January 2004
Total Page:16
File Type:pdf, Size:1020Kb
Load more
Recommended publications
-
Assigning Folds to the Proteins Encoded by the Genome of Mycoplasma Genitalium (Protein Fold Recognition͞computer Analysis of Genome Sequences)
Proc. Natl. Acad. Sci. USA Vol. 94, pp. 11929–11934, October 1997 Biophysics Assigning folds to the proteins encoded by the genome of Mycoplasma genitalium (protein fold recognitionycomputer analysis of genome sequences) DANIEL FISCHER* AND DAVID EISENBERG University of California, Los Angeles–Department of Energy Laboratory of Structural Biology and Molecular Medicine, Molecular Biology Institute, University of California, Los Angeles, Box 951570, Los Angeles, CA 90095-1570 Contributed by David Eisenberg, August 8, 1997 ABSTRACT A crucial step in exploiting the information genitalium (MG) (10), as a test of the capabilities of our inherent in genome sequences is to assign to each protein automatic fold recognition server and as a case study to sequence its three-dimensional fold and biological function. identify the difficulties facing automated fold assignment. Here we describe fold assignment for the proteins encoded by the small genome of Mycoplasma genitalium. The assignment MATERIALS AND METHODS was carried out by our computer server (http:yywww.doe- mbi.ucla.eduypeopleyfrsvryfrsvr.html), which assigns folds to The MG Sequences. The 468 MG sequences were obtained amino acid sequences by comparing sequence-derived predic- from The Institute for Genome Research (TIGR) through its tions with known structures. Of the total of 468 protein ORFs, Web address: http:yywww.tigr.orgytdbymdbymgdbymgd- 103 (22%) can be assigned a known protein fold with high b.html. Three types of annotation (based on searches in the confidence, as cross-validated with tests on known structures. sequence database) accompany each TIGR sequence (10): (i) Of these sequences, 75 (16%) show enough sequence similarity functional assignment—a clear sequence similarity with a to proteins of known structure that they can also be detected protein of known function from another organism was found by traditional sequence–sequence comparison methods. -
Practical Structure-Sequence Alignment of Pseudoknotted Rnas Wei Wang
Practical structure-sequence alignment of pseudoknotted RNAs Wei Wang To cite this version: Wei Wang. Practical structure-sequence alignment of pseudoknotted RNAs. Bioinformatics [q- bio.QM]. Université Paris Saclay (COmUE), 2017. English. NNT : 2017SACLS563. tel-01697889 HAL Id: tel-01697889 https://tel.archives-ouvertes.fr/tel-01697889 Submitted on 31 Jan 2018 HAL is a multi-disciplinary open access L’archive ouverte pluridisciplinaire HAL, est archive for the deposit and dissemination of sci- destinée au dépôt et à la diffusion de documents entific research documents, whether they are pub- scientifiques de niveau recherche, publiés ou non, lished or not. The documents may come from émanant des établissements d’enseignement et de teaching and research institutions in France or recherche français ou étrangers, des laboratoires abroad, or from public or private research centers. publics ou privés. 1 NNT : 2017SACLS563 Thèse de doctorat de l’Université Paris-Saclay préparée à L’Université Paris-Sud Ecole doctorale n◦580 (STIC) Sciences et Technologies de l’Information et de la Communication Spécialité de doctorat : Informatique par M. Wei WANG Alignement pratique de structure-séquence d’ARN avec pseudonœuds Thèse présentée et soutenue à Orsay, le 18 Décembre 2017. Composition du Jury : Mme Hélène TOUZET Directrice de Recherche (Présidente) CNRS, Université Lille 1 M. Guillaume FERTIN Professeur (Rapporteur) Université de Nantes M. Jan GORODKIN Professeur (Rapporteur) University of Copenhagen Mme Johanne COHEN Directrice de Recherche (Examinatrice) -
Mala Radhakrishnan an Interview by Mindy Levine
DED UN 18 O 98 F http://www.nesacs.org N Y O T R E I T H C E N O A E S S S L T A E A C R C I th N S M 90 Anniversary Issue of The NUCLEUS S E E H C C TI N November 2011 Vol. XC, No. 3 O CA N • AMERI Monthly Meeting 2011 James Flack Norris Award to Prof. Peter Mahaffy Meeting at Astra-Zeneca, Waltham Mala Radhakrishnan An Interview by Mindy Levine ACS Governance A Summary from the Fall ACS Meeting Arno Heyn Award 2011 Award to Harvey C. Steiner 2 The Nucleus November 2011 The Northeastern Section of the American Chemical Society, Inc. Contents Office: Anna Singer, 12 Corcoran Road, Burlington, MA 01803 (Voice or FAX) 781-272-1966. Mala Radhakrishnan ____________________________________4 e-mail: secretary(at)nesacs.org NESACS Homepage: An interview by Mindy Levine http://www.NESACS.org Officers 2011 Monthly Meeting _______________________________________5 Chair: 2011 James Flack Norris Award to Prof. Peter Mahaffy Patrick M. Gordon 1 Brae Circle Meeting at Astra-Zeneca, Waltham Woburn, MA 01801 [email protected] ACS Awards to NESACS Members _________________________6 Chair-Elect Ruth Tanner To be presented at the 243rd ACS National Meeting, San Diego, CA Olney Hall 415B March 27, 2012 Lowell, MA 01854 University of Mass Lowell Ruth_Tanner(at)uml.edu Report from Denver ____________________________________6 978-934-3662 Revamping the MCAT Exams. By Morton Z. Hoffman Immediate Past Chair: John McKew Historical Notes 7 John.McKew(at)gmail.com _______________________________________ Secretary: Virginia C. -
UC San Diego UC San Diego Electronic Theses and Dissertations
UC San Diego UC San Diego Electronic Theses and Dissertations Title Analysis and applications of conserved sequence patterns in proteins Permalink https://escholarship.org/uc/item/5kh9z3fr Author Ie, Tze Way Eugene Publication Date 2007 Peer reviewed|Thesis/dissertation eScholarship.org Powered by the California Digital Library University of California UNIVERSITY OF CALIFORNIA, SAN DIEGO Analysis and Applications of Conserved Sequence Patterns in Proteins A dissertation submitted in partial satisfaction of the requirements for the degree Doctor of Philosophy in Computer Science by Tze Way Eugene Ie Committee in charge: Professor Yoav Freund, Chair Professor Sanjoy Dasgupta Professor Charles Elkan Professor Terry Gaasterland Professor Philip Papadopoulos Professor Pavel Pevzner 2007 Copyright Tze Way Eugene Ie, 2007 All rights reserved. The dissertation of Tze Way Eugene Ie is ap- proved, and it is acceptable in quality and form for publication on microfilm: Chair University of California, San Diego 2007 iii DEDICATION This dissertation is dedicated in memory of my beloved father, Ie It Sim (1951–1997). iv TABLE OF CONTENTS Signature Page . iii Dedication . iv Table of Contents . v List of Figures . viii List of Tables . x Acknowledgements . xi Vita, Publications, and Fields of Study . xiii Abstract of the Dissertation . xv 1 Introduction . 1 1.1 Protein Homology Search . 1 1.2 Sequence Comparison Methods . 2 1.3 Statistical Analysis of Protein Motifs . 4 1.4 Motif Finding using Random Projections . 5 1.5 Microbial Gene Finding without Assembly . 7 2 Multi-Class Protein Classification using Adaptive Codes . 9 2.1 Profile-based Protein Classifiers . 14 2.2 Embedding Base Classifiers in Code Space . -
ABSTRACT DATA DRIVEN APPROACHES to IDENTIFY DETERMINANTS of HEART DISEASES and CANCER RESISTANCE Avinash Das Sahu, Doctor Of
ABSTRACT Title of dissertation: DATA DRIVEN APPROACHES TO IDENTIFY DETERMINANTS OF HEART DISEASES AND CANCER RESISTANCE Avinash Das Sahu, Doctor of Philosophy, 2016 Dissertation directed by: Professor Sridhar Hannenhalli Department of Computer Science Cancer and cardio-vascular diseases are the leading causes of death world-wide. Caused by systemic genetic and molecular disruptions in cells, these disorders are the manifestation of profound disturbance of normal cellular homeostasis. People suffering or at high risk for these disorders need early diagnosis and personalized therapeutic intervention. Successful implementation of such clinical measures can significantly improve global health. However, development of effective therapies is hindered by the challenges in identifying genetic and molecular determinants of the onset of diseases; and in cases where therapies already exist, the main challenge is to identify molecular determinants that drive resistance to the therapies. Due to the progress in sequencing technologies, the access to a large genome-wide biolog- ical data is now extended far beyond few experimental labs to the global research community. The unprecedented availability of the data has revolutionized the ca- pabilities of computational researchers, enabling them to collaboratively address the long standing problems from many different perspectives. Likewise, this thesis tackles the two main public health related challenges using data driven approaches. Numerous association studies have been proposed to identify genomic variants that determine disease. However, their clinical utility remains limited due to their inability to distinguish causal variants from associated variants. In the presented thesis, we first propose a simple scheme that improves association studies in su- pervised fashion and has shown its applicability in identifying genomic regulatory variants associated with hypertension. -
Australian Biochemist the Magazine of the Australian Society for Biochemistry and Molecular Biology Inc
ISSN 1443-0193 Australian Biochemist The Magazine of the Australian Society for Biochemistry and Molecular Biology Inc. Volume 47 AUGUST 2016 No.2 SHOWCASE ON RESEARCH Protein Misfolding and Proteostasis THIS ISSUE INCLUDES Showcase on Research Regular Departments A Short History of Amyloid SDS (Students) Page Molecular Chaperones: The Cutting Edge Guardians of the Proteome Off the Beaten Track When Proteostasis Goes Bad: Intellectual Property Protein Aggregation in the Cell Our Sustaining Members Extracellular Chaperones and Forthcoming Meetings Proteostasis Directory INSIDE ComBio2016 International Speaker Profiles Vol 47 No 2 August 2016 AUSTRALIAN BIOCHEMIST Page 1 ‘OSE’ Fill-in Puzzle We have another competition for the readers of the Australian Biochemist. All correct entries received by the Editor (email [email protected]) before 3 October 2016 will enter the draw to receive a gift voucher. With thanks to Rebecca Lew. The purpOSE is to choOSE from thOSE words listed and transpOSE them into the grid. So, clOSE your door, repOSE in a chair, and diagnOSE the answers – you don’t want to lOSE! 6 letters 8 letters ALDOSE FRUCTOSE FUCOSE FURANOSE HEXOSE PYRANOSE KETOSE RIBOSE 9 letters XYLOSE CELLULOSE GALACTOSE 7 letters RAFFINOSE AMYLOSE TREHALOSE GLUCOSE LACTOSE 11 letters MALTOSE DEOXYRIBOSE PENTOSE Australian Biochemist – Editor Chu Kong Liew, Editorial Officer Liana Friedman © 2016 Australian Society for Biochemistry and Molecular Biology Inc. All rights reserved. Page 2 AUSTRALIAN BIOCHEMIST Vol 47 No 2 August 2016 SHOWCASE ON RESEARCH EDITORIAL Molecular Origami: the Importance of Managing Protein Folding In my humble opinion, the most important biological transcription, RNA processing and transport, translation, molecule is the protein. -
Etwork Inference from Vector Representations of Words
RZ 3918 (# ZUR1801-015) 01/09/2018 Computer Science/Mathematics 19 pages Research Report INtERAcT: Interaction Network Inference from Vector Representations of Words Matteo Manica, Roland Mathis, Maria Rodriguez Martinez IBM Research – Zurich 8803 Rüschlikon Switzerland LIMITED DISTRIBUTION NOTICE This report has been submitted for publication outside of IBM and will probably be copyrighted if accepted for publication. It has been issued as a Research Report for early dissemination of its contents. In view of the transfer of copyright to the outside pub- lisher, its distribution outside of IBM prior to publication should be limited to peer communications and specific requests. After outside publication, requests should be filled only by reprints or legally obtained copies (e.g., payment of royalties). Some re- ports are available at http://domino.watson.ibm.com/library/Cyberdig.nsf/home. Research Africa • Almaden • Austin • Australia • Brazil • China • Haifa • India • Ireland • Tokyo • Watson • Zurich INtERAcT: Interaction Network Inference from Vector Representations of Words Matteo Manica1,2,*, Roland Mathis1,*, Mar´ıa Rodr´ıguez Mart´ınez1, y ftte,lth,[email protected] 1 IBM Research Z¨urich, S¨aumerstrasse4, 8803 R¨uschlikon, Switzerland 2 ETH Z¨urich, Institute f¨urMolekulare Systembiologie, Auguste-Piccard-Hof 1 8093, Z¨urich, Switzerland * Shared first authorship y Corresponding author Abstract Background In recent years, the number of biomedical publications made freely available through literature archives is steadfastly growing, resulting in a rich source of untapped new knowledge. Most biomedical facts are however buried in the form of unstructured text, and their exploitation requires expert-knowledge and time-consuming manual curation of published articles. -
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. -
Postmaster & the Merton Record 2020
Postmaster & The Merton Record 2020 Merton College Oxford OX1 4JD Telephone +44 (0)1865 276310 Contents www.merton.ox.ac.uk College News From the Warden ..................................................................................4 Edited by Emily Bruce, Philippa Logan, Milos Martinov, JCR News .................................................................................................8 Professor Irene Tracey (1985) MCR News .............................................................................................10 Front cover image Merton Sport .........................................................................................12 Wick Willett and Emma Ball (both 2017) in Fellows' Women’s Rowing, Men’s Rowing, Football, Squash, Hockey, Rugby, Garden, Michaelmas 2019. Photograph by John Cairns. Sports Overview, Blues & Haigh Ties Additional images (unless credited) Clubs & Societies ................................................................................24 4: © Ian Wallman History Society, Roger Bacon Society, Neave Society, Christian 13: Maria Salaru (St Antony’s, 2011) Union, Bodley Club, Mathematics Society, Quiz Society, Art Society, 22: Elina Cotterill Music Society, Poetry Society, Halsbury Society, 1980 Society, 24, 60, 128, 236: © John Cairns Tinbergen Society, Chalcenterics 40: Jessica Voicu (St Anne's, 2015) 44: © William Campbell-Gibson Interdisciplinary Groups ...................................................................40 58, 117, 118, 120, 130: Huw James Ockham Lectures, History of the Book -
The Eagle 2020
The Eagle 2020 The Eagle 2020 Photo: Emma Dellar, Lead Clinical Nurse, living on-site during the lockdown Credit: (2017) VOLUME 102 THE EAGLE 2020 1 WELCOME Published in the United Kingdom in 2020 by St John’s College, Cambridge First published in the United Kingdom in 1858 by St John’s College, Cambridge Cover photo credit: Jo Tynan Designed by Out of the Bleu (07759 919440; www.outofthebleu.co.uk) Printed by CDP (01517 247000; www.cdp.co.uk) The Eagle is published annually by St John’s College, Cambridge, and is provided free of charge to members of the College and other interested parties. 2 Photo: Komorebi Credit: Paul Everest WELCOME THE EAGLE 2020 3 WELCOME Contents Welcome Contributors .................................................................................................... 6 Editorial .......................................................................................................... 7 Message from the Vice-Master . 8 Articles Research at the Centre for Misfolding Diseases ...................................................... 14 A word for Wordsworth .................................................................................... 18 Dyslexia, poetry, rhythm and the brain . 21 Portrait of a Lady ............................................................................................. 24 The Cambridge Carthaginians ............................................................................ 27 Innovation and entrepreneurship at St John’s ......................................................... 31 The academic -
Communicating Biochemistry: Meetings and Events
© The Authors. Volume compilation © 2011 Portland Press Limited Chapter 3 Communicating Biochemistry: Meetings and Events Ian Dransfield and Brian Beechey Scientific conferences organized by the Biochemical Society represent a key facet of activity throughout the Society’s history and remain central to the present mission of promoting the advancement of molecular biosciences. Importantly, scientific conferences are an important means of communicating research findings, establishing collaborations and, critically, a means of cementing the community of biochemical scientists together. However, in the past 25 years, we have seen major changes to the way in which science is communicated and also in the way that scientists interact and establish collabo- rations. For example, the ability to show videos, “fly through” molecular structures or show time-lapse or real-time movies of molecular events within cells has had a very positive impact on conveying difficult concepts in presentations. However, increased pressures on researchers to obtain/maintain funding can mean that there is a general reluctance to present novel, unpublished data. In addition, the development of email and electronic access to scientific journals has dramatically altered the potential for communi- cation and accessibility of information, perhaps reducing the necessity of attending meetings to make new contacts and to hear exciting new science. The Biochemical Society has responded to these challenges by progressive development of the meetings format to better match the -
Protein Engineering Design & Selection
ISSN 1741-0126 (PRINT) ISSN 1741-0134 (ONLINE) peds protein engineering design & selection protein pedsprotein engineering design & selection Special Issue: Computational Protein Structure Assessment and Design: Part III Methods VOLUME GADIS: Algorithm for designing sequences to achieve target secondary structure profiles of intrinsically disordered proteins protein engineering design & selection 29 | peds Tyler S. Harmon, Michael D. Crabtree, Sarah L. Shammas, Ammon E. Posey, Jane Clarke, and Rohit V. Pappu 339 Original Articles NUMBER Conformational dynamics of cancer-associated MyD88-TIR domain mutant L252P (L265P) allosterically tilts the landscape VOLUME 29 NUMBER 9 2016 | | SEPTEMBER toward homo-dimerization 9 | S Chendi Zhan, Ruxi Qi, Guanghong Wei, Emine Guven-Maiorov, Ruth Nussinov, and Buyong Ma 347 E Efficient laboratory evolution of computationally designed enzymes with low starting activities using fluorescence-activated PT EMBER droplet sorting Special Issue: Computational Protein Structure Assessment and Design: Part III Richard Obexer, Moritz Pott, Cathleen Zeymer, Andrew D. Griffiths, and Donald Hilvert 355 2016 Steric interactions determine side-chain conformations in protein cores D. Caballero, A. Virrueta, C.S. O’Hern, and L. Regan 367 www.peds.oxfordjournals.org An in silico algorithm for identifying stabilizing pockets in proteins: test case, the Y220C mutant of the p53 tumor suppressor protein Dennis Bromley, Matthias R. Bauer, Alan R. Fersht, and Valerie Daggett 377 Structural difficulty index: a reliable measure