Hupo 4Th Annual World Congress from Defining the Proteome to Understanding Function
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ISCB Ebola Award for Important Future Research on the Computational Biology of Ebola Virus
ISCB Ebola Award for Important Future Research on the Computational Biology of Ebola Virus Journal Information Article/Issue Information Journal ID (nlm-ta): F1000Res Self URI: f1000research-4-6464.pdf Journal ID (iso-abbrev): F1000Res Date accepted: 13 January 2015 Journal ID (pmc): F1000Research Publication date (electronic): 15 January 2015 Title: F1000Research Publication date (collection): 2015 ISSN (electronic): 2046-1402 Volume: 4 Publisher: F1000Research (London, UK) Electronic Location Identifier: 12 Article Id (accession): PMC4457108 Article Id (pmcid): PMC4457108 Article Id (pmc-uid): 4457108 PubMed ID: 26097686 DOI: 10.12688/f1000research.6038.1 Funding: The author(s) declared that no grants were involved in supporting this work. Categories Subject: Editorial Categories Subject: Articles Subject: Bioinformatics Subject: Theory & Simulation Subject: Tropical & Travel-Associated Diseases Subject: Viral Infections (without HIV) Subject: Virology ISCB Ebola Award for Important Future Research on the Computational Biology of Ebola Virus v1; ref status: not peer reviewed Peter D. Karp Bonnie Berger Diane Kovats Thomas Lengauer Michal Linial Pardis Sabeti Winston Hide Burkhard Rost 1 1International Society for Computational Biology, La Jolla, CA, USA 2 2SRI International, Menlo Park, CA, USA 3 3Department of Mathematics, Massachusetts Institute of Technology, Cambridge, MA, USA 4 4Computational Biology and Applied Algorithmics, Max Planck Institute for Informatics, Saarbruecken, Germany 5 5Hebrew University & Institute of Advanced -
©Copyright 2015 Samuel Tabor Marionni Native Ion Mobility Mass Spectrometry: Characterizing Biological Assemblies and Modeling Their Structures
©Copyright 2015 Samuel Tabor Marionni Native Ion Mobility Mass Spectrometry: Characterizing Biological Assemblies and Modeling their Structures Samuel Tabor Marionni A dissertation submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy University of Washington 2015 Reading Committee: Matthew F. Bush, Chair Robert E. Synovec Dustin J. Maly James E. Bruce Program Authorized to Offer Degree: Chemistry University of Washington Abstract Native Ion Mobility Mass Spectrometry: Characterizing Biological Assemblies and Modeling their Structures Samuel Tabor Marionni Chair of the Supervisory Committee: Assistant Professor Matthew F. Bush Department of Chemistry Native mass spectrometry (MS) is an increasingly important structural biology technique for characterizing protein complexes. Conventional structural techniques such as X-ray crys- tallography and nuclear magnetic resonance (NMR) spectroscopy can produce very high- resolution structures, however large quantities of protein are needed, heterogeneity com- plicates structural elucidation, and higher-order complexes of biomolecules are difficult to characterize with these techniques. Native MS is rapid and requires very small amounts of sample. Though the data is not as high-resolution, information about stoichiometry, subunit topology, and ligand-binding, is readily obtained, making native MS very complementary to these techniques. When coupled with ion mobility, geometric information in the form of a collision cross section (Ω) can be obtained as well. Integrative modeling approaches are emerging that integrate gas-phase techniques — such as native MS, ion mobility, chemical cross-linking, and other forms of protein MS — with conventional solution-phase techniques and computational modeling. While conducting the research discussed in this dissertation, I used native MS to investigate two biological systems: a mammalian circadian clock protein complex and a series of engineered fusion proteins. -
Personal and Contact Details
CURRICULUM VITAE Carol Vivien Robinson DBE FRS FMedSci Personal and Contact Details Date of Birth 10th April 1956 Maiden Name Bradley Nationality British Contact details Department of Physical and Theoretical Chemistry University of Oxford South Parks Road Oxford OX1 3QZ Tel : +44 (0)1865 275473 E-mail : [email protected] Web : http://robinsonweb.chem.ox.ac.uk/Default.aspx Education and Appointments 2009 Professorial Fellow, Exeter College, Oxford 2009 Dr Lee’s Professor of Physical and Theoretical Chemistry, University of Oxford 2006 - 2016 Royal Society Research Professorship 2003 - 2009 Senior Research Fellow, Churchill College, University of Cambridge 2001 - 2009 Professor of Mass Spectrometry, Dept. of Chemistry, University of Cambridge 1999 - 2001 Titular Professor, University of Oxford 1998 - 2001 Research Fellow, Wolfson College, Oxford 1995 - 2001 Royal Society University Research Fellow, University of Oxford 1991 - 1995 Postdoctoral Research Fellow, University of Oxford. Supervisor: Prof. C. M. Dobson FRS 1991 - 1991 Postgraduate Diploma in Information Technology, University of Keele 1983 - 1991 Career break: birth of three children 1982 - 1983 MRC Training Fellowship, University of Bristol Medical School 1980 - 1982 Doctor of Philosophy, University of Cambridge. Supervisor: Prof. D. H. Williams FRS 1979 - 1980 Master of Science, University of Wales. Supervisor: Prof. J. H. Beynon FRS 1976 - 1979 Graduate of the Royal Society of Chemistry, Medway College of Technology, Kent 1972 - 1976 ONC and HNC in Chemistry, Canterbury -
From Fragmentation Mechanisms to Sequencing: Tandem Mass Spectrometry Based Peptide and Protein Identification
B American Society for Mass Spectrometry, 2012 J. Am. Soc. Mass Spectrom. (2012) 23:575Y576 DOI: 10.1007/s13361-012-0358-2 FOCUS: MS/MS PEPTIDE IDENTIFICATION: CONFERENCE REVIEW 23rd Sanibel Conference on Mass Spectrometry: From Fragmentation Mechanisms to Sequencing: Tandem Mass Spectrometry Based Peptide and Protein Identification Béla Paizs,1 Matthias Mann2 1German Cancer Research Center, Heidelberg, Germany 2Max-Planck Institute of Biochemistry, Martinsried, Germany he 23rd Sanibel Conference, sponsored by the American sequencing strategy. As a direct result of this parallel and TSociety for Mass Spectrometry, was held January 21– independent development, recent mechanistic insights into 24, 2011, at the TradeWinds Island Grand Hotel, St. Pete peptide fragmentation are seldom incorporated into the most Beach, Florida. The topic of this year was “From popular peptide identification or sequencing algorithms. Fragmentation Mechanisms to Sequencing: Tandem Mass These software packages are mainly based on peptide Spectrometry-Based Peptide and Protein Identification.” fragmentation models developed in the mid 1990s. The conference was co-organized by Béla Paizs, German The purpose of the 23rd Sanibel conference was to Cancer Research Center, Heidelberg, Germany, and bring the peptide fragmentation and bioinformatics Matthias Mann, Max-Planck Institute of Biochemistry, communities closer to each other by offering a forum Martinsried, Germany. to create a common language, exchange ideas, and A key information unit in the use of tandem mass establish joint research projects. This initiative was spectrometry (MS/MS) in proteomics is the product-ion well-appreciated by the community, and the conference spectrum of peptides or intact proteins. Most of the basic attracted a record attendance in the history of Sanibel biological and clinical investigations in proteomics face meetings with 200 participants presenting 27 invited the problem of peptide or protein sequencing by using lectures and submitting 77 poster abstracts. -
2Nd ANNUAL NORTH AMERICAN MASS SPECTROMETRY SUMMER SCHOOL
2nd ANNUAL NORTH AMERICAN MASS SPECTROMETRY SUMMER SCHOOL JULY 21-24, 2019 | MADISON, WISCONSIN Parabola of Neon (1913) Featured on the cover is an early 20th century parabola mass spectrograph. The early mass spectrometers, pioneered by J. J. Thomson, used electric and magnetic fields to disperse ion populations on photographic plates. Depending on their masses, the ions were dispersed along parabolic lines with those of the highest energy landing in the center and those with the least extending to the outermost edges. Positive ions are imaged on the upper half of the parabola while negative ions are deflected to the bottom half. Note that Ne produces two lines in the spectrum. Francis Aston, a former Thomson student, concluded from these data that stable elements also must have isotopes. These observations won Aston the Nobel Prize in Chemistry in 1922. Grayson, M.A. Measuring Mass: From Positive Rays to Proteins. 2002. Chemical Heritage Press, Philadelphia. Welcome to the 2nd Annual North American Mass Spectrometry Summer School We are proud to assemble world-leading experts in mass spectrometry for this second annual mass spectrometry summer school. We aim for you to experience an engaging and inspiring program covering the fundamentals of mass spectrometry and how to apply this tool to study biology. Also infused in the course are several workshops aimed to promote professional development. We encourage you to actively engage in discussion during all lectures, workshops, and events. This summer school is made possible through generous funding from the National Science Foundation (Plant Genome Research Program, Grant No. 1546742), the National Institutes of Health National Center for Quantitative Biology of Complex Systems (P41 GM108538), and the Morgridge Institute for Research. -
58TH ASMS CONFERENCE on MASS SPECTROMETRY MAY 23 – 27, 2010 Z SHORT COURSES: MAY 22 - 23, 2010 Salt Lake City, Utah
58TH ASMS CONFERENCE ON MASS SPECTROMETRY MAY 23 – 27, 2010 z SHORT COURSES: MAY 22 - 23, 2010 Salt Lake City, Utah LOCATION. The conference and short courses will be held at the Salt Palace Convention Center, 100 South West Temple, Salt Lake City, UT 84101. All oral sessions, poster sessions, exhibit booths and hospitality suites will be located in the convention center. REGISTRATION. On-site conference registration will open 2:00 pm, Saturday, May 22 in the convention center. There is no on-site registration for short courses. For more information: www.asms.org American Society for Mass Spectrometry 2019 Galisteo Street, Building I-1, Santa Fe, NM 87505 Phone: (505) 989-4517 Fax: (505) 989-1073 [email protected] www.asms.org Vice President for Programs: Scott A. McLuckey TABLE OF CONTENTS New This Year ........................................................ S2 ASMS Awards ........................................................ S3 Research Awards .................................................... S4 Program Overview .................................................. S5 Workshops .............................................................. S7 Sunday Program .................................................... S10 Monday Morning Oral Sessions ........................... S10 Monday Afternoon Oral Sessions ......................... S13 Tuesday Morning Oral Sessions ........................... S15 Tuesday Afternoon Oral Sessions ......................... S17 Wednesday Morning Oral Sessions ...................... S20 Wednesday Afternoon -
Focus on Proteomics in Honor of Ruedi Aebersold, 2002 Biemann Awardee
EDITORIAL Focus on Proteomics in Honor of Ruedi Aebersold, 2002 Biemann Awardee It is a pleasure to introduce this series of articles “Trypsin Catalyzed 16O-to-18O Exchange for Compara- honouring the achievements of Ruedi Aebersold, the tive Proteomics: Tandem Mass Spectrometry Compari- 2002 recipient of the ASMS Biemann Medal. During the son using MALDI-TOF, ESI-QTOF and ESI-Ion Trap last decade enormous progress has been made in the Mass Spectrometers” by Manfred Heller, Hassan Mat- application of mass spectrometry to proteomics, an area tou, Christoph Menzel, and Xudong Yao illustrates the to which Ruedi has contributed both generally and use of alternative labeling strategies involving 16Oto specifically with his isotope labelling strategies. In his 18O, in conjunction with enzymatic digestion for iden- opening Account and Perspective, “A Mass Spectromet- tifying proteins in human plasma. Of additional interest ric Journey into Protein and Proteome Research,” Ruedi in this article is the comparison of the many different poses the interesting question ‘does technology drive mass spectrometry platforms emerging for analysing biology or is the converse the case, where the biological such data including LC MALDI MS/MS approaches. question drives the technological development?’ This of Chromatographic separation is at the heart of many course remains an open question but the accompanying successful proteomic strategies, and an alternative ap- series of articles exemplify the tremendous synergy proach is exemplified by Figeys and colleagues in their between biology and methodological development. article, “On-line Strong Cation Exchange -HPLC-ESI- An important biological question prompts the first of MS/MS for Protein Identification and Process Optimi- the research articles; “Quantitative Proteomic Analysis zation.” Using a strong cation exchange micro LC of Chromatin-associated Factors” by Yuzuru Shiio, Eu- method for identification of proteins in mixtures, they gene C. -
Using Bayesian Networks to Analyze Expression Data
JOURNAL OFCOMPUTATIONAL BIOLOGY Volume7, Numbers 3/4,2000 MaryAnn Liebert,Inc. Pp. 601–620 Using Bayesian Networks to Analyze Expression Data NIR FRIEDMAN, 1 MICHAL LINIAL, 2 IFTACH NACHMAN, 3 andDANA PE’ER 1 ABSTRACT DNAhybridization arrayssimultaneously measurethe expression level forthousands of genes.These measurementsprovide a “snapshot”of transcription levels within the cell. Ama- jorchallenge in computationalbiology is touncover ,fromsuch measurements,gene/ protein interactions andkey biological features ofcellular systems. In this paper,wepropose a new frameworkfor discovering interactions betweengenes based onmultiple expression mea- surements. This frameworkbuilds onthe use of Bayesian networks forrepresenting statistical dependencies. ABayesiannetwork is agraph-basedmodel of joint multivariateprobability distributions thatcaptures properties ofconditional independence betweenvariables. Such models areattractive for their ability todescribe complexstochastic processes andbecause theyprovide a clear methodologyfor learning from(noisy) observations.We start byshowing howBayesian networks can describe interactions betweengenes. W ethen describe amethod forrecovering gene interactions frommicroarray data using tools forlearning Bayesiannet- works.Finally, we demonstratethis methodon the S.cerevisiae cell-cycle measurementsof Spellman et al. (1998). Key words: geneexpression, microarrays, Bayesian methods. 1.INTRODUCTION centralgoal of molecularbiology isto understand the regulation of protein synthesis and its Areactionsto external -
Download Link at Figshare.Com/Articles/Bint Fishmovie32 100 Mat/5009840)
Distribution Agreement In presenting this thesis or dissertation as a partial fulfillment of the requirements for an advanced degree from Emory University, I hereby grant to Emory University and its agents the non-exclusive license to archive, make accessible, and display my thesis or dissertation in whole or in part in all forms of media, now or hereafter known, including display on the world wide web. I understand that I may select some access restrictions as part of the online submission of this thesis or dissertation. I retain all ownership rights to the copyright of the thesis or dissertation. I also retain the right to use in future works (such as articles or books) all or part of this thesis or dissertation. Signature: Joseph L. Natale Date Inference, Dynamics, and Coarse-Graining of Large-Scale Biological Networks By Joseph L. Natale Doctor of Philosophy Physics Ilya Nemenman, Ph.D. Advisor Gordon Berman, Ph.D. Committee Member Avani Gadani, Ph.D. Committee Member H. George E. Hentschel, Ph.D. Committee Member Daniel Weissman, Ph.D. Committee Member Accepted: Lisa A. Tedesco, Ph.D. Dean of the James T. Laney School of Graduate Studies Date Inference, Dynamics, and Coarse-Graining of Large-Scale Biological Networks By Joseph L. Natale B.S., Stevens Institute of Technology, NJ, 2012 M.S., Stevens Institute of Technology, NJ, 2013 Advisor: Ilya Nemenman, Ph.D. An abstract of A dissertation submitted to the Faculty of the James T. Laney School of Graduate Studies of Emory University in partial fulfillment of the requirements for the degree of Doctor of Philosophy in Physics 2020 Inference, Dynamics, and Coarse-Graining of Large-Scale Biological Networks By Joseph L. -
Nature Milestones Mass Spectrometry October 2015
October 2015 www.nature.com/milestones/mass-spec MILESTONES Mass Spectrometry Produced with support from: Produced by: Nature Methods, Nature, Nature Biotechnology, Nature Chemical Biology and Nature Protocols MILESTONES Mass Spectrometry MILESTONES COLLECTION 4 Timeline 5 Discovering the power of mass-to-charge (1910 ) NATURE METHODS: COMMENTARY 23 Mass spectrometry in high-throughput 6 Development of ionization methods (1929) proteomics: ready for the big time 7 Isotopes and ancient environments (1939) Tommy Nilsson, Matthias Mann, Ruedi Aebersold, John R Yates III, Amos Bairoch & John J M Bergeron 8 When a velocitron meets a reflectron (1946) 8 Spinning ion trajectories (1949) NATURE: REVIEW Fly out of the traps (1953) 9 28 The biological impact of mass-spectrometry- 10 Breaking down problems (1956) based proteomics 10 Amicable separations (1959) Benjamin F. Cravatt, Gabriel M. Simon & John R. Yates III 11 Solving the primary structure of peptides (1959) 12 A technique to carry a torch for (1961) NATURE: REVIEW 12 The pixelation of mass spectrometry (1962) 38 Metabolic phenotyping in clinical and surgical 13 Conquering carbohydrate complexity (1963) environments Jeremy K. Nicholson, Elaine Holmes, 14 Forming fragments (1966) James M. Kinross, Ara W. Darzi, Zoltan Takats & 14 Seeing the full picture of metabolism (1966) John C. Lindon 15 Electrospray makes molecular elephants fly (1968) 16 Signatures of disease (1975) 16 Reduce complexity by choosing your reactions (1978) 17 Enter the matrix (1985) 18 Dynamic protein structures (1991) 19 Protein discovery goes global (1993) 20 In pursuit of PTMs (1995) 21 Putting the pieces together (1999) CITING THE MILESTONES CONTRIBUTING JOURNALS UK/Europe/ROW (excluding Japan): The Nature Milestones: Mass Spectroscopy supplement has been published as Nature Methods, Nature, Nature Biotechnology, Nature Publishing Group, Subscriptions, a joint project between Nature Methods, Nature, Nature Biotechnology, Nature Chemical Biology and Nature Protocols. -
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. -
Aggregation, Dissemination, and Analysis of High- Throughput Scientific Data Sets in the Field of Proteomics
AGGREGATION, DISSEMINATION, AND ANALYSIS OF HIGH- THROUGHPUT SCIENTIFIC DATA SETS IN THE FIELD OF PROTEOMICS by Jayson A. Falkner A dissertation submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy (Bioinformatics) in The University of Michigan 2008 Doctoral Committee Professor Philip C. Andrews, Chair Professor Daniel M. Burns Jr Assistant Professor Matthew A. Young Assistant Professor Alexey Nesvizhskii © Jayson A. Falkner 2008 I dedicate this to my parents and family for supporting me in pursuit of over-education to the fullest. Thankfully I've learned that academics, science, and the pursuit of intellect are of little to benefit an individual. Friends, family, and society give purpose to both work and life. One is not without the other. Thanks Mom and Dad. ii Acknowledgments Phil Andrews has been a constant source of ideas, enthusiasm, and support for my work. Pretty much every part of this thesis was inspired in one way or another by Phil, and I feel very fortunate to have had a mentor that wanted include me in most everything. Even sending me around the world for countless conferences, workshops, and meetings. I think that all mentors work in mysterious and unmeasurable ways, and I have been unbelievably lucky to have such a good mentor and friend. Pete Ulintz, Eric Simon, Anastasia Yocum, Bryan Smith, James “Augie” Hill, and the rest of Phil's lab have been great friends and contributed in many ways to my work. Dan Burns, David States, Brian Athey, Gil Omenn, Alexey Nesvizhskii, Matt Young, Heather Carlson, David Burke, and others in the program are all to thank for advice, guidance, and teaching me about what getting a PhD is really about.