Friday (August 4) Intelligent Systems for Molecular Biology
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SD Gross BFI0403
Janet Thornton Bioinformatician avant la lettre Michael Gross B ioinformatics is very much a buzzword of our time, with new courses and institutes dedicated to it sprouting up almost everywhere. Most significantly, the flood of genome data has raised the gen- eral awareness of the need to deve-lop new computational approaches to make sense of all the raw information collected. Professor Janet Thornton, the current director of the European Bioinformatics Institute (EBI), an EMBL outpost based at the Hinxton campus near Cambridge, has been in the field even before there was a word for it. Coming to structural biology with a physics degree from the University of Nottingham, she was already involved with computer-generated structural im- ages in the 1970s, when personal comput- ers and user-friendly programs had yet to be invented. The Early Years larities. Within 15 minutes, the software From there to the EBI, her remarkable Janet Thornton can check all 2.4 billion possible re- career appears to be organised in lationships and pick the ones relevant decades. During the 1970s, she did doc- software to compare structures to each to the question at hand. In comparison toral and post-doctoral research at other, recognise known folds and spot to publicly available bioinformatics the Molecular Biophysics Laboratory in new ones. Such work provides both packages such as Blast or Psiblast, Oxford and at the National Institute for fundamental insights into the workings Biopendium can provide an additional Medical Research in Mill Hill, near Lon- of evolution on a molecular level, and 30 % of annotation, according to Inphar- don. -
The EMBL-European Bioinformatics Institute the Hub for Bioinformatics in Europe
The EMBL-European Bioinformatics Institute The hub for bioinformatics in Europe Blaise T.F. Alako, PhD [email protected] www.ebi.ac.uk What is EMBL-EBI? • Part of the European Molecular Biology Laboratory • International, non-profit research institute • Europe’s hub for biological data, services and research The European Molecular Biology Laboratory Heidelberg Hamburg Hinxton, Cambridge Basic research Structural biology Bioinformatics Administration Grenoble Monterotondo, Rome EMBO EMBL staff: 1500 people Structural biology Mouse biology >60 nationalities EMBL member states Austria, Belgium, Croatia, Denmark, Finland, France, Germany, Greece, Iceland, Ireland, Israel, Italy, Luxembourg, the Netherlands, Norway, Portugal, Spain, Sweden, Switzerland and the United Kingdom Associate member state: Australia Who we are ~500 members of staff ~400 work in services & support >53 nationalities ~120 focus on basic research EMBL-EBI’s mission • Provide freely available data and bioinformatics services to all facets of the scientific community in ways that promote scientific progress • Contribute to the advancement of biology through basic investigator-driven research in bioinformatics • Provide advanced bioinformatics training to scientists at all levels, from PhD students to independent investigators • Help disseminate cutting-edge technologies to industry • Coordinate biological data provision throughout Europe Services Data and tools for molecular life science www.ebi.ac.uk/services Browse our services 9 What services do we provide? Labs around the -
Functional Effects Detailed Research Plan
GeCIP Detailed Research Plan Form Background The Genomics England Clinical Interpretation Partnership (GeCIP) brings together researchers, clinicians and trainees from both academia and the NHS to analyse, refine and make new discoveries from the data from the 100,000 Genomes Project. The aims of the partnerships are: 1. To optimise: • clinical data and sample collection • clinical reporting • data validation and interpretation. 2. To improve understanding of the implications of genomic findings and improve the accuracy and reliability of information fed back to patients. To add to knowledge of the genetic basis of disease. 3. To provide a sustainable thriving training environment. The initial wave of GeCIP domains was announced in June 2015 following a first round of applications in January 2015. On the 18th June 2015 we invited the inaugurated GeCIP domains to develop more detailed research plans working closely with Genomics England. These will be used to ensure that the plans are complimentary and add real value across the GeCIP portfolio and address the aims and objectives of the 100,000 Genomes Project. They will be shared with the MRC, Wellcome Trust, NIHR and Cancer Research UK as existing members of the GeCIP Board to give advance warning and manage funding requests to maximise the funds available to each domain. However, formal applications will then be required to be submitted to individual funders. They will allow Genomics England to plan shared core analyses and the required research and computing infrastructure to support the proposed research. They will also form the basis of assessment by the Project’s Access Review Committee, to permit access to data. -
Ismb/Eccb 2015
Research Collection Journal Article ISMB/ECCB 2015 Author(s): Moreau, Yves; Beerenwinkel, Niko Publication Date: 2015 Permanent Link: https://doi.org/10.3929/ethz-b-000102416 Originally published in: Bioinformatics 31(12), http://doi.org/10.1093/bioinformatics/btv303 Rights / License: Creative Commons Attribution-NonCommercial 4.0 International This page was generated automatically upon download from the ETH Zurich Research Collection. For more information please consult the Terms of use. ETH Library Bioinformatics, 31, 2015, i1–i2 doi: 10.1093/bioinformatics/btv303 ISMB/ECCB 2015 Editorial ISMB/ECCB 2015 This special issue of Bioinformatics serves as the proceedings of the 175 external reviewers recruited as sub-reviewers by program com- joint 23rd annual meeting of Intelligent Systems for Molecular mittee members. Table 1 provides a summary of the areas, area Biology (ISMB) and 14th European Conference on Computational chairs and a review summary by area. The conference used a two- Biology (ECCB), which took place in Dublin, Ireland, July 10–14, tier review system—a continuation and refinement of a process that 2015 (http://www.iscb.org/ismbeccb2015). ISMB/ECCB 2015, the begun with ISMB/ECCB 2013 in an effort to better ensure thorough official conference of the International Society for Computational and fair reviewing. Under the revised process, each of the 241 sub- Biology (ISCB, http://www.iscb.org/), was accompanied by nine missions was first reviewed by at least three expert referees, with a Special Interest Group meetings of 1 or 2 days each, and two satel- subset receiving between four and six reviews, as needed. lite meetings. -
Meeting Review: Bioinformatics and Medicine – from Molecules To
Comparative and Functional Genomics Comp Funct Genom 2002; 3: 270–276. Published online 9 May 2002 in Wiley InterScience (www.interscience.wiley.com). DOI: 10.1002/cfg.178 Feature Meeting Review: Bioinformatics And Medicine – From molecules to humans, virtual and real Hinxton Hall Conference Centre, Genome Campus, Hinxton, Cambridge, UK – April 5th–7th Roslin Russell* MRC UK HGMP Resource Centre, Genome Campus, Hinxton, Cambridge CB10 1SB, UK *Correspondence to: Abstract MRC UK HGMP Resource Centre, Genome Campus, The Industrialization Workshop Series aims to promote and discuss integration, automa- Hinxton, Cambridge CB10 1SB, tion, simulation, quality, availability and standards in the high-throughput life sciences. UK. The main issues addressed being the transformation of bioinformatics and bioinformatics- based drug design into a robust discipline in industry, the government, research institutes and academia. The latest workshop emphasized the influence of the post-genomic era on medicine and healthcare with reference to advanced biological systems modeling and simulation, protein structure research, protein-protein interactions, metabolism and physiology. Speakers included Michael Ashburner, Kenneth Buetow, Francois Cambien, Cyrus Chothia, Jean Garnier, Francois Iris, Matthias Mann, Maya Natarajan, Peter Murray-Rust, Richard Mushlin, Barry Robson, David Rubin, Kosta Steliou, John Todd, Janet Thornton, Pim van der Eijk, Michael Vieth and Richard Ward. Copyright # 2002 John Wiley & Sons, Ltd. Received: 22 April 2002 Keywords: bioinformatics; -
• La Gestion Efficace De L’Énergie • Le Réseautage Planétaire • Les Processus Géophysiques • L’Économie Globale, La Sécurité Et La Stabilité
SupérieureS atiqueS athéM e M inaire D SéM The planet on which we live and the challenges that we face on this planet become increasingly complex as ecological, economic and social systems are large intertwined networks governed by dynamic processes and feedback loops. Mathematical models are indispensable in understanding and managing such systems since they provide insight into governing processes; they help predict future behavior; and they allow for risk-free evaluation of possible interventions. The goal of this thematic program is to tackle pressing and emerging challenges in population and ecosystem health, including understanding and controlling major transmissible diseases, optimizing and monitoring vaccination, predicting the impacts of climate change on invasive species, protecting biodiversity and managing ecosystems sustainably. This pan-Canadian program will bring together the international community of researchers who work on these topics in a series of workshops to foster exchange and stimulate cross-disciplinary research between all scientific areas involved, to discuss perspectives and directions for future advances in the field, including new models and methods and to foster tighter links between the research community, government agencies and policy makers. Three summer schools will introduce graduate students and postdoctoral fellows to the art of modeling living systems and to the latest tools and techniques to analyze these models. SCIENTIFIC COMMITTEE Jacques Bélair Mark Lewis (Montréal) Models and Methods in Ecology (Alberta) Frithjof Lutscher and Epidemiology Mathematical Modeling James Watmough (Ottawa) February 6-8, 2013 (UNB) of Indigenous Population Jianhong Wu CRM, Montréal (York) Organizers: Jacques Bélair (Montréal), Health Jianhong Wu (York) September 28-29, 2013 AISENSTADT CHAIRS BIRS Bryan Grenfell (Princeton), May 2013 Graphic Design: www.neograf.ca Simon A. -
The Principled Design of Large-Scale Recursive Neural Network Architectures–DAG-Rnns and the Protein Structure Prediction Problem
Journal of Machine Learning Research 4 (2003) 575-602 Submitted 2/02; Revised 4/03; Published 9/03 The Principled Design of Large-Scale Recursive Neural Network Architectures–DAG-RNNs and the Protein Structure Prediction Problem Pierre Baldi [email protected] Gianluca Pollastri [email protected] School of Information and Computer Science Institute for Genomics and Bioinformatics University of California, Irvine Irvine, CA 92697-3425, USA Editor: Michael I. Jordan Abstract We describe a general methodology for the design of large-scale recursive neural network architec- tures (DAG-RNNs) which comprises three fundamental steps: (1) representation of a given domain using suitable directed acyclic graphs (DAGs) to connect visible and hidden node variables; (2) parameterization of the relationship between each variable and its parent variables by feedforward neural networks; and (3) application of weight-sharing within appropriate subsets of DAG connec- tions to capture stationarity and control model complexity. Here we use these principles to derive several specific classes of DAG-RNN architectures based on lattices, trees, and other structured graphs. These architectures can process a wide range of data structures with variable sizes and dimensions. While the overall resulting models remain probabilistic, the internal deterministic dy- namics allows efficient propagation of information, as well as training by gradient descent, in order to tackle large-scale problems. These methods are used here to derive state-of-the-art predictors for protein structural features such as secondary structure (1D) and both fine- and coarse-grained contact maps (2D). Extensions, relationships to graphical models, and implications for the design of neural architectures are briefly discussed. -
120421-24Recombschedule FINAL.Xlsx
Friday 20 April 18:00 20:00 REGISTRATION OPENS in Fira Palace 20:00 21:30 WELCOME RECEPTION in CaixaForum (access map) Saturday 21 April 8:00 8:50 REGISTRATION 8:50 9:00 Opening Remarks (Roderic GUIGÓ and Benny CHOR) Session 1. Chair: Roderic GUIGÓ (CRG, Barcelona ES) 9:00 10:00 Richard DURBIN The Wellcome Trust Sanger Institute, Hinxton UK "Computational analysis of population genome sequencing data" 10:00 10:20 44 Yaw-Ling Lin, Charles Ward and Steven Skiena Synthetic Sequence Design for Signal Location Search 10:20 10:40 62 Kai Song, Jie Ren, Zhiyuan Zhai, Xuemei Liu, Minghua Deng and Fengzhu Sun Alignment-Free Sequence Comparison Based on Next Generation Sequencing Reads 10:40 11:00 178 Yang Li, Hong-Mei Li, Paul Burns, Mark Borodovsky, Gene Robinson and Jian Ma TrueSight: Self-training Algorithm for Splice Junction Detection using RNA-seq 11:00 11:30 coffee break Session 2. Chair: Bonnie BERGER (MIT, Cambrige US) 11:30 11:50 139 Son Pham, Dmitry Antipov, Alexander Sirotkin, Glenn Tesler, Pavel Pevzner and Max Alekseyev PATH-SETS: A Novel Approach for Comprehensive Utilization of Mate-Pairs in Genome Assembly 11:50 12:10 171 Yan Huang, Yin Hu and Jinze Liu A Robust Method for Transcript Quantification with RNA-seq Data 12:10 12:30 120 Zhanyong Wang, Farhad Hormozdiari, Wen-Yun Yang, Eran Halperin and Eleazar Eskin CNVeM: Copy Number Variation detection Using Uncertainty of Read Mapping 12:30 12:50 205 Dmitri Pervouchine Evidence for widespread association of mammalian splicing and conserved long range RNA structures 12:50 13:10 169 Melissa Gymrek, David Golan, Saharon Rosset and Yaniv Erlich lobSTR: A Novel Pipeline for Short Tandem Repeats Profiling in Personal Genomes 13:10 13:30 217 Rory Stark Differential oestrogen receptor binding is associated with clinical outcome in breast cancer 13:30 15:00 lunch break Session 3. -
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. -
Fall 2016 Is Available in the Laboratory of Dr
RNA Society Newsletter Aug 2016 From the Desk of the President, Sarah Woodson Greetings to all! I always enjoy attending the annual meetings of the RNA Society, but this year’s meeting in Kyoto was a standout in my opinion. This marked the second time that the RNA meeting has been held in Kyoto as a joint meeting with the RNA Society of Japan. (The first time was in 2011). Particular thanks go to the local organizers Mikiko Siomi and Tom Suzuki who took care of many logistical details, and to all of the organizers, Mikiko, Tom, Utz Fischer, Wendy Gilbert, David Lilley and Erik Sontheimer, for putting together a truly exciting and stimulating scientific program. Of course, the real excitement in the annual RNA meetings comes from all of you who give the talks and present the posters. I always enjoy meeting old friends and colleagues, but the many new participants in this year’s meeting particularly encouraged me. (Continued on p2) In this issue : Desk of the President, Sarah Woodson 1 Highlights of RNA 2016 : Kyoto Japan 4 Annual Society Award Winners 4 Jr Scientist activities 9 Mentor Mentee Lunch 10 New initiatives 12 Desk of our CEO, James McSwiggen 15 New Volunteer Opportunities 16 Chair, Meetings Committee, Benoit Chabot 17 Desk of the Membership Chair, Kristian Baker 18 Thank you Volunteers! 20 Meeting Reports: RNA Sponsored Meetings 22 Upcoming Meetings of Interest 27 Employment 31 1 Although the graceful city of Kyoto and its cultural months. First, in May 2016, the RNA journal treasures beckoned from just beyond the convention instituted a uniform price for manuscript publication hall, the meeting itself held more than enough (see p 12) that simplifies the calculation of author excitement to keep ones attention! Both the quality fees and facilitates the use of color figures to and the “polish” of the scientific presentations were convey scientific information. -
Deep Learning in Chemoinformatics Using Tensor Flow
UC Irvine UC Irvine Electronic Theses and Dissertations Title Deep Learning in Chemoinformatics using Tensor Flow Permalink https://escholarship.org/uc/item/963505w5 Author Jain, Akshay Publication Date 2017 Peer reviewed|Thesis/dissertation eScholarship.org Powered by the California Digital Library University of California UNIVERSITY OF CALIFORNIA, IRVINE Deep Learning in Chemoinformatics using Tensor Flow THESIS submitted in partial satisfaction of the requirements for the degree of MASTER OF SCIENCE in Computer Science by Akshay Jain Thesis Committee: Professor Pierre Baldi, Chair Professor Cristina Videira Lopes Professor Eric Mjolsness 2017 c 2017 Akshay Jain DEDICATION To my family and friends. ii TABLE OF CONTENTS Page LIST OF FIGURES v LIST OF TABLES vi ACKNOWLEDGMENTS vii ABSTRACT OF THE THESIS viii 1 Introduction 1 1.1 QSAR Prediction Methods . .2 1.2 Deep Learning . .4 2 Artificial Neural Networks(ANN) 5 2.1 Artificial Neuron . .5 2.2 Activation Function . .7 2.3 Loss function . .8 2.4 Optimization . .8 3 Deep Recursive Architectures 10 3.1 Recurrent Neural Networks (RNN) . 10 3.2 Recursive Neural Networks . 11 3.3 Directed Acyclic Graph Recursive Neural Networks (DAG-RNN) . 11 4 UG-RNN for small molecules 14 4.1 DAG Generation . 16 4.2 Local Information Vector . 16 4.3 Contextual Vectors . 17 4.4 Activity Prediction . 17 4.5 UG-RNN With Contracted Rings (UG-RNN-CR) . 18 4.6 Example: UG-RNN Model of Propionic Acid . 20 5 Implementation 24 6 Data & Results 26 6.1 Aqueous Solubility Prediction . 26 6.2 Melting Point Prediction . 28 iii 7 Conclusions 30 Bibliography 32 A Source Code 37 A.1 UGRNN . -
Computational Biology and Bioinformatics
Vol. 30 ISMB 2014, pages i1–i2 BIOINFORMATICS EDITORIAL doi:10.1093/bioinformatics/btu304 Editorial This special issue of Bioinformatics serves as the proceedings of The conference used a two-tier review system, a continuation the 22nd annual meeting of Intelligent Systems for Molecular and refinement of a process begun with ISMB 2013 in an effort Biology (ISMB), which took place in Boston, MA, July 11–15, to better ensure thorough and fair reviewing. Under the revised 2014 (http://www.iscb.org/ismbeccb2014). The official confer- process, each of the 191 submissions was first reviewed by at least ence of the International Society for Computational Biology three expert referees, with a subset receiving between four and (http://www.iscb.org/), ISMB, was accompanied by 12 Special eight reviews, as needed. These formal reviews were frequently Interest Group meetings of one or two days each, two satellite supplemented by online discussion among reviewers and Area meetings, a High School Teachers Workshop and two half-day Chairs to resolve points of dispute and reach a consensus on tutorials. Since its inception, ISMB has grown to be the largest each paper. Among the 191 submissions, 29 were conditionally international conference in computational biology and bioinfor- accepted for publication directly from the first round review Downloaded from matics. It is expected to be the premiere forum in the field for based on an assessment of the reviewers that the paper was presenting new research results, disseminating methods and tech- clearly above par for the conference. A subset of 16 papers niques and facilitating discussions among leading researchers, were viewed as potentially in the top tier but raised significant practitioners and students in the field.