Bioinformatic Methods in Applied Genomic Research
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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. -
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. -
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. -
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. -
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. -
Predicting Protein Folding Pathways Using Ensemble Modeling and Sequence Information
Predicting Protein Folding Pathways Using Ensemble Modeling and Sequence Information by David Becerra McGill University School of Computer Science Montr´eal, Qu´ebec, Canada A thesis submitted to McGill University in partial fulfillment of the requirements of the degree of Doctor of Philosophy c David Becerra 2017 Dedicated to my GRANDMOM. Thanks for everything. You are such a strong woman i Acknowledgements My doctoral program has been an amazing adventure with ups and downs. The most valuable fact is that I am a different person with respect to the one who started the program five years ago. I am not better or worst, I am just different. I would like to express my gratitude to all the people who helped me during my time at McGill. This thesis contains only my name as author, but it should have the name of all the people who played an important role in the completion of this thesis (and they are a lot of people). I am certain I would have not reached the end of my thesis without the help, advises and support of all people around me. First at all, I want to thank my country Colombia. Being abroad, I learnt to value my culture, my roots and my south-american positiveness, happiness and resourcefulness. I am really proud of being Colombian and of showing to the world a bit of what our wonderful land has given to us. I would also like to thank all Colombians, because with your taxes (via Colciencia’s funding) I was able to complete this dream. -
In Systems Physiology
IN SYSTEMS PHYSIOLOGY Interpretation of the consequences of mutations in protein kinases: combined use of bioinformatics and text mining Jose M.G. Izarzugaza, Martin Krallinger and Alfonso Valencia Journal Name: Frontiers in Physiology ISSN: 1664-042X Article type: Review Article Received on: 23 May 2012 Accepted on: 23 Jul 2012 Provisional PDF published on: 23 Jul 2012 Frontiers website link: www.frontiersin.org Citation: Izarzugaza JM, Krallinger M and Valencia A(2012) Interpretation of the consequences of mutations in protein kinases: combined use of bioinformatics and text mining. Front. Physio. 3:323. doi:10.3389/fphys.2012.00323 Article URL: http://www.frontiersin.org/Journal/Abstract.aspx?s=1092& name=systems%20physiology&ART_DOI=10.3389/fphys.2012.00323 (If clicking on the link doesn't work, try copying and pasting it into your browser.) Copyright statement: © 2012 Izarzugaza, Krallinger and Valencia. This is an open‐access article distributed under the terms of the Creative Commons Attribution License, which permits use, distribution and reproduction in other forums, provided the original authors and source are credited and subject to any copyright notices concerning any third-party graphics etc. This Provisional PDF corresponds to the article as it appeared upon acceptance, after rigorous peer-review. Fully formatted PDF and full text (HTML) versions will be made available soon. Interpretation of the consequences of mutations in protein kinases: combined use of bioinformatics and text mining Jose MG Izarzugaza, Martin Krallinger and Alfonso Valencia Abstract Protein kinases play a crucial role in a plethora of significant physiological functions and a number of mutations in this superfamily have been reported in the literature to disrupt protein structure and/or function. -
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. -
BIOINFORMATICS Doi:10.1093/Bioinformatics/Btu322
Vol. 30 ISMB 2014, pages i3–i8 BIOINFORMATICS doi:10.1093/bioinformatics/btu322 ISMB 2014 PROCEEDINGS PAPERS COMMITTEE PROCEEDINGS PAPERS COMMITTEE CHAIRS F. Gene Regulation and Transcriptomics Serafim Batzoglu, Stanford University, United States Alexander Haremink, Duke University, Durham, United States Russell Schwartz, Carnegie Mellon University, Pittsburgh, Zohar Yakhini, Agilent, Haifa, Israel United States G. Mass Spectrometry and Proteomics Olga Vitek, Purdue University, West Lafayette, United States Bill Noble, University of Washington, Seattle, United States PROCEEDINGS PAPERS-AREA CHAIRS A. Applied Bioinformatics H. Metabolic Networks Thomas Lengauer, Max Planck Institute for Informatics, Jason Papin, University of Virginia, Charlottesville, United Saarbrucken, Germany States Lenore Cowen, Tufts University, Medford, United States I. Population Genomics Eran Halperin, Tel-Aviv University, Israel B. Bioimaging and Data Visualization Itsik Pe’er, Columbia University, New York, United States Robert Murphy, Carnegie Mellon University, Pittsburgh, United States J. Protein Interactions and Molecular Networks Mona Singh, Princeton University, United States C. Databases and Ontologies and Text Mining Trey Ideker, UC San Diego, United States Hagit Shatkay, University of Delaware, Newark, United States Alex Bateman, European Bioinformatics Institute (EMBL-EBI), K. Protein Structure and Function Wellcome Trust Genome Campus, Hinxton, United Kingdom Jie Liang, University of Illinois at Chicago, United States Jinbo Xu, Toyota Technical Institute, -
Text Skip-Gram Model [BGJM17] Was Trained to Learn the Individual Word Vectors for Which the Dimensionality of the Vector Was Set to 1
PREDICTING TRANSPORTER PROTEINS AND THEIR SUBSTRATE SPECIFICITY Munira Alballa A Thesis in the department of Computer Science and Software Engineering Presented in Partial Fulfillment of the Requirements For the Degree of Doctor of Philosophy (Computer Science) Concordia University Montreal,´ Quebec,´ Canada June, 2020 c Munira Alballa, 2020 Concordia University School of Graduate Studies This is to certify that the thesis prepared By: Munira Alballa Entitled: Predicting transporter proteins and their substrate specificity and submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy (Computer Science) complies with the regulations of this University and meets the accepted standards with respect to originality and quality. Signed by the final examining committee: Chair Dr. Ciprian Alecsandru External Examiner Dr. Anthony J. Kusalik Examiner Dr. Leila Kosseim Examiner Dr. Adam Krzyzak Examiner Dr. Jia Yuan Yu Supervisor Dr. Gregory Butler Approved Dr. Leila Kosseim, Graduate Program Director June 5, 2020 Dr. Amir Asif, Dean Faculty of Engineering and Computer Science Abstract Predicting transporter proteins and their substrate specificity Munira Alballa, Ph.D. Concordia University, 2020 The publication of numerous genome projects has resulted in an abundance of protein sequences, a significant number of which are still unannotated. Membrane proteins such as transporters, receptors, and enzymes are among the least characterized proteins due to their hydrophobic surfaces and lack of conformational stability. This research aims to build a proteome-wide system to determine transporter substrate specificity, which involves three phases: 1) distinguishing membrane proteins, 2) differentiating transporters from other functional types of membrane proteins, and 3) detecting the substrate specificity of the transporters. -
University of Bologna International Master Course in Bioinformatics Interdepartmental Center “Luigi Galvani” Department of Pharmacy and Biotechnology
University of Bologna International Master Course in Bioinformatics Interdepartmental Center “Luigi Galvani” Department of Pharmacy and Biotechnology ORGANISATION:AIRBBC (Associazione Italiana per la Ricerca in Biofisica e Biologia Computazionale) WITH THE SUPPORT OF: SIB (Italian Society of Biochemistry and Molecular Biology) ELIXIR-IIB 21st BOLOGNA WINTER SCHOOL in BIOINFORMATICS What can we learn from protein structure? February 17-21, 2020, BOLOGNA (Italy) LECTURERS: Montserrat Corominas (University of Barcelona, ES); Piero Fariselli (University of Turin, IT), Roderic Guigò (University Pompeu Fabra, Barcelona, ES); David Jones (Francis Crick Institute and University College of London, UK); Anders Krogh (University of Copenhagen, DK); Christine Orengo (University College of London, UK); Graziano Pesole (CNR Institute of Biomembrane and Bioenergetics and University of Bari, IT); Burkhard Rost (Technical University of Munich, DE); Silvio Tosatto (University of Padova, IT); Mauno Vihinen (University of Lund, SE). SCIENTIFIC COMMITTEE: Rita Casadio, David Jones. ORGANIZING COMMITTEE: P.L. Martelli, C. Savojardo, G. Babbi, D. Baldazzi, E. Capriotti, G. Madeo, M. Manfredi, G. Tartari, T.Tavella. ORGANIZING SECRETARY: AIRBBC c/o Dept. of Pharmacy and Biotechnology, University of Bologna Via San Giacomo 9/2, 40126, Bologna, ITALY. Tel: (+39) 051 2094005 http://www.biocomp.unibo.it/~school2020 21th Bologna Winter School: Programme What can we learn from protein structure? Bologna (Italy, February 17-21, 2020) Caffè della Corte, Corte Isolani 5/B, Bologna Monday, February 17 10:00-13:00 Christine Orengo 15:00- 17:30 Burkhard Rost Tuesday, February 18 10:00-13:00 David Jones 15:00- 17:30 Round Table Discussion on ELIXIR Participants: G. Pesole, S. Tosatto, G.