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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 -
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). -
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 -
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 -
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). -
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. -
A Glance Into the Evolution of Template-Free Protein Structure Prediction Methodologies Arxiv:2002.06616V2 [Q-Bio.QM] 24 Apr 2
A glance into the evolution of template-free protein structure prediction methodologies Surbhi Dhingra1, Ramanathan Sowdhamini2, Frédéric Cadet3,4,5, and Bernard Offmann∗1 1Université de Nantes, CNRS, UFIP, UMR6286, F-44000 Nantes, France 2Computational Approaches to Protein Science (CAPS), National Centre for Biological Sciences (NCBS), Tata Institute for Fundamental Research (TIFR), Bangalore 560-065, India 3University of Paris, BIGR—Biologie Intégrée du Globule Rouge, Inserm, UMR_S1134, Paris F-75015, France 4Laboratory of Excellence GR-Ex, Boulevard du Montparnasse, Paris F-75015, France 5DSIMB, UMR_S1134, BIGR, Inserm, Faculty of Sciences and Technology, University of La Reunion, Saint-Denis F-97715, France Abstract Prediction of protein structures using computational approaches has been explored for over two decades, paving a way for more focused research and development of algorithms in com- parative modelling, ab intio modelling and structure refinement protocols. A tremendous suc- cess has been witnessed in template-based modelling protocols, whereas strategies that involve template-free modelling still lag behind, specifically for larger proteins (> 150 a.a.). Various improvements have been observed in ab initio protein structure prediction methodologies over- time, with recent ones attributed to the usage of deep learning approaches to construct protein backbone structure from its amino acid sequence. This review highlights the major strategies undertaken for template-free modelling of protein structures while discussing few tools devel- arXiv:2002.06616v2 [q-bio.QM] 24 Apr 2020 oped under each strategy. It will also briefly comment on the progress observed in the field of ab initio modelling of proteins over the course of time as seen through the evolution of CASP platform. -
Janga-Phd-Thesis.Pdf (PDF, 9Mb)
Exploiting network-based approaches for understanding gene regulation and function Sarath Chandra Janga A dissertation submitted to the University of Cambridge in candidature for the degree of Doctorate of Philosophy April 2010 Darwin College, University of Cambridge MRC Laboratory of Molecular Biology Cambridge, United Kingdom Previous page: A portrait of the transcriptional regulatory network of the budding yeast, Saccharomyces Cerevisiae. Each circle represents the network of transcriptional interconnections between all other chromosomes to one of the chromosomes. Evidently all chromosomes are transcriptionally controlled by factors encoded on many of the 16 chromosomes in this organism marked by the letters ‘a’ through ‘p’. iii Declaration of originality This dissertation describes work I carried out at the Medical Research Council Laboratory of Molecular Biology in Cambridge between January 2008 and April 2010. The contents are my original work, although much has been influenced by the collaborations in which I took part. I have not submitted the work in this dissertation for any other degree or qualification at any other university. Sarath Chandra Janga April, 2010 Cambridge, United Kingdom iv Acknowledgements First of all I would like to express my gratitude to Dr. Madan Babu with out whose continuous support all along my doctoral work, it would have just remained a dream for me to carry out my thesis work at MRC Laboratory of Molecular Biology. Madan has not only been an excellent supervisor but a good friend who was always supportive of my research interests, by allowing me to work independently on a wide range of problems during my stay here. He has been a source of great inspiration on various occasions and a great scientific colleague to work with. -
BIO-CHEM-00.Pdf
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 -
CV Burkhard Rost
Burkhard Rost CV BURKHARD ROST TUM Informatics/Bioinformatics i12 Boltzmannstrasse 3 (Rm 01.09.052) 85748 Garching/München, Germany & Dept. Biochemistry & Molecular Biophysics Columbia University New York, USA Email [email protected] Tel +49-89-289-17-811 Photo: © Eckert & Heddergott, TUM Web www.rostlab.org Fax +49-89-289-19-414 Document: CV Burkhard Rost TU München Affiliation: Columbia University TOC: • Tabulated curriculum vitae • Grants • List of publications Highlights by numbers: • 186 invited talks in 29 countries (incl. TedX) • 250 publications (187 peer-review, 168 first/last author) • Google Scholar 2016/01: 30,502 citations, h-index=80, i10=179 • PredictProtein 1st Internet server in mol. biol. (since 1992) • 8 years ISCB President (International Society for Computational Biology) • 143 trained (29% female, 50% foreigners from 32 nations on 6 continents) Brief narrative: Burkhard Rost obtained his doctoral degree (Dr. rer. nat.) from the Univ. of Heidelberg (Germany) in the field of theoretical physics. He began his research working on the thermo-dynamical properties of spin glasses and brain-like artificial neural networks. A short project on peace/arms control research sketched a simple, non-intrusive sensor networks to monitor aircraft (1988-1990). He entered the field of molecular biology at the European Molecular Biology Laboratory (EMBL, Heidelberg, Germany, 1990-1995), spent a year at the European Bioinformatics Institute (EBI, Hinxton, Cambridgshire, England, 1995), returned to the EMBL (1996-1998), joined the company LION Biosciences for a brief interim (1998), became faculty in the Medical School of Columbia University in 1998, and joined the TUM Munich to become an Alexander von Humboldt professor in 2009. -
Scientific Program
Program ECCB’2003 Saturday, September 27 9h30 Registration opens, welcome coffee 12h-13h Light buffet 13h15-13h30 Welcoming speeches 13h30-14h20 Invited talk Chair: Shoshana Wodak Thomas Lengauer Analyzing resistance phenomena in HIV with bioinformatics methods Contributed talks - Genetic networks Chair: David Gilbert 14h20-14h45 A description of dynamical graphs associated to elementary regulatory circuits. Elisabeth Rémy, Brigitte Mossé, Claudine Chaouiya, Denis Thieffry 14h45-15h00 Using ChIP data to decipher regulatory logic of MBF and SBF during the Yeast cell cycle.F eng Gao, Harmen Bussemaker 15h00-15h15 Validation of noisy dynamical system models of gene regulation inferred from time-course gene expression data at arbitrary time intervals. Michiel de Hoon, Sascha Ott, Seiya Imoto, Satoru Miyano 15h15-15h30 Accuracy of the models for gene regulation - a comparison of two modeling methods. Kimmo Palin 15h30-16h10 Coffee Break Contributed talks - Genetic networks and gene expression Chair: Stéphane Robin 16h10-16h35 Extracting active pathways from gene expression data. Jean-Philippe Vert, Minoru Kanehisa 16h35-17h00 Gene networks inference using dynamic Bayesian networks. Bruno-Edouard Perrin, Liva Ralaivola, Florence d'Alché-Buc, Samuele Bottani, Aurélien Mazurie 17h00-17h25 Estimating gene networks from gene expression data by combining Bayesian network model with promoter element detection .Yoshinori Tamada, Sunyong Kim, Hideo Bannai, Seiya Imoto, Kousuke Tashiro, Satoru Kuhara, Satoru Miyano 17h25-17h50 Biclustering microarray -
Full Program Book
1 Welcome On behalf of the ECCB’14 Organizing and Steering Committees we are very happy to welcome you to Strasbourg, Heart of Europe. We hope that you will enjoy the many facets of the conference: keynote lectures, oral communications, workshops and tutorials, demos, posters, booths. This dense and attractive program is intended to be the substrate of fruitful discussions and networking among all of you. We are proud to welcome seven distinguished Keynote Speakers: Nobel Prize laureate Jean-Marie Lehn (Strasbourg University, Nobel Prize in Chemistry in 1987), Patrick Aloy (Institute for Research in Biomedicine, Barcelona, Spain), Alice McHardy (Heinrich Heine University, Düsseldorf and Helmholtz Center for Infection Biology, Braunschweig, Germany), Nada Lavrač (Jožef Stefan Institute and University of Nova Gorica, Slovenia), Ewan Birney (European Bioinformatics Institute, Hinxton, United Kingdom), Doron Lancet (The Weizmann Institute of Science, Rehovot, Israel) and Eric Westhof (Strasbourg University, France). A large variety of Workshops, Tutorials and Satellite Meetings will take place on Saturday, September 6 and Sunday, September 7 to kick off the conference! We would like to stress the interest in the conference by the Council of Europe, whose headquarters are in Strasbourg. An invited talk by Laurence Lwoff, Head of the Bioethics Unit, is scheduled during the opening ceremony, in which she will share the Council of Europe’s concerns about the bio-ethical challenges raised by the usage of biobanks and biomedical data in research and its applications. The Council of Europe will also host the Gala Evening on Tuesday in its nice reception hall and gardens along the Ill river.