CURRICULUM VITAE George M. Weinstock, Ph.D
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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]. -
Synergistic Cytotoxicity of Renieramycin M and Doxorubicin in MCF-7 Breast Cancer Cells
marine drugs Article Synergistic Cytotoxicity of Renieramycin M and Doxorubicin in MCF-7 Breast Cancer Cells Jortan O. Tun 1,*, Lilibeth A. Salvador-Reyes 1,2 , Michael C. Velarde 3 , Naoki Saito 4 , Khanit Suwanborirux 5 and Gisela P. Concepcion 1,2,* 1 The Marine Science Institute, University of the Philippines Diliman, Quezon City 1101, Philippines; [email protected] 2 Philippine Genome Center, University of the Philippines Diliman, Quezon City 1101, Philippines 3 Institute of Biology, University of the Philippines Diliman, Quezon City 1101, Philippines; [email protected] 4 Graduate School of Pharmaceutical Sciences, Meiji Pharmaceutical University, Tokyo 204-8588, Japan; [email protected] 5 Department of Pharmacognosy and Pharmaceutical Botany, Faculty of Pharmaceutical Sciences, Center for Bioactive Natural Products from Marine Organisms and Endophytic Fungi (BNPME), Chulalongkorn University, Pathumwan, Bangkok 10330, Thailand; [email protected] * Correspondence: [email protected] (J.O.T.); [email protected] (G.P.C.); Tel.: +632-922-3959 (J.O.T. & G.P.C.) Received: 23 July 2019; Accepted: 7 August 2019; Published: 16 September 2019 Abstract: Renieramycin M (RM) is a KCN-stabilized tetrahydroisoquinoline purified from the blue sponge Xestospongia sp., with nanomolar IC50s against several cancer cell lines. Our goal is to evaluate its combination effects with doxorubicin (DOX) in estrogen receptor positive MCF-7 breast cancer cells. MCF-7 cells were treated simultaneously or sequentially with various combination ratios of RM and DOX for 72 h. Cell viability was determined using the MTT assay. Synergism or antagonism was determined using curve-shift analysis, combination index method and isobologram analysis. -
Alejandra C. Ortiz 425D Mann Hall 2501 Stinson Dr
Alejandra C. Ortiz 425D Mann Hall 2501 Stinson Dr. Raleigh, NC 27695 Phone: (919) 515-8392 E-Mail: [email protected] Appointments Assistant Professor, Department of Civil, Construction, and Environmental Engineering, North Carolina State University. 2017-Present National Center for Earth Surface Dynamics 2 Synthesis Postdoctoral Fellow, Department of Geological Sciences at Indiana University. 2015 – 2016. Adviser: Dr. Doug Edmonds Education Ph.D. MIT-WHOI Joint Program in Oceanography and Applied Ocean Science & Engineering. 2010 – 2015. Marine Geology & Geophysics Department. Investigating the Evolution and Formation of Coastlines and the Response to Sea-Level Rise. Dr. Andrew D. Ashton. M.S. MIT. 2010 - 2012. Civil and Environmental Engineering Department. Investigation of the Effect of a Circular Patch of Vegetation on Turbulence Generation and Sediment Deposition Using Four Case Studies. Dr. Heidi M. Nepf. B.A. Wellesley College. 2006 – 2010. Geosciences & Classical Civilizations. Honors in Geosciences & cum laude. Sigma Psi. Senior Thesis in Geosciences: Investigating the Effect of Wave Energy on Coastal Morphology and Beach Sedimentology Using Real and Modeled Wave Data. Dr. Britt Argow. Research Interests • Coastal Geomorphology • Numerical Modeling • Coastal Response to Climate Change • Fluvial Ecogeomorphology • Coastal Sedimentology Academic Experience Teaching • Teaching Assistant. MIT – 12.717. Coastal Geomorphology. Planned class field trip, 2015 planed and graded homework assignments. Graduate Students. • Teaching Assistant. MIT – 1.69. Transport Processes in the Environment. Planned and 2013 prepped 1 lab and 2 lectures. Undergraduates. • Teaching Assistant. MIT – 12.747. Modeling, Data Analysis, and Numerical Techniques 2012 for Geochemistry. MatLab Programming. Graduate Students. • Teaching Assistant. Wellesley College – CS 112. Computation for the Sciences. MatLab 2009-2010 Programming. -
Masthead (PDF)
Proceedings of the National Academy ofPNAS Sciences of the United States of America www.pnas.org PRESIDENT OF Robert G. Roeder Geophysics John J. Mekalanos THE ACADEMY Michael Rosbash Michael L. Bender Peter Palese Ralph J. Cicerone David D. Sabatini Thomas E. Shenk Gertrud M. Schupbach Human Environmental Thomas J. Silhavy SENIOR EDITOR Robert Tjian Sciences Peter K. Vogt Solomon H. Snyder Susan Hanson Cellular and Molecular Physics ASSOCIATE EDITORS Neuroscience Immunology Anthony Leggett William C. Clark Pietro V. De Camilli Peter Cresswell Paul C. Martin Alan Fersht Richard L. Huganir Douglas T. Fearon Jack Halpern L. L. Iversen Richard A. Flavell Physiology and Jeremy Nathans Charles F. Stevens Dan R. Littman Pharmacology Thomas C. Su¨dhof Tak Wah Mak Susan G. Amara Joseph S. Takahashi William E. Paul David Julius EDITORIAL BOARD Hans Thoenen Michael Sela Ramon Latorre Ralph M. Steinman Masashi Yanagisawa Animal, Nutritional, and Chemistry Applied Microbial Sciences Stephen J. Benkovic Mathematics Plant Biology David L. Denlinger Bruce J. Berne Richard V. Kadison Maarten J. Chrispeels R. Michael Roberts Harry B. Gray Robion C. Kirby Enrico Coen Robert Haselkorn Linda J. Saif Mark A. Ratner George H. Lorimer Ryuzo Yanagimachi Barry M. Trost Medical Genetics, Hematology, and Nicholas J. Turro Anthropology Oncology Plant, Soil, and Charles T. Esmon Microbial Sciences Jeremy A. Sabloff Computer and Joseph L. Goldstein Roger N. Beachy Information Sciences Mark T. Groudine Steven E. Lindow Applied Mathematical Sciences Shafrira Goldwasser David O. Siegmund Tony Hunter M. S. Swaminathan Philip W. Majerus Susan R. Wessler Economic Sciences Newton E. Morton Applied Physical Sciences Ronald W. -
Computational Pan-Genomics: Status, Promises and Challenges
bioRxiv preprint doi: https://doi.org/10.1101/043430; this version posted March 12, 2016. 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. Computational Pan-Genomics: Status, Promises and Challenges Tobias Marschall1,2, Manja Marz3,60,61,62, Thomas Abeel49, Louis Dijkstra6,7, Bas E. Dutilh8,9,10, Ali Ghaffaari1,2, Paul Kersey11, Wigard P. Kloosterman12, Veli M¨akinen13, Adam Novak15, Benedict Paten15, David Porubsky16, Eric Rivals17,63, Can Alkan18, Jasmijn Baaijens5, Paul I. W. De Bakker12, Valentina Boeva19,64,65,66, Francesca Chiaromonte20, Rayan Chikhi21, Francesca D. Ciccarelli22, Robin Cijvat23, Erwin Datema24,25,26, Cornelia M. Van Duijn27, Evan E. Eichler28, Corinna Ernst29, Eleazar Eskin30,31, Erik Garrison32, Mohammed El-Kebir5,33,34, Gunnar W. Klau5, Jan O. Korbel11,35, Eric-Wubbo Lameijer36, Benjamin Langmead37, Marcel Martin59, Paul Medvedev38,39,40, John C. Mu41, Pieter Neerincx36, Klaasjan Ouwens42,67, Pierre Peterlongo43, Nadia Pisanti44,45, Sven Rahmann29, Ben Raphael46,47, Knut Reinert48, Dick de Ridder50, Jeroen de Ridder49, Matthias Schlesner51, Ole Schulz-Trieglaff52, Ashley Sanders53, Siavash Sheikhizadeh50, Carl Shneider54, Sandra Smit50, Daniel Valenzuela13, Jiayin Wang70,71,72, Lodewyk Wessels56, Ying Zhang23,5, Victor Guryev16,12, Fabio Vandin57,34, Kai Ye68,69,72 and Alexander Sch¨onhuth5 1Center for Bioinformatics, Saarland University, Saarbr¨ucken, Germany; 2Max Planck Institute for Informatics, Saarbr¨ucken, -
Serratia Marcescens: Outer Membrane Porins and Comparative Genomics
Serratia marcescens: Outer Membrane Porins and Comparative Genomics By Alexander Diamandas A Thesis submitted to the Faculty of Graduate Studies of The University of Manitoba In partial fulfillment of the requirements of the degree of Master of Science Department of Microbiology University of Manitoba Winnipeg Copyright © 2019 by Alexander Diamandas Table of Contents Abstract ........................................................................................................................................................ v Acknowledgments ...................................................................................................................................... vi List of Tables .............................................................................................................................................. vii List of Figures ............................................................................................................................................ viii 1. Literature Review: ............................................................................................................................ 10 1.1. Serratia marcescens .................................................................................................................... 10 1.1.1. Species ................................................................................................................................ 11 1.1.2. Incidence and Mortality ..................................................................................................... -
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We gratefully acknowledge the following Authors from the Originating laboratories responsible for obtaining the specimens, as well as the Submitting laboratories where the genome data were generated and shared via GISAID, on which this research is based. All Submitters of data may be contacted directly via www.gisaid.org Authors are sorted alphabetically. Accession ID Originating Laboratory Submitting Laboratory Authors EPI_ISL_1562503 Aegis Sciences Corporation Centers for Disease Control and Prevention Division of Viral Dakota Howard, Dhwani Batra, Peter W. Cook, Kara Moser, Adrian Paskey, Jason Caravas, Benjamin Rambo-Martin, Shatavia Morrison, Christopher Diseases, Pathogen Discovery Gulvick, Scott Sammons, Yvette Unoarumhi, Darlene Wagner, Matthew Schmerer, Cyndi Clark, Patrick Campbell, Rob Case, Vikramsinha Ghorpade, Holly Houdeshell, Ola Kvalvaag, Dillon Nall, Ethan Sanders, Alec Vest, Shaun Westlund, Matthew Hardison, Clinton R. Paden, Duncan MacCannell EPI_ISL_1648208 Quest Diagnostics Incorporated Centers for Disease Control and Prevention Division of Viral Dakota Howard, Dhwani Batra, Peter W. Cook, Kara Moser, Adrian Paskey, Jason Caravas, Benjamin Rambo-Martin, Shatavia Morrison, Christopher Diseases, Pathogen Discovery Gulvick, Scott Sammons, Yvette Unoarumhi, Darlene Wagner, Matthew Schmerer, S. H. Rosenthal, A. Gerasimova, R. M. Kagan, B. Anderson, M. Hua, Y. Liu, L.E. Bernstein, K.E. Livingston, A. Perez, I. A. Shlyakhter, R. V. Rolando, R. Owen, P. Tanpaiboon, F. Lacbawan, Clinton R. Paden, Duncan MacCannell EPI_ISL_1660458 -
28 June 2019 25 – 28 Fjuneaculty of 2019 Scienc E Kasetsart University, Bangkok Faculty of Science Kasetsart University, Bangkok
25 - 28 June 2019 25 – 28 FJuneaculty of 2019 Scienc e Kasetsart University, Bangkok Faculty of Science Kasetsart University, Bangkok This page is intentionally left blank. T A B L E O F C ONTENT Workshop schedule 2 Opening and Welcome speeches 6 Sponsors’ Info 11 Organizing Committee 15 Presenters’ Biographies 17 Participants’ Info 27 Invited Talks and Talks 31 Lecture Summary 44 Poster Abstracts 50 1 W O R K S H O P S CHEDULE 08:00-08:40 Registration 08:40-08:45 Celebration of Coronation of King Rama X 08:45-09:05 Welcome and opening ceremony Group Photo 09:05-09:15 Overview of the Empowering agricultural research through (meta)genomics workshop Alexie Papanicolaou 09:15-10:15 Plenary Talk: “Genomes, Genes, Allele and Mechanisms.” Roger Hellens 10:15:10:30 Tea break and networking (Room 352) 10:30-10:50 Invited Talk: High Resolution Profiling of Bacterial Communities using Full-Length 16S rRNA Sequence Data from PacBio SMRT Sequencing System Wirulda Pootakarm 10:50-11:10 Invited Talk: From Omics to System Biology: Impact on Industrial Biotechnology and Human Health Wanwipa Vongsangnak 11:10-11:50 Invited talk: Functional Genomics of Tropical Plants Goh Hoe Han 11:50-13:00 Lunch and Product presentation by Sponsors (Room 352) 12:00-12.20: Advancing metagenomics research with Illumina solutions - Cara Lim 12:20-12:40: QIAGEN’s Innovative Solutions for Advancing Microbiome Research from Challenging Samples to Insight with Confidence - Wasin Sakulkoo 2 12:40-12:50: Sequencing solution on DNBSEQ platform - Honghong Liu 13:00:13:40 Invited -
Here She Received a NASA Earth Systems Science Fellowship (1996- 1999) and Completed Her Ph.D
TRAIT-BASED APPROACHES TO OCEAN LIFE traitspace.com Keynotes Brian Enquist Lionel Guidi Image: Erik Selander Alexandra Worden Neil Banas CHICHELEY HALL, BUCKINGHAMSHIRE, UK 18th to 21st August, 2019 FOURTH WORKSHOP ON TRAIT-BASED APPROACHES TO OCEAN LIFE Table of Contents Schedule ...................................................................................................................................... 2 Keynote Speakers ........................................................................................................................ 5 Abstracts ..................................................................................................................................... 7 1 Schedule Sunday 13:00-14:00 Lunch 18th August 14:00-14:10 Welcome & Introduction Session 1: Traits, environments, ecology and evolution 14:10-15:10 Keynote: Brian Enquist The past, present, and future of trait- based ecology: Toward a more predictive framework 15:10-15:30 Davi Castro Tavares Traits shared by marine megafauna and their relationships with ecosystem functions and services 15:30-15:50 Stephanie Dutkiewicz Biogeochemical and ecological redundancy in phytoplankton communities 15:50-16:10 Tea/Coffee 16:10-16:30 Stephanie Green A traits-based framework to account for the influence of predator-prey interactions on species distribution under global change 16:30-16:50 David Talmy Trade-offs modify ecosystem biomass structure along trophic gradients 16:50-17:10 Aleksandra Does initial diversity influence Lewandowska phytoplankton response -
Mutation Rates of Escherichia Coli with Different Balanced Growth Rates: a New Fluctuation Test Protocol and Phenotypic Lag Adju
Mutation rates of Escherichia coli with different balanced growth rates: a new fluctuation test protocol and phenotypic lag adjustments by Christian Terry Henderson Barna A thesis presented to the University of Waterloo in fulfilment of the thesis requirement for the degree of Master of Mathematics in Applied Mathematics Waterloo, Ontario, Canada, 2020 c Christian Terry Henderson Barna 2020 Author's Declaration I hereby declare that I am the sole author of this thesis. This is a true copy of the thesis, including any required final revisions, as accepted by my examiners. I understand that my thesis may be made electronically available to the public. ii Abstract Bacteria are the oldest, most abundant life form on the planet, and every other organ- ism's livelihood is dependent on them. The bacteria Escherichia coli (E. coli) is commonly used in microbiology as a model organism to give insight into the functions of bacteria and cells in general. Of particular interest in these studies is the methods with which bacteria grow and evolve. Growth is what propagates a bacteria's species; whereas evolution is what allows them to adapt to the ever-changing world. Evolution is made possible by mutations which change a bacterium's DNA. In 1943, Luria and Delbr¨uck developed a method, called a “fluctuation test", to estimate mutation rates from the number of mutants in a collection of parallel cultures exposed to a selecting agent after growth. The original fluctuation test methodology suffers from two major limitations. First, the bacteria are not in a re- producible, balanced state of growth throughout the test. -
2009 NIH Director's Transformative Research Award Reviewers
2009 NIH Director’s Transformative Research Award Reviewers Editorial Board Members Chairs David Botstein Keith Robert Yamamoto Princeton University University of California, San Francisco Members John T. Cacioppo Myron P. Gutmann University of Chicago Inter-University Consortium for Political and Social Research Aravinda Chakravarti Johns Hopkins School of Medicine Nola M. Hylton-Watson University of California, San Francisco Garret A. Fitzgerald Cecil B. Pickett University of Pennsylvania Biogen Idec Alfred G. Gilman Susan S. Taylor University of Texas Southwestern Medical University of California at San Diego Center Michael J. Welsh University of Iowa Mail Reviewers Craig Kendall Abbey Margaret Ashcroft University of California, Santa Barbara Division of Medicine Samuel Achilefu Richard Herbert Aster School of Medicine Blood Research Institute Manuel Ares Arleen D. Auerbach University of California Rockefeller University Bruce A. Armitage J. Thomas August Carnegie Mellon University Johns Hopkins University Mark A. Arnold Kevin A. Ault University of Iowa Emory University School of Medicine David C. Aron Jennifer Bates Averill Case Western Reserve University University of New Mexico 1 Mary Helen Barcellos-Hoff Leslie A. Bruggeman New York University School of Medicine Case Western Reserve University David P. Bartel Peter Burkhard New Cambrige Center University of Connecticut Ralf Bartenschlager Alma L. Burlingame University of Heidelberg University of California, San Francisco Rashid Bashir Frederic D. Bushman University of Illinois at Urbana – Champaign University of Pennsylvania Carl A. Batt Robert William Caldwell Cornell University Medical College of Georgia Mark T. Bedford Phil Gordon Campbell Research Division Carnegie Mellon University Kevin D. Belfield Joseph Nicholas Cappella University of Central Florida University of Pennsylvania Andrew Steven Belmont William A. -
Science & Policy Meeting Jennifer Lippincott-Schwartz Science in The
SUMMER 2014 ISSUE 27 encounters page 9 Science in the desert EMBO | EMBL Anniversary Science & Policy Meeting pageS 2 – 3 ANNIVERSARY TH page 8 Interview Jennifer E M B O 50 Lippincott-Schwartz H ©NI Membership expansion EMBO News New funding for senior postdoctoral In perspective Georgina Ferry’s enlarges its membership into evolution, researchers. EMBO Advanced Fellowships book tells the story of the growth and ecology and neurosciences on the offer an additional two years of financial expansion of EMBO since 1964. occasion of its 50th anniversary. support to former and current EMBO Fellows. PAGES 4 – 6 PAGE 11 PAGES 16 www.embo.org HIGHLIGHTS FROM THE EMBO|EMBL ANNIVERSARY SCIENCE AND POLICY MEETING transmissible cancer: the Tasmanian devil facial Science meets policy and politics tumour disease and the canine transmissible venereal tumour. After a ceremony to unveil the 2014 marks the 50th anniversary of EMBO, the 45th anniversary of the ScienceTree (see box), an oak tree planted in soil European Molecular Biology Conference (EMBC), the organization of obtained from countries throughout the European member states who fund EMBO, and the 40th anniversary of the European Union to symbolize the importance of European integration, representatives from the govern- Molecular Biology Laboratory (EMBL). EMBO, EMBC, and EMBL recently ments of France, Luxembourg, Malta, Spain combined their efforts to put together a joint event at the EMBL Advanced and Switzerland took part in a panel discussion Training Centre in Heidelberg, Germany, on 2 and 3 July 2014. The moderated by Marja Makarow, Vice President for Research of the Academy of Finland.