pollard, T. Wood, F. Luo, R. Stevenson O2 Phenome-wide association study for smoking- and drinking-associated genes in 26,394 American women with African, Asian, European, and Hispanic descents R. Polimanti, J. Gelernter O3 Effects of prenatal environment, genotype and DNA methylation on birth weight and subsequent postnatal outcomes: findings from GUSTO, an Asian birth cohort X. Lin, I. Y. Lim, Y. Wu, A. L. Teh, L. Chen, I. M. Aris, S. E. Soh, M. T. Tint, J. L. MacIsaac, F. Yap, K. Kwek, S. M. Saw, M. S. Kobor, M. J. Meaney, K. M. Godfrey, Y. S. Chong, J. D. Holbrook, Y. S. Lee, P. D. Gluckman, N. Karnani, GUSTO study group O4 High-throughput identification of specific qt interval modulating enhancers at the SCN5A locus A. Kapoor, D. Lee, A. Chakravarti O5 Identification of extracellular matrix components inducing cancer cell migration in the supernatant of cultivated mesenchymal stem cells C. Maercker, F. Graf, M. Boutros O6 Single cell allele specific expression (ASE) IN T21 and common trisomies: a novel approach to understand DOWN syndrome and other aneuploidies G. Stamoulis, F. Santoni, P. Makrythanasis, A. Letourneau, M. Guipponi, N. Panousis, M. Garieri, P. Ribaux, E. Falconnet, C. Borel, S. E. Antonarakis O7 Role of microRNA in LCL to IPSC reprogramming S. Kumar, J. Curran, J. Blangero O8 Multiple enhancer variants disrupt gene regulatory network in Hirschsprung disease S. Chatterjee, A. Kapoor, J. Akiyama, D. Auer, C. Berrios, L. Pennacchio, A. Chakravarti O9 Metabolomic profiling for the diagnosis of neurometabolic disorders T. R. Donti, G. Cappuccio, M. Miller, P. Atwal, A. Kennedy, A. Cardon, C. Bacino, L. Emrick, J. Hertecant, F. Baumer, B. Porter, M. Bainbridge, P. Bonnen, B. Graham, R. Sutton, Q. Sun, S. Elsea O10 A novel causal methylation network approach to Alzheimer’s

关键词： Pulmonary Arterial Hypertension Oral Squamous Cell Carcinoma Deep Neural Network Autosomal Recessive Polycystic Kidney Disease Whole Genome Bisulfite Sequencing

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Tree template matching in ranked ordered trees by pushdown automata

Tree template matching in ranked ordered trees by pushdown a...

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作者： Flouri, Tomáš Iliopoulos, Costas S. Janoušek, Jan Melichar, Bořivoj Pissis, Solon P. Czech Technical University in Prague Faculty of Information Technology Dept. of Theoretical Computer Science Czech Republic King's College London Dept. of Informatics United Kingdom Curtin University Digital Ecosystems and Business Intelligence Institute Center for Stringology and Applications Australia

We consider the problem of tree template matching in ranked ordered trees, and propose a solution based on the bottom-up technique. Specifically, we transform the tree pattern matching problem to a string matching problem, by transforming the tree template and the subject tree to strings representing their postfix notation, and then use pushdown automata as the computational model. The method is analogous to the construction of string pattern matchers. The given tree template is preprocessed once, by constructing a nondeterministic pushdown automaton, which is then transformed to the equivalent deterministic one. Although we prove that the space required for preprocessing is exponential to the size of the tree template in the worst case, the space required for a specific class of tree templates is linear. The time required for the searching phase is linear to the size of the subject tree in both cases. © 2012 Elsevier B.V. All rights reserved.

关键词： Template matching

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On left and right seeds of a string

On left and right seeds of a string

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作者： Christou, Michalis Crochemore, Maxime Guth, Ondrej Iliopoulos, Costas S. Pissis, Solon P. King's College London Dept. of Informatics United Kingdom Czech Technical University in Prague Faculty of Information Technology Dept. of Theoretical Computer Science Czech Republic Curtin University Digital Ecosystems and Business Intelligence Institute Center for Stringology and Applications Australia Université Paris-Est France

We consider the problem of finding the repetitive structure of a given string y of length n. A factor u of y is a cover of y, if every letter of y lies within some occurrence of u in y. A string v is a seed of y, if it is a cover of a superstring of y. A left seed of y is a prefix of y, that is a cover of a superstring of y. Similarly, a right seed of y is a suffix of y, that is a cover of a superstring of y. An integer array LS is the minimal left-seed (resp. maximal left-seed) array of y, if LS[i] is the minimal (resp. maximal) length of left seeds of y[0.i]. The minimal right-seed (resp. maximal right-seed) array RS of y is defined in a similar fashion. In this article, we present linear-time algorithms for computing all left and right seeds of y, a linear-time algorithm for computing the minimal left-seed array of y, a linear-time solution for computing the maximal left-seed array of y, an O(nlogn)-time algorithm for computing the minimal right-seed array of y, and a linear-time solution for computing the maximal right-seed array of y. All algorithms use linear auxiliary space. © 2012 Elsevier B.V. All rights reserved.

关键词： Clustering algorithms

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Smart home network mechanism via cloud computing

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Journal of Computational information Systems 2012年第23期8卷 10035-10042页

作者： Liu, Li Fu, Xiaodong Jiang, Hong Lv, Yang Faculty of Information Engineering and Automation Kunming University of Science and Technology Kunming 650500 China Computer Technology Application Key Lab of Yunnan Province Kunming 650500 China National Engineering Research Center of Digital Life State-Province Joint Laboratory of Digital Home Interactive Applications Sun Yat-sen University Guangzhou 510006 China

Traditional smart home system based on TCP/IP network applies TC35i cell phone module in smart home controller, and realizes function of short message service by GSM network. This realization model is complex, high-cost, hard to test, and it cannot ensure the short messages could be received and sent successfully. Using the advantages of Cloud computing system, we present a kind of smart home network mechanism solution based on Cloud computing in this paper. Two important constituents in the proposed solution, i.e., SGIP exterior short message gateway and residential quarter information system are described in detail. Moreover, the error ratio of system decreases markedly by improving the short message interface. The proposed smart home network mechanism solution via Cloud computing can be a referential model of the digital life application research based on Cloud computing platform. ©2012 by Binary information Press.

关键词： Cloud computing

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Poster abstracts

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Sleep and Biological Rhythms 2016年第1期5卷 A1-A189页

作者： J. Ferrie M. Shipley F. Cappuccio E. Brunner M. Miller M. Kumari M. Marmot A. Coenen J. L. Castillo F. Araya G. Bustamante L. Montecino C. Torres S. Oporto J. Gronli E. Fiske R. Murison B. Bjorvatn E. Sorensen R. Ursin C. M. Portas S. Rajaraman A. Gribok N. Wesensten T. Balkin J. Reifman N. Dursunoglu S. Ozkurt S. Baser O. Delen S. Sarikaya P. Sadler P. Mitchell D. Françon M. Decobert B. Herve A. Richard G. Griebel P. Avenet B. Scatton G. L. Fur D. Eckert A. Jordan A. Wellman S. Smith A. Malhotra D. White D. Bruck I. Thomas A. Kritikos W. Oertel K. Stiasny-Kolster D. Garcia-Borreguero W. Poewe B. Hoegl R. Kohnen E. Schollmayer J. Keffel C. Trenkwalder A. Valle S. Roizenblatt F. Fregni P. Boggio S. Tufik K. Ward L. Robertson L. Palmer P. Eastwood D. Hillman J. Lee S. Mukherjee V. de Padova G. Barbato G. Ficca I. Zilli P. Salzarulo M. Veldi T. Hion V. Vasar M. Kull L. Nowak J. Davis Y. Latzer O. Tzischinsky S. Crowley M. Carskadon M. Anca-Herschkovitsch D. Frey J. Ortega C. Wiseman C. Farley K. Wright A. Campbell A. Neill K. Spiegel R. Leproult E. Tasali N. Scherberg E. van Cauter A. T. Noradina N. A. Karim I. Norlinah A. A. Raymond R. Sahathevan B. Hamidon E. Werth R. Poryazova R. Khatami C. Bassetti R. G. Beran L. Ainley G. Holand J. Duncan H. Kinney B. Davis B. Hood S. Frey C. Schmidt M. Hofstetter P. Peigneux C. Cajochen W.-P. Hu J.-D. Li C. Zhang L. Boehmer J. Siegel Q.-Y. Zhou Y. Sagawa H. Kondo T. Takemura H. Kanayama Y. Kaneko M. Sato T. Kanbayashi Y. Hishikawa T. Shimizu A. Viola L. James L. Schlangen D.-J. Dijk R. Andretic Y.-C. Kim K.-A. Han F. Jones R. Greenspan L. Sanford L. Yang X. Tang K. Dieter E. Uta H. Sven M. Richard N. Oyane S. Pallesen F. Holsten Y. Inoue M. Fujita N. Emura K. Kuroda N. Uchimura A. Johnston J. Astbury G. Kennedy K. Hoedlmoser M. Schabus T. Pecherstorfer S. Moser G. Gruber P. Anderer W. Klimesch N. Naidoo M. Ferber A. Pack D. Neu O. Mairesse G. Hoffmann A. Dris L. Lambrecht P. Linkowski P. Verbanck O. Le Bon N. Matsuura M. Yamao N. Adachi R. Aritomi Y. Komada H. Tanaka S. Shirak University College London London UK University College London London USA Warwick Medical School London UK Warwick Medical School Coventry USA Radboud University Nijmegen Nijmegen Netherlands Department of Neurology University of Chile Santiago Chile Neurology Service Hospital del Salvador Santiago Chile Family Health Center Juan Pablo II Santiago Chile Department of Biomedicine Section on Physiology Univeristy of Bergen Bergen Norway Department of Public Health and Primary Health Care Univeristy of Bergen Bergen Norway Department of Public Health and Primary Health Care University of Bergen Bergen Norway Norwegian Competence Center for Sleep Disorders Haukeland University Hospital Bergen Norway Department of Child and Adolescent Psychiatry Haukeland University Hospital Univeristy of Bergen Bergen Norway Department of Biomedicine University of Bergen Bergen Norway US Army Medical Research and Materiel Command Fort Detrick Frederick USA Walter Reed Army Institute of Research Silver Spring USA Department of Behavioral Biology Walter Reed Army Institute of Research Silver Spring USA Faculty Department of Pulmonology Pamukkale University Medical Denizli Turkey University of Ballarat Ballarat Australia Sanofi-Aventis Recherche et Developpement Paris France Brigham and Women’s Hospital Harvard Medical School Boston USA The University of Queensland Adelaide Australia School of Psychology University of Queensland Brisbane Australia The University of Queensland Brisbane Australia Victoria University Melbourne Australia Department of Psychology Victoria University Melbourne Australia School of Psychology Victoria University Melbourne Australia Philips-Universität Marburg Germany Philips-Universitaet-Marburg Marburg Germany Instituto de Investigaciones del Sueno Madrid Spain Universitätsklinik für Neurologie Innsbruck Austria Universitaetsklinik fuer Neurologie Innsbruck Austria IMEREM GmbH Nuernberg Germany Schwarz Pharma AG Monheim Germany

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DynMap: Mapping short reads to multiple related genomes 11

DynMap: Mapping short reads to multiple related genomes

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2011 ACM Conference on Bioinformatics, Computational Biology and Biomedicine, ACM-BCB 2011

作者： Flouri, Tomáš Iliopoulos, Costas S. Pissis, Solon P. Czech Technical University in Prague Faculty of Information Technology Dept. of Theoretical Computer Science Czech Republic King's College London Dept. of Informatics Strand London WC2R 2LS United Kingdom Curtin University Digital Ecosystems and Business Intelligence Institute Centre for Stringology and Applications GPO Box U1987 Perth WA 6845 Australia

ISBN: (纸本)9781450307963

The constant advances in sequencing technology have redefined the way genome sequencing is performed. They are able to produce millions of short sequences (reads) during a single experiment, and with a much lower cost than previously possible. Due to the dramatic increase in the amount of data generated, efficient algorithms for aligning (mapping) these reads to reference genomes are in great demand, and recently, there has been ample work for publishing such algorithms. In this paper, we study a different version of this problem;mapping these reads to multiple related genomes (e.g. individuals of the same species). We present DynMap, a new practical algorithm, which employs a suitable data structure that takes into account potential inherent genomic variability (replacements, insertions, deletions) between related genomes. Therefore, if a small number of differences occurs within a reference sequence, the already mapped reads can be altered dynamically. The presented experimental results demonstrate that DynMap can match or even outperform the most popular tools in terms of sensitivity, accuracy, and speed. Copyright © 2011 ACM.

关键词： Mapping

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Approximate string-matching with a single gap for sequence alignment 11

Approximate string-matching with a single gap for sequence a...

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2011 ACM Conference on Bioinformatics, Computational Biology and Biomedicine, ACM-BCB 2011

作者： Flouri, Tomáš Frousios, Kimon Iliopoulos, Costas S. Park, Kunsoo Pissis, Solon P. Tischler, German Czech Technical University in Prague Faculty of Information Technology Dept. of Theoretical Computer Science Czech Republic King's College London Dept. of Informatics Strand London WC2R 2LS United Kingdom School of Computer Science and Engineering Seoul National University Seoul 151-742 Korea Republic of University of Würzburg Lehrstuhl für Informatik II Am Hubland 97074 Würzburg Germany Curtin University Digital Ecosystems and Business Intelligence Institute Centre for Stringology and Applications GPO Box U1987 Perth WA 6845 Australia

ISBN: (纸本)9781450307963

This paper deals with the approximate string-matching problem with Hamming distance and a single gap for sequence alignment. We consider an extension of the approximate string-matching problem with Hamming distance, by also allowing the existence of a single gap, either in the text, or in the pattern. This problem is strongly and directly motivated by the next-generation re-sequencing procedure. We present a general algorithm that requires O(nm) time, where n is the length of the text and m is the length of the pattern, but this can be reduced to O(mβ) time, if the maximum length β of the gap is given. Copyright © 2011 ACM.

关键词： Hamming distance

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Optimal computerized model for designing cellular manufacturing systems using neural network

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Journal of Applied Sciences 2011年第15期11卷 2837-2842页

作者： Mukattash, Adnan Idwan, Sahar Ashhab, Moh'd Sami Samhouri, Murad Matar, Izzeddin A. Department of Industrial Engineering The Hashemite University P.O. Box 150459 Zarqa 13115 Jordan Department of Computer Science and Applications The Hashemite University P.O. Box 150459 Zarqa 13115 Jordan Department of Mechanical Engineering The Hashemite University P.O. Box 150459 Zarqa 13115 Jordan Department of Software Engineering Faculty of Information Technology Petra University Queen Alia International Road P.O. Box 961343 Amman 11196 Jordan

In this study, a computerized model has been developed to obtain the optimal distribution of the machines on three cells based on Artificial Neural Network (ANN's). These networks rely on the historical input-output data to learn input output implicit mapping. They are trained using back propagation algorithm. Comparing the results with those in the literature, it has been proved that the artificial neural network is superior in finding all the possible optimal solution (s) since it gives the minimum sum of voids and/or exceptions for all the possible ways of forming three cells from n machines. Taking all the possible ways of forming the cells is of great advantage since;it will provide the designer with more flexibility. An important feature of the optimization model is that it finds the solution fast regardless the number of machines and parts. The distinct superiority of the proposed model is that, machine cells and part families are identified and done concurrently which will decrease the computational time. Results are verified with the aid of computer simulation. © 2011 Asian Network for Scientific information.

关键词： Cellular manufacturing

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Invisible calibration pattern based on human visual perception

IEEJ Transactions on Electronics, Information and Systems

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IEEJ Transactions on Electronics, information and Systems 2010年第8期130卷 1440-1447+19页

作者： Takimoto, Hironori Yoshimori, Seiki Mitsukura, Yasue Fukumi, Minoru Faculty of Computer Science and Syst. Eng. Okayama Prefectural University 111 Kuboki Soja Okayama 719-1197 Japan Dept. of Media Technologies Faculty of Eng. Nippon Bunri University 1727 Ichigi Oita Oita 870-0397 Japan Graduate School of Bio-Applications and System Enginner-ing Tokyo University of Agriculture and Technology 2-24-16 Nakamachi Koganei Tokyo 184-8588 Japan Dept. of Information Science and Intteligent Syst. Faculty of Eng. University of Tokushima 2-1 Minami-Josanjima Tokushima Tokushima 770-8506 Japan

In this paper, we propose an arrangement and detection method of an invisible calibration pattern based on characteristics of human visual perception. A calibration pattern is arranged around contents where invisible data is embedded, as some feature points between an original image and the scanned image for normalization of the scanned image. However, it is clear that conventional methods interfere with page layout and artwork of contents. Moreover, conventional visible patterns show a third person the position of embedded data. Therefore, visible calibration patterns are not suitable for security service. The most important part of human visual perception in the proposed method is the spectral luminous efficiency characteristic and the chromatic spatial frequency characteristic. In addition, a back ground color in surrounding of contents is not restricted to uniform color by using the proposed calibration pattern. It is suggest that the proposed method protect page layout and artwork. © 2010 The Institute of Electrical Engineers of Japan.

关键词： Image processing

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An age estimation system on the AIBO

An age estimation system on the AIBO

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International Conference on Control, Automation and Systems ( ICCAS)

作者： Hironobu Fukai Yuuki Nishie Kohki Abiko Yasue Mitsukura Minoru Fukumi Masahiro Tanaka Graduate School of Bio-Applications & Systems Engineering Tokyo University of Agriculture슠and슠Technology Tokyo Japan Department of Computer and Information Science Tokyo University of Agriculture슠and슠Technology Tokyo Japan Faculty of Engineering University of Tokushima Tokushima Japan Department of Information Science and Systems Engineering Konan University Hyogo Japan

In this paper, we propose an age estimation system on the AIBO. AIBO is an entertainment robot produced by SONY co., Ltd.. AIBO has many sensors to get information around itself and moves according to its instinct. This autonomous action is considerably natural. However, it is inadequate to communicate with people. If AIBO can estimate the human age from a face image, it becomes more excellent entertainment robot. Then, we propose the age estimation method on the AIBO by using face image. In this paper, the apparent age feature is extracted by the fast Fourier transform (FFT), and it is selected by the GA. Moreover, the age is estimated by the 1-dimensional SOM. In order to show the effectiveness of the proposed method, we show the simulation examples.

关键词： Humans Robot sensing systems Agricultural engineering Systems engineering and theory Agriculture information science Face Feature extraction Genetic algorithms Organizing

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