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IEEE Workshop on Computational Intelligence in Production and Logistics Systems (CIPLS)

作者： Yan Jiang Thomas Weise Jörg Lässig Raymond Chiong Rukshan Athauda Joint USTC-Birmingham Research Institute in Intelligent Computation and Its Applications (UBRI) University of Science and Technology of China Hefei Anhui China Department of Computer Science University of Applied Sciences Zittau/Görlitz Görlitz Germany Faculty of Science and Information Technology The University of Newcastle Callaghan NSW Australia

Benchmarking is one of the most important ways to investigate the performance of metaheuristic optimization algorithms. Yet, most experimental algorithm evaluations in the literature limit themselves to simple statistics for comparing end results. Furthermore, comparisons between algorithms from different “families” are rare. In this study, we use the TSP Suite - an open source software framework - to investigate the performance of the Branch and Bound (BB) algorithm for the Traveling Salesman Problem (TSP). We compare this BB algorithm to an Evolutionary Algorithm (EA), an Ant Colony Optimization (ACO) approach, as well as three different Local Search (LS) algorithms. Our comparisons are based on a variety of different performance measures and statistics computed over the entire optimization process. The experimental results show that the BB algorithm performs well on very small TSP instances, but is not a good choice for any medium to large-scale problem instances. Subsequently, we investigate whether hybridizing BB with LS would give rise to similar positive results like the hybrid versions of EA and ACO have. This turns out to be true - the “Memetic” BB algorithms are able to improve the performance of pure BB algorithms significantly. It is worth pointing out that, while the results presented in this paper are consistent with previous findings in the literature, our results have been obtained through a much more comprehensive and solid experimental procedure.

关键词： Algorithm design and analysis Runtime Software algorithms Cities and towns Complexity theory Optimization Benchmark testing

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Abstracts from the 3rd International Genomic Medicine Conference (3rd IGMC 2015) : Jeddah, Kingdom of Saudi Arabia. 30 November - 3 December 2015

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BMC genomics 2016年第6期17 Suppl 6卷 487页

作者： Jerry W. Shay Noriko Homma Ruyun Zhou Muhammad Imran Naseer Adeel G. Chaudhary Mohammed Al-Qahtani Nobutaka Hirokawa Maryam Goudarzi Albert J. Fornace Saleh Baeesa Deema Hussain Mohammed Bangash Fahad Alghamdi Hans-Juergen Schulten Angel Carracedo Ishaq Khan Hanadi Qashqari Nawal Madkhali Mohamad Saka Kulvinder S. Saini Awatif Jamal Jaudah Al-Maghrabi Adel Abuzenadah Adeel Chaudhary Mohammed Al Qahtani Ghazi Damanhouri Heba Alkhatabi Anne Goodeve Laura Crookes Nikolas Niksic Nicholas Beauchamp Adel M. Abuzenadah Jim Vaught Bruce Budowle Mourad Assidi Abdelbaset Buhmeida Leena Merdad Sudhir Kumar Sayaka Miura Karen Gomez Mahmood Rasool Ahmed Rebai Sajjad Karim Hend F. Nour Eldin Heba Abusamra Elham M. Alhathli Nada Salem Mohammed H. Al-Qahtani Hossam Faheem Ashok Agarwa Eberhard Nieschlag Joachim Wistuba Oliver S. Damm Mohd A. Beg Taha A. Abdel-Meguid Hisham A. Mosli Osama S. Bajouh Serdar Coskun Muhammad Abu-Elmagd Ashraf Dallol Sahar Hakamy Wejdan Al-Qahtani Asia Al-Harbi Shireen Hussain Burak Ozkosem Rick DuBois Safia S. Messaoudi Maryam T. Dandana Touhami Mahjoub Wassim Y. Almawi S. Abdalla M. Nabil Al-Aama Asmaa Elzawahry Tsuyoshi Takahashi Sachiyo Mimaki Eisaku Furukawa Rie Nakatsuka Isao Kurosaka Takahiko Nishigaki Hiromi Nakamura Satoshi Serada Tetsuji Naka Seiichi Hirota Tatsuhiro Shibata Katsuya Tsuchihara Toshirou Nishida Mamoru Kato Sajid Mehmood Naeem Mahmood Ashraf Awais Asif Muhammad Bilal Malik Siddique Mehmood Aadil Hussain Qazi Mohammad Sajid Jamal Mughees Uddin Siddiqui Mohammad A. Alzohairy Mohammad A. Al Karaawi Taoufik Nedjadi Heba Al-Khattabi Adel Al-Ammari Ahmed Al-Sayyad Hédia Zitouni Nozha Raguema Marwa Ben Ali Wided Malah Raja Lfalah Wassim Almawi Mohammed Elanbari Andrey Ptitsyn Sana Mahjoub Rabeb El Ghali Bechir Achour Nidhal Ben Amor Brahim N’siri Hamid Morjani Esam Azhar Vera Chayeb Maryam Dendena Hedia Zitouni Khedija Zouari-Limayem Bassem Refaat Ahmed M. Ashshi Sarah A. Batwa Hazem Ramadan Amal Awad Ahmed Ateya Adel Galal Ahmed El-Shemi Ahmad Ashshi Mohammed Basalamah Youjin Na Cha University of Texas Southwestern Medical Center Dallas USA Department of Cell Biology and Anatomy Graduate School of Medicine the University of Tokyo Tokyo Japan Center of Excellence in Genomic Medicine Research King Abdulaziz University Jeddah Saudi Arabia Department of Biochemistry and Molecular & Cellular Biology Lombardi Comprehensive Cancer Center Georgetown University Washington USA Department of Oncology Lombardi Comprehensive Cancer Center Georgetown University Washington USA Department of Radiation Medicine Lombardi Comprehensive Cancer Center Georgetown University Washington USA Center of Excellence in Genomic Medicine Research (CEGMR) King Abdulaziz University Jeddah Kingdom of Saudi Arabia King Fahd Medical Research Centre King Abdulaziz University Jeddah Saudi Arabia Centre of Excellence in Genomic Medicine Research King Abdulaziz University Jeddah Saudi Arabia Sheffield Diagnostic Genetic Service Sheffield Children’s NHS Foundation Trust Western Bank Sheffield UK Center of Innovations in Personalized Medicine King Abdulaziz University Jeddah Saudi Arabia President ISBER Editor-in-Chief Biopreservation & Biobanking ᅟ USA Institute of Applied Genetics Department of Molecular and Medical Genetics University of North Texas Health Science Center Fort Worth USA Department of Dental Public Health Faculty of Dentistry King Abdulaziz University Jeddah Saudi Arabia Institute for Genomics and Evolutionary Medicine Temple University Philadelphia USA Center of Excellence in Genomic Medicine King Abdulaziz University Jeddah Kingdom of Saudi Arabia Laboratory of Molecular and Cellular Screening Processes (Bioinformatics Group) Centre of Biotechnology of Sfax Sfax Tunisia Fujitsu Technology Solutions International ᅟ ᅟ Case Western Reserve University School of Medicine and Lerner College of Medicine Cleveland Clinic Foundation Cleveland USA American Center for Reproductive Medicine Andrology Center Cleveland USA Center for Reproductive Medicine and

O1 Regulation of genes by telomere length over long distances Jerry W. Shay O2 The microtubule destabilizer KIF2A regulates the postnatal establishment of neuronal circuits in addition to prenatal cell survival, cell migration, and axon elongation, and its loss leading to malformation of cortical development and severe epilepsy Noriko Homma, Ruyun Zhou, Muhammad Imran Naseer, Adeel G. Chaudhary, Mohammed Al-Qahtani, Nobutaka Hirokawa O3 Integration of metagenomics and metabolomics in gut microbiome research Maryam Goudarzi, Albert J. Fornace Jr. O4 A unique integrated system to discern pathogenesis of central nervous system tumors Saleh Baeesa, Deema Hussain, Mohammed Bangash, Fahad Alghamdi, Hans-Juergen Schulten, Angel Carracedo, Ishaq Khan, Hanadi Qashqari, Nawal Madkhali, Mohamad Saka, Kulvinder S. Saini, Awatif Jamal, Jaudah Al-Maghrabi, Adel Abuzenadah, Adeel Chaudhary, Mohammed Al Qahtani, Ghazi Damanhouri O5 RPL27A is a target of miR-595 and deficiency contributes to ribosomal dysgenesis Heba Alkhatabi O6 Next generation DNA sequencing panels for haemostatic and platelet disorders and for Fanconi anaemia in routine diagnostic service Anne Goodeve, Laura Crookes, Nikolas Niksic, Nicholas Beauchamp O7 Targeted sequencing panels and their utilization in personalized medicine Adel M. Abuzenadah O8 International biobanking in the era of precision medicine Jim Vaught O9 Biobank and biodata for clinical and forensic applications Bruce Budowle, Mourad Assidi, Abdelbaset Buhmeida O10 Tissue microarray technique: a powerful adjunct tool for molecular profiling of solid tumors Jaudah Al-Maghrabi O11 The CEGMR biobanking unit: achievements, challenges and future plans Abdelbaset Buhmeida, Mourad Assidi, Leena Merdad O12 Phylomedicine of tumors Sudhir Kumar, Sayaka Miura, Karen Gomez O13 Clinical implementation of pharmacogenomics for colorectal cancer treatment Angel Carracedo, Mahmood Rasool O14 From association to causality: translation of GWAS findings for genomic me

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Integrated model of photovoltaic solar system with the sound biometric techniques

Integrated model of photovoltaic solar system with the sound...

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International Conference & Exhibition on the applications Of information technology To Renewable Energy Processes And Systems (IT-DREPS)

作者： Kenza Meridji Khalid T. Al-Sarayreh Ebaa Fayyoumi Sahar Idwan Faculty of Information Technology University of Petra Amman Jordan Departments of Software Engineering and Computer Science and Applications Hashemite University Zarqa Jordan

Photovoltaic system (PVS) is used for generating electric power by using solar cells to convert energy from the sun light into a flow of direct current electricity, which can be used to power equipment or to recharge a battery. In addition, the Sound biometric techniques can enable PVS to listen and understand their surrounding auditory environment since turning the lights on all the nights will get through a lot of energy which it might be used in other significant concerns. This paper proposed a model of combination between PVS to generate power energy (electricity) from the sunlight controlled by a sound biometric technique to reduce the consumption of the generated power energy by turning the lights on for the highways only when there are cars on the highway and only for some period of time to make the driving out of harmful ways and trouble-free; followed by an implementation of the proposed combination model between the PVS and biometric sound chip and a presentation of a discussion of the proposed system results.

关键词： Feature extraction Road transportation Vectors Electricity Batteries Photovoltaic systems

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Single and multi trusted third party: Comparison, identification and reduction of malicious conduct by trusted third party in secure multiparty computing protocol

Single and multi trusted third party: Comparison, identifica...

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2nd International Conference on computer Science, Engineering and applications, ICCSEA 2012

作者： Shaikh, Zulfa Garg, Poonam Faculty of Computer Applications Acropolis Institute of Technology and Research Indore M.P. India Deptt. of Information Technology Institute of Management Technology Ghaziabad India

ISBN: (纸本)9783642301100

SMC is a problem of n parties with inputs (x1, x 2...xn) , hand over their inputs to third party for computation f(x1, x2...xn) and third party announces the result in the form of y. During joint computation of inputs, all the organizations involved in computation wish to preserve privacy of their inputs. So need is to define a protocol which maintains privacy, security and correctness parameters of SMC. In this paper, single third party and multi third party model are defined and compared. The probabilistic evidences for single and multi third party SMC model have been analyzed with security analysis graphs. In this paper, we have also worked on identification and reduction of malicious conduct of TTPs in multi TTP environment. © 2012 Springer-Verlag GmbH.

关键词： Cryptography

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

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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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