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Curriculum Vitae 01/13/2014
Curriculum Vitae 01/13/2014 Dimitris Papamichail Assistant Professor Department of Computer Science The College of New Jersey P.O. Box 7718 Ewing, NJ 08628-0718, USA Phone (office): (609) 771-2268 E-mail: [email protected] Webpage: www.tcnj.edu/~papamicd RESEARCH INTERESTS Applied algorithms, data structures, computational biology. EDUCATION Ph.D. Computer Science, SUNY at Stony Brook, USA, 8/02-8/07 M.S. Computer Science, University of Arizona, USA, 8/96-5/98 B.E. Computer Engineering and Informatics, University of Patras, Greece, 9/91-6/96 WORK EXPERIENCE • Assistant Professor, Department of Computer Science, The College of New Jersey, 8/13 – present. • Assistant Professor, Department of Computer Science, University of Miami, 8/07 – 8/13 • Research Assistant, Brookhaven National Laboratory, Upton, USA, 10/04 - 8/07 • Research Assistant, Computer Science department, SUNY at Stony Brook, Stony Brook, USA, 9/03 - 8/07 • Teaching Assistant, Computer Science department, SUNY at Stony Brook, Stony Brook, USA, 8/02 - 7/03 • Computer Programmer, Division of Research and Informatics, Greek Army, Greece, 9/00 - 3/02 • Site Engineer, Modular Mining Systems Inc., Tucson, Arizona, USA, 8/98 - 4/00 • Teaching assistant, Computer Science department, University of Arizona, Arizona, USA, 8/97 - 5/98 • Programmer, Lunar and Planetary Laboratory, University of Arizona, Tucson, Arizona, USA, 1/97 - 6/97 • Programmer, National Electric Company of Greece, Athens, Greece, 6/94 - 8/94 • Systems Operator, Computer Institute of Technology, Patras, Greece, 6/92 - 9/93 AWARDS/DISTINCTIONS • University of Miami Faculty Learning Community (FLC) Fellow, 2010. • Best paper award, Graduate Research Conference 2004, Computer Science Department, Stony Brook University. -
Replication of Picornaviruses I
JouRNAL oF VnoLoGy, Dec. 1975, p. 1512-1527 Vol. 16, No. 6 Copyright ©) 1975 American Society for Microbiology Printed in U.SA. Replication of Picornaviruses I. Evidence from In Vitro RNA Synthesis that Poly(A) of the Poliovirus Genome is Genetically Coded KAROLINE DORSCH-HASLER, YOSHIAKI YOGO,' AND ECKARD WIMMER* Department ofMicrobiology, St. Louis University School ofMedicine, St. Louis, Missouri 63104, and Department ofMicrobiology, School ofBasic Health Sciences, State University ofNew York at Stony Brook, Stony Brook, New York 11794 * Received for publication 3 July 1975 A crude replication complex has been isolated from poliovirus-infected HeLa cells and used for synthesis of poliovirus replicative intermediate (RI) RNA, replicative form (RF) RNA, and single-stranded (SS) RNA in vitro. All three classes of virus-specific RNA synthesized in vitro are shown to contain poly(A). Poly(A) of RF and of SS RNA [RF-poly(A) and SS-poly(A)] has a chain length (50 to 70 nucleotides) that is shorter than that of poly(A) of in vivo-synthesized RNAs. Poly(A) of RI [RI-poly(A)], however, is at least 200 nucleotides long and, therefore, larger than poly(A) of RI isolated from HeLa cells 4 h after infection. The crude membrane-bound replication complex contains a terminal adenylate transferase activity that is stimulated by Mn2+ and the addition of an (Ap),AoH primer. This transferase activity is found also in extracts of mock-infected cells. Partial purification of the replication complex in a stepwise sucrose gradient, in which the viral replicase is associated with the smooth cytoplasmic membrane fraction, does not remove the terminal transferase. -
Abstract Book (Pdf)
6th EMBO/EMBL Conference on Science and Society Science and Security 28 – 29 October 2005 at the European Molecular Biology Laboratory Heidelberg, Germany Organising Committee: Andrew Moore (EMBO, Chair), Halldòr Stefànsson (EMBL), Alessandra Bendiscioli (EMBO), Frank Gannon (EMBO), Iain Mattaj (EMBL) Welcome message n September this year, plans for a new bio-defence laboratory in Montana, USA, were Iunveiled. In the $66.5 million facility, researchers will apply similar scientific knowledge to that which makes bio-terrorism or biological warfare a possibility in the first place. The double-edged sword of science application can hardly be more evident. How successfully can we prevent the misuse of research findings that otherwise give us important insights into the workings of nature and prospects of useful applications? What would be the consequences of tackling this problem by constraining research, the mobility of researchers and the funding and publication of their research? Could we, indeed, ever successfully define “research that should not be done”? How much thought should scientists give to the downstream consequences of their work when deciding what to research, or which experiments to do? In June this year, the USA announced that it would delay the introduction of compulsory biometric passports for travellers from 27 countries in Europe and the Asia-Pacific region until October 2006. But whenever they appear, biometric passports will be part of normal life in the future. In the era of international terrorism, this could, indeed, lead to a safer world; an example of a beneficial use of science. On the other hand, it increases the perception by normal citizens that they are being unnecessarily “watched” by an all- seeing, all-controlling state – the so-called Big Brother of Orwell’s 1984. -
“Let There Be Life”
Focus: Brave New World “We have reason to believe that the disease is created by a man-made super pathogen...” AND MAN SAID, “LETa short story THERE BE LIFE” By Lawrence Valverde e have reason to believe the nearly 200 scientists simmered with “Wdisease is caused by a man- mumbled comments. The researcher made super-pathogen. The construc- whose speech had been interrupted tion seems to be loosely based on the straightened himself and raised his smallpox virus, but with significant voice in response. modifications, including genes encod- “I hear your concern, Dr. Boots, ing immune system antagonists. It but we have not confirmed whether or also seems to have been specifically not this is, in fact, a terrorist act…” engineered to resist known antivi- “Who else would do such a thing, ral…” Dr. Cervantes?” Dr. Boots demanded. “What do you mean specifically “It wasn’t necessarily done on engineered!” boomed an overweight purpose…” said Dr. Cervantes—the man as he hauled himself out of speaker—but he was interrupted by his chair. “Are you proposing that the clamor that erupted as scientists terrorists may have the technology jump up from their seats. Dr. Cervantes to synthetically create their own vi- frowned. Trying to speak over the ruses?” The surrounding panel of crowd was clearly a lost cause. When credit: Clipart courtesy FCIT. http://etc.usf.edu/clipart credit: Clipart courtesy FCIT. fall 2008 • Harvard Science Review 9 valverde.indd 9 2/9/2009 11:24:54 PM Focus: Brave New World did this whole business with artificially Dr. Boots sputtered. -
Curriculum Vitae
1 CURRICULUM VITAE Name: StevenSkiena Date of birth: January 30, 1961 Office: Dept. of Computer Science Home: 6Storyland Lane StonyBrook University Setauket, NY 11733 StonyBrook, NY 11794 Tel.: (631) 689-5477 Tel.: (631)-632-8470/9026 email: [email protected] URL: http://www.cs.stonybrook.edu/˜skiena Education University of Illinois at Urbana-Champaign, Fall 1983 to Spring 1988. M.S. in Computer Science May 1985, Ph.D in Computer Science May 1988. Cumulative GPA 4.87/5.00. University of Virginia, Charlottesville VA, Fall 1979 to Spring 1983. B.S. in Computer Science with High Distinction, May 1983. Final GPA3.64/4.0, with 4.0+ GPAinComputer Science. Rodman Scholar,Intermediate Honors, Tau Beta Pi. Employment Founding Director,Institute for AI-DrivenDiscovery and Innovation (IAIDDI), August 2018 to date. College of Engineering and Applied Science, StonyBrook University. StonyBrook University,Empire Innovation Professor,fall 2018 to date. Distinguished Teaching Pro- fessor of Computer Science, spring 2009 to date. Professor of Computer Science, fall 2001 to spring 2009. Associate Professor of Computer Science, fall 1994 to spring 2001. Assistant Professor of Computer Science, fall 1988 to spring 1994. Also, Adjunct Professor of Applied Mathematics, spring 1991 to date. Affiliated faculty,Dept. of Biomedical Engineering, Institute for Advanced Computa- tional Science (IACS), and Graduate Program in Genetics. Yahoo Labs/Research, Visiting Scientist, NewYork, NY.summer 2015 to summer 2016. Chief Scientist, General Sentiment Inc. (www.generalsentiment.com) Woodbury NY spring 2009 to spring 2015. Hong Kong University of Science and Technology (HKUST), Visiting Professor,Dept. of Computer Science and Engineering, fall 2008 to summer 2009. -
Profile of Eckard Wimmer
PROFILE Profile of Eckard Wimmer he finding caused an uproar. vitalism—the belief that chemicals in liv- Researchers at Stony Brook Uni- ing systems are somehow distinct from Tversity in New York had engi- the chemicals in inorganic systems, such neered poliovirus in a test tube as salt and rocks. That notion was shat- (1). The discovery, led by Eckard Wimmer, tered in 1828, when German chemist elected in 2012 to the National Academy Friedrich Wöhler synthesized the organic of Sciences, dispelled the belief that compound urea from inorganic pre- viruses require a live host to grow cursors (5). and spread. By the 1940s, theoretical physicists and The thought of synthetic viruses terrified biochemists had begun to wonder about an American public still reeling from 9/11 what constitutes life. Wimmer was en- and the subsequent anthrax attacks. What thralled. Biochemistry squared perfectly if the technology to engineer viruses with his worldview, the idea that something wound up in the hands of bioterrorists? as seemingly profound as life could be pared However, today, just a decade later, it is down to its simplest—chemical—form. widely accepted that the ability to engineer While completing his second post- viruses also allows researchers to develop doctoral fellowship at the University of viruses that work as synthetic vaccines, British Columbia in Vancouver in the to carry genetic material into a cell for use mid-1960s, Wimmer attended a talk on in gene therapies, or to preferentially viruses and had his eureka moment. “It attack cancer cells (2). was clear, even though it wasn’t men- Wimmer says his motivations for engi- tioned in that talk, that if viruses can be neering polio were strictly scientific. -
Bert Lawrence Semler
Curriculum Vitae: Bert Lawrence Semler Contact Information Department of Microbiology and Molecular Genetics School of Medicine, Med Sci B237 University of California Irvine, CA 92697 USA E-mail: [email protected] Phone: (949) 824-7573 FAX: (949) 824-2694 Education 1970-1974 University of California, Irvine Bachelor of Science - Biological Sciences 1974-1979 University of California, San Diego Doctor of Philosophy - Biology Research and Professional Experience 1972-1974 Undergraduate research with Professor H. W. Moore Department of Chemistry, University of California, Irvine 1975-1979 Graduate student with Professor John J. Holland Department of Biology, University of California, San Diego 1979-1983 Postdoctoral fellow with Professor Eckard Wimmer, Department of Microbiology, State University of New York at Stony Brook 1983-1987 Assistant Professor, Department of Microbiology and Molecular Genetics College of Medicine, University of California, Irvine 1987-1991 Associate Professor, Department of Microbiology and Molecular Genetics College of Medicine, University of California, Irvine 1991-2018 Professor, Department of Microbiology and Molecular Genetics School of Medicine, University of California, Irvine 1996-2006 Chair, Department of Microbiology and Molecular Genetics School of Medicine, University of California, Irvine 2000-2010 Associate Director, Center for Virus Research University of California, Irvine 2010-present Director, Center for Virus Research University of California, Irvine 2018-present Distinguished Professor, Department -
NAT265 NEW Mx
news Poliovirus advance sparks fears of data curbs Erika Check, Washington The recent laboratory synthesis of an infec- tious poliovirus is prompting fears among SCIENCE US biologists that the publication of results GETTY IMAGES deemed potentially useful to terrorists may be restricted. The virus was synthesized by a team led by virologist Eckard Wimmer at the State University of New York at Stony Brook. The results, published online by Science on 11 July (J. Cello, A. V. Paul & E. Wimmer Science 10.1126/science.1072266), sparked media reports worldwide suggesting that similar techniques might be used by terrorists to synthesize the Ebola virus or even smallpox. For Eckard Wimmer, his results brought a ‘scary Culture shock: researchers have synthesized this Geneticists fear that the report — the first realization’ that viruses can be recreated. infectious poliovirus in the laboratory. demonstration that a published genome can be turned into an infectious virus — will been used to demonstrate the technique. sequence information. He claims that the encourage calls for a clampdown on the open Wimmer defends his group’s decision to latest research proves that the world can publication of gene sequences of viruses. publish, saying that they are only pointing never stop vaccinating against polio. “You US government officials have been floating out the fact that terrorists could misuse cannot eliminate a virus from existence,” he the idea of such restrictions since the terror- published data. “We’ve been criticized for says. “Somebody can always resynthesize it, ist attacks last autumn (see Nature 414, playing into the hands of a bioterrorist, but and that’s a scary realization.” 237–238; 2001). -
Defective Interfering Particles of Poliovirus I
JOURNAL OF VIROLOGY, Apr. 1971, p. 478-485 Vol. 7, No. 4 Copyright © 1971 American Society for Microbiology Printed int U.S.A. Defective Interfering Particles of Poliovirus I. Isolation and Physical Properties CHARLES N. COLE, DONNA SMOLER, ECKARD WIMMER, AND DAVID BALTIMORE Departmenit of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139 Received for publication 8 January 1971 A class of defective interfering (DI) poliovirus particles has been identified. The first was found as a contaminant of a viral stock; others have been isolated by serial passage at a high multiplicity of infection. The DI particles are less dense than standard virus and sediment more slowly. Their ribonucleic acid (RNA) sediments more slowly than standard RNA and has a higher electrophoretic mobility. Compe- tition hybridization experiments with double-stranded viral RNA indicate that DI RNA is 80 to 90'- of the length of standard RNA. The proteins of DI particles are indistinguishable from those of standard poliovirus. Defective interfering (DI) particles are found (ii) virus diluted serially in medium; (iii) HeLa cells in stocks of many different types of viruses (9). washed twice with medium and resuspended at 107/ml These particles are a natural form of mutant in medium plus 1 horse serum. A mixture of 0.2 which could be useful in the study of viral multi- ml of a given virus dilution with 0.6 ml of cells and 0.6 ml of agar were spread rapidly over base layer plication. They are also of interest because of plates at room temperature, and plates were incu- their possible role in viral disease processes (9). -
Synthetic Biology: Synthesis and Modification of a Chemical Called Poliovirus
Synthetic biology: Synthesis and modification of a chemical called poliovirus Steffen Mueller, Dimitris Papamichail, John Robert Coleman, Jeronimo Cello, Aniko Paul, Steven Skiena, and Eckard Wimmer SUNY–Stony Brook, U.S.A. Synthetic biology is a newly emerging scientific field, encompassing knowledge of different disciplines, such as engineering, physics, chemistry, computer sciences, mathematics, and biology. Synthetic biology aims to create novel biological systems with functions that do not exist in nature. There seem infinite possibilities of constructing unique derivatives of existing organisms (bacteria, yeast, viruses). Apart from designing novel building elements for engineering biological systems, a fundamental requirement in synthetic biology is the ability of large-scale DNA synthesis and DNA sequencing. Viruses can be described in chemical terms; the empirical formula of the organic matter of poliovirus being:1 C332,652H492,388N98,245O131,196P7,501S2,340. Placing these atoms into order, a particle of high symmetry emerges2 with all the properties required for its proliferation and “survival” in nature. These properties are encoded in the viral genome, which is a single stranded nucleic acid (RNA) of about 7,500 nucleotides. Guided by the published nucleotide sequence,3 we have recently synthesized the DNA equivalent of the polio RNA genome and converted it by simple biochemical manipulations in a cell-free environment (outside living cells) into authentic poliovirus particles.4 The synthesis of a replicating "organism" in the absence of a natural template was without precedence at the time of publication4 and it provoked widespread responses – good and bad. Poliovirus is a human virus that replicates after ingestion in the gastrointestinal tract. -
Profile of Eckard Wimmer
PROFILE Profile of Eckard Wimmer he finding caused an uproar. vitalism—the belief that chemicals in liv- Researchers at Stony Brook Uni- ing systems are somehow distinct from Tversity in New York had engi- the chemicals in inorganic systems, such neered poliovirus in a test tube as salt and rocks. That notion was shat- (1). The discovery, led by Eckard Wimmer, tered in 1828, when German chemist elected in 2012 to the National Academy Friedrich Wöhler synthesized the organic of Sciences, dispelled the belief that compound urea from inorganic pre- viruses require a live host to grow cursors (5). and spread. By the 1940s, theoretical physicists and The thought of synthetic viruses terrified biochemists had begun to wonder about an American public still reeling from 9/11 what constitutes life. Wimmer was en- and the subsequent anthrax attacks. What thralled. Biochemistry squared perfectly if the technology to engineer viruses with his worldview, the idea that something wound up in the hands of bioterrorists? as seemingly profound as life could be pared However, today, just a decade later, it is down to its simplest—chemical—form. widely accepted that the ability to engineer While completing his second post- viruses also allows researchers to develop doctoral fellowship at the University of viruses that work as synthetic vaccines, British Columbia in Vancouver in the to carry genetic material into a cell for use mid-1960s, Wimmer attended a talk on in gene therapies, or to preferentially viruses and had his eureka moment. “It attack cancer cells (2). was clear, even though it wasn’t men- Wimmer says his motivations for engi- tioned in that talk, that if viruses can be neering polio were strictly scientific. -
Doctor Atomic and Doctor Genomic
GENDER MEDICINE/VOL. 5, NO. 4, 2008 Editorial Doctor Atomic and Doctor Genomic As I watched Doctor Atomic, John Adams’ fascinating new production with The Metropolitan Opera that dramatizes the Manhattan Project’s creation of the atomic bomb, I applauded the brilliant portrayal of the dilemma that our greatest scientific achievements pose. Because of their completely novel and tremen- dous power, these achievements have the potential for both enormous good and unimaginably terrible consequences. The opera’s libretto used original sources, and in their own words described the gut-wrenching tensions among the scientists involved in making the bomb. No imagined dialogue could possibly have been more compelling. Edward Teller and Robert Wilson tried, unsuccessfully, to persuade their colleagues to petition President Truman to refrain from dropping the bomb on Japan. Yet Robert Oppenheimer, the complex, highly cultured, and charismatic project leader whom Adams dubbed “Dr. Atomic,” pushed the testing of the device to completion, despite his own misgivings. He later said, “As I watched the explosion, I thought of a quotation from the Bhagavad Gita: ‘I am become death, the destroyer of worlds.’” The average age of the more than 300 men and women who worked on the Manhattan Project was 25. At Los Alamos, beer drinking, lovemaking, and frenzied devotion to finishing the project were all, predict- ably, going on at once. Many worked to the point of exhaustion: one young scientist was hospitalized with a nervous breakdown. The opera touched on the thousand difficulties faced by Oppenheimer as he knit the project together despite the disparate enthusiasms, misgivings, and diametrically opposed moti- vations of the gifted scholars, many of them Nobel laureates, who worked to complete it.