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Author Correction: A systems biology approach uncovers cell-specific gene regulatory effects of genetic associations in multiple sclerosis

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Nature communications 2019年第1期10卷 2956页

作者： Lohith Madireddy Kicheol Kim Xiaoming Jia Adam Santaniello Stacy J. Caillier Bruce A. C. Cree Roland Henry Stephen L. Hauser Jorge R. Oksenberg Sergio E. Baranzini Nikolaos A. Patsopoulos Philip De Jager Chris Cotsapas Matthew R. Lincoln David A. Hafler Steffan D. Bos Hanne F. Harbo Tone Berge Elisabeth G. Celius Ashley Beecham Jacob McCauley Margaret A. Pericak-Vance Till F. M. Andlauer Christiane Gasperi Bernhard Hemmer Lisa F. Barcellos Luisa Bernardinelli Filippo Martinelli-Boneschi David R. Booth Graeme J. Stewart Farren Briggs Jonathan Haines Manuel Comabella Giancarlo Comi Federica Esposito Sandra D’Alfonso Katrina Dedham Pierre Duquette Efthimios Dardiotis Bertrand Fontaine An Goris Bénédicte Dubois Pierre-Antoine Gourraud Georgios Hadjigeorgiou Clive Hawkins Seema Kalra Rogier Hintzen Dana Horakova Noriko Isobe Jun-ichi Kira Michael Khalil Ingrid Kockum Tomas Olsson Christina M. Lill Felix Luessi Frauke Zipp Roland Martin Annette Oturai Aarno Palotie Janna Saarela Adrian Ivinson Bruce V. Taylor Alastair Compston Stephen Sawcer Weill Institute for Neurosciences Department of Neurology University of California San Francisco San Francisco CA 94158 USA Bakar Institute for Computational Health Science. University of California San Francisco San Francisco CA 94158 USA Systems Biology and Computer Science Program Ann Romney Center for Neurological Diseases Department of Neurology and Division of Genetics Department of Medicine Brigham & Women’s Hospital Harvard Medical School Boston MA 02115 USA Broad Institute of Harvard University and Massachusetts Institute of Technology Cambridge MA 02142 USA Department of Neurology Center for Translational and Computational Neuroimmunology and Multiple Sclerosis Center Columbia University Medical Center New York NY 10032 USA Departments of Neurology Yale School of Medicine 300 George St New Haven CT 06511 USA Department of Genetics Yale School of Medicine 300 George St New Haven CT 06511 USA Institute of Clinical Medicine University of Oslo Oslo 0318 Norway Department of Neurology Oslo University Hospital Oslo 0424 Norway Department of Mechanical Electronics and Chemical Engineering Oslo Metropolitan University Oslo 0167 Norway Institute of Health and Society University of Oslo Oslo 0318 Norway John P. Hussman Institute for Human Genomics University of Miami Miller School of Medicine Miami FL 33136 USA Dr. John T. Macdonald Foundation Department of Human Genetics University of Miami Miller School of Medicine Miami FL 33136 USA Department of Neurology Klinikum rechts der Isar School of Medicine Technical University of Munich 81675 Munich Germany Munich Cluster for Systems Neurology (SyNergy) 81377 Munich Germany Division of Epidemiology School of Public HealthUniversity of California 324 Stanley Hall MC#3220 Berkeley CA 94720 USA Section of Biostatistics Neurophyisiology and Psychiatry Unit of medical and genomic statistics Universita of Pavia Pavia 27100 Italy Department of Biomedical Sciences for Health Univers

An amendment to this paper has been published and can be accessed via a link at the top of the paper.

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Author Correction: Reference component analysis of single-cell transcriptomes elucidates cellular heterogeneity in human colorectal tumors

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Nature genetics 2018年第12期50卷 1754页

作者： Huipeng Li Elise T Courtois Debarka Sengupta Yuliana Tan Kok Hao Chen Jolene Jie Lin Goh Say Li Kong Clarinda Chua Lim Kiat Hon Wah Siew Tan Mark Wong Igor Cima Min-Han Tan Lawrence J K Wee Axel M Hillmer Iain Beehuat Tan Paul Robson Shyam Prabhakar Computational and Systems Biology Genome Institute of Singapore Singapore Singapore. Developmental Cellomics Laboratory Genome Institute of Singapore Singapore Singapore. Department of Computer Science and Engineering and Center for Computational Biology Indraprastha Institute of Information Technology Delhi India. Synthetic Biology Genome Institute of Singapore Singapore Singapore. Cancer Therapeutics and Stratified Oncology Genome Institute of Singapore Singapore Singapore. Department of Medical Oncology National Cancer Centre Singapore Singapore Singapore. Department of Pathology Singapore General Hospital Singapore Singapore. Department of Colorectal Surgery Singapore General Hospital Singapore Singapore. Institute of Bioengineering and Nanotechnology Singapore Singapore. Data Analytics Department Institute for Infocomm Research Singapore Singapore. Cancer Therapeutics and Stratified Oncology Genome Institute of Singapore Singapore Singapore. iain.tan.b.h@singhealth.com.sg. Department of Medical Oncology National Cancer Centre Singapore Singapore Singapore. iain.tan.b.h@singhealth.com.sg. Program in Cancer and Stem Cell Biology Duke-NUS Medical School Singapore Singapore. iain.tan.b.h@singhealth.com.sg. Developmental Cellomics Laboratory Genome Institute of Singapore Singapore Singapore. paul.robson@***. The Jackson Laboratory for Genomic Medicine Farmington Connecticut USA. paul.robson@***. Department of Genetics and Genome Sciences Institute for Systems Genomics University of Connecticut Farmington Connecticut USA. paul.robson@***. Department of Biological Sciences National University of Singapore Singapore Singapore. paul.robson@***. Computational and Systems Biology Genome Institute of Singapore Singapore Singapore. prabhakars@gis.a-star.edu.sg.

In the version of the article published, the author list is not accurate. Igor Cima and Min-Han Tan should have been authors, appearing after Mark Wong in the author list, while Paul Jongjoon Choi should not have been listed as an author. Igor Cima and Min-Han Tan both have the affiliation Institute of Bioengineering and Nanotechnology, Singapore, Singapore, and their contributions should have been noted in the Author Contributions section as "I.C. preprocessed Primary Cell Atlas data with inputs from M.-H.T." The following description of the contribution of Paul Jongjoon Choi should not have appeared: "P.J.C. supported the smFISH experiments." In the 'RCA: global panel' section of the Online Methods, the following sentence should have appeared as the second sentence, "An expression atlas of human primary cells (the Primary Cell Atlas) was preprocessed similarly to in ref. 55," with new reference 55 (Cima, I. et al. Tumor-derived circulating endothelial cell clusters in colorectal cancer. science Transl. Med. 8, 345ra89, 2016).

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Creation and analysis of biochemical constraint-based models: The COBRA Toolbox v3.0

arXiv

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arXiv 2017年

作者： Heirendt, Laurent Arreckx, Sylvain Pfau, Thomas Mendoza, Sebastián N. Richelle, Anne Heinken, Almut Haraldsdóttir, Hulda S. Wachowiak, Jacek Keating, Sarah M. Vlasov, Vanja Magnusdóttir, Stefania Ng, Chiam Yu Preciat, German Žagare, Alise Chan, Siu H.J. Aurich, Maike K. Clancy, Catherine M. Modamio, Jennifer Sauls, John T. Noronha, Alberto Bordbar, Aarash Cousins, Benjamin El Assal, Diana C. Valcarcel, Luis V. Apaolaza, Iñigo Ghaderi, Susan Ahookhosh, Masoud Guebila, Marouen Ben Kostromins, Andrejs Sompairac, Nicolas Le, Hoai M. Ma, Ding Sun, Yuekai Wang, Lin Yurkovich, James T. Oliveira, Miguel A.P. Vuong, Phan T. El Assal, Lemmer P. Kuperstein, Inna Zinovyev, Andrei Scott Hinton, H. Bryant, William A. Aragón Artacho, Francisco J. Planes, Francisco J. Stalidzans, Egils Maass, Alejandro Vempala, Santosh Hucka, Michael Saunders, Michael A. Maranas, Costas D. Lewis, Nathan E. Sauter, Thomas Palsson, Bernhard Ø. Thiele, Ines Fleming, Ronan M.T. Luxembourg Centre for Systems Biomedicine University of Luxembourg 6 avenue du Swing BelvauxL-4367 Luxembourg Life Sciences Research Unit University of Luxembourg 6 avenue du Swing BelvauxL-4367 Luxembourg University of Chile Blanco Encalada 2085 Santiago Chile Department of Pediatrics University of California San Diego School of Medicine San DiegoCA92093 United States Hinxton CambridgeCB10 1SD United Kingdom Department of Chemical Engineering Pennsylvania State University University University ParkPA16802 United States Department of Physics University of California San Diego 9500 Gilman Dr. San DiegoCA92093 United States Bioinformatics and Systems Biology Program University of California San Diego San DiegoCA United States Sinopia Biosciences San DiegoCA United States School of Computer Science Algorithms and Randomness Center Georgia Institute of Technology AtlantaGA United States Biomedical Engineering and Sciences Department TECNUN University of Navarra Paseo de Manuel Lardizabal 13 San Sebastian20018 Spain Institute of Microbiology and Biotechnology University of Latvia Jelgavas iela 1 RigaLV-1004 Latvia Department of Management Science and Engineering Stanford University StanfordCA94305-4026 United States Bioengineering Department University of California San Diego San DiegoCA United States Utah State University Research Foundation 1695 North Research Park Way North LoganUT84341 United States Centre for Integrative Systems Biology and Bioinformatics Department of Life Sciences Imperial College London London United Kingdom Department of Mathematics University of Alicante Spain California Institute of Technology Computing and Mathematical Sciences MC 305-16 1200 E. California Blvd. PasadenaCA91125 United States Mathomics Center for Mathematical Modeling University of Chile Beauchef 851 Santiago Chile Novo Nordisk Foundation Center for Biosustainability University of California San Diego San DiegoCA92093 Uni

COnstraint-Based Reconstruction and Analysis (COBRA) provides a molecular mechanistic framework for integrative analysis of experimental data and quantitative prediction of physicochemically and biochemically feasible phenotypic states. The COBRA Toolbox is a comprehensive software suite of interoperable COBRA methods. It has found widespread applications in biology, biomedicine, and biotechnology because its functions can be flexibly combined to implement tailored COBRA protocols for any biochemical network. Version 3.0 includes new methods for quality controlled reconstruction, modelling, topological analysis, strain and experimental design, network visualisation as well as network integration of chemoinformatic, metabolomic, transcriptomic, proteomic, and thermochemical data. New multi-lingual code integration also enables an expansion in COBRA application scope via high-precision, high-performance, and nonlinear numerical optimisation solvers for multi-scale, multi-cellular and reaction kinetic modelling, respectively. This protocol can be adapted for the generation and analysis of a constraint-based model in a wide variety of molecular systems biology scenarios. This protocol is an update to the COBRA Toolbox 1.0 and 2.0. The COBRA Toolbox 3.0 provides an unparalleled depth of constraint-based reconstruction and analysis methods. Copyright © 2017, The Authors. All rights reserved.

关键词： Data integration

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Multi-Layered Alert Filtration and Feedback Cycle using Brahms Model

Multi-Layered Alert Filtration and Feedback Cycle using Brah...

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International Conference on Advanced computer science Applications and Technologies

作者： Abid Ghaffar Mohamed Ridza Wahiddin Asadullah Shaikh Akhlaq Ahmad Department of Computer Science Foundation Year Program Umm Al-Qura University Department of Computer Science Kulliyyah of Information and Communication Technology International Islamic University Malaysia Department of Computer Science and Information Systems Najran University College of Engineering and Islamic Architecture Umm Al Qura University

ISBN: (纸本)9781509004256

Customer service improvement is directly related with organizational standards and productivity. Employees activities have certain objectives to be followed but sometimes outcomes are different than expected. Human error while performing regular job activities cause sufficient losses and difficult to address. Management faces real challenges while dealing with employee related issues and sometimes becomes unproductive. We propose Brahms Model with multi layered alert filtration and feedback cycle which would address the human error in the system and generate the filtered alerts in the form of sms or by emails. This is especially useful for Human-computer Interfacing (HCI) Scenarios. Controlling human error and addressing real issues may protect any institution from severe damage and losses. Efficiency of a customer service department can be improved and maximized by multi-layered alert filtration system using Brahms Model.

关键词： Brahms Model Customer Service Improvement Context Aware Applications Alert Generation and Filtration Organizational behaviour Human computer Interfacing

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Wave algorithm for recruitment in swarm robotics

Lecture Notes in Computer Science (including subseries Lectu...

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Lecture Notes in computer science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics) 2015年 9156卷 3-13页

作者： Silva, Luneque Nedjah, Nadia Systems Engineering and Computer Science Program Federal University of Rio de Janeiro Rio de Janeiro Brazil Department of Electronics Engineering and Telecommunications State University of Rio de Janeiro Rio de Janeiro Brazil

In the last decades, studies on swarm robotics have grown significantly, with different new aspects becoming of interest in research. Although the primary interest in swarm robotics should be the application, which is the task that robots should perform, other aspects are also studied. For instance, in a robotic swarm, it may be necessary to select the robots that would perform a given task, aiming at a division of labor among the members. A similar problem is that of robot recruitment, required when a specific robot needs assistance to execute some tasks and thus needs to recruit other robots of the swarm to do so. In this paper, a distributed algorithm, termed the wave algorithm, is exploited to perform the recruitment based mainly on robot message passing to neighboring robots. © Springer International Publishing Switzerland 2015.

关键词： Message passing

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Correction: Liquid-capped encoded microcapsules for multiplex assays

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Lab on a chip 2017年第4期17卷 738页

作者： Younghoon Song Yunjin Jeong Taehong Kwon Daewon Lee Dong Yoon Oh Tae-Joon Park Junhoi Kim Jiyun Kim Sunghoon Kwon Institutes of Entrepreneurial BioConvergence Seoul National University Seoul 151-742 Republic of Korea. skwon@snu.ac.kr and Department of Electrical and Computer Science Seoul National University Seoul 151-742 Republic of Korea. Institutes of Entrepreneurial BioConvergence Seoul National University Seoul 151-742 Republic of Korea. skwon@snu.ac.kr and Interdisciplinary Program of Bioengineering Seoul National University Seoul 151-742 Republic of Korea. Nano Systems Institute Seoul National University Seoul 151-742 Republic of Korea. Department of Materials Science and Engineering Ulsan National Institute of Science and Technology Ulsan 44919 Republic of Korea. Institutes of Entrepreneurial BioConvergence Seoul National University Seoul 151-742 Republic of Korea. skwon@snu.ac.kr and Department of Electrical and Computer Science Seoul National University Seoul 151-742 Republic of Korea and Interdisciplinary Program of Bioengineering Seoul National University Seoul 151-742 Republic of Korea and Nano Systems Institute Seoul National University Seoul 151-742 Republic of Korea and Seoul National University Hospital Biomedical Research Institute Seoul National University Hospital Seoul 151-742 Republic of Korea and Quantamatrix Inc. Seoul 151-742 Republic of Korea.

Correction for 'Liquid-capped encoded microcapsules for multiplex assays' by Younghoon Song et al., Lab Chip, 2017, DOI: .

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Using HMM in strategic games 9

Using HMM in strategic games

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9th International Workshop on Developments in Computational Models, DCM 2013

作者： Benevides, Mario Lima, Isaque Nader, Rafael Rougemont, Pedro Systems and Computer Engineering Program and Computer Science Department Federal University of Rio de Janeiro Brazil

In this paper we describe an approach to resolve strategic games in which players can assume different types along the game. Our goal is to infer which type the opponent is adopting at each moment so that we can increase the player's odds. To achieve that we use Markov games combined with hidden Markov model. We discuss a hypothetical example of a tennis game whose solution can be applied to any game with similar characteristics. © M. Benevides, I. Lima, R. Nader & P. Rougemont This work is licensed under the Creative Commons Attribution License.

关键词： Tennis

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Towards autonomous navigation of unsignalized intersections under uncertainty of human driver intent

Towards autonomous navigation of unsignalized intersections ...

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IEEE/RSJ International Conference on Intelligent Robots and systems

作者： V. Sezer T. Bandyopadhyay D. Rus E. Frazzoli D. Hsu Department of Mechanical Engineering Istanbul Technical University Istanbul Turkey Tirthankar Bandyopadhyay is with Autonomous Systems Program Commonwealth Scientific and Industrial Research Organization Australia Daniela Rus and Emilio Frazzoli are with the Department of Electri-cal&Engineering and Aeronautics&Astronautic respectively Massachusetts Institute of Technology USA Department of Computer Science National University of Singapore Singapore

In a mixed environment of autonomous driverless vehicles and human driven vehicles operating on the same road, identifying intentions of human drivers and interacting with them in a compliant and responsible manner becomes a challenging problem for the driverless vehicles. In this paper, the problem of vehicle interaction at an intersection merging scenario is formulated as an Intention-Aware motion planning problem using the tools from Mixed Observability Markov Decision Process (MOMDP). We utilize the tools from recent intention aware planning framework to demonstrate a merging behavior in the presence of human drivers by trying to infer and act according to the intentions of the human drivers. A driver behavior model for T-junction intersections is developed in order to calculate the probabilistic state transition functions of the MOMDP model. With proposed solution, it is demonstrated that using intention aware planning improves performance in comparison to present time to merge approach by lowering accident probability and intersection navigation duration. The proposed method is tested on a real autonomous vehicle (AV) in the presence of human driven vehicles to validate our approach.

关键词： Vehicles Navigation Mobile robots Roads Hidden Markov models Uncertainty

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Using PepExplorer to Filter and Organize De Novo Peptide Sequencing Results

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Current Protocols in Bioinformatics 2015年第1期51卷 13.27.1-13.27.9页

作者： da Veiga Leprevost, Felipe Barbosa, Valmir C. Carvalho, Paulo Costa Computational Mass Spectrometry Group Carlos Chagas Institute–Fiocruz. Curitiba Paraná Brazil Department of Pathology University of Michigan Ann Arbor United States Systems Engineering and Computer Science Program Federal University of Rio de Janeiro Rio de Janeiro Brazil

PepExplorer aids in the biological interpretation of de novo sequencing results;this is accomplished by assembling a list of homolog proteins obtained by aligning results from widely adopted de novo sequencing tools against a target-decoy sequence database. Our tool relies on pattern recognition to ensure that the results satisfy a user-given false-discovery rate (FDR). For this, it employs a radial basis function neural network that considers the precursor charge states, de novo sequencing scores, the peptide lengths, and alignment scores. PepExplorer is recommended for studies addressing organisms with no genomic sequence available. PepExplorer is integrated into the PatternLab for proteomics environment, which makes available various tools for downstream data analysis, including the resources for quantitative and differential proteomics. © 2015 by John Wiley & Sons, Inc. © 2015 John Wiley & Sons, Inc.

关键词： de novo sequencing mass spectrometry proteomics

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Methods for Evaluating Medical Tests and Biomarkers

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Diagnostic and Prognostic Research 2017年第1期1卷 1-34页

作者： Gowri Gopalakrishna Miranda Langendam Patrick Bossuyt Mariska Leeflang Rob Scholten Anna Noel-Storr James Thomas Iain Marshall Byron Wallace Penny Whiting Clare Davenport Gowri GopalaKrishna Isabel de Salis Sue Mallett Robert Wolff Marie Westwood Jos Kleinen Richard Riley Gary Collins Hans Reitsma Karel Moons Antonia Zapf Katharina Kramer Annika Hoyer Oliver Kuss J. Ensor R. D. Riley J. J. Deeks E. C. Martin Gerta Rücker Martin Schumacher Susanne Steinhauser Joie Ensor Kym Snell Brian Willis Jon Deeks Thomas Debray Lavinia Ferrante di Ruffano Sian Taylor-Phillips Chris Hyde Stuart A. Taylor Gauraang Batnagar Lavinia Ferrante Di Ruffano Farah Seedat Aileen Clarke Sarah Byron Frances Nixon Rebecca Albrow Thomas Walker Carla Deakin Zhivko Zhelev Harriet Hunt Yaling Yang Lucy Abel James Buchanan Thomas Fanshawe Bethany Shinkins Laure Wynants Sabine Van Huffel Jan Verbakel Dirk Timmerman Ben Van Calster Aeliko Zwinderman Jason Oke Jack O’Sullivan Rafael Perera Brian Nicholson Hannah L. Bromley Tracy E. Roberts Adele Francis Denniis Petrie G. Bruce Mann Kinga Malottki Holly Smith Lucinda Billingham Alice Sitch Oke Gerke Mie Holm-Vilstrup Eivind Antonsen Segtnan Ulrich Halekoh Poul Flemming Høilund-Carlsen Bernard G. Francq Jac Dinnes Julie Parkes Walter Gregory Jenny Hewison Peter Selby Doug Altman William Rosenberg Julien Asselineau Paul Perez Aïssatou Paye Emilie Bessede Cécile Proust-Lima Christiana Naaktgeboren Joris de Groot Johannes Reitsma Anne Rutjes Emmanuel Ogundimu Jonathan Cook Yannick Le Manach Yvonne Vergouwe Romin Pajouheshnia Rolf Groenwold Karen Moons Linda Peelen Bavo De Cock Daan Nieboer Ewout W. Steyerberg Micael J. Pencina Jennifer Cooper Nick Parsons Chris Stinton Steve Smith Andy Dickens Rachel Jordan Alexandra Enocson David Fitzmaurice Peymane Adab Charles Boachie Gaj Vidmar Karoline Freeman Martin Connock Rachel Court Carl Moons Jessica Harris Zoe Plummer Barnaby Reeves Chris Rogers Andrew Mumford Kurtis Lee Veerle Verheyden Gianni D. Angelini Gavin J. Murphy Jeremy Huddy Melody Ni George Hanna Department of Clinical Epidemiology Biostatistics & Bioinformatics Academic Medical Center University of Amsterdam Amsterdam The Netherlands Department of Clinical Epidemiology and Biostatistics Academic Medical Center University of Amsterdam Amsterdam Netherlands Cochrane Netherlands Julius Center for Health Sciences and Primary Care University Medical Center Utrecht Utrecht Netherlands Cochrane Dementia and Cognitive Improvement Group University of Oxford Oxford UK EPPI-Centre Department of Social Science University College London London UK Division of Health and Social Care Research King’s College London London UK College of Computer and Information Science Northeastern University Boston USA University Hospitals Bristol NHS Foundation Trust School of Social and Community Medicine Bristol UK Institute of Applied Health Research University of Birmingham Birmingham UK School of Social and Community Medicine University of Bristol Bristol UK Kleijnen Systematic Reviews Ltd York UK Research Institute for Primary Care and Health Sciences Keele University Keele UK Centre for Statistics in Medicine Nuffield Department of Orthopaedics Rheumatology and Musculoskeletal Sciences University of Oxford Oxford UK Julius Center for Health Sciences and Primary Care University Medical Center Utrecht Utrecht The Netherlands Cochrane Netherlands University Medical Center Utrecht Utrecht The Netherlands Julius Center for Health Sciences and Primary Care University Medical Center Utrecht 3584 CG Utrecht Netherlands Department of Medical Statistics University Medical Center Göttingen Göttingen Germany Institute for Biometry and Epidemiology German Diabetes Center Leibniz Institute for Diabetes Research at Heinrich Heine University Düsseldorf Germany Manchester Pharmacy School University of Manchester Manchester UK Institute for Medical Biometry and Statistics Faculty of Medicine and Medical Center – University of Freiburg Stefan-Meier-Str. 26 79104 Freiburg Germany

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