DOCSLIB.ORG

Hot Topics in Structural Genomics†

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
Hot Topics in Structural Genomics† Comparative and Functional Genomics Comp Funct Genom 2003; 4: 394–396. Published online in Wiley InterScience (www.interscience.wiley.com). DOI: 10.1002/cfg.314 Conference Report The 4th Bologna Winter School: hot topics in structural genomics† Rita Casadio* Department of Biology/CIRB, University of Bologna, Via Irnerio 42, 40126 Bologna, Italy *Correspondence to: Abstract Rita Casadio, Department of Biology/CIRB, University of The 4th Bologna Winter School on Biotechnologies was held on 9–15 February Bologna, Via Irnerio 42, 40126 2003 at the University of Bologna, Italy, with the specific aim of discussing recent Bologna, Italy. developments in bioinformatics. The school provided an opportunity for students E-mail: [email protected] and scientists to debate current problems in computational biology and possible solutions. The course, co-supported (as last year) by the European Science Foundation program on Functional Genomics, focused mainly on hot topics in structural genomics, including recent CASP and CAPRI results, recent and promising genome- Received: 3 June 2003 wide predictions, protein–protein and protein–DNA interaction predictions and Revised: 5 June 2003 genome functional annotation. The topics were organized into four main sections Accepted: 5 June 2003 (http://www.biocomp.unibo.it). Published in 2003 by John Wiley & Sons, Ltd. Predictive methods in structural Predictive methods in functional genomics genomics • Contemporary challenges in structure prediction • Prediction of protein function (Arthur Lesk, and the CASP5 experiment (John Moult, Uni- University of Cambridge, Cambridge, UK). versity of Maryland, Rockville, MD, USA). • Microarray data analysis and mining (Raf- • Contemporary challenges in structure prediction faele Calogero, University of Torino, Torino, (Anna Tramontano, University ‘La Sapienza’, Italy). Rome, Italy). • Prediction of protein function and protein net- • Prediction of protein structure and function at the works (Søren Brunak Technical University of genomic scale (Jeffrey Skolnick, Buffalo Center Denmark, Lyngby, Denmark, and Alfonso Valen- of Excellence in Bioinformatics, Buffalo, NY, cia, National Centre of Biotechnology, Canto- USA). blanco, Spain). • Advanced automated machine learning appr- oaches (David Jones, University College, Lon- don, UK). • Fully automated ab initio protein structure pre- Prediction of membrane protein diction (Chris Bystroff, Rensselaer Polytechnic structure Institute, Troy, NY, USA). • Automatic fold recognition prediction (Daniel • Fischer, Ben Gurion University, Be’er Sheva, The prediction of membrane protein topology Israel). (Gunnar von Heijne, University of Stockholm, Stockholm, Sweden, and Stephen White, Uni- versity of California, Irvine, CA, USA). † This article is an adaptation of the Conference Report on this • workshop (published to satisfy the requirements of the ESF Application of structural genomics tools to fish- funding) previously published on the Integrated Approaches for ing for new membrane proteins (Rita Casadio, Functional Genomics website. University of Bologna, Italy). Published in 2003 by John Wiley & Sons, Ltd. 4th Bologna Winter School: hot topics in structural genomics 395 Prediction of protein–protein What about predicting function? and protein–DNA interaction • The CAPRI experiment and the prediction of Raffaele Calogero discussed DNA microarray tech- protein–protein interactions (Joel Janin, LEBS, nology, a high-throughput method for gaining CNRS, Gif sur Yvette, France). information on gene function. However, genomes • Prediction of protein complexes based on evolu- can only be completely annotated when we can tionary information (Patrick Aloy, EMBL Hei- predict the function, possibly starting from the delberg, Germany). sequence. This is presently a really difficult and • Prediction of protein–DNA complexes (Sue challenging task, as Arthur Lesk pointed out in Jones, European Bioinformatics Institute, Hinx- his talk. Søren Brunak has used a suite of pro- ton, UK). grams, integrating predictions of different structural • Prediction of functional patches in proteins and functional properties, to successfully address (Manuela Helmer Citterich University of Tor this problem. Alfonso Valencia described how pre- Vergata, Rome, Italy, and Nir Ben Tal, Tel Aviv dictions are of a quality similar to the exper- University, Tel Aviv, Israel). imental data, when different interacting protein networks (at the basis of systems biology, and obtained using both theoretical and experimental What can we predict in the post genomic approaches) are compared. Also, the interactions era? Is it feasible to perform large-scale detected by more than one method have a substan- prediction on entire genomes? How can tially higher confidence. we cope with predictive tools? The CASP (critical assessment of protein structure prediction techniques) experiment reports on how Good results are being achieved in the different methods perform in specific predictive case of globular proteins, but when it tasks. The results had been debated just 2 months comes to membrane proteins, the earlier at the CASP5 meeting in Asilomar on 1–5 situation is much worse December 2002 (http://predictioncenter.llnl.gov/ casp5/Casp5.html). Apparently, as explained by its organizer (John Moult) and one of its asses- Less than 1% of PDB structures are membrane sors (Anna Tramontano, assessor of the homology proteins and, as a result, building by homol- building section), one cannot state that a partic- ogy is hampered by the paucity of examples, ular method is the best. There are several excel- except possibly in the case of outer membrane lent tools that, when integrated into meta-servers proteins. The β-barrel architecture is rather con- (as described by Daniel Fisher), can perform fold served and the changes that are seen are in recognition in a very satisfactory way. Therefore, the number of antiparallel beta strands. Once integrated knowledge will help us in solving the this is predicted, a 3D model can be computed folding problem also on a genome-wide scale. Jef- with a threading procedure (as explained in my frey Skolnick is modelling most of the protein own presentation). In the case of inner mem- content of presently available known proteomes, brane proteins, one is mainly left with the pre- including some functional properties, based on a diction of topological models. Gunnar von Hei- sequence-to-structure-to-function paradigm. With a jne presented some recent advances in the iden- very low rate of false positives, his tools can also tification of membrane protein topology and its predict folds of some 30–50% of the proteins. prediction with bioinformatic methods. Stephen Machine learning approaches form the basis of the White described two Web-based tools, MPEx most successful tools for prediction of structural (http://blanco.biomol.uci.edu/mpex) and MPtopo features, including secondary structure of proteins, (http://blanco.biomol.uci.edu/mptopo), which are as David Jones reported. Chris Bystroff explained based on chemical-physical properties of trans- that proteins can also be predicted ab initio,pro- membrane α-helices and ‘designed to help experi- vided that an HMM-based method, predicting pro- mentalists explore the topology of membrane pro- tein contact maps, is used. teins of unknown 3D structure’. Published in 2003 by John Wiley & Sons, Ltd. Comp Funct Genom 2003; 4: 394–396. 396 R. Casadio Can we predict protein–protein characterization (Alessandro Desideri, University and protein–DNA interactions? of Tor Vergata, Rome, Italy, and Richard Wag- ner, University of Osnabruck,¨ Germany), protein Joel Janin described the CAPRI (critical assessment structure determination with NMR (Henriette Moli- of predicted interactions; http://capri.ebi.ac.uk) nari, University of Verona, Italy), and protein fold- experiment. Inspired by CASP, it similarly accepts ing studies with atomic force microscopy (Bruno predictions of proteins interacting in complexes, Samori, University of Bologna, Italy). whose structures are known only after the submis- The take home message was that bioinformatics sion is closed. The results of the last edition (which can offer solutions to problems, provided that were evaluated by Shoshana Wodak and Raul theoreticians and experimentalists work in close Mendez, Free University of Brussels, Belgium) collaboration to benefit from both a computational show significant success on some of the targets. and an experimental approach. However, the predictions failed on other targets, and Joel believes that progress is necessary ‘in the Acknowledgements score functions, and in the way docking procedures handle conformation changes and non-structural The school was made possible thanks to the invaluable information, before large-scale predictions of pro- help of Piero Fariselli, Pier Luigi Martelli, Ivan Rossi, Gianluca Tasco, Emidio Capriotti, Luca Malaguti, Remo tein–protein interactions can be made reliably’ Calabrese and Mario Compiani, all at the Biocomputing (http://www.biocomp.unibo.it/school/html2003). Unit, and the precious collaboration of Professor Lanfranco Sue Jones detailed some interesting features of pro- Masotti (Co-chairman of the School) at the Department tein–DNA complexes and Patrick Aloy explained of Biochemistry, University of Bologna. Other supporting how protein interactions can be predicted through organizations were: the University of Bologna, the Interde- tertiary structure. If we know the structure, we can partmental Centre for Biotechnological
Load more

Recommended publications
  • RECENT ADVANCES in BIOLOGY, BIOPHYSICS, BIOENGINEERING and COMPUTATIONAL CHEMISTRY
    RECENT ADVANCES in BIOLOGY, BIOPHYSICS, BIOENGINEERING and COMPUTATIONAL CHEMISTRY Proceedings of the 5th WSEAS International Conference on CELLULAR and MOLECULAR BIOLOGY, BIOPHYSICS and BIOENGINEERING (BIO '09) Proceedings of the 3rd WSEAS International Conference on COMPUTATIONAL CHEMISTRY (COMPUCHEM '09) Puerto De La Cruz, Tenerife, Canary Islands, Spain December 14-16, 2009 Recent Advances in Biology and Biomedicine A Series of Reference Books and Textbooks Published by WSEAS Press ISSN: 1790-5125 www.wseas.org ISBN: 978-960-474-141-0 RECENT ADVANCES in BIOLOGY, BIOPHYSICS, BIOENGINEERING and COMPUTATIONAL CHEMISTRY Proceedings of the 5th WSEAS International Conference on CELLULAR and MOLECULAR BIOLOGY, BIOPHYSICS and BIOENGINEERING (BIO '09) Proceedings of the 3rd WSEAS International Conference on COMPUTATIONAL CHEMISTRY (COMPUCHEM '09) Puerto De La Cruz, Tenerife, Canary Islands, Spain December 14-16, 2009 Recent Advances in Biology and Biomedicine A Series of Reference Books and Textbooks Published by WSEAS Press www.wseas.org Copyright © 2009, by WSEAS Press All the copyright of the present book belongs to the World Scientific and Engineering Academy and Society Press. All rights reserved. No part of this publication may be reproduced, stored in a retrieval system, or transmitted in any form or by any means, electronic, mechanical, photocopying, recording, or otherwise, without the prior written permission of the Editor of World Scientific and Engineering Academy and Society Press. All papers of the present volume were peer reviewed
    [Show full text]
  • ISMB 2008 Toronto
    ISMB 2008 Toronto The Harvard community has made this article openly available. Please share how this access benefits you. Your story matters Citation Linial, Michal, Jill P. Mesirov, B. J. Morrison McKay, and Burkhard Rost. 2008. ISMB 2008 Toronto. PLoS Computational Biology 4(6): e1000094. Published Version doi:10.1371/journal.pcbi.1000094 Citable link http://nrs.harvard.edu/urn-3:HUL.InstRepos:11213310 Terms of Use This article was downloaded from Harvard University’s DASH repository, and is made available under the terms and conditions applicable to Other Posted Material, as set forth at http:// nrs.harvard.edu/urn-3:HUL.InstRepos:dash.current.terms-of- use#LAA Message from ISCB ISMB 2008 Toronto Michal Linial1,2, Jill P. Mesirov1,3, BJ Morrison McKay1*, Burkhard Rost1,4 1 International Society for Computational Biology (ISCB), University of California San Diego, La Jolla, California, United States of America, 2 Sudarsky Center, The Hebrew University of Jerusalem, Jerusalem, Israel, 3 Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America, 4 Department of Biochemistry and Molecular Biophysics, Columbia University, New York, New York, United States of America the integration of students, and for the of ISMB. One meeting in South Asia support of young leaders in the field. (InCoB; http://incob.binfo.org.tw/) has ISMB has also become a forum for already been sponsored by ISCB, and reviewing the state of the art in the many another one in North Asia is going to fields of this growing discipline, for follow. ISMB itself has also been held in introducing new directions, and for an- Australia (2003) and Brazil (2006).
    [Show full text]
  • Methodology for Predicting Semantic Annotations of Protein Sequences by Feature Extraction Derived of Statistical Contact Potentials and Continuous Wavelet Transform
    Universidad Nacional de Colombia Sede Manizales Master’s Thesis Methodology for predicting semantic annotations of protein sequences by feature extraction derived of statistical contact potentials and continuous wavelet transform Author: Supervisor: Gustavo Alonso Arango Dr. Cesar German Argoty Castellanos Dominguez A thesis submitted in fulfillment of the requirements for the degree of Master’s on Engineering - Industrial Automation in the Department of Electronic, Electric Engineering and Computation Signal Processing and Recognition Group June 2014 Universidad Nacional de Colombia Sede Manizales Tesis de Maestr´ıa Metodolog´ıapara predecir la anotaci´on sem´antica de prote´ınaspor medio de extracci´on de caracter´ısticas derivadas de potenciales de contacto y transformada wavelet continua Autor: Tutor: Gustavo Alonso Arango Dr. Cesar German Argoty Castellanos Dominguez Tesis presentada en cumplimiento a los requerimientos necesarios para obtener el grado de Maestr´ıaen Ingenier´ıaen Automatizaci´onIndustrial en el Departamento de Ingenier´ıaEl´ectrica,Electr´onicay Computaci´on Grupo de Procesamiento Digital de Senales Enero 2014 UNIVERSIDAD NACIONAL DE COLOMBIA Abstract Faculty of Engineering and Architecture Department of Electronic, Electric Engineering and Computation Master’s on Engineering - Industrial Automation Methodology for predicting semantic annotations of protein sequences by feature extraction derived of statistical contact potentials and continuous wavelet transform by Gustavo Alonso Arango Argoty In this thesis, a method to predict semantic annotations of the proteins from its primary structure is proposed. The main contribution of this thesis lies in the implementation of a novel protein feature representation, which makes use of the pairwise statistical contact potentials describing the protein interactions and geometry at the atomic level.
    [Show full text]
  • Biocreative II.5 Workshop 2009 Special Session on Digital Annotations
    BioCreative II.5 Workshop 2009 Special Session on Digital Annotations The purified IRF-4 was also The main role of BRCA2 shown to be capable of binding appears to involve regulating the DNA in a PU.1-dependent manner function of RAD51 in the repair by by electrophoretic mobility shift homologous recombination . analysis. brca2 irf4 We found that cells ex- Moreover, expression of pressing Olig2, Nkx2.2, and NG2 Carma1 induces phosphorylation were enriched among virus- of Bcl10 and activation of the infected, GFP-positive (GFP+) transcription factor NF-kappaB. cells. carma1 BB I O olig2 The region of VHL medi- The Rab5 effector ating interaction with HIF-1 alpha Rabaptin-5 and its isoform C R E A T I V E overlapped with a putative Rabaptin-5delta differ in their macromolecular binding site within ability to interact with the rsmallab5 the crystal structure. GTPase Rab4. vhl Translocation RCC, bearing We show that ERBB2-dependenterbb2 atf1 TFE3 or TFEB gene fusions, are Both ATF-1 homodimers and tfe3 medulloblastoma cell invasion and ATF-1/CREB heterodimers bind to recently recognized entities for prometastatic gene expression can the CRE but not to the related which risk factors have not been be blocked using the ERBB tyrosine phorbol ester response element. identified. kinase inhibitor OSI-774. C r i t i c a l A s s e s s m e n t o f I n f o r m a t i o n E x t r a c t i o n i n B i o l o g y October 7th - 9th, 2009 www.BioCreative.org BioCreative II.5 Workshop 2009 special session | Digital Annotations Auditorium of the Spanish National
    [Show full text]
  • Bioinformatic Methods in Applied Genomic Research
    Alma mater studiorum - Università di Bologna Dottorato in Biotecnologie Cellulari e Molecolari: XXIII ciclo Settore scientifico disciplinare di afferenza: BIO11 BIOINFORMATIC METHODS IN APPLIED GENOMIC RESEARCH Presentato da Raffaele Fronza Coordinatore Dottorato: Supervisore: Prof. Santi Mario Spampinato Prof. Rita Casadio Esame finale anno 2011 ii Abstract Here I will focus on three main topics that best address and include the projects I have been working in during my three year PhD period that I have spent in different research laboratories addressing both computationally and practically important problems all related to modern molecular genomics. The first topic is the use of livestock species (pigs) as a model of obesity, a complex hu- man dysfunction. My efforts here concern the detection and annotation of Single Nucleotide Polymorphisms. I developed a pipeline for mining human and porcine sequences. Starting from a set of human genes related with obesity the platform returns a list of annotated porcine SNPs extracted from a new set of potential obesity-genes. 565 of these SNPs were analyzed on an Illumina chip to test the involvement in obesity on a population composed by more than 500 pigs. Results will be discussed. All the computational analysis and experiments were done in collaboration with the Biocomputing group and Dr.Luca Fontanesi, respectively, under the direction of prof. Rita Casadio at the Bologna University, Italy. The second topic concerns developing a methodology, based on Factor Analysis, to simul- taneously mine information from different levels of biological organization. With specific test cases we develop models of the complexity of the mRNA-miRNA molecular interaction in brain tumors measured indirectly by microarray and quantitative PCR.
    [Show full text]
  • BIOINFORMATICS Doi:10.1093/Bioinformatics/Btq499
    Vol. 26 ECCB 2010, pages i409–i411 BIOINFORMATICS doi:10.1093/bioinformatics/btq499 ECCB 2010 Organization CONFERENCE CHAIR B. Comparative Genomics, Phylogeny, and Evolution Yves Moreau, Katholieke Universiteit Leuven, Belgium Martijn Huynen, Radboud University Nijmegen Medical Centre, The Netherlands PROCEEDINGS CHAIR Yves Van de Peer, Ghent University & VIB, Belgium Jaap Heringa, Free University of Amsterdam, The Netherlands C. Protein and Nucleotide Structure LOCAL ORGANIZING COMMITTEE Anna Tramontano, University of Rome ‘La Sapienza’, Italy Jan Gorodkin, University of Copenhagen, Denmark Yves Moreau, Katholieke Universiteit Leuven, Belgium Jaap Heringa, Free University of Amsterdam, The Netherlands D. Annotation and Prediction of Molecular Function Gert Vriend, Radboud University, Nijmegen, The Netherlands Yves Van de Peer, University of Ghent & VIB, Belgium Nir Ben-Tal, Tel-Aviv University, Israel Kathleen Marchal, Katholieke Universiteit Leuven, Belgium Fritz Roth, Harvard Medical School, USA Jacques van Helden, Université Libre de Bruxelles, Belgium Louis Wehenkel, Université de Liège, Belgium E. Gene Regulation and Transcriptomics Antoine van Kampen, University of Amsterdam & Netherlands Jaak Vilo, University of Tartu, Estonia Bioinformatics Center (NBIC) Zohar Yakhini, Agilent Laboratories, Tel-Aviv & the Tech-nion, Peter van der Spek, Erasmus MC, Rotterdam, The Netherlands Haifa, Israel STEERING COMMITTEE F. Text Mining, Ontologies, and Databases Michal Linial (Chair), Hebrew University, Jerusalem, Israel Alfonso Valencia, National
    [Show full text]
  • Springer A++ Viewer
    PublisherInfo PublisherName : BioMed Central PublisherLocation : London PublisherImprintName : BioMed Central European Virtual Institute for Genome Annotation receives €12 million ArticleInfo ArticleID : 4907 ArticleDOI : 10.1186/gb-spotlight-20040127-01 ArticleCitationID : spotlight-20040127-01 ArticleSequenceNumber : 259 ArticleCategory : Research news ArticleFirstPage : 1 ArticleLastPage : 2 RegistrationDate : 2004–1–27 ArticleHistory : OnlineDate : 2004–1–27 ArticleCopyright : BioMed Central Ltd2004 ArticleGrants : ArticleContext : 130594411 Genome Biology Email: [email protected] Janet Thornton, Director of the European Bioinformatics Institute(EBI; Hinxton, UK), is coordinator of the BioSapiens project. "The BioSapiens Network of Excellence ... will coordinate and focus excellent research in bioinformatics, by creating a Virtual Institute for Genome Annotation. The Institute will also establish a permanent European School of Bioinformatics, to train bioinformaticians and to encourage best practice in the exploitation of genome annotation data for biologists," she adds. The annotations will be integrated and made freely accessible via a web portal, and will be used to guide future experiments. Annotations will be integrated using the Open Source Distributed Annotation System(DAS) developed by Lincoln Stein and colleagues at Cold Spring Harbor Laboratory (USA) for exchanging genome annotations. "The development of methods, tools, and servers in close interaction with experimentalists is one feature that distinguishes the
    [Show full text]
  • The 4Th Bologna Winter School: Hot Topics in Structural Genomics†
    Comparative and Functional Genomics Comp Funct Genom 2003; 4: 394–396. Published online in Wiley InterScience (www.interscience.wiley.com). DOI: 10.1002/cfg.314 Conference Report The 4th Bologna Winter School: hot topics in structural genomics† Rita Casadio* Department of Biology/CIRB, University of Bologna, Via Irnerio 42, 40126 Bologna, Italy *Correspondence to: Abstract Rita Casadio, Department of Biology/CIRB, University of The 4th Bologna Winter School on Biotechnologies was held on 9–15 February Bologna, Via Irnerio 42, 40126 2003 at the University of Bologna, Italy, with the specific aim of discussing recent Bologna, Italy. developments in bioinformatics. The school provided an opportunity for students E-mail: [email protected] and scientists to debate current problems in computational biology and possible solutions. The course, co-supported (as last year) by the European Science Foundation program on Functional Genomics, focused mainly on hot topics in structural genomics, including recent CASP and CAPRI results, recent and promising genome- Received: 3 June 2003 wide predictions, protein–protein and protein–DNA interaction predictions and Revised: 5 June 2003 genome functional annotation. The topics were organized into four main sections Accepted: 5 June 2003 (http://www.biocomp.unibo.it). Published in 2003 by John Wiley & Sons, Ltd. Predictive methods in structural Predictive methods in functional genomics genomics • Contemporary challenges in structure prediction • Prediction of protein function (Arthur Lesk, and the CASP5 experiment (John Moult, Uni- University of Cambridge, Cambridge, UK). versity of Maryland, Rockville, MD, USA). • Microarray data analysis and mining (Raf- • Contemporary challenges in structure prediction faele Calogero, University of Torino, Torino, (Anna Tramontano, University ‘La Sapienza’, Italy).
    [Show full text]
  • Dear Delegates,History of Productive Scientific Discussions of New Challenging Ideas and Participants Contributing from a Wide Range of Interdisciplinary fields
    3rd IS CB S t u d ent Co u ncil S ymp os ium Welcome To The 3rd ISCB Student Council Symposium! Welcome to the Student Council Symposium 3 (SCS3) in Vienna. The ISCB Student Council's mis- sion is to develop the next generation of computa- tional biologists. We would like to thank and ac- knowledge our sponsors and the ISCB organisers for their crucial support. The SCS3 provides an ex- citing environment for active scientific discussions and the opportunity to learn vital soft skills for a successful scientific career. In addition, the SCS3 is the biggest international event targeted to students in the field of Computational Biology. We would like to thank our hosts and participants for making this event educative and fun at the same time. Student Council meetings have had a rich Dear Delegates,history of productive scientific discussions of new challenging ideas and participants contributing from a wide range of interdisciplinary fields. Such meet- We are very happy to welcomeings have you proved all touseful the in ISCBproviding Student students Council and postdocs Symposium innovative inputsin Vienna. and an Afterincreased the network suc- cessful symposiums at ECCBof potential 2005 collaborators. in Madrid and at ISMB 2006 in Fortaleza we are determined to con- tinue our efforts to provide an event for students and young researchers in the Computational Biology community. Like in previousWe ar yearse extremely our excitedintention to have is toyou crhereatee and an the opportunity vibrant city of Vforienna students welcomes to you meet to our their SCS3 event. peers from all over the world for exchange of ideas and networking.
    [Show full text]
  • I S C B N E W S L E T T
    ISCB NEWSLETTER FOCUS ISSUE {contents} President’s Letter 2 Member Involvement Encouraged Register for ISMB 2002 3 Registration and Tutorial Update Host ISMB 2004 or 2005 3 David Baker 4 2002 Overton Prize Recipient Overton Endowment 4 ISMB 2002 Committees 4 ISMB 2002 Opportunities 5 Sponsor and Exhibitor Benefits Best Paper Award by SGI 5 ISMB 2002 SIGs 6 New Program for 2002 ISMB Goes Down Under 7 Planning Underway for 2003 Hot Jobs! Top Companies! 8 ISMB 2002 Job Fair ISCB Board Nominations 8 Bioinformatics Pioneers 9 ISMB 2002 Keynote Speakers Invited Editorial 10 Anna Tramontano: Bioinformatics in Europe Software Recommendations11 ISCB Software Statement volume 5. issue 2. summer 2002 Community Development 12 ISCB’s Regional Affiliates Program ISCB Staff Introduction 12 Fellowship Recipients 13 Awardees at RECOMB 2002 Events and Opportunities 14 Bioinformatics events world wide INTERNATIONAL SOCIETY FOR COMPUTATIONAL BIOLOGY A NOTE FROM ISCB PRESIDENT This newsletter is packed with information on development and dissemination of bioinfor- the ISMB2002 conference. With over 200 matics. Issues arise from recommendations paper submissions and over 500 poster submis- made by the Society’s committees, Board of sions, the conference promises to be a scientific Directors, and membership at large. Important feast. On behalf of the ISCB’s Directors, staff, issues are defined as motions and are discussed EXECUTIVE COMMITTEE and membership, I would like to thank the by the Board of Directors on a bi-monthly Philip E. Bourne, Ph.D., President organizing committee, local organizing com- teleconference. Motions that pass are enacted Michael Gribskov, Ph.D., mittee, and program committee for their hard by the Executive Committee which also serves Vice President work preparing for the conference.
    [Show full text]
  • Optimization and Machine Learning Applications to Protein Sequence and Structure
    Optimization and Machine Learning Applications to Protein Sequence and Structure A DISSERTATION SUBMITTED TO THE FACULTY OF THE GRADUATE SCHOOL OF THE UNIVERSITY OF MINNESOTA BY Kevin W. DeRonne IN PARTIAL FULFILLMENT OF THE REQUIREMENTS FOR THE DEGREE OF Doctor of Philosophy George Karypis January, 2013 c Kevin W. DeRonne 2013 ALL RIGHTS RESERVED Acknowledgements This thesis represents the culmination of over ten years of work. Not once over those ten years did I actually expect to be writing these words, and it is only through the stalwart, foolish, patient love and support of a great many people that I am. There are far too many names I need to list, so I can only name a few, but to the others who do not appear here: you are by no means forgotten. Professors Cavan Reilly, Ravi Janardan and Vipin Kumar: thank you for taking the time to serve on my preliminary and final examination committees. It is an honor to have people of such quality reviewing my work. Professor George Karypis: I have no idea why you put up with me for so long, but here we are. Despite my repeated attempts to force you to give up on me, you never did. The only way I can be succinct about what you have done for me is this: I have become the computer scientist I am because of you. Patrick Coleman Saunders: in death as in life, you made me a better person. Chas Kennedy, David Mulvihill, Dan O'Brien, Adam Meyer, Andrew Owen, Huzefa Rangwala, Jeff Rostis, David Seelig, Neil Shah and Nikil Wale: I hope you know that you are all like brothers to me.
    [Show full text]
  • Emidio Capriotti Phd CURRICULUM VITÆ
    Emidio Capriotti PhD CURRICULUM VITÆ Name: Emidio Capriotti Nationality: Italian Date of birth: February, 1973 Place of birth: Roma, Italy Languages: Italian, English, Spanish Positions Oct 2019 Associate Professor: Department of Pharmacy and Biotechnology (FaBiT). University of Bologna, Bologna, Italy 2016-2019 Senior Assistant Professor (RTD type B): Department of Pharmacy and Biotechnology (FaBiT) and Department of Biological, Geological, and Environmental Sciences (BiGeA). University of Bologna, Bologna, Italy. 2015-2016 Junior Group Leader: Institute of Mathematical Modeling of Biological Systems, University of Düsseldorf, Düsseldorf, Germany 2012-2015 Assistant Professor: Division of Informatics, Department of Pathology, University of Alabama at Birmingham (UAB), Birmingham (AL), USA. 2011-2012 Marie-Curie IOF: Contracted Researcher at the Department of Mathematics and Computer Science, University of Balearic Islands (UIB), Palma de Mallorca, Spain. 2009-2011 Marie-Curie IOF: Postdoctoral Researcher at the Helix Group, Department of Bioengineering, Stanford University, Stanford (CA), USA. 2006-2009 Postdoctoral Researcher in the Structural Genomics Group at Department of Bioinformatics and Genetics, Prince Felipe Research Center (CIPF) Valencia, Spain. 2004-2006 Contract researcher at Department of Biology, University of Bologna, Bologna, Italy. 2001-2003 Ph.D student in Physical Sciences at University of Bologna, Bologna, Italy. Education Sep 2004 Master in Bioinformatics (first level) University of Bologna, Bologna (Italy). Jun 2004 Ph.D. in Physical Sciences University of Bologna, Bologna (Italy). Jul 1999 Laurea (B.S.) Degree in Physical Sciences, score 106/110 University of Bologna, Bologna (Italy). Visiting Jun 2012 – Jul 2012 Prof. Frederic Rousseau and Prof. Joost Schymkowitz, VIB Switch Laboratory, KU Leuven, Leuven (Belgium) May 2009 Prof.
    [Show full text]