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View of to Begin With, AHC Treats Each Data Object As a Separate the Data to the User, Frequently Achieved Using Clustering
BioData Mining BioMed Central Research Open Access Fast approximate hierarchical clustering using similarity heuristics Meelis Kull*1,2 and Jaak Vilo*1,2 Address: 1Institute of Computer Science, University of Tartu, Liivi 2, 50409 Tartu, Estonia and 2Quretec Ltd. Ülikooli 6a, 51003 Tartu, Estonia Email: Meelis Kull* - [email protected]; Jaak Vilo* - [email protected] * Corresponding authors Published: 22 September 2008 Received: 8 April 2008 Accepted: 22 September 2008 BioData Mining 2008, 1:9 doi:10.1186/1756-0381-1-9 This article is available from: http://www.biodatamining.org/content/1/1/9 © 2008 Kull and Vilo; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. Abstract Background: Agglomerative hierarchical clustering (AHC) is a common unsupervised data analysis technique used in several biological applications. Standard AHC methods require that all pairwise distances between data objects must be known. With ever-increasing data sizes this quadratic complexity poses problems that cannot be overcome by simply waiting for faster computers. Results: We propose an approximate AHC algorithm HappieClust which can output a biologically meaningful clustering of a large dataset more than an order of magnitude faster than full AHC algorithms. The key to the algorithm is to limit the number of calculated pairwise distances to a carefully chosen subset of all possible distances. We choose distances using a similarity heuristic based on a small set of pivot objects. -
Introductory Guide for Authors This Guide Is for Early-Career Researchers Who Are Beginning to Write Papers for Publication
Introductory guide for authors This guide is for early-career researchers who are beginning to write papers for publication. publishingsupport.iopscience.org publishingsupport.iopscience.org This guide is for early-career researchers who are beginning to write papers for publication. Academic publishing is rapidly changing, with new technologies and publication models giving authors much more choice over where and how to publish their work. Whether you are writing up the results of a PhD chapter or submitting your first paper, knowing how to prepare your work for publication is essential. This guide will provide an overview of academic publishing and advice on how to make the most of the process for sharing your research. For more information and to download a digital version of this guide go to publishingsupport.iopscience.org. c o n t e n t s Page Choosing where to submit your paper 4 Writing and formatting 6 Peer-review process 8 Revising and responding to referee reports 10 Acceptance and publication 12 Promoting your published work 13 Copyright and ethical integrity 14 Frequently asked questions 15 Publishing glossary 16 IOP publications 18 Introductory guide for authors 3 publishingsupport.iopscience.org Choosing where to submit your paper It can be tempting to begin writing a paper before giving much thought to where it might be published. However, choosing a journal to target before you begin to prepare your paper will enable you to tailor your writing to the journal’s audience and format your paper according to its specific guidelines, which you may find on the journal’s website. -
Diverse Convergent Evidence in the Genetic Analysis of Complex Disease
Dartmouth College Dartmouth Digital Commons Dartmouth Scholarship Faculty Work 6-30-2014 Diverse Convergent Evidence in the Genetic Analysis of Complex Disease: Coordinating Omic, Informatic, and Experimental Evidence to Better Identify and Validate Risk Factors Timothy H. Ciesielski Dartmouth College Sarah A. Pendergrass Pennsylvania State University, University Park Marquitta J. White Dartmouth College Nuri Kodaman Dartmouth College Rafal S. Sobota Dartmouth College Follow this and additional works at: https://digitalcommons.dartmouth.edu/facoa See next page for additional authors Part of the Medicine and Health Sciences Commons Dartmouth Digital Commons Citation Ciesielski, Timothy H.; Pendergrass, Sarah A.; White, Marquitta J.; Kodaman, Nuri; Sobota, Rafal S.; Huang, Minjun; Bartlett, Jacquelaine; Li, Jing; Pan, Qinxin; Gui, Jiang; Selleck, Scott B.; Amos, Christopher I.; Ritchie, Marylyn D.; Moore, Jason H.; and Williams, Scott M., "Diverse Convergent Evidence in the Genetic Analysis of Complex Disease: Coordinating Omic, Informatic, and Experimental Evidence to Better Identify and Validate Risk Factors" (2014). Dartmouth Scholarship. 2650. https://digitalcommons.dartmouth.edu/facoa/2650 This Article is brought to you for free and open access by the Faculty Work at Dartmouth Digital Commons. It has been accepted for inclusion in Dartmouth Scholarship by an authorized administrator of Dartmouth Digital Commons. For more information, please contact [email protected]. Authors Timothy H. Ciesielski, Sarah A. Pendergrass, Marquitta J. White, Nuri Kodaman, Rafal S. Sobota, Minjun Huang, Jacquelaine Bartlett, Jing Li, Qinxin Pan, Jiang Gui, Scott B. Selleck, Christopher I. Amos, Marylyn D. Ritchie, Jason H. Moore, and Scott M. Williams This article is available at Dartmouth Digital Commons: https://digitalcommons.dartmouth.edu/facoa/2650 Ciesielski et al. -
SCIENCE CITATION INDEX EXPANDED - JOURNAL LIST Total Journals: 8631
SCIENCE CITATION INDEX EXPANDED - JOURNAL LIST Total journals: 8631 1. 4OR-A QUARTERLY JOURNAL OF OPERATIONS RESEARCH 2. AAPG BULLETIN 3. AAPS JOURNAL 4. AAPS PHARMSCITECH 5. AATCC REVIEW 6. ABDOMINAL IMAGING 7. ABHANDLUNGEN AUS DEM MATHEMATISCHEN SEMINAR DER UNIVERSITAT HAMBURG 8. ABSTRACT AND APPLIED ANALYSIS 9. ABSTRACTS OF PAPERS OF THE AMERICAN CHEMICAL SOCIETY 10. ACADEMIC EMERGENCY MEDICINE 11. ACADEMIC MEDICINE 12. ACADEMIC PEDIATRICS 13. ACADEMIC RADIOLOGY 14. ACCOUNTABILITY IN RESEARCH-POLICIES AND QUALITY ASSURANCE 15. ACCOUNTS OF CHEMICAL RESEARCH 16. ACCREDITATION AND QUALITY ASSURANCE 17. ACI MATERIALS JOURNAL 18. ACI STRUCTURAL JOURNAL 19. ACM COMPUTING SURVEYS 20. ACM JOURNAL ON EMERGING TECHNOLOGIES IN COMPUTING SYSTEMS 21. ACM SIGCOMM COMPUTER COMMUNICATION REVIEW 22. ACM SIGPLAN NOTICES 23. ACM TRANSACTIONS ON ALGORITHMS 24. ACM TRANSACTIONS ON APPLIED PERCEPTION 25. ACM TRANSACTIONS ON ARCHITECTURE AND CODE OPTIMIZATION 26. ACM TRANSACTIONS ON AUTONOMOUS AND ADAPTIVE SYSTEMS 27. ACM TRANSACTIONS ON COMPUTATIONAL LOGIC 28. ACM TRANSACTIONS ON COMPUTER SYSTEMS 29. ACM TRANSACTIONS ON COMPUTER-HUMAN INTERACTION 30. ACM TRANSACTIONS ON DATABASE SYSTEMS 31. ACM TRANSACTIONS ON DESIGN AUTOMATION OF ELECTRONIC SYSTEMS 32. ACM TRANSACTIONS ON EMBEDDED COMPUTING SYSTEMS 33. ACM TRANSACTIONS ON GRAPHICS 34. ACM TRANSACTIONS ON INFORMATION AND SYSTEM SECURITY 35. ACM TRANSACTIONS ON INFORMATION SYSTEMS 36. ACM TRANSACTIONS ON INTELLIGENT SYSTEMS AND TECHNOLOGY 37. ACM TRANSACTIONS ON INTERNET TECHNOLOGY 38. ACM TRANSACTIONS ON KNOWLEDGE DISCOVERY FROM DATA 39. ACM TRANSACTIONS ON MATHEMATICAL SOFTWARE 40. ACM TRANSACTIONS ON MODELING AND COMPUTER SIMULATION 41. ACM TRANSACTIONS ON MULTIMEDIA COMPUTING COMMUNICATIONS AND APPLICATIONS 42. ACM TRANSACTIONS ON PROGRAMMING LANGUAGES AND SYSTEMS 43. ACM TRANSACTIONS ON RECONFIGURABLE TECHNOLOGY AND SYSTEMS 44. -
Genomic Analyses with Biofilter 2.0: Knowledge Driven
Pendergrass et al. BioData Mining 2013, 6:25 http://www.biodatamining.org/content/6/1/25 BioData Mining SOFTWARE ARTICLE Open Access Genomic analyses with biofilter 2.0: knowledge driven filtering, annotation, and model development Sarah A Pendergrass, Alex Frase, John Wallace, Daniel Wolfe, Neerja Katiyar, Carrie Moore and Marylyn D Ritchie* * Correspondence: [email protected] Abstract Center for Systems Genomics, Department of Biochemistry and Background: The ever-growing wealth of biological information available through Molecular Biology, The Pennsylvania multiple comprehensive database repositories can be leveraged for advanced State University, Eberly College of analysis of data. We have now extensively revised and updated the multi-purpose Science, The Huck Institutes of the Life Sciences, University Park, software tool Biofilter that allows researchers to annotate and/or filter data as well as Pennsylvania, PA, USA generate gene-gene interaction models based on existing biological knowledge. Biofilter now has the Library of Knowledge Integration (LOKI), for accessing and integrating existing comprehensive database information, including more flexibility for how ambiguity of gene identifiers are handled. We have also updated the way importance scores for interaction models are generated. In addition, Biofilter 2.0 now works with a range of types and formats of data, including single nucleotide polymorphism (SNP) identifiers, rare variant identifiers, base pair positions, gene symbols, genetic regions, and copy number variant (CNV) location information. Results: Biofilter provides a convenient single interface for accessing multiple publicly available human genetic data sources that have been compiled in the supporting database of LOKI. Information within LOKI includes genomic locations of SNPs and genes, as well as known relationships among genes and proteins such as interaction pairs, pathways and ontological categories. -
Graphene and Other 2D Materials a Selection of Cutting-Edge Research from Across the IOP Materials Portfolio Iopscience.Org/Graphene Contents
Graphene and other 2D materials A selection of cutting-edge research from across the IOP materials portfolio iopscience.org/graphene contents Foreword 3 2D Materials 6 Applied Physics Express 8 EPL 10 Japanese Journal of Applied Physics 12 Journal of Physics: Condensed Matter 14 Journal of Physics D: Applied Physics 16 Modelling and Simulation in Materials Science and Engineering 18 Nanotechnology 20 New Journal of Physics 22 Physica Scripta 24 Research on Progress in Physics 26 Science and Technology of Advanced Materials 28 Semiconductor Science and Technology 30 Physics World 32 Stay updated on graphene research by visiting Are you interested in other areas of science? iopscience.org/graphene. Visit our subject collections homepage to explore Latest articles, special issues, videos and news similar collections in other key topics. will be posted regularly. iopscience.org/subjects graphene and other 2D materials Driven by the discovery of new fundamental science and the potential for wide-ranging novel applications, research on graphene has expanded like no other recent field attracting the attention of thousands of scientists from across physics, chemistry, engineering, medicine and industry. This research activity has also triggered the emergence of a new generation of atomically thin “2D materials” demonstrating the potential for equally novel properties and technological innovations. Cover image: Coloured scanning electron micrograph (SEM) of a crumpled layer of graphene. Credit: Andre Geim, Kostya Novoselov/Science In response to this rapid pace of development, we are Photo Library. pleased to present a selection of high-impact articles from across the IOP materials journals portfolio covering a range of 2D materials that includes: • Graphene and graphene-derived materials • Silicene and germanene/silicane and germanane • Boron nitride • Transition metal dichalcogenides • 2D topological insulators • Complex oxides • Composite materials All of the featured articles are also collected online at iopscience.org/graphene. -
No-Boundary Thinking in Bioinformatics
Huang et al. BioData Mining 2013, 6:19 http://www.biodatamining.org/content/6/1/19 BioData Mining REVIEW Open Access No-boundary thinking in bioinformatics research Xiuzhen Huang1*, Barry Bruce2, Alison Buchan3, Clare Bates Congdon4, Carole L Cramer5, Steven F Jennings6, Hongmei Jiang7, Zenglu Li8, Gail McClure9, Rick McMullen10, Jason H Moore11, Bindu Nanduri12, Joan Peckham13, Andy Perkins14, Shawn W Polson15, Bhanu Rekepalli16, Saeed Salem17, Jennifer Specker18, Donald Wunsch19, Donghai Xiong20, Shuzhong Zhang21 and Zhongming Zhao22 * Correspondence: [email protected] Abstract 1Department of Computer Science, Arkansas State University, Jonesboro, Currently there are definitions from many agencies and research societies defining AR 72467, USA “bioinformatics” as deriving knowledge from computational analysis of large volumes of Full list of author information is biological and biomedical data. Should this be the bioinformatics research focus? We will available at the end of the article discuss this issue in this review article. We would like to promote the idea of supporting human-infrastructure (HI) with no-boundary thinking (NT) in bioinformatics (HINT). Keywords: No-boundary thinking, Human infrastructure The Big-data paradigm Today’s data-intensive computing (“big data”) was advocated by the 1998 Turing Award1 recipient, Jim Gray, as the fourth paradigm for scientific discovery [1] after direct experimentation, theoretical mathematical physics and chemistry, and computer simulation. With the rapid advance of biotechnologies and development of clinical record systems, we have witnessed an exponential growth of data ranging from “omics” (such as genomics, proteomics, metabolomics, and pharmacogenomics), imaging data, to electronic medical record data. Last year, the federal funding agencies National Institutes of Health (NIH) and National Science Foundation (NSF) exer- cised a joint effort to launch big-data initiatives and consortia to promote and support big-data projects [2]. -
Impact Factor Journals in Physics
Impact Factor Journals in Physics Indexed in ISI Web of Science (JCR SCI, 2019) ______________________________________________________________________________________________________________________ Compiled By: Arslan Sheikh In Charge Reference & Research Section Junaid Zaidi Library COMSATS University Islamabad Park Road, Islamabad-Pakistan. Cell: 92+321-9423071 [email protected] 2019 Impact Rank Journal Title Factor 1 REVIEWS OF MODERN PHYSICS 45.037 2 NATURE MATERIALS 38.663 3 Living Reviews in Relativity 35.429 4 Nature Photonics 31.241 5 ADVANCED MATERIALS 27.398 6 MATERIALS SCIENCE & ENGINEERING R-REPORTS 26.625 7 PHYSICS REPORTS-REVIEW SECTION OF PHYSICS LETTERS 25.798 8 Advanced Energy Materials 25.245 9 Nature Physics 19.256 10 Applied Physics Reviews 17.054 11 REPORTS ON PROGRESS IN PHYSICS 17.032 12 ADVANCED FUNCTIONAL MATERIALS 16.836 13 Nano Energy 16.602 14 ADVANCES IN PHYSICS 16.375 15 Annual Review of Fluid Mechanics 16.306 16 Annual Review of Condensed Matter Physics 14.833 17 PROGRESS IN PARTICLE AND NUCLEAR PHYSICS 13.421 18 Physical Review X 12.577 19 Nano-Micro Letters 12.264 20 Small 11.459 21 NANO LETTERS 11.238 22 Laser & Photonics Reviews 10.655 23 Materials Today Physics 10.443 24 SURFACE SCIENCE REPORTS 9.688 25 CURRENT OPINION IN SOLID STATE & MATERIALS SCIENCE 9.571 26 npj 2D Materials and Applications 9.324 27 PROGRESS IN NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY 8.892 28 Annual Review of Nuclear and Particle Science 8.778 29 PHYSICAL REVIEW LETTERS 8.385 1 | P a g e Junaid Zaidi Library, COMSATS -
Biodata Mining Biomed Central
BioData Mining BioMed Central Research Open Access Search extension transforms Wiki into a relational system: A case for flavonoid metabolite database Masanori Arita*1,2,3 and Kazuhiro Suwa1 Address: 1Department of Computational Biology, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwanoha 5-1-5 CB05, Kashiwa, Japan, 2Metabolome Informatics Unit, Plant Science Center, RIKEN, Japan and 3Institute for Advanced Biosciences, Keio University, Japan Email: Masanori Arita* - [email protected]; Kazuhiro Suwa - [email protected] * Corresponding author Published: 17 September 2008 Received: 23 May 2008 Accepted: 17 September 2008 BioData Mining 2008, 1:7 doi:10.1186/1756-0381-1-7 This article is available from: http://www.biodatamining.org/content/1/1/7 © 2008 Arita and Suwa; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. Abstract Background: In computer science, database systems are based on the relational model founded by Edgar Codd in 1970. On the other hand, in the area of biology the word 'database' often refers to loosely formatted, very large text files. Although such bio-databases may describe conflicts or ambiguities (e.g. a protein pair do and do not interact, or unknown parameters) in a positive sense, the flexibility of the data format sacrifices a systematic query mechanism equivalent to the widely used SQL. Results: To overcome this disadvantage, we propose embeddable string-search commands on a Wiki-based system and designed a half-formatted database. -
Memoria Curso Académico 2010-2011 DEPARTAMENTO DE
Memoria Curso Académico 2010-2011 Departamentos DEPARTAMENTO DE DEPORTE E INFORMÁTICA DIRECCIÓN DEL DEPARTAMENTO Director: Prof. Dr. D. Francisco José Berral de la Rosa Subdirector: Prof. Dr. D. Federico Divina Secretario: Prof. Dr. D. Roberto Ruiz Sánchez Sesiones y Principales Acuerdos Adoptados Sesión ordinaria, celebrada el 5 de octubre de 2010 Se aprueba por asentimiento la solicitud de convocatoria de plaza de profesor/a funcionario/a docente para el Área de Educación Física y Deportiva del Departamento con los siguientes datos: Cuerpo docente: profesor/a titular de universidad. Área de Conocimiento: Educación Física y Deportiva Perfil: Planificación y Gestión del Deporte. Calidad Servicios Deportivos. Comisión titular: Presidente: Dr. D. Francisco José Berral de la Rosa. Profesor titular de universidad (Universidad Pablo de Olavide). Vocal: Dr.ª D.ª Belén Tabernero Sánchez. Profesora titular de universidad (Universidad de Salamanca). Secretario: Dr. D. Juan José González Badillo. Profesor Titular de Universidad (Universidad Pablo de Olavide). Comisión suplente: Presidente: Dr. D. José Antonio Casajús Mallén. Profesor titular de universidad (Universidad de Zaragoza). Vocal: Dr.ª D.ª M.ª Perla Arroyo Moreno. Profesora titular de Universidad (Universidad de Extremadura). Secretario: Dr. D. Manuel Delgado Fernández. Profesor titular de universidad (Universidad de Granada). -1- Memoria Curso Académico 2010-2011 Departamentos Se aprueba por asentimiento la propuesta de contratación de un profesor/a sustituto/a para el Área de Lenguaje y Sistemas Informáticos, debido a que han quedado plazas de profesores/as desiertas. El candidato es D. Francisco Gómez Vela. Se aprueba por asentimiento la contratación de un profesor/a sustituto/a para el Área de Educación Física y Deportiva, debido a la renuncia del profesor D. -
O Brave New World That Has Such Machines in It James D Malley1, Karen G Malley2 and Jason H Moore3*
Malley et al. BioData Mining 2014, 7:26 http://www.biodatamining.org/content/7/1/26 BioData Mining EDITORIAL Open Access O brave new world that has such machines in it James D Malley1, Karen G Malley2 and Jason H Moore3* * Correspondence: Machine learning is a critical component of any biological data mining. Given its [email protected] established advantages, there remain challenges that need to be addressed before it can 3Departments of Genetics and Community and Family Medicine, be considered practical and persuasive. Institute for Quantitative Biomedical The Tempest Sciences, The Geisel School of Thus, not quite (Act V, Scene One), above, but Shakespeare would still Medicine, Dartmouth College, One have understood: learning machines have achieved stunning success in a stunning Medical Center Dr., Lebanon, NH — — 03756, USA range of areas, but they are still often correctly seen as strange and mysterious. Full list of author information is They make predictions {tumor, not tumor} with ease and rapidity, but how do we available at the end of the article understand the forecasts? How were the forecasts made, and how do they apply to this patient, with this set of symptoms and exposure factors? How does a low mean square error translate into guidance for patient treatment and care? How is any machine translated? These questions point to an unfortunate separation between the advances of learning machines and the needs of biomedical research or patient care. We have written about the nearly invisible interest shown by computer science groups in the shared task of communication and joint application, and a dis- connect between some statistical teaching practices and the needs of researchers and medical practitioners [1]. -
— Messages from STAM 02 NIMS NOW International 2013 October Expanding Scientifi C Communication — Messages from STAM
2013 No. 8 October Expanding Scientific Communication — Messages from STAM 02 NIMS NOW International 2013 October Expanding Scientifi c Communication — Messages from STAM About 2.4 million scientific articles are published every year, and this number keeps growing. Amid the fi erce competition toward a higher impact factor, which now even affects national policy, the situation surrounding science and article publication is changing at an ever-increasing pace. Scientists, readers and publishers are being asked about the reasons for writing an article and selecting a journal for publication. Science and Technology of Advanced Materials (STAM), a materials science open-access journal supported by NIMS, is in the middle of this trend. How can science reach people? How should STAM select articles for publication? We aim to communicate our answers to these questions through our editing and publishing activities. NIMS NOW International 2013 October 03 Expanding Scientific Communication — Messages from STAM Special Discussion: Future of academic journals and STAM Science and Technology of Advanced Materials (STAM) is increasing its presence as a materials science journal not only in Japan, but also abroad. How is STAM received at materials science research sites? What kind of journal does STAM aim to become in the future? These and other topics are discussed below by Masakazu Aono, Director-General of the International Center for Materi- als Nanoarchitectonics (MANA), Toyonobu Yoshida, Editor-in-Chief of STAM, and Mikiko Tanifuji, publisher of STAM and Head of the Scientific Information Office at NIMS. Importance of having a Japanese important new research on elementary parti- the citation number (CN) of each of the enor- materials science journal cles into the spotlight.