Mary Ann Handel, Ph.D. Education Positions And
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Chapter 14: Functional Genomics Learning Objectives
Chapter 14: Functional Genomics Learning objectives Upon reading this chapter, you should be able to: ■ define functional genomics; ■ describe the key features of eight model organisms; ■ explain techniques of forward and reverse genetics; ■ discuss the relation between the central dogma and functional genomics; and ■ describe proteomics-based approaches to functional genomics. Outline : Functional genomics Introduction Relation between genotype and phenotype Eight model organisms E. coli; yeast; Arabidopsis; C. elegans; Drosophila; zebrafish; mouse; human Functional genomics using reverse and forward genetics Reverse genetics: mouse knockouts; yeast; gene trapping; insertional mutatgenesis; gene silencing Forward genetics: chemical mutagenesis Functional genomics and the central dogma Approaches to function; Functional genomics and DNA; …and RNA; …and protein Proteomic approaches to functional genomics CASP; protein-protein interactions; protein networks Perspective Albert Blakeslee (1874–1954) studied the effect of altered chromosome numbers on the phenotype of the jimson-weed Datura stramonium, a flowering plant. Introduction: Functional genomics Functional genomics is the genome-wide study of the function of DNA (including both genes and non-genic regions), as well as RNA and proteins encoded by DNA. The term “functional genomics” may apply to • the genome, transcriptome, or proteome • the use of high-throughput screens • the perturbation of gene function • the complex relationship of genotype and phenotype Functional genomics approaches to high throughput analyses Relationship between genotype and phenotype The genotype of an individual consists of the DNA that comprises the organism. The phenotype is the outward manifestation in terms of properties such as size, shape, movement, and physiology. We can consider the phenotype of a cell (e.g., a precursor cell may develop into a brain cell or liver cell) or the phenotype of an organism (e.g., a person may have a disease phenotype such as sickle‐cell anemia). -
Masterpath: Network Analysis of Functional Genomics Screening Data
MasterPATH: network analysis of functional genomics screening data Natalia Rubanova, Guillaume Pinna, Jeremie Kropp, Anna Campalans, Juan Pablo Radicella, Anna Polesskaya, Annick Harel-Bellan, Nadya Morozova To cite this version: Natalia Rubanova, Guillaume Pinna, Jeremie Kropp, Anna Campalans, Juan Pablo Radicella, et al.. MasterPATH: network analysis of functional genomics screening data. BMC Genomics, BioMed Central, 2020, 21 (1), pp.632. 10.1186/s12864-020-07047-2. hal-02944249 HAL Id: hal-02944249 https://hal.archives-ouvertes.fr/hal-02944249 Submitted on 26 Nov 2020 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. Rubanova et al. BMC Genomics (2020) 21:632 https://doi.org/10.1186/s12864-020-07047-2 METHODOLOGY ARTICLE Open Access MasterPATH: network analysis of functional genomics screening data Natalia Rubanova1,2,3* , Guillaume Pinna4, Jeremie Kropp1, Anna Campalans5,6,7, Juan Pablo Radicella5,6,7, Anna Polesskaya8, Annick Harel-Bellan1 and Nadya Morozova1,4 Abstract Background: Functional genomics employs several experimental approaches to investigate gene functions. High- throughput techniques, such as loss-of-function screening and transcriptome profiling, allow to identify lists of genes potentially involved in biological processes of interest (so called hit list). -
The Economic Impact and Functional Applications of Human Genetics and Genomics
The Economic Impact and Functional Applications of Human Genetics and Genomics Commissioned by the American Society of Human Genetics Produced by TEConomy Partners, LLC. Report Authors: Simon Tripp and Martin Grueber May 2021 TEConomy Partners, LLC (TEConomy) endeavors at all times to produce work of the highest quality, consistent with our contract commitments. However, because of the research and/or experimental nature of this work, the client undertakes the sole responsibility for the consequence of any use or misuse of, or inability to use, any information or result obtained from TEConomy, and TEConomy, its partners, or employees have no legal liability for the accuracy, adequacy, or efficacy thereof. Acknowledgements ASHG and the project authors wish to thank the following organizations for their generous support of this study. Invitae Corporation, San Francisco, CA Regeneron Pharmaceuticals, Inc., Tarrytown, NY The project authors express their sincere appreciation to the following indi- viduals who provided their advice and input to this project. ASHG Government and Public Advocacy Committee Lynn B. Jorde, PhD ASHG Government and Public Advocacy Committee (GPAC) Chair, President (2011) Professor and Chair of Human Genetics George and Dolores Eccles Institute of Human Genetics University of Utah School of Medicine Katrina Goddard, PhD ASHG GPAC Incoming Chair, Board of Directors (2018-2020) Distinguished Investigator, Associate Director, Science Programs Kaiser Permanente Northwest Melinda Aldrich, PhD, MPH Associate Professor, Department of Medicine, Division of Genetic Medicine Vanderbilt University Medical Center Wendy Chung, MD, PhD Professor of Pediatrics in Medicine and Director, Clinical Cancer Genetics Columbia University Mira Irons, MD Chief Health and Science Officer American Medical Association Peng Jin, PhD Professor and Chair, Department of Human Genetics Emory University Allison McCague, PhD Science Policy Analyst, Policy and Program Analysis Branch National Human Genome Research Institute Rebecca Meyer-Schuman, MS Human Genetics Ph.D. -
Human Functional Genomics Project Begins Unraveling Links Between
Human Functional Genomics Project Begins Unraveling Links Between Genes, Immune Response Jul 28, 2016 | Elizabeth Newbern Premium NEW YORK (GenomeWeb) – Earlier this month, researchers involved in the Human Functional Genomics Project (HFGP) published data on the relationship between genetics and human cytokine response in Nature Medicine. The data was derived from a first cohort, the 200 Functional Genomics project, and the researchers plan to publish more data from this cohort in Nature Medicine in August. In addition, the HFGP just finished collecting patient data from a second cohort made up of 500 healthy individuals from Western Europe and aptly named the 500 Functional Genomics project, late last year. The HFGP researchers also recently finished collecting data from their LifeLines-deep cohort, made up of 1,600 healthy individuals from Western Europe. The researchers are assessing and analyzing the 500 FG and LifeLines-deep data now and hope to publish preliminary results at the end of this year, Mihai Netea, member of the HFGP's scientific advisory board and professor of the Radboud Center for Infectious Diseases (RCI) in the Netherlands, told GenomeWeb. They also finished recruitment and started data collection for their 300 Functional Genomics project, which is a cohort of 300 obese individuals, he added. The human immune system is composed of a complex network of organs, tissues, cells, and molecules and has evolved to both protect the host against infections and to play roles in immune surveillance. However, it has previously been unclear what role genetics plays in influencing cytokine responses in health and disease. The HFGP researchers aim to find out more about the role of genetics in immune response by characterizing and better understanding variation in human response through the use of various omics analyses — genomic, transcriptomic, metabolomic, and microbiomic — and in-depth functional phenotyping. -
High-Throughput Automated Microfluidic Sample Preparation for Accurate Microbial Genomics
High-throughput automated microfluidic sample preparation for accurate microbial genomics The MIT Faculty has made this article openly available. Please share how this access benefits you. Your story matters. Citation Kim, Soohong et al. “High-Throughput Automated Microfluidic Sample Preparation for Accurate Microbial Genomics.” Nature Communications 8 (2017): 13919. © 2017 Macmillan Publishers Limited As Published http://dx.doi.org/10.1038/ncomms13919 Publisher Nature Publishing Group Version Final published version Citable link http://hdl.handle.net/1721.1/108270 Terms of Use Creative Commons Attribution 4.0 International License Detailed Terms http://creativecommons.org/licenses/by/4.0/ ARTICLE Received 14 Oct 2016 | Accepted 11 Nov 2016 | Published 27 Jan 2017 DOI: 10.1038/ncomms13919 OPEN High-throughput automated microfluidic sample preparation for accurate microbial genomics Soohong Kim1,2, Joachim De Jonghe1,3, Anthony B. Kulesa1,2, David Feldman1,4, Tommi Vatanen1,5, Roby P. Bhattacharyya1,6, Brittany Berdy7, James Gomez1, Jill Nolan1, Slava Epstein7 & Paul C. Blainey1,2 Low-cost shotgun DNA sequencing is transforming the microbial sciences. Sequencing instruments are so effective that sample preparation is now the key limiting factor. Here, we introduce a microfluidic sample preparation platform that integrates the key steps in cells to sequence library sample preparation for up to 96 samples and reduces DNA input requirements 100-fold while maintaining or improving data quality. The general-purpose microarchitecture we demonstrate supports workflows with arbitrary numbers of reaction and clean-up or capture steps. By reducing the sample quantity requirements, we enabled low-input (B10,000 cells) whole-genome shotgun (WGS) sequencing of Mycobacterium tuberculosis and soil micro-colonies with superior results. -
IBM Functional Genomics Platform, a Cloud-Based Platform for Studying Microbial Life at Scale
IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS , VOL. 16, NO. 7, DECEMBER 2019 1 IBM Functional Genomics Platform, A Cloud-Based Platform for Studying Microbial Life at Scale Edward E. Seabolt*, Gowri Nayar*, Harsha Krishnareddy, Akshay Agarwal, Kristen L. Beck, Ignacio Terrizzano, Eser Kandogan, Mark Kunitomi, Mary Roth, Vandana Mukherjee, and James H. Kaufman Abstract—The rapid growth in biological sequence data is revolutionizing our understanding of genotypic diversity and challenging conventional approaches to informatics. With the increasing availability of genomic data, traditional bioinformatic tools require substantial computational time and the creation of ever-larger indices each time a researcher seeks to gain insight from the data. To address these challenges, we pre-computed important relationships between biological entities spanning the Central Dogma of Molecular Biology and captured this information in a relational database. The database can be queried across hundreds of millions of entities and returns results in a fraction of the time required by traditional methods. In this paper, we describe IBM Functional Genomics Platform (formerly known as OMXWare), a comprehensive database relating genotype to phenotype for bacterial life. Continually updated, IBM Functional Genomics Platform today contains data derived from 200,000 curated, self-consistently assembled genomes. The database stores functional data for over 68 million genes, 52 million proteins, and 239 million domains with associated biological activity annotations from Gene Ontology, KEGG, MetaCyc, and Reactome. IBM Functional Genomics Platform maps all of the many-to-many connections between each biological entity including the originating genome, gene, protein, and protein domain. Various microbial studies, from infectious disease to environmental health, can benefit from the rich data and connections. -
CC Little Hall Name Task Force
C.C. Little Hall Name Task Force University of Maine Final Report for Committee Review 23 June 2020 Purpose and Scope of the Task Force Partly in response to a student petition to remove the name of Clarence C. Little from UMaine’s Little Hall, a resolution passed by the UMaine Student Government in support of that petition, and a letter from the campus organization Decolonizing UMaine, President Joan Ferrini-Mundy created a task force of university stakeholders to address the issue with the following charge: 1. Recommend criteria for deciding whether an individual’s name should be removed from a physical facility named for them. 2. Recommend whether to remove Clarence C. Little’s name from the campus building bearing his name, with pros and cons, and rationale. If you recommend removal, please also suggest replacement names, if any and rationale for the naming. 3. If a name replacement is recommended, what criteria did you consider for the name replacement? Task Force Members Hailey Cedor, undergraduate, Class of 2021 Thomas Connolly, Assistant General Counsel-Contracting, University of Maine System John Dieffenbacher-Krall, Assistant Director, Research, College of Natural Sciences, Forestry, and Agriculture Stewart Harvey, Executive Director of Facilities and Capital Management Services Jeffery Mills, President/CEO, UMaine Foundation Liam Riordan, Professor, History Joyce Rumery, Dean of Libraries Kenda Scheele, Associate Vice President, Student Life Howard Segal, Professor, History David Townsend, Professor, School of Marine Sciences and President, Faculty Senate Executive Summary Clarence Cook Little (1888-1971) was the president of the University of Maine from 1922 to 1925. Little Hall was named for him in a dedication ceremony of the new building in June 1966. -
THE JACKSON LABORATORY Taxable Bonds, Series 2018
NEW ISSUE – BOOK-ENTRY ONLY RATING: Moody’s: “A1” See “RATING” herein. $159,585,000 THE JACKSON LABORATORY Taxable Bonds, Series 2018 Dated: Date of Delivery Due: July 1, as shown on the inside cover The Jackson Laboratory Taxable Bonds, Series 2018 (the “Bonds”) will be issued pursuant to the terms of an Indenture of Trust, dated as of March 1, 2018 (the “Indenture”), by and between The Jackson Laboratory (the “Institution”) and U.S. Bank National Association, as Trustee (the “Trustee”). The Institution has authorized the issuance of the Bonds. The Bonds will be issued in fully-registered form in denominations of $1,000 or any integral multiple thereof and, when issued, will be registered under a book-entry system in the name of Cede & Co., as nominee of The Depository Trust Company, New York, New York (“DTC”). DTC will act as securities depository for the Bonds. Individual purchases will be made in book-entry form only, in principal amounts of $1,000 or any integral multiple thereof. Purchasers of the Bonds will not receive physical certificates (except under certain circumstances described in the Indenture) representing their ownership interests in Bonds purchased. See “BOOK-ENTRY SYSTEM AND GLOBAL CLEARANCE PROCEDURES” herein. Interest on the Bonds will be payable on January 1 and July 1 of each year, commencing on July 1, 2018. So long as the Bonds are held by DTC, the principal of and interest on or Redemption Price (as defined herein) of the Bonds will be payable by wire transfer to DTC, which in turn is required to remit such principal and interest or Redemption Price to the DTC Participants (as defined herein) for subsequent disbursement to the Beneficial Owners of the Bonds, as more fully described in “BOOK-ENTRY SYSTEM AND GLOBAL CLEARANCE PROCEDURES” herein. -
Maine Public Broadcasting Network from the President & CEO
Annual Report | 2013 Maine Public Broadcasting Network From the President & CEO Friends, T HAS BEEN AN EXCITING YEAR at MPBN, and I am pleased to tell you that we Ihave weathered all of our challenges, embraced our successes and believe that MPBN, in keeping with our mission, stands tall as Maine’s primary source for quality news, information, and entertainment. MPBN’s award-winning news department continues to be relied on across Maine for the depth of our coverage, and that strength was reinforced with the launch of the Maine Capitol Connection which offered statewide TV coverage of the Legislature for the first time in Maine history. We saw additional popularity in the expansion of our noontime Maine Calling. Our election coverage, both on radio and television and additionally online, was lauded by our viewers, listeners, and members as being comprehensive and essential in charting the voting season in Maine and across the country. The news team has been busy! Our radio listenership itself continued to rise as program changes resulting from listener feedback and our Community Advisory Board hit their mark. Local programming like In Tune with Sara Willis and Jazz Tonight with Rich Tozier grew audience share and legions of new followers. Our strategy for radio pledge, the one-day “Super Thursday” format, tapped into listeners’ enthusiasm to keep the programs interruption-free as much as possible and has proven to be a true success. The television side, too, experienced an exciting year, led of course by the juggernaut known as Downton Abbey. The quality and breadth of programs coming to us from PBS – from NOVAto new Masterpiece offerings – continue to really impress us and excite our audience. -
After the Draft Sequence, What Next for the Human Genome Mapping Project Resource Centre?
Comparative and Functional Genomics Comp Funct Genom 2001; 2: 176–179. DOI: 10.1002/cfg.83 Interview: Duncan Campbell After the draft sequence, what next for the Human Genome Mapping Project Resource Centre? Dr R. Duncan Campbell is the Director of the Medical Research Council (MRC) funded UK Human Genome Mapping Project Resource Centre (HGMP-RC), on the Wellcome Trust Genome Campus at Hinxton, near Cambridge, UK. The Centre provides both biological and bioinformatics resources to the UK genomics community, and also has research groups supporting these activities and investigating separate projects. CFG: The HGMP-RC is broadly arranged into three tools for DNA and protein sequence analysis, Divisions: Bioinformatics, Biology Services and which will expand the functions offered by the Research. Let’s tackle these one at a time. The Genetics Computer Group (GCG) package. We are draft sequence release will no doubt have encouraged currently redeveloping our website in order to make many researchers to get on-line and use bio- it bigger, better and more interactive for our users, informatics tools to mine the dataset, can you tell and our hope is that we will have a new website me about the projects that the Bioinformatics team which will go live in the next few months. The site are working on to facilitate such investigations? will include access and ordering for the existing services and information and support for new RDC: With the huge amount of draft sequence now services as they come on-line. available, we have seen increased use of the bioinformatics tools already on offer from the CFG: The Biology Services Division supplies a HGMP-RC, such as NIX and PIX. -
Toward a Protein–Protein Interaction Map of the Budding Yeast: A
Toward a protein–protein interaction map of the budding yeast: A comprehensive system to examine two-hybrid interactions in all possible combinations between the yeast proteins Takashi Ito*†, Kosuke Tashiro‡, Shigeru Muta‡, Ritsuko Ozawa*§, Tomoko Chiba*§, Mayumi Nishizawa‡, Kiyoshi Yamamoto‡, Satoru Kuhara‡, and Yoshiyuki Sakaki*§ *Human Genome Center, Institute of Medical Science, University of Tokyo, 4-6-1 Shirokanedai, Minato-ku, Tokyo 108-8639, Japan; ‡Molecular Gene Technics, Graduate School of Genetic Resources Technology, Kyushu University, 6-10-1 Hakozaki, Higashi-ku, Fukuoka 812-8581, Japan; and §RIKEN Genomic Sciences Center, Wako, Saitama 351-0198, Japan Communicated by Satoshi Omura, The Kitasato Institute, Tokyo, Japan, November 22, 1999 (received for review October 15, 1999) Protein–protein interactions play pivotal roles in various aspects of interaction modules contributes not only to the studies of the the structural and functional organization of the cell, and their particular pathway but also to much wider fields of biomedical complete description is indispensable to thorough understanding research. A large set of protein–protein interaction data would of the cell. As an approach toward this goal, here we report a lay a foundation for the search of such modules by both comprehensive system to examine two-hybrid interactions in all of experimental and computational means. the possible combinations between proteins of Saccharomyces Despite the need for comprehensive studies on protein– cerevisiae. We cloned all of the yeast ORFs individually as a protein interactions, no efforts for a genome-wide scale screen- DNA-binding domain fusion (‘‘bait’’) in a MATa strain and as an ing have ever been reported, although pioneering works using activation domain fusion (‘‘prey’’) in a MAT␣ strain, and subse- the yeast two-hybrid system (2) were reported on Drosophila cell quently divided them into pools, each containing 96 clones. -
A Massively Parallel Barcoded Sequencing Pipeline Enables Generation of the First Orfeome and Interactome Map for Rice
A massively parallel barcoded sequencing pipeline enables generation of the first ORFeome and interactome map for rice Shayne D. Wierbowskia,b,1, Tommy V. Vob,1,2, Pascal Falter-Braunc,d, Timothy O. Jobee, Lars H. Krusef, Xiaomu Weia, Jin Liangb, Michael J. Meyera,b, Nurten Akturkb, Christen A. Rivera-Erickb, Nicolas A. Corderob, Mauricio I. Paramob,g, Elnur E. Shayhidinb, Marta Bertolottib, Nathaniel D. Tippensa,b, Kazi Aktherh, Rita Sharmai, Yuichi Katayosej, Kourosh Salehi-Ashtianik,l,m,n, Tong Haol,m, Pamela C. Ronaldo,p,q, Joseph R. Eckerr,s, Peter A. Schweitzert, Shoshi Kikuchiu, Hiroshi Mizunov, David E. Hilll,m, Marc Vidall,m, Gaurav D. Moghef, Susan R. McCouchh,3, and Haiyuan Yua,b,3 aDepartment of Biological Statistics and Computational Biology, Cornell University, Ithaca, NY 14853; bWeill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY 14853; cInstitute of Network Biology, Helmholtz Zentrum München, German Research Center for Environmental Health, 85764 Munich, Germany; dMicrobe-Host Interactions, Faculty of Biology, Ludwig-Maximilians-Universität München, 80539 Munich, Germany; eBotanical Institute, Cluster of Excellence on Plant Sciences (CEPLAS), University of Cologne, 50674 Cologne, Germany; fPlant Biology Section, School of Integrative Plant Sciences, Cornell University, Ithaca, NY 14853; gDepartment of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853; hSection of Plant Breeding and Genetics, School of Integrated Plant Sciences, Cornell University, Ithaca, NY 14853-1901; iSchool