Immunoinformatics
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Editorial Computational and Bioinformatics Techniques for Immunology
Hindawi Publishing Corporation BioMed Research International Volume 2014, Article ID 263189, 2 pages http://dx.doi.org/10.1155/2014/263189 Editorial Computational and Bioinformatics Techniques for Immunology Francesco Pappalardo,1 Vladimir Brusic,2 Filippo Castiglione,3 and Christian Schönbach2 1 Department of Drug Sciences, University of Catania, 95125 Catania, Italy 2School of Science and Technology, Nazarbayev University, Astana 010000, Kazakhstan 3Istituto Applicazioni del Calcolo “M. Picone”, Consiglio Nazionale delle Ricerche, Via dei Taurini 19, 00185 Rome, Italy Correspondence should be addressed to Francesco Pappalardo; [email protected] Received 22 July 2014; Accepted 22 July 2014; Published 31 December 2014 Copyright © 2014 Francesco Pappalardo et al. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. Computational immunology and immunological bioinfor- biology spanning different scales: an open challenge”by matics are well-established and rapidly evolving research F. Castiglione et al. fields. Whereas the former aims to develop mathematical Exploring the connections between classical mathemat- and/or computational methods to study the dynamics of ical modeling (at different scales) and bioinformatics pre- cellular and molecular entities during the immune response dictions of omic scope along with specific aspects of the [1–4], the latter targets proposing methods to analyze large immune system in combination with concepts and methods genomic and proteomic immunological-related datasets and like computer simulations, mathematics and statistics for the derive (i.e., predict) new knowledge mainly by statistical discovery, design, and optimization of drugs, vaccines, and inference and machine learning algorithms. -
Download the Abstract Book
1 Exploring the male-induced female reproduction of Schistosoma mansoni in a novel medium Jipeng Wang1, Rui Chen1, James Collins1 1) UT Southwestern Medical Center. Schistosomiasis is a neglected tropical disease caused by schistosome parasites that infect over 200 million people. The prodigious egg output of these parasites is the sole driver of pathology due to infection. Female schistosomes rely on continuous pairing with male worms to fuel the maturation of their reproductive organs, yet our understanding of their sexual reproduction is limited because egg production is not sustained for more than a few days in vitro. Here, we explore the process of male-stimulated female maturation in our newly developed ABC169 medium and demonstrate that physical contact with a male worm, and not insemination, is sufficient to induce female development and the production of viable parthenogenetic haploid embryos. By performing an RNAi screen for genes whose expression was enriched in the female reproductive organs, we identify a single nuclear hormone receptor that is required for differentiation and maturation of germ line stem cells in female gonad. Furthermore, we screen genes in non-reproductive tissues that maybe involved in mediating cell signaling during the male-female interplay and identify a transcription factor gli1 whose knockdown prevents male worms from inducing the female sexual maturation while having no effect on male:female pairing. Using RNA-seq, we characterize the gene expression changes of male worms after gli1 knockdown as well as the female transcriptomic changes after pairing with gli1-knockdown males. We are currently exploring the downstream genes of this transcription factor that may mediate the male stimulus associated with pairing. -
Toward Computational Modelling on Immune System Function Francesco Pappalardo1*, Marzio Pennisi2, Pedro A
Pappalardo et al. BMC Bioinformatics 2019, 20(Suppl 6):622 https://doi.org/10.1186/s12859-019-3239-x INTRODUCTION Open Access Toward computational modelling on immune system function Francesco Pappalardo1*, Marzio Pennisi2, Pedro A. Reche3 and Giulia Russo1 From 2nd International Workshop on Computational Methods for the Immune System Function Madrid, Spain. 3–6 December 2018 Abstract The 2nd Computational Methods for the Immune System function Workshop has been held in Madrid in conjunction with the IEEE International Conference on Bioinformatics and Biomedicine (BIBM 2018) in Madrid, Spain, from December 3 to 6, 2018. The workshop has been obtained 100% more submissions in respect to the first edition, highlighting a growing interest for the treated topics. The best papers (9) have been selected for extension in this special issue, with themes about immune system and disease simulation, computer-aided design of novel candidate vaccines, methods for the analysis of immune system involved diseases based on statistical methods, meta-heuristics and game theory, and modelling strategies for improving the simulation of the immune system dynamics. Introduction modeling of the Immune system function, along with their The constant and rapid increasing of computing power application in understanding the pathogenesis of specific has favoured the diffusion of computational methods diseases (e.g., infectious diseases, cancers, hypersensitivi- into immunology, giving the birth to computational ties, autoimmune disorders) has been in our minds for -
An Interdisciplinary Perspective on Artificial Immune Systems
Evol. Intel. (2008) 1:5–26 DOI 10.1007/s12065-007-0004-2 REVIEW ARTICLE An interdisciplinary perspective on artificial immune systems J. Timmis Æ P. Andrews Æ N. Owens Æ E. Clark Received: 7 September 2007 / Accepted: 11 October 2007 / Published online: 10 January 2008 Ó Springer-Verlag 2008 Abstract This review paper attempts to position the area 1 Introduction of Artificial Immune Systems (AIS) in a broader context of interdisciplinary research. We review AIS based on an Artificial Immune Systems (AIS) is a diverse area of established conceptual framework that encapsulates math- research that attempts to bridge the divide between ematical and computational modelling of immunology, immunology and engineering and are developed through abstraction and then development of engineered systems. the application of techniques such as mathematical and We argue that AIS are much more than engineered systems computational modelling of immunology, abstraction from inspired by the immune system and that there is a great those models into algorithm (and system) design and deal for both immunology and engineering to learn from implementation in the context of engineering. Over recent each other through working in an interdisciplinary manner. years there have been a number of review papers written on AIS with the first being [25] followed by a series of others Keywords Artificial immune systems Á that either review AIS in general, for example, [29, 30, 43, Immunological modelling Á Mathematical modelling Á 68, 103], or more specific aspects of AIS such as data Computational modelling Á mining [107], network security [71], applications of AIS Applications of artificial immune systems Á [58], theoretical aspects [103] and modelling in AIS [39]. -
Computational Immunology Workshop
Computational Immunology Workshop On the 16th of November, with the support of the Pole Rabelais, the SIRIC Montpellier Cancer, and the IRCM, we organize a 1-day workshop on the theme Computational Immunology. The meeting will take place at IRCM auditorium. We will discuss computational or bioinformatics aspects of immunology and the cancer microenvironment. Recent developments in DNA sequencing and functional proteomics have made possible remarkably successful data driven research in these fields. It requires bioinformatics and computational abilities to transform data into information. The workshop is a unique opportunity to learn from experts who applied such techniques to conduct meaningful biological and translational research. We will welcome prestigious international and French speakers: • Dr Andreas Pichlmair, Max Plank Institute, Munich, innate immunity ; • Dr Fatima Mechta-Grigoriou, Institut Curie, Paris, tumor microenvironment ; • Pr Zlatko Trajanoski, Biocenter, Innsbruck, oncoimmunology ; • Dr Monsef Benkirane, IGH, Montpellier, immunology ; • Pr Marie-Paule Lefranc, IGH, Montpellier, immunoinformatics. Registration is free but mandatory: Inscription In addition, YOU are invited to submit an abstract for an oral or poster presentation (send to [email protected]) and contribute to the success of this workshop. The organizers: Ula Hibner (IGMM), Sofia Kossida (IGH), Jacques Colinge (IRCM). Preliminary Program 08:45 Registration 09:00 Opening and introductory remarks Session 1 Innate and adaptive immunity 09:00 Keynote -
The Bio Revolution: Innovations Transforming and Our Societies, Economies, Lives
The Bio Revolution: Innovations transforming economies, societies, and our lives economies, societies, our and transforming Innovations Revolution: Bio The The Bio Revolution Innovations transforming economies, societies, and our lives May 2020 McKinsey Global Institute Since its founding in 1990, the McKinsey Global Institute (MGI) has sought to develop a deeper understanding of the evolving global economy. As the business and economics research arm of McKinsey & Company, MGI aims to help leaders in the commercial, public, and social sectors understand trends and forces shaping the global economy. MGI research combines the disciplines of economics and management, employing the analytical tools of economics with the insights of business leaders. Our “micro-to-macro” methodology examines microeconomic industry trends to better understand the broad macroeconomic forces affecting business strategy and public policy. MGI’s in-depth reports have covered more than 20 countries and 30 industries. Current research focuses on six themes: productivity and growth, natural resources, labor markets, the evolution of global financial markets, the economic impact of technology and innovation, and urbanization. Recent reports have assessed the digital economy, the impact of AI and automation on employment, physical climate risk, income inequal ity, the productivity puzzle, the economic benefits of tackling gender inequality, a new era of global competition, Chinese innovation, and digital and financial globalization. MGI is led by three McKinsey & Company senior partners: co-chairs James Manyika and Sven Smit, and director Jonathan Woetzel. Michael Chui, Susan Lund, Anu Madgavkar, Jan Mischke, Sree Ramaswamy, Jaana Remes, Jeongmin Seong, and Tilman Tacke are MGI partners, and Mekala Krishnan is an MGI senior fellow. -
Guide to Biotechnology 2008
guide to biotechnology 2008 research & development health bioethics innovate industrial & environmental food & agriculture biodefense Biotechnology Industry Organization 1201 Maryland Avenue, SW imagine Suite 900 Washington, DC 20024 intellectual property 202.962.9200 (phone) 202.488.6301 (fax) bio.org inform bio.org The Guide to Biotechnology is compiled by the Biotechnology Industry Organization (BIO) Editors Roxanna Guilford-Blake Debbie Strickland Contributors BIO Staff table of Contents Biotechnology: A Collection of Technologies 1 Regenerative Medicine ................................................. 36 What Is Biotechnology? .................................................. 1 Vaccines ....................................................................... 37 Cells and Biological Molecules ........................................ 1 Plant-Made Pharmaceuticals ........................................ 37 Therapeutic Development Overview .............................. 38 Biotechnology Industry Facts 2 Market Capitalization, 1994–2006 .................................. 3 Agricultural Production Applications 41 U.S. Biotech Industry Statistics: 1995–2006 ................... 3 Crop Biotechnology ...................................................... 41 U.S. Public Companies by Region, 2006 ........................ 4 Forest Biotechnology .................................................... 44 Total Financing, 1998–2007 (in billions of U.S. dollars) .... 4 Animal Biotechnology ................................................... 45 Biotech -
Adapting to a Changing World: RAG Genomics and Evolution Maristela Martins De Camargo1and Laila Alves Nahum2*
REVIEW Adapting to a changing world: RAG genomics and evolution Maristela Martins de Camargo1and Laila Alves Nahum2* 1 Department of Immunology, Institute of Biomedical Sciences, University of Sa˜o Paulo, Sa˜o Paulo, SP 05508-900, Brazil 2 Department of Biological Science, Louisiana State University, Baton Rouge, LA 70803, USA * Correspondence to: Tel: þ11 225 578 8798; Fax: þ11 225 578 2597; E-mail: [email protected] Date received (in revised form): 21th March 2005 Abstract The origin of the recombination-activating genes (RAGs) is considered to be a foundation hallmark for adaptive immunity, characterised by the presence of antigen receptor genes that provide the ability to recognise and respond to specific peptide antigens. In vertebrates, a diverse repertoire of antigen-specific receptors, T cell receptors and immunoglobulins is generated by V(D)J recombination performed by the RAG-1 and RAG-2 protein complex. RAG homologues were identified in many jawed vertebrates. Despite their crucial importance, no homologues have been found in jawless vertebrates and invertebrates. This paper focuses on the RAG homologues in humans and other vertebrates for which the genome is completely sequenced, and also discuses the main contribution of the use of RAG homologues in phylogenetics and vertebrate evolution. Since mutations in both genes cause a spectrum of severe combined immunodeficiencies, including the Omenn syndrome (OS), these topics are discussed in detail. Finally, the relevance to genomic diversity and implications to immunomics are addressed. The search for homologues could enlighten us about the evolutionary processes that shaped the adaptive immune system. Understanding the diversity of the adaptive immune system is crucially important for the design and development of new therapies to modulate the immune responses in humans and/or animal models. -
How Do We Evaluate Artificial Immune Systems?
How Do We Evaluate Artificial Immune Systems? Simon M. Garrett [email protected] Computational Biology Group, Department of Computer Science, University of Wales, Aberystwyth, Wales, SY23 3DB. UK Abstract The field of Artificial Immune Systems (AIS) concerns the study and development of computationally interesting abstractions of the immune system. This survey tracks the development of AIS since its inception, and then attempts to make an assessment of its usefulness, defined in terms of ‘distinctiveness’ and ‘effectiveness.’ In this paper, the standard types of AIS are examined—Negative Selection, Clonal Selection and Im- mune Networks—as well as a new breed of AIS, based on the immunological ‘danger theory.’ The paper concludes that all types of AIS largely satisfy the criteria outlined for being useful, but only two types of AIS satisfy both criteria with any certainty. Keywords Artificial immune systems, critical evaluation, negative selection, clonal selection, im- mune network models, danger theory. 1 Introduction What is an artificial immune system (AIS)? One answer is that an AIS is a model of the immune system that can be used by immunologists for explanation, experimentation and prediction activities that would be difficult or impossible in ‘wet-lab’ experiments. This is also known as ‘computational immunology.’ Another answer is that an AIS is an abstraction of one or more immunological processes. Since these processes protect us on a daily basis, from the ever-changing onslaught of biological and biochemical entities that seek to prosper at our expense, it is reasoned that they may be computa- tionally useful. It is this form of AIS—methods based on immune abstractions—that will be studied here. -
Vaccinology in the Genome Era
Vaccinology in the genome era C. Daniela Rinaudo, … , Rino Rappuoli, Kate L. Seib J Clin Invest. 2009;119(9):2515-2525. https://doi.org/10.1172/JCI38330. Review Series Vaccination has played a significant role in controlling and eliminating life-threatening infectious diseases throughout the world, and yet currently licensed vaccines represent only the tip of the iceberg in terms of controlling human pathogens. However, as we discuss in this Review, the arrival of the genome era has revolutionized vaccine development and catalyzed a shift from conventional culture-based approaches to genome-based vaccinology. The availability of complete bacterial genomes has led to the development and application of high-throughput analyses that enable rapid targeted identification of novel vaccine antigens. Furthermore, structural vaccinology is emerging as a powerful tool for the rational design or modification of vaccine antigens to improve their immunogenicity and safety. Find the latest version: https://jci.me/38330/pdf Review series Vaccinology in the genome era C. Daniela Rinaudo, John L. Telford, Rino Rappuoli, and Kate L. Seib Novartis Vaccines, Siena, Italy. Vaccination has played a significant role in controlling and eliminating life-threatening infectious diseases through- out the world, and yet currently licensed vaccines represent only the tip of the iceberg in terms of controlling human pathogens. However, as we discuss in this Review, the arrival of the genome era has revolutionized vaccine develop- ment and catalyzed a shift from conventional culture-based approaches to genome-based vaccinology. The availabili- ty of complete bacterial genomes has led to the development and application of high-throughput analyses that enable rapid targeted identification of novel vaccine antigens. -
Quantitative Immunology for Physicists
bioRxiv preprint doi: https://doi.org/10.1101/696567; this version posted July 28, 2019. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission. Quantitative Immunology for Physicists Gr´egoireAltan-Bonnet,1, ∗ Thierry Mora,2, ∗ and Aleksandra M. Walczak2, ∗ 1Immunodynamics Section, Cancer & Inflammation Program, National Cancer Institute, Bethesda MD 20892, USA 2Laboratoire de physique de l'Ecole´ normale sup´erieure (PSL University), CNRS, Sorbonne Universit´e,Universit´ede Paris, 75005 Paris, France Abstract. The adaptive immune system is a dynamical, self-organized multiscale system that protects vertebrates from both pathogens and internal irregularities, such as tumours. For these reason it fascinates physicists, yet the multitude of different cells, molecules and sub-systems is often also petrifying. Despite this complexity, as experiments on different scales of the adaptive immune system become more quantitative, many physicists have made both theoretical and experimental contributions that help predict the behaviour of ensembles of cells and molecules that participate in an immune response. Here we review some recent contributions with an emphasis on quantitative questions and methodologies. We also provide a more general methods section that presents some of the wide array of theoretical tools used in the field. CONTENTS A. Cytokine signaling and the JAK-STAT pathway 14 I. Introduction 2 1. Cytokine binding and signaling at equilibrium 15 II. Physical chemistry of ligand-receptor 2. Tunability of cytokine responses. 15 interaction: specificity, sensitivity, kinetics. 4 3. Regulation by cytokine consumption 17 A. Diffusion-limited reaction rates 4 4. -
Advancing the Development of Therapeutics with the Deep Immunomics Platform
Advancing the development of therapeutics with the Deep Immunomics platform February 2021 ImmunoScape today • Venture-backed company with 2 major investors: Anzu Partners and UTEC (University of Tokyo Edge Capital) • Company offices and laboratories now established in both Singapore and San Diego, CA • 29 FTEs, including 13 PhD scientists • Deep in-house expertise in mass cytometry, high-dimensional flow cytometry, analysis of complex data sets, and bioinformatics • Extensive history of collaborating with big pharma/biotech, small biotech companies, and top-tier academic medical centers • 35 total projects including ongoing efforts with 10+ pharma/biotech companies and 10+ academic centers • 1,400 antigens* screened across 6 HLA types using TargetScape *Antigens include tumor neoantigens, tumor-associated antigens, viral antigens from influenza virus, SARS-CoV-2, CMV, EBV, HBV, HIV 2 Introduction to the Deep Immunomics technology platform Understanding each patient’s immunome, and how it evolves in response to treatment, is the key to developing next-generation immunotherapies At ImmunoScape, we believe that these outcomes can be Immunotherapy Immunodynamic understood by deep treatment changes characterization of the immunome at scale. • Immunomic data generated across many patients at multiple timepoints, pre- and post-treatment Patient at baseline Non-responder • Multiple immune cell compartments studied Responder Serious adverse event • Hundreds of T cell specificities and dozens of markers analyzed per sample 4 ImmunoScape’s Deep Immunomics