Multiscale Modeling in Systems Biology
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Applied Category Theory for Genomics – an Initiative
Applied Category Theory for Genomics { An Initiative Yanying Wu1,2 1Centre for Neural Circuits and Behaviour, University of Oxford, UK 2Department of Physiology, Anatomy and Genetics, University of Oxford, UK 06 Sept, 2020 Abstract The ultimate secret of all lives on earth is hidden in their genomes { a totality of DNA sequences. We currently know the whole genome sequence of many organisms, while our understanding of the genome architecture on a systematic level remains rudimentary. Applied category theory opens a promising way to integrate the humongous amount of heterogeneous informations in genomics, to advance our knowledge regarding genome organization, and to provide us with a deep and holistic view of our own genomes. In this work we explain why applied category theory carries such a hope, and we move on to show how it could actually do so, albeit in baby steps. The manuscript intends to be readable to both mathematicians and biologists, therefore no prior knowledge is required from either side. arXiv:2009.02822v1 [q-bio.GN] 6 Sep 2020 1 Introduction DNA, the genetic material of all living beings on this planet, holds the secret of life. The complete set of DNA sequences in an organism constitutes its genome { the blueprint and instruction manual of that organism, be it a human or fly [1]. Therefore, genomics, which studies the contents and meaning of genomes, has been standing in the central stage of scientific research since its birth. The twentieth century witnessed three milestones of genomics research [1]. It began with the discovery of Mendel's laws of inheritance [2], sparked a climax in the middle with the reveal of DNA double helix structure [3], and ended with the accomplishment of a first draft of complete human genome sequences [4]. -
Tsvi Tlusty – C.V
TSVI TLUSTY – C.V. 06/2021 Center for Soft and Living Matter, Institute for Basic Science, Bldg. (#103), Ulsan National Institute of Science and Technology, 50 UNIST-gil, Ulju-gun, Ulsan 44919, Korea email: [email protected] homepage: life.ibs.re.kr EDUCATION AND EMPLOYMENT 2015– Distinguished Professor, Department of Physics, UNIST, Ulsan 2015– Group Leader, Center for Soft and Living Matter, Institute for Basic Science 2011–2015 Long-term Member, Institute of Advanced Study, Princeton. 2005–2013 Senior researcher, Physics of Complex Systems, Weizmann Institute. 2000–2004 Fellow, Center for Physics and Biology, Rockefeller University, New York. Host: Prof. Albert Libchaber 1995–2000 Ph.D. in Physics, Weizmann Institute, “Universality in Microemulsions”, Supervisor: Prof. Samuel A. Safran. 1991–1995 M.Sc. in Physics, Weizmann Institute. 1988–1990 B.Sc. in Physics and Mathematics (Talpyot), Hebrew University, Jerusalem. Teaching: Landmark Experiments in Biology (2006); Statistical Physics (2007, 2017-20); Information in Biology (2012); Errors and Codes (IAS, 2012); Theory of Living Matter (2016); Students and post-doctoral fellows (03/2020) Pineros William (postdoc, 2019- ) John Mcbride (postdoc, 2018- ) Somya Mani (postdoc, 2018- ) Tamoghna Das (postdoc, 2018- ) Ashwani Tripathi (postdoc, 2018- ) Sandipan Dutta (postdoc, 2016-2021), Prof. at BIRS Pileni, India Vladimir Reinharz (postdoc, 2018-2020), Prof. at U. Montreal. YongSeok Jho (research fellow, 2016-2017), Prof. at GyeongSang U. Yoni Savir (Ph.D., 2005-2011) Prof. at Technion. Adam Lampert (Ph.D., 2008-2012) Prof. at U. Arizona. Arbel Tadmor (M.Sc., 2006-2008) researcher at TRON. Maria Rodriguez Martinez (Postdoc, 2007-2009), PI at IBM Zurich Tamar Friedlander (Postdoc, 2009 -2012) Prof. -
UNIVERSITY of CALIFORNIA SAN DIEGO Making Sense of Microbial
UNIVERSITY OF CALIFORNIA SAN DIEGO Making sense of microbial populations from representative samples A dissertation submitted in partial satisfaction of the requirements for the degree Doctor of Philosophy in Computer Science by James T. Morton Committee in charge: Professor Rob Knight, Chair Professor Pieter Dorrestein Professor Rachel Dutton Professor Yoav Freund Professor Siavash Mirarab 2018 Copyright James T. Morton, 2018 All rights reserved. The dissertation of James T. Morton is approved, and it is acceptable in quality and form for publication on microfilm and electronically: Chair University of California San Diego 2018 iii DEDICATION To my friends and family who paved the road and lit the journey. iv EPIGRAPH The ‘paradox’ is only a conflict between reality and your feeling of what reality ‘ought to be’ —Richard Feynman v TABLE OF CONTENTS Signature Page . iii Dedication . iv Epigraph . .v Table of Contents . vi List of Abbreviations . ix List of Figures . .x List of Tables . xi Acknowledgements . xii Vita ............................................. xiv Abstract of the Dissertation . xvii Chapter 1 Methods for phylogenetic analysis of microbiome data . .1 1.1 Introduction . .2 1.2 Phylogenetic Inference . .4 1.3 Phylogenetic Comparative Methods . .6 1.4 Ancestral State Reconstruction . .9 1.5 Analysis of phylogenetic variables . 11 1.6 Using Phylogeny-Aware Distances . 15 1.7 Challenges of phylogenetic analysis . 18 1.8 Discussion . 19 1.9 Acknowledgements . 21 Chapter 2 Uncovering the horseshoe effect in microbial analyses . 23 2.1 Introduction . 24 2.2 Materials and Methods . 34 2.3 Acknowledgements . 35 Chapter 3 Balance trees reveal microbial niche differentiation . 36 3.1 Introduction . -
Standardised Benchmarking in the Quest for Orthologs
View metadata, citation and similar papers at core.ac.uk brought to you by CORE provided by Harvard University - DASH Standardised Benchmarking in the Quest for Orthologs The Harvard community has made this article openly available. Please share how this access benefits you. Your story matters Citation Altenhoff, A. M., B. Boeckmann, S. Capella-Gutierrez, D. A. Dalquen, T. DeLuca, K. Forslund, J. Huerta-Cepas, et al. 2016. “Standardised Benchmarking in the Quest for Orthologs.” Nature methods 13 (5): 425-430. doi:10.1038/nmeth.3830. http://dx.doi.org/10.1038/ nmeth.3830. Published Version doi:10.1038/nmeth.3830 Citable link http://nrs.harvard.edu/urn-3:HUL.InstRepos:29408292 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 HHS Public Access Author manuscript Author ManuscriptAuthor Manuscript Author Nat Methods Manuscript Author . Author manuscript; Manuscript Author available in PMC 2016 October 04. Published in final edited form as: Nat Methods. 2016 May ; 13(5): 425–430. doi:10.1038/nmeth.3830. Standardised Benchmarking in the Quest for Orthologs Adrian M. Altenhoff1,2, Brigitte Boeckmann3, Salvador Capella-Gutierrez4,5,6, Daniel A. Dalquen7, Todd DeLuca8, Kristoffer Forslund9, Jaime Huerta-Cepas9, Benjamin Linard10, Cécile Pereira11,12, Leszek P. Pryszcz4, Fabian Schreiber13, Alan Sousa da Silva13, Damian Szklarczyk14,15, Clément-Marie Train1, Peer Bork9,16,17, Odile Lecompte18, Christian von Mering14,15, Ioannis Xenarios3,19,20, Kimmen Sjölander21, Lars Juhl Jensen22, Maria J. -
Mechanistic Mathematical Modeling of Spatiotemporal Microtubule Dynamics and Regulation in Vivo
Research Collection Doctoral Thesis Mechanistic mathematical modeling of spatiotemporal microtubule dynamics and regulation in vivo Author(s): Widmer, Lukas A. Publication Date: 2018 Permanent Link: https://doi.org/10.3929/ethz-b-000328562 Rights / License: In Copyright - Non-Commercial Use Permitted This page was generated automatically upon download from the ETH Zurich Research Collection. For more information please consult the Terms of use. ETH Library diss. eth no. 25588 MECHANISTICMATHEMATICAL MODELINGOFSPATIOTEMPORAL MICROTUBULEDYNAMICSAND REGULATION INVIVO A thesis submitted to attain the degree of DOCTOR OF SCIENCES of ETH ZURICH (dr. sc. eth zurich) presented by LUKASANDREASWIDMER msc. eth cbb born on 11. 03. 1987 citizen of luzern and ruswil lu, switzerland accepted on the recommendation of Prof. Dr. Jörg Stelling, examiner Prof. Dr. Yves Barral, co-examiner Prof. Dr. François Nédélec, co-examiner Prof. Dr. Linda Petzold, co-examiner 2018 Lukas Andreas Widmer Mechanistic mathematical modeling of spatiotemporal microtubule dynamics and regulation in vivo © 2018 ACKNOWLEDGEMENTS We are all much more than the sum of our work, and there is a great many whom I would like to thank for their support and encouragement, without which this thesis would not exist. I would like to thank my supervisor, Prof. Jörg Stelling, for giving me the opportunity to conduct my PhD research in his group. Jörg, you have been a great scientific mentor, and the scientific freedom you give your students is something I enjoyed a lot – you made it possible for me to develop my own theories, and put them to the test. I thank you for the trust you put into me, giving me a challenge to rise up to, and for always having an open door, whether in times of excitement or despair. -
Causal Queries from Observational Data in Biological Systems Via Bayesian Networks: an Empirical Study in Small Networks
Causal Queries from Observational Data in Biological Systems via Bayesian Networks: An Empirical Study in Small Networks Alex White and Matthieu Vignes Abstract Biological networks are a very convenient modelling and visualisation tool to discover knowledge from modern high-throughput genomics and post- genomics data sets. Indeed, biological entities are not isolated, but are components of complex multi-level systems. We go one step further and advocate for the con- sideration of causal representations of the interactions in living systems. We present the causal formalism and bring it out in the context of biological networks, when the data is observational. We also discuss its ability to decipher the causal infor- mation flow as observed in gene expression. We also illustrate our exploration by experiments on small simulated networks as well as on a real biological data set. Key words: Causal biological networks, Gene regulatory network reconstruction, Direct Acyclic Graph inference, Bayesian networks 1 Introduction Throughout their lifetime, organisms express their genetic program, i.e. the instruc- tion manual for molecular actions in every cell. The products of the expression of this program are messenger RNA (mRNA); the blueprints to produce proteins, the cornerstones of the living world. The diversity of shapes and the fate of cells is a re- sult of different readings of the genetic material, probably because of environmental factors, but also because of epigenetic organisational capacities. The genetic mate- rial appears regulated to produce what the organism needs in a specific situation. We now have access to rich genomics data sets. We see them as instantaneous images of cell activity from varied angles, through different filters. -
OMA, a Comprehensive, Automated Project for the Identification of Orthologs from Complete Genome Data: Introduction and First Achievements
OMA, A Comprehensive, Automated Project for the Identification of Orthologs from Complete Genome Data: Introduction and First Achievements Christophe Dessimoz, Gina Cannarozzi, Manuel Gil, Daniel Margadant, Alexander Roth, Adrian Schneider, and Gaston H. Gonnet ETH Zurich, Institute of Computational Science, CH-8092 Z¨urich [email protected] Abstract. The OMA project is a large-scale effort to identify groups of orthologs from complete genome data, currently 150 species. The algo- rithm relies solely on protein sequence information and does not require any human supervision. It has several original features, in particular a verification step that detects paralogs and prevents them from being clustered together. Consistency checks and verification are performed throughout the process. The resulting groups, whenever a comparison could be made, are highly consistent both with EC assignments, and with assignments from the manually curated database HAMAP. A highly ac- curate set of orthologous sequences constitutes the basis for several other investigations, including phylogenetic analysis and protein classification. Complete genomes give scientists a valuable resource to assign functions to se- quences and to analyze their evolutionary history. These analyses rely heavily on gene comparison through sequence alignment algorithms that output the level of similarity, which gives an indication of homology. When homologous sequences are of interest, care must often be taken to distinguish between orthologous and paralogous proteins [1]. Both orthologs and paralogs come from the same ancestral sequence, and therefore are homologous, but they differ in the way they arise: paralogous se- quences are the product of gene duplication, while orthologous sequences are the product of speciation. -
Advancing a Systems Cell-Free Metabolic Engineering Approach to Natural Product Synthesis and Discovery
University of Tennessee, Knoxville TRACE: Tennessee Research and Creative Exchange Doctoral Dissertations Graduate School 12-2020 Advancing a systems cell-free metabolic engineering approach to natural product synthesis and discovery Benjamin Mohr University of Tennessee Follow this and additional works at: https://trace.tennessee.edu/utk_graddiss Recommended Citation Mohr, Benjamin, "Advancing a systems cell-free metabolic engineering approach to natural product synthesis and discovery. " PhD diss., University of Tennessee, 2020. https://trace.tennessee.edu/utk_graddiss/6837 This Dissertation is brought to you for free and open access by the Graduate School at TRACE: Tennessee Research and Creative Exchange. It has been accepted for inclusion in Doctoral Dissertations by an authorized administrator of TRACE: Tennessee Research and Creative Exchange. For more information, please contact [email protected]. To the Graduate Council: I am submitting herewith a dissertation written by Benjamin Mohr entitled "Advancing a systems cell-free metabolic engineering approach to natural product synthesis and discovery." I have examined the final electronic copy of this dissertation for form and content and recommend that it be accepted in partial fulfillment of the equirr ements for the degree of Doctor of Philosophy, with a major in Energy Science and Engineering. Mitchel Doktycz, Major Professor We have read this dissertation and recommend its acceptance: Jennifer Morrell-Falvey, Dale Pelletier, Michael Simpson, Robert Hettich Accepted for the Council: Dixie L. Thompson Vice Provost and Dean of the Graduate School (Original signatures are on file with official studentecor r ds.) Advancing a systems cell-free metabolic engineering approach to natural product synthesis and discovery A Dissertation Presented for the Doctor of Philosophy Degree The University of Tennessee, Knoxville Benjamin Pintz Mohr December 2019 c by Benjamin Pintz Mohr, 2019 All Rights Reserved. -
REST API and the Packages for R and Python Omadb
F1000Research 2019, 8:42 Last updated: 12 APR 2019 SOFTWARE TOOL ARTICLE Expanding the Orthologous Matrix (OMA) programmatic interfaces: REST API and the OmaDB packages for R and Python [version 2; peer review: 2 approved] Klara Kaleb1, Alex Warwick Vesztrocy 1,2, Adrian Altenhoff 2,3, Christophe Dessimoz 1,2,4-6 1Centre for Life’s Origins and Evolution, Department of Genetics, Evolution and Environment, University College London, London, WC1E 6BT, UK 2Swiss Institute of Bioinformatics, Lausanne, Switzerland 3Department of Computer Science, ETH Zurich, Zurich, Switzerland 4Department of Computer Science, University College London, London, WC1E 6BT, Switzerland 5Department of Computational Biology, University of Lausanne, Lausanne, 1015, Switzerland 6Center for Integrative Genomics, University of Lausanne, Lausanne, 1015, Switzerland First published: 10 Jan 2019, 8:42 ( Open Peer Review v2 https://doi.org/10.12688/f1000research.17548.1) Latest published: 29 Mar 2019, 8:42 ( https://doi.org/10.12688/f1000research.17548.2) Referee Status: Abstract Invited Referees The Orthologous Matrix (OMA) is a well-established resource to identify 1 2 orthologs among many genomes. Here, we present two recent additions to its programmatic interface, namely a REST API, and user-friendly R and Python packages called OmaDB. These should further facilitate the incorporation of version 2 report report OMA data into computational scripts and pipelines. The REST API can be published freely accessed at https://omabrowser.org/api. The R OmaDB package is 29 Mar 2019 available as part of Bioconductor at http://bioconductor.org/packages/OmaDB/, and the omadb Python package is available from the Python Package Index version 1 (PyPI) at https://pypi.org/project/omadb/. -
Daniel Aalberts Scott Aa
PLOS Computational Biology would like to thank all those who reviewed on behalf of the journal in 2015: Daniel Aalberts Jeff Alstott Benjamin Audit Scott Aaronson Christian Althaus Charles Auffray Henry Abarbanel Benjamin Althouse Jean-Christophe Augustin James Abbas Russ Altman Robert Austin Craig Abbey Eduardo Altmann Bruno Averbeck Hermann Aberle Philipp Altrock Ferhat Ay Robert Abramovitch Vikram Alva Nihat Ay Josep Abril Francisco Alvarez-Leefmans Francisco Azuaje Luigi Acerbi Rommie Amaro Marc Baaden Orlando Acevedo Ettore Ambrosini M. Madan Babu Christoph Adami Bagrat Amirikian Mohan Babu Frederick Adler Uri Amit Marco Bacci Boris Adryan Alexander Anderson Stephen Baccus Tinri Aegerter-Wilmsen Noemi Andor Omar Bagasra Vera Afreixo Isabelle Andre Marc Baguelin Ashutosh Agarwal R. David Andrew Timothy Bailey Ira Agrawal Steven Andrews Wyeth Bair Jacobo Aguirre Ioan Andricioaei Chris Bakal Alaa Ahmed Ioannis Androulakis Joseph Bak-Coleman Hasan Ahmed Iris Antes Adam Baker Natalie Ahn Maciek Antoniewicz Douglas Bakkum Thomas Akam Haroon Anwar Gabor Balazsi Ilya Akberdin Stefano Anzellotti Nilesh Banavali Eyal Akiva Miguel Aon Rahul Banerjee Sahar Akram Lucy Aplin Edward Banigan Tomas Alarcon Kevin Aquino Martin Banks Larissa Albantakis Leonardo Arbiza Mukul Bansal Reka Albert Murat Arcak Shweta Bansal Martí Aldea Gil Ariel Wolfgang Banzhaf Bree Aldridge Nimalan Arinaminpathy Lei Bao Helen Alexander Jeffrey Arle Gyorgy Barabas Alexander Alexeev Alain Arneodo Omri Barak Leonidas Alexopoulos Markus Arnoldini Matteo Barberis Emil Alexov -
1. Introduction
Reviews in Computational Biology 1. Introduction ! Christophe Dessimoz and James Smith January 2012 1 Today Course introduction Review writing 2 About Christophe • Diploma in Biology • PhD in Computer Science • Now: Visiting Scientist at EBI • Relevant experience: ~25 research articles ~50 peer-reviews for 14 journals ~15 funding proposals Guest editor of Briefings in Bioinformatics 3 - ETH Zurich, Northwestern, Tsinghua University, Chulalongkorn (Bangkok) About James • Biological Sciences & Pathway Biochemistry • PhD in Comp. Pharmacology (Drug Design) • Now: Scientist in Comp. Biochemistry • Previous experience: Research Fellow in Comp. Systems Biology ~20 research articles ~20 peer-reviews for 8 journals 12 funding proposals (myself & students) Experience as a technical editor 4 - BSc(Hons) Biological Sciences (Leicester) – halfway into a DPhil Biochemistry (Oxford) was lured to Pharmacology in Cambridge on an industrial scholarship, so jumped :-) – collaborations with universities/institutes in the USA, UK, Germany (inc EMBL), France and some pharmaceutical companies. What is doctoral training? • Mechanism for interdisciplinary research eg. at the interface between life and physical/computational sciences • CCBI http://en.wikipedia.org/wiki/Doctoral_Training_Centredoesn't have a DTC so we are piloting this course module 5 What is a Academic Training & Transferable Skills Course? Doctoral training has been around in diferent forms other European countries In the UK, doctoral training is a strategic mechanism for interdisciplinary research at the interface between the life and physical sciences or between disciplines DTC modules are conventionally for 1st/2nd years of a 3 or 4-year programme that augment the background of interdisciplinary projects and help researchers interact in new domains. They act as bridges between disciplines. -
Annual Scientific Report 2011 Annual Scientific Report 2011 Designed and Produced by Pickeringhutchins Ltd
European Bioinformatics Institute EMBL-EBI Annual Scientific Report 2011 Annual Scientific Report 2011 Designed and Produced by PickeringHutchins Ltd www.pickeringhutchins.com EMBL member states: Austria, Croatia, Denmark, Finland, France, Germany, Greece, Iceland, Ireland, Israel, Italy, Luxembourg, the Netherlands, Norway, Portugal, Spain, Sweden, Switzerland, United Kingdom. Associate member state: Australia EMBL-EBI is a part of the European Molecular Biology Laboratory (EMBL) EMBL-EBI EMBL-EBI EMBL-EBI EMBL-European Bioinformatics Institute Wellcome Trust Genome Campus, Hinxton Cambridge CB10 1SD United Kingdom Tel. +44 (0)1223 494 444, Fax +44 (0)1223 494 468 www.ebi.ac.uk EMBL Heidelberg Meyerhofstraße 1 69117 Heidelberg Germany Tel. +49 (0)6221 3870, Fax +49 (0)6221 387 8306 www.embl.org [email protected] EMBL Grenoble 6, rue Jules Horowitz, BP181 38042 Grenoble, Cedex 9 France Tel. +33 (0)476 20 7269, Fax +33 (0)476 20 2199 EMBL Hamburg c/o DESY Notkestraße 85 22603 Hamburg Germany Tel. +49 (0)4089 902 110, Fax +49 (0)4089 902 149 EMBL Monterotondo Adriano Buzzati-Traverso Campus Via Ramarini, 32 00015 Monterotondo (Rome) Italy Tel. +39 (0)6900 91402, Fax +39 (0)6900 91406 © 2012 EMBL-European Bioinformatics Institute All texts written by EBI-EMBL Group and Team Leaders. This publication was produced by the EBI’s Outreach and Training Programme. Contents Introduction Foreword 2 Major Achievements 2011 4 Services Rolf Apweiler and Ewan Birney: Protein and nucleotide data 10 Guy Cochrane: The European Nucleotide Archive 14 Paul Flicek: