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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 -
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. -
Diversity Data Report 2019 Diversity Data Report 2019 Issued: November 2020 DES6507
Diversity data report 2019 Diversity data report 2019 Issued: November 2020 DES6507 The text of this work is licensed under the terms of the Creative Commons Attribution License which permits unrestricted use, provided the original author and source are credited. The license is available at: creativecommons.org/licenses/by/4.0 Images are not covered by this license. This report can be viewed online at: royalsociety.org/diversity Contents Introduction .....................................................4 The Fellowship ..................................................11 Committees, panels and working groups ..........................19 Research Fellowship Grants ......................................26 Scientific programmes ...........................................38 Public engagement .............................................50 Publishing ......................................................62 Schools engagement ............................................67 Royal Society staff ..............................................72 Gender pay gap .................................................75 Definitions .....................................................77 DIVERSITY DATA REPORT 2019 3 Introduction The Royal Society is a Fellowship of many of the world’s most eminent scientists and is the oldest scientific academy in continuous existence. The Society is committed to increasing sections of this report such as organisers, diversity in science, technology, engineering chairs and speakers at scientific meetings, and mathematics (‘STEM’) -
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). -
From DNA Sequence to Chromatin Dynamics: Computational Analysis of Transcriptional Regulation
From DNA Sequence to Chromatin Dynamics: Computational Analysis of Transcriptional Regulation Thesis submitted for the degree of “Doctor of Philosophy” by Tommy Kaplan Submitted to the Senate of the Hebrew University May 2008 This work was carried out under the supervision of Prof. Nir Friedman and Prof. Hanah Margalit Abstract All cells of a living organism share the same DNA. Yet, they differ in structure, activities and interactions. These differences arise through a tight regulatory system which activates different genes and pathways to fit the cell’s specialization, condition, and requirements. Deciphering the regulatory mechanisms underlying a living cell is one of the fundamental challenges in biology. Such knowledge will allow us to better understand how cells work, how they respond to external stimuli, what goes wrong in diseases like cancer (which often involves disruption of gene regulation), and how it can be fought. In my PhD, I focus on regulation of gene expression from three perspectives. First, I present an innovative algorithm for identifying the target genes of novel transcription factors, based on their protein sequence (Chapter 1). Second, I consider how several transcription factors cooperate to process external stimuli and alter the behavior of the cell (Chapter 2). Finally, I study how the genomic position of nucleosomes and their covalent modifications modulate the accessibility of DNA to transcription factors, thus adding a fascinating dimension to transcriptional regulation (Chapters 3 and 4). To understand transcriptional regulation, one should first reconstruct the architecture of the cell’s regulatory map, thus identifying which genes are regulated by which transcription factors (TFs). -
Program Book
Pacific Symposium on Biocomputing 2016 January 4-8, 2016 Big Island of Hawaii Program Book PACIFIC SYMPOSIUM ON BIOCOMPUTING 2016 Big Island of Hawaii, January 4-8, 2016 Welcome to PSB 2016! We have prepared this program book to give you quick access to information you need for PSB 2016. Enclosed you will find • Logistics information • Menus for PSB hosted meals • Full conference schedule • Call for Session and Workshop Proposals for PSB 2017 • Poster/abstract titles and authors • Participant List Conference materials are also available online at http://psb.stanford.edu/conference-materials/. PSB 2016 gratefully acknowledges the support the Institute for Computational Biology, a collaborative effort of Case Western Reserve University, the Cleveland Clinic Foundation, and University Hospitals; the National Institutes of Health (NIH), the National Science Foundation (NSF); and the International Society for Computational Biology (ISCB). If you or your institution are interested in sponsoring, PSB, please contact Tiffany Murray at [email protected] If you have any questions, the PSB registration staff (Tiffany Murray, Georgia Hansen, Brant Hansen, Kasey Miller, and BJ Morrison-McKay) are happy to help you. Aloha! Russ Altman Keith Dunker Larry Hunter Teri Klein Maryln Ritchie The PSB 2016 Organizers PACIFIC SYMPOSIUM ON BIOCOMPUTING 2016 Big Island of Hawaii, January 4-8, 2016 SPEAKER INFORMATION Oral presentations of accepted proceedings papers will take place in Salon 2 & 3. Speakers are allotted 10 minutes for presentation and 5 minutes for questions for a total of 15 minutes. Instructions for uploading talks were sent to authors with oral presentations. If you need assistance with this, please see Tiffany Murray or another PSB staff member. -
Modeling and Analysis of RNA-Seq Data: a Review from a Statistical Perspective
Modeling and analysis of RNA-seq data: a review from a statistical perspective Wei Vivian Li 1 and Jingyi Jessica Li 1;2;∗ Abstract Background: Since the invention of next-generation RNA sequencing (RNA-seq) technolo- gies, they have become a powerful tool to study the presence and quantity of RNA molecules in biological samples and have revolutionized transcriptomic studies. The analysis of RNA-seq data at four different levels (samples, genes, transcripts, and exons) involve multiple statistical and computational questions, some of which remain challenging up to date. Results: We review RNA-seq analysis tools at the sample, gene, transcript, and exon levels from a statistical perspective. We also highlight the biological and statistical questions of most practical considerations. Conclusion: The development of statistical and computational methods for analyzing RNA- seq data has made significant advances in the past decade. However, methods developed to answer the same biological question often rely on diverse statical models and exhibit dif- ferent performance under different scenarios. This review discusses and compares multiple commonly used statistical models regarding their assumptions, in the hope of helping users select appropriate methods as needed, as well as assisting developers for future method development. 1 Introduction RNA sequencing (RNA-seq) uses the next generation sequencing (NGS) technologies to reveal arXiv:1804.06050v3 [q-bio.GN] 1 May 2018 the presence and quantity of RNA molecules in biological samples. Since its invention, RNA- seq has revolutionized transcriptome analysis in biological research. RNA-seq does not require any prior knowledge on RNA sequences, and its high-throughput manner allows for genome-wide profiling of transcriptome landscapes [1,2]. -
Autumn 2005 SCIENCE in PARLIAMENT
Autumn 2005 SCIENCE IN PARLIAMENT State of the Nation Plastic Waste Private Finance Initiative Visions of Science Airbus Launches the New A350 The Journal of the Parliamentary and Scientific Committee http://www.scienceinparliament.org.uk THE STATE OF THE NATION 2005 An assessment of the UK’s infrastructure by the Institution of Civil Engineers PUBLISHED 18 OCTOBER 2005 About the Institution of Civil Engineers About the report As a professional body, the The State of the Nation Report For more information on the Institution of Civil Engineers (ICE) is compiled each year by a panel background to the State of the is one of the most important of civil engineering experts. The Nation Report, contact ICE sources of professional expertise report’s aim is to stimulate debate External Relations: in road and rail transport, water and to highlight the actions that supply and treatment, flood ICE believes need to be taken to t +44 (0)20 7665 2151 management, waste and energy – improve the UK’s infrastructure. e [email protected] our infrastructure. Established in It has been produced since 2000. w www.uk-infrastructure.org.uk 1818, it has over 75,000 members This year, six regional versions throughout the world – including of the State of the Nation Report – over 60,000 in the UK. covering Northern Ireland, Scotland, Wales as well as the North West, South West and West Midlands of England – are being produced, in conjunction with the UK-wide publication. To read the complete report please visit www.uk-infrastructure.org.uk Registered Charity No. -
24019 - Probabilistic Graphical Models
Year : 2019/20 24019 - Probabilistic Graphical Models Syllabus Information Academic Course: 2019/20 Academic Center: 337 - Polytechnic School Study: 3379 - Bachelor's (degree) programme in Telecommunications Network Engineering Subject: 24019 - Probabilistic Graphical Models Credits: 5.0 Course: 3 Teaching languages: Theory: Grup 1: English Practice: Grup 101: English Grup 102: English Seminar: Grup 101: English Grup 102: English Teachers: Vicente Gomez Cerda Teaching Period: Second Quarter Schedule: --- Presentation Probabilistic graphical models (PGMs) are powerful modeling tools for reasoning and decision making under uncertainty. PGMs have many application domains, including computer vision, natural language processing, efficient coding, and computational biology. PGMs connects graph theory and probability theory, and provide a flexible framework for modeling large collections of random variables with complex interactions. This is an introductory course which focuses on two main principles: (1) emphasizing the role of PGMs as a unifying language in machine learning that allows a natural specification of many problem domains with inherent uncertainty, and (2) providing a set of computational tools for probabilistic inference (making predictions that can be used to aid decision making), and learning (estimating the graph structure and their parameters from data). Associated skills Basic Competences That the students can apply their knowledge to their work or vocation of a professional form in a professional way and possess the competences which are usually proved by means of the elaboration and defense of arguments and solving the solution of problems within their study area. That the students have the ability of collecting and interpreting relevant data (normally within their study area) to issue judgements which include a reflection about relevant topics of social, scientific or ethical nature. -
Volume 2: Prizes and Scholarships
Issue 16: Volume 2 – Prizes, Awards & Scholarships (January – March, 2014) RESEARCH OPPORTUNITIES ALERT! Issue 16: Volume 2 PRIZES, AWARDS AND SCHOLARSHIPS (QUARTER: JANUARY - MARCH, 2014) A Compilation by the Research Services Unit Office of Research, Innovation and Development (ORID) December 2013 1 A compilation of the Research Services Unit of the Office of Research, Innovation & Development (ORID) Issue 16: Volume 2 – Prizes, Awards & Scholarships (January – March, 2014) JANUARY 2014 RUCE WASSERMAN YOUNG INVESTIGATOR AWARD American Association of Cereal Chemists Foundation B Description: Deadline information: Call has not yet been The American Association of Cereal Chemists announced by sponsor but this is the Foundation invites nominations for the Bruce approximate deadline we expect. This call is Wasserman young investigator award. This repeated once a year. award recognises young scientists who have Posted date: 12 Nov 10 made outstanding contributions to the field of Award type: Prizes cereal biotechnology. The work can either be Award amount max: $1,000 basic or applied. For the purposes of this Website: award, cereal biotechnology is broadly http://www.aaccnet.org/divisions/divisionsd defined, and encompasses any significant etail.cfm?CODE=BIOTECH body of research using plants, microbes, genes, proteins or other biomolecules. Eligibility profile Contributions in the disciplines of genetics, ---------------------------------------------- molecular biology, biochemistry, Country of applicant institution: Any microbiology and fermentation engineering are all included. Disciplines ---------------------------------------------- Nominees must be no older than 40 by July 1 Grains, Food Sciences, Cereals, Biotechnology, 2010, but nominations of younger scientists Biology, Molecular, Fermentation, are particularly encouraged. AACC Microbiology, Plant Genetics, Plant Sciences, international membership is not required for Biochemistry, Biological Sciences (RAE Unit nomination. -
A Hidden Markov Model Framewrok for Studying Regulation from Chromatin Through RNA
Submitted in part fulfilment of the requirements for the degree of Master of Science in Computer Science and Computational Biology A Hidden Markov Model Framewrok For Studying Regulation From Chromatin Through RNA Eran Rosenthal Supervisor: Dr. Tommy Kaplan October 2017 Hebrew University of Jerusalem Faculty of Science - Computer Science and Engineering Acknowledgments I would like to deeply thank Tommy, for being a great supervisor, giving very useful advices and scientific tutoring. Tommy has great ability to express complex concepts in simple, illustrative stories, and he introduced me to different kinds of experimental data and computational approaches. I would like also to thank for the members of the lab, for the interesting ideas and discussions. I would like to thank for all the people I had worked in collaboration in my master: • Moshe Oren and Gilad Fuchs for the providing me their experimental data of nascent RNA with RNF20 knockdown for studying the role of monoubiquity- lation of H2B. • Michael Berger and Yuval Malka for the exciting project of studying post- transcriptional 3’UTR cleavage of mRNA transcripts, and for Hanah Margalit and Avital Shimony who helped us in the analysis of miRNA regulation in this project. i Abstract Information flows from DNA to RNA, through transcription, followed by trans- lation of the RNA transcript to protein. A viable cell must have proper regulation on genes expression. There are varieties of regulation mechanisms along the way, which include regulation on the DNA and expression level of genes, post-transcriptional regulation, and post-translation regulation. Most of the cells in our body share the same DNA, but they have different func- tions. -
Curriculum Vitae—Nir Friedman
Nir Friedman Last update: February 14, 2019 Curriculum Vitae|Nir Friedman School of Computer Science and Engineering email: [email protected] Alexander Silberman Institute of Life Sciences Office: +972-73-388-4720 Hebrew University of Jerusalem Cellular: +972-54-882-0432 Jerusalem 91904, ISRAEL Professional History Professor 2009{present Alexander Silberman Institute of Life Sciences The Hebrew University of Jerusalem Professor 2007{present School of Computer Science & Engineering The Hebrew University of Jerusalem Associate Professor 2002{2007 School of Computer Science & Engineering The Hebrew University of Jerusalem Senior Lecturer 1998{2002 School of Computer Science & Engineering The Hebrew University of Jerusalem Postdoctoral Scholar 1996{1998 Division of Computer Science University of California, Berkeley Education Ph.D. Computer Science, Stanford University 1992{1997 M.Sc. Math. & Computer Science, Weizmann Institute of Science 1990{1992 B.Sc. Math. & Computer Science, Tel-Aviv University 1983{1987 Awards Alexander von Humboldt Foundation Research Award 2015 Fellow of the International Society of Computational Biology 2014 European Research Council \Advanced Grant" research award 2014-2018 \Test of Time" Award Research in Computational Molecular Biology (RECOMB) 2012 Most cited paper in 12-year window in RECOMB Michael Bruno Memorial Award 2010 \Israeli scholars and scientists of truly exceptional promise, whose achievements to date sug- gest future breakthroughs in their respective fields” [age < 50] European Research Council \Advanced