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João C. Setubal Nalvo F. Almeida (Eds.) Advances in Bioinformatics and LNBI 8213 Computational Biology 8th Brazilian Symposium on Bioinformatics, BSB 2013 Recife, Brazil, November 2013 Proceedings 123 Lecture Notes in Bioinformatics 8213 Edited by S. Istrail, P. Pevzner, and M. Waterman Editorial Board: A. Apostolico S. Brunak M. Gelfand T. Lengauer S. Miyano G. Myers M.-F. Sagot D. Sankoff R. Shamir T. Speed M. Vingron W. Wong Subseries of Lecture Notes in Computer Science João C. Setubal Nalvo F. Almeida (Eds.) Advances in Bioinformatics and Computational Biology 8th Brazilian Symposium on Bioinformatics, BSB 2013 Recife, Brazil, November 3-7, 2013 Proceedings 13 Volume Editors João C. Setubal University of São Paulo, Institute of Chemistry Avenida Prof. Lineu Prestes, 748 sala 911, 05508-000 São Paulo, SP, Brazil E-mail: [email protected] Nalvo F. Almeida Federal University of Mato Grosso do Sul, School of Computing Facom-UFMS, CP 549, 79070-900 Campo Grande, MS, Brazil E-mail: [email protected] ISSN 0302-9743 e-ISSN 1611-3349 ISBN 978-3-319-02623-7 e-ISBN 978-3-319-02624-4 DOI 10.1007/978-3-319-02624-4 Springer Cham Heidelberg New York Dordrecht London Library of Congress Control Number: 2013949541 CR Subject Classification (1998): J.3, F.2, H.2, I.5, I.2, F.1, I.5 LNCS Sublibrary: SL 8 – Bioinformatics © Springer International Publishing Switzerland 2013 This work is subject to copyright. All rights are reserved by the Publisher, whether the whole or part of the material is concerned, specifically the rights of translation, reprinting, reuse of illustrations, recitation, broadcasting, reproduction on microfilms or in any other physical way, and transmission or information storage and retrieval, electronic adaptation, computer software, or by similar or dissimilar methodology now known or hereafter developed. Exempted from this legal reservation are brief excerpts in connection with reviews or scholarly analysis or material supplied specifically for the purpose of being entered and executed on a computer system, for exclusive use by the purchaser of the work. Duplication of this publication or parts thereof is permitted only under the provisions of the Copyright Law of the Publisher’s location, in its current version, and permission for use must always be obtained from Springer. Permissions for use may be obtained through RightsLink at the Copyright Clearance Center. Violations are liable to prosecution under the respective Copyright Law. The use of general descriptive names, registered names, trademarks, service marks, etc. in this publication does not imply, even in the absence of a specific statement, that such names are exempt from the relevant protective laws and regulations and therefore free for general use. While the advice and information in this book are believed to be true and accurate at the date of publication, neither the authors nor the editors nor the publisher can accept any legal responsibility for any errors or omissions that may be made. The publisher makes no warranty, express or implied, with respect to the material contained herein. Typesetting: Camera-ready by author, data conversion by Scientific Publishing Services, Chennai, India Printed on acid-free paper Springer is part of Springer Science+Business Media (www.springer.com) Preface This volume contains the papers selected for presentation at the 8th Brazilian Symposium on Bioinformatics (BSB 2013), held during November 3–6, 2013, in Recife, Brazil. BSB is an international conference that covers all aspects of bioin- formatics and computational biology. This year the event was jointly organized by the special interest group in Computational Biology of the Brazilian Com- puter Society (SBC), which has been the organizer of BSB for the past several years, and by the Brazilian Association for Bioinformatics and Computational Biology (AB3C), which has been the organizer of another event, the X-Meeeting, also for the past several years. This year for the first time the two events were co-located. As in previous editions, BSB 2013 had an international Program Committee (PC) of 46 members. After a rigorous review process by the PC, 18 papers were accepted to be orally presented at the event, and are printed in this volume. In addition to the technical presentations, BSB 2013 featured keynote talks from David Roos (University of Pennsylvania), Peter Stadler (University of Leipzig), and Martin Tompa (University of Washington). Peter Stadler graciously con- tributed an invited paper to these proceedings (“The Trouble with Long-Range Base Pairs in RNA Folding”). BSB 2013 was made possible by the dedication and work of many people and organizations. We would like to express our sincere thanks to all PC members, as well as to the external reviewers. Their names are listed in the pages that follow. We are also grateful to the local organizers and volunteers for their valuable help; the sponsors for making the event financially viable; Guilherme P. Telles and Peter Stadler for assisting in the preparation of the proceedings; and Springer for agreeing to publish this volume. Finally, we would like to thank all authors for their time and effort in submitting their work and the invited speakers for having accepted our invitation. This year selected BSB 2013 papers were invited for submission in expanded format to a special issue of the IEEE/ACM Transactions on Computational Biology and Bioinformatics. We thank Ying Xu (Editor-in-Chief) and Dong Xu (Associate Editor-in-Chief) for this opportunity. November 2013 Jo˜ao C. Setubal Nalvo F. Almeida Organization BSB 2013 was organized by Universidade Federal de Pernambuco. Conference Chairs Katia S. Guimar˜aes Universidade Federal de Pernambuco, Brazil Paulo Gustavo S. Fonseca Universidade Federal de Pernambuco, Brazil Ana Benko Iseppon Universidade Federal de Pernambuco, Brazil Valdir Balbino Universidade Federal de Pernambuco, Brazil Program Chairs Jo˜ao C. Setubal Universidade de S˜ao Paulo, Brazil Nalvo F. Almeida Universidade Federal de Mato Grosso do Sul, Brazil Steering Comittee Guilherme P. Telles (President) Universidade Estadual de Campinas, Brazil Ivan G. Costa Filho Universidade Federal de Pernambuco, Brazil Luis Antonio Kowada Universidade Federal Fluminense, Brazil Marcelo de Macedo Br´ıgido Universidade de Bras´ılia, Brazil Marcilio C.P. de Souto Universit´e d’Orl´eans, France Osmar Norberto de Souza PUC Rio Grande do Sul, Brazil S´ergio Vale Aguiar Campos Universidade Federal de Minas Gerais, Brazil Sponsors Sociedade Brasileira de Computa¸c˜ao (SBC) Associa¸c˜ao Brasileira de Bioinform´atica e Biologia Computacional (AB3C) Funding Conselho Nacional de Desenvolvimento Cient´ıfico e Tecnol´ogico (CNPq) Coordena¸c˜ao de Aperfei¸coamento de Pessoal de N´ıvel Superior (CAPES) Funda¸c˜ao de Amparo `aCiˆencia e Tecnologia de Pernambuco (FACEPE) VIII Organization Program Committee Said S. Adi Universidade Federal de Mato Grosso do Sul, Brazil Nalvo F. Almeida Universidade Federal de Mato Grosso do Sul, Brazil Fernando Alvarez-Val´´ ın Universidad de la Republica, Uruguay Ana L.C. Bazzan Universidade Federal do Rio Grande do Sul, Brazil Ana M. Benko-Iseppon Universidade Federal de Pernambuco, Brazil Mar´ılia D.V. Braga Inmetro, Brazil Marcelo de Macedo Br´ıgido Universidade de Bras´ılia, Brazil Sergio Campos Universidade Federal de Minas Gerais, Brazil Alessandra Carbone Pierre and Marie Curie University, France Ivan Gesteira Costa Universidade Federal de Pernambuco, Brazil Andr´e C.P.L.F. de Carvalho Universidade de S˜ao Paulo/S˜ao Carlos, Brazil Marcilio de Souto Universit´e d’Orl´eans, France Emanuel Maltempi de Souza Universidade Federal do Paran´a, Brazil Osmar Norberto de Souza PUC Rio Grande do Sul, Brazil Luciano Digiampietri Universidade de S˜ao Paulo, Brazil Alan Durham Universidade de S˜ao Paulo, Brazil Carlos E. Ferreira Universidade de S˜ao Paulo, Brazil Andr´e Fujita Universidade de S˜ao Paulo, Brazil Katia S. Guimar˜aes Universidade Federal de Pernambuco, Brazil Lenny Heath Virginia Tech, USA Dirk Husmeier University of Glasgow, UK Andre Kashiwabara Universidade Tecnol´ogica Federal do Paran´a, Brazil Ney Lemke Universidade Est. Paulista J´ulio Mesquita Filho, Brazil Sergio Lifschitz PUC Rio de Janeiro, Brazil Ana Carolina Lorena Universidade Federal do ABC, Brazil Wellington Martins Universidade Federal de Goi´as, Brazil Marta Mattoso Universidade Federal do Rio de Janeiro, Brazil Satoru Miyano University of Tokyo, Japan Houtan Noushmehr Universidade de S˜ao Paulo, Brazil Guilherme Oliveira Funda¸c˜ao Oswaldo Cruz, Minas Gerais, Brazil Alexey Onufriev Virginia Tech, USA Miguel Ortega Universidade Federal de Minas Gerais, Brazil Sergio Pantano Instituto Pasteur de Montevideo, Uruguay Alexandre Rossi Paschoal Universidade Tecnol´ogica Federal do Paran´a, Brazil Duncan Ruiz PUC Rio Grande do Sul, Brazil Marie-France Sagot Inria, France Alexander Schliep Rutgers University, USA Organization IX Jo˜ao Setubal Universidade de S˜ao Paulo, Brazil Peter F. Stadler University of Leipzig, Germany Jens Stoye University of Bielefeld, Germany Guilherme P. Telles Universidade Estadual de Campinas, Brazil Thiago Venancio Universidade Federal Fluminense, Brazil Maria Emilia T. Walter Universidade de Bras´ılia, Brazil Additional Reviewers Poly Hannah Da Silva Universidade Federal Fluminense, Brazil Marcelo Henriques de Carvalho Universidade Federal de Mato Grosso do Sul, Brazil Zanoni Dias Universidade Estadual de Campinas, Brazil Marcio Dorn Universidade Federal do Rio Grande do Sul, Brazil Alessandra Faria-Campos
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  • CDC123 Antibody (RQ6088)

    CDC123 Antibody (RQ6088)

    CDC123 Antibody (RQ6088) Catalog No. Formulation Size RQ6088 0.5mg/ml if reconstituted with 0.2ml sterile DI water 100 ug Bulk quote request Availability 1-3 business days Species Reactivity Human Format Antigen affinity purified Clonality Polyclonal (rabbit origin) Isotype Rabbit IgG Purity Affinity purified Buffer Lyophilized from 1X PBS with 2% Trehalose and 0.025% sodium azide UniProt O75794 Localization Cytoplasmic Applications Western blot : 1-2ug/ml Immunohistochemistry (FFPE) : 2-5ug/ml Immunofluorescence : 5ug/ml Flow cytometry : 1-3ug/million cells Direct ELISA : 0.1-0.5ug/ml Limitations This CDC123 antibody is available for research use only. Immunofluorescent staining of FFPE human A431 cells with CDC123 antibody (green) and DAPI nuclear stain (blue). HIER: steam section in pH6 citrate buffer for 20 min. IHC staining of FFPE human pancreatic cancer with CDC123 antibody. HIER: boil tissue sections in pH8 EDTA for 20 min and allow to cool before testing. IHC staining of FFPE human bladder cancer with CDC123 antibody. HIER: boil tissue sections in pH8 EDTA for 20 min and allow to cool before testing. IHC staining of FFPE human appendicitis tissue with CDC123 antibody. HIER: boil tissue sections in pH8 EDTA for 20 min and allow to cool before testing. IHC staining of FFPE human ovarian cancer with CDC123 antibody. HIER: boil tissue sections in pH8 EDTA for 20 min and allow to cool before testing. IHC staining of FFPE human liver cancer with CDC123 antibody. HIER: boil tissue sections in pH8 EDTA for 20 min and allow to cool before testing. IHC staining of FFPE human gastric cancer with CDC123 antibody.