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Dr. George Pieczenik (born 1944) ( ... )
Saved Wikipedia (June 2, 2021) - "Ruth Nussinov"
Saved Wikipedia (June 2, 2021) - "Ruth Nussinov"
https://en.wikipedia.org/wiki/Ruth_Nussinov
2021-06-02-wikipedia-org-ruth-nussinov.pdf
https://drive.google.com/file/d/14hkhuwtF7SfFWm8IMOJQG-DVmcV5BPn4/view?usp=sharing
Alma mater Rutgers University
Known for Nucleic acid structure prediction, PLoS Computational Biology, Nussinov plots, Equilibrium unfolding, Protein–protein interaction prediction
Awards
Biophysical Society Fellow Award (2011)
ISCB Fellow (2013)
ISCB Senior Scientist Award (2018)
Scientific career
Fields Bioinformatics
Institutions Tel Aviv University, Weizmann Institute, Berkeley, Harvard
Thesis Secondary structure analysis of nucleic acids (1977)
Website http://ccr.cancer.gov/staff/staff.asp?profileid=6892
Ruth Nussinov (Hebrew: פרופסור רות נוסינוב) is an Israeli-American biologist who works as a Professor in the Department of Human Genetics, School of Medicine at Tel Aviv University and is the Senior Principal Scientist and Principal Investigator at the National Cancer Institute, National Institutes of Health.[1] Nussinov is also the Editor in Chief for the journal PLOS Computational Biology.[2]
Nussinov proposed the first dynamic programming approach for nucleic acid secondary structure prediction, this method is now known as the Nussinov algorithm.[3][4]
Career[edit]
Ruth Nussinov received her B.Sc in Microbiology from University of Washington in 1966, her M.Sc in Biochemistry from Rutgers University in 1967 and her Ph.D. in Biochemistry from Rutgers in 1977. Her thesis was titled Secondary structure analysis of nucleic acids.[5] She was a fellow at the Weizmann Institute and worked as a visiting scientist at Berkeley and at Harvard. She took a position at Tel Aviv University in 1985 as Associate Professor and was promoted to Professor in 1990.[2]
Besides her work on nucleic acid secondary structure prediction, Nussinov is also regarded as a pioneer in DNA sequence analysis for her work in the early 1980s.[2]
Nussinov has authored over 500 scientific papers and is the Editor in Chief of the journal PLOS Computational Biology.[2] She also serves on the editorial boards of the journals Physical Biology, Proteins, BMC Bioinformatics and the Journal of Biological Chemistry.[6][7][8][9]
Awards[edit]
Nussinov was made a Fellow of the Biophysical Society in 2011, for her "extraordinary contributions to advances in computational biology on both nucleic acids and proteins".[10] She became a Fellow of the International Society for Computational Biology (ISCB) in 2013.[11] In 2018, Nussinov was awarded the ISCB Senior Scientist Award.[12] In 2020, Nussinov was elected Fellow of the American Physical Society.[13]
References[edit]
^ "Tel Aviv University Staff Page". Retrieved 5 February 2013.
^ Jump up to: a b c d "PLOS Computational Biology Editors-in-Chief". Retrieved 13 January 2014.
^ Nussinov, Ruth; Pieczenik, George; Griggs, Jerrold R.; Kleitman, Daniel J. (1 July 1978). "Algorithms for Loop Matchings". SIAM Journal on Applied Mathematics. 35 (1): 68–82. doi:10.1137/0135006.
^ Nussinov, R; Jacobson, AB (Nov 1980). "Fast algorithm for predicting the secondary structure of single-stranded RNA". Proceedings of the National Academy of Sciences of the United States of America. 77 (11): 6309–6313. Bibcode:1980PNAS...77.6309N. doi:10.1073/pnas.77.11.6309. PMC 350273. PMID 6161375.
^ "Ruth Nussinov - Curriculum Vitae" (PDF). Archived from the original (PDF) on 12 September 2015. Retrieved 11 August 2015.
^ "Editorial Board - Physical Biology - IOPscience". Retrieved 11 August 2015.
^ "Proteins: Structure, Function, and Bioinformatics". Wiley Online Library. Retrieved 5 May 2021.
^ "BMC Bioinformatics - Editorial Board". Retrieved 11 August 2015.
^ "jbc Editorial Board". Retrieved 11 August 2015.
^ "2011 Society Fellows Press Release" (PDF). Retrieved 11 August 2015.
^ Fogg, Christiana N.; Kovats, Diane E. (22 August 2013). "International Society for Computational Biology Welcomes Its Newest Class of Fellows". PLOS Computational Biology. 9 (8): e1003199. Bibcode:2013PLSCB...9E3199F. doi:10.1371/journal.pcbi.1003199. PMC 3749946. PMID 23990772.
^ "February 14, 2018: ISCB Congratulates the 2018 ISCB Award Winners!". www.iscb.org. Retrieved 15 February 2018.
^ "APS Fellows Archive". Retrieved 2020-10-09.
https://www.youtube.com/watch?v=vzGJFg-eRAo
CURRICULUM VITAEName: Ruth Nussinov, Ph.D.Education:1964 Biology, Hebrew University, Jerusalem, Israel1964-1966 B.Sc. (Microbiology), University of Washington, Seattle, Washington1966-1967 M.Sc. (Biochemistry), Rutgers University, New Brunswick, New Jersey1967-1975 Time off;1975-1977 Ph.D. (Biochemistry), Rutgers University, New Brunswick, New JerseyBrief Chronology of Employment:1977-1980 Postdoctoral Fellow, Structural Chemistry Department, Weizmann Institute, Rehovot, Israel1980-1981 Visiting Scientist, Chemistry Department, University of California at Berkeley, California1981-1981 Visiting Scientist, Biochemistry Department, Harvard University, Cambridge, Massachusetts1981-1981 Visiting Scientist, Chemistry Department, Cornell University, Ithaca, New York1981-1983 Senior Lecturer, Dept. of Computer Sciences, School of Mathematics, Tel Aviv University, Tel Aviv, Israel1983-1983 Visiting Scientist, Los Alamos National Laboratory, Los Alamos, New Mexico1983-1984 Visiting Associate, NIH, National Child Health and Human Development, Bethesda, Maryland1984-1990 Associate Professor, Sackler Institute of Molecular Medicine, Medical School, Tel Aviv University, Tel Aviv, Israel1985-2001 Senior Scientist, SAIC, NCI-FCRDC, Frederick, Maryland1990-2012 Professor of Biochemistry, Department of Human Genetics, Sackler Institute of Molecular Medicine, Medical School, Tel Aviv University, Tel Aviv, Israel2001-2013 Senior Principal Scientist, SAIC, Computational Structural Biology Section, Nanobiology Program (formerly LECB), Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD2002-2013 Senior Principal Investigator, Leidos Biomedical Research (formerly SAIC), Head, Computational Structural Biology Section, Nanobiology Program (formerly LECB), Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MDNussinov-12012-Present Professor Emeritus of Biochemistry, Department of Human Genetics, Sackler Institute of Molecular Medicine, Medical School, Tel Aviv University, Tel Aviv, Israel2013-Present Senior Principal Investigator, Leidos Biomedical Research, Head, Computational Structural Biology Section, Cancer and Inflammation Program, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MDSocieties:• Protein Society• Biophysical Society• American Chemical Society• International Society for Computational Biology• American Society for Biochemistry and Molecular BiologyEditor /Editorial Boards - Journals:• Biophysical Journal (two terms)• BMC Bioinformatics• Editor-in-Chief, PLOS Computational Biology• Journal of Biological Chemistry (JBC)• Current Opinion in Structural Biology• Journal of Molecular Recognition• Physical Biology• Proteins: Structure, Function and Bioinformatics• Protein Engineering, Design and selectivity• Intrinsically disordered proteinsEditor – Books/Issues:• Methods in Molecular Biology Series: Protocols in Protein Folding (co-edit with Yawen Bai), Humana Press, Totowa, NJ, September 2006• Methods in Molecular Biology Series: Protocols in Nano Structure Design (co-edit with Ehud Gazit), Humana Press, Totowa, NJ• Computational Protein-Protein Interactions, CRC Series Press, Taylor and Francis Group (co-edit with Gideon Schreiber)• Focus Issues in Physical Biology. Three issues:• Protein-protein Interactions• Nanobiology (with Carlos Aleman)• Protein Folding with (Rohit Pappu)• Molecular Crowding (with Giuseppe Foffi, Francesco Piazza, Annalisa Pastore)• Reviews Editor, Frontiers in Molecular and Structural Endocrinology (area of allostericRegulationNussinov-2• A Special Issue on "The free energy landscape: from folding to cellular function" Physical Chemistry Chemical Physics (PCCP), (co-edited with Peter Wolynes), 2013• Invited by Tom Blundell to co-edit an issue in Progress in Biophysics and Molecular Biology on Structural Bioinformatics of Protein-Protein Interactions• Guest Editor, Chemical Reviews, Special Issue “Protein Ensembles and Allostery”, 2015• Co-Editor, Current Opinion Structural Biology, Section of “Folding and Binding”, 2015Reviews:Journals:• Reviewer for Biochemistry, J. Molecular Biology, TIBS, Proceedings National Academy of Science (USA), Protein Science, Protein Engineering, JACS, Biopolymers, J. Biomolecular Structure and Dynamics, Structure, J. Theoretical Biology, Biophysical J., Proteins, Nucleic Acids Research, Bioinformatics, PLoS, J. Med. Chem., J. Physical Chemistry, J. Chemical Physics, Physical Biology, Trends in Biotechnology, FEBS Lett., PEDS, BMC Series Journals, Nature journals, and many others.Honors & Other Special Scientific Recognition:• Scholarship, University of Washington, Seattle WA (1965)• John Russel Scholarship, Rutgers University, New Brunswick, NJ (1976)• Weizmann Fellowship (1977)• On the Presidents’ list of the Researchers Attaining the Most External Funding in Tel Aviv University• Top CCR, NCI Science Advances (2009)• Recommended by Faculty of 1000: Protein allostery, signal transmission and dynamics: A classification scheme of allosteric mechanisms “A way to categorize allosteric change is proposed on conformational change”• Among the most highly downloaded PNAS paper (2010)• Among the most highly downloaded review on the Mechanisms of transcription factor selectivity Trends in Genetics paper (2010)• Member of the Center for Cancer Research, National Cancer Institute Advisory Board (advises the Scientific Director and the CCR Director)• Voted unanimously "Distinguished Speaker" by the students of the Molecular Biophysics Program, Northwestern University (June 2010)• Voted A Fellow of the 2011 Biophysical Society "for her extraordinary contributions to advances in computational biology on both nucleic acids and proteins"• Lecture in the Institute Pasteur, Paris; a seminar series given by eminent scientists (2010)• Invited by the Chairman of the Board of Directors of Forschungszentrum Jülich, and the Partnership for Advanced Computing in Europe, to Chair the External Overview the Genomic/Biocomputational initiative, Aachen, Germany (January 2011)Nussinov-3• The paper, “Allostery: absence of a change in shape does not imply that allostery is not at play”, Tsai, C-J, del Sol, A., and Nussinov, R., J. Mol Biol. 378(1): 1-11, 2008, is among the top 10 cited JMB papers since 2008 (the year of its publication).• The paper, “Comparing interfacial dynamics in protein-protein complexes: an elastic network approach”, Zen, A., Micheletti, C., Keskin, O., and Nussinov, R., BMC Structural Biology, 10:26 (08 Aug 2010) is among the “Highly Accessed”.• Top ten most accessed articles in Molecular Biosystems: “Towards inferring time dimensionality in protein-protein interaction networks by integrating structures: the p53 example”, Tuncbag, N., Kar, G., Gursoy, A., Keskin, O., and Nussinov, R., Mol. Biosyst. 5(10): 1770-1778, 2009.• Citation in the Coordinator’s Report for Technical and Management Report of the National Cancer Institute as “a recognized leader in the field and having exemplary record of accomplishments” and “for having a great record of training and mentoring”, 2011• Our paper, “Antimicrobial protegrin-1 forms amyloid-like fibrils with rapid kinetics suggestion a functional link”, Biophysical Journal was selected for the “New and Notable” highlights, 2011• Distinguished J. Clarence Karcher (Rosetta Barton) Lecturer in “Frontiers in Chemical Research”, University of Oklahoma.• Fellow, Institute of Physics, London, UK.• Cited by SAIC, NCI-Frederick as being “Internationally recognized leader”, 2011• Author of one of the top 1% most highly cited papers in the field worldwide according to the Council of Canadian Academies letter, 2011• Placed by Thomson Reuters in the top 5% of cited authors for journals in Biology and Chemistry, 2011• Distinguished Ulam Scholar, The Center for Nonlinear Studies (CNLS), Los Alamos National labs, 2012• Paper, “How do dynamic cellular signals travel long distances?” in Mol. Biosyst. has been selected as “Hot paper”, 2012• Paper, “How do dynamic cellular signals travel long distances?” in Mol. Biosyst. is top accessed paper, 2012• Max Planck Institute for the Physics of Complex Systems, Institute Colloquium Speaker, Dresden, Germany, 2012• Paper on, “Protein dynamics and conformational selection in bidirectional signal transduction”, in BMC Biology, has achieved a ‘Highly Accessed’ level, 2012• Our Current Opinion In Structural Biology paper "Constructing structural networks of signaling pathways on the proteome scale" is among the most read/downloaded papers, 2012• Nussinov R, Ma B: Protein dynamics and conformational selection in bidirectional signal transduction. BMC Biol; 2012;10:2 PMID: 22277130 heads the top 20 articles in its domain in its domain in BioMedLib since its publication, 2012• Our TiBS paper “Allosteric post-translational modification codes is among the most downloaded/read• Identified by Thomson Reuters as “a scientist with prestigious publication history in biology and biochemistryNussinov-4• The manuscript on Enriching the human apoptosis pathway by predicting the structures of protein-protein complexes was featured in Global Medical Discovery• Nominated for the President of the Biophysical Society, narrowly losing to Jane Richardson• The paper "Allosteric post-translational modification codes", Nussinov et al. TiBS, stood out as the outstanding winner among all winners of the STFC 2012 Publication Awards, NCI for" pointing the way to a body of new research, 2012• Elected Fellow of the International Society of Computational Biology (ISCB), for significant contributions to the fields of computational biology and biochemistry, particularly through her work in the areas of protein alignment and docking, protein structure and function, and the proposition and development of the conformational selection and population shift model for binding, and allostery. Nussinov has authored over 450 scientific papers, and is highly cited, 2013• Publication selected for Spotlight by the NCI- Basic Science Program: Nussinov R, Tsai C-J: Allostery in disease and in drug discovery. Cell 153(2): 293-305, 2013The article Allostery in disease and in drug discovery. Nussinov R, Tsai CJ: Cell 153: 293-305, 2013 highlighted in F1000 Structural Biology: "So far, allostery has been largely described as a molecular event that occurs in a population of a single-protein species. But, in this insightful review, Nussinov and Tsai suggest that the concept should be extended to explain the regulation of functional cellular networks in which multiple protein components participate. Another important take-home message is that the new concept can be a useful theoretical framework for drug-development strategies. The authors also nicely present the historical overview on the efforts to explain the allostery at a molecular level. So, I strongly recommend this review to students in the wide areas such as biochemistry, biophysics, and pharmacology”, 2013• The manuscript "Single Mutations in Tau Modulate the Populations of Fibril Conformers through Seed Selection" in Angewandte Chemie has been designated a "Hot Paper", 2014• Awarded the The Michael and Ada Anbar Lectureship in the Biophysical Sciences, Buffalo University, 2014• The biophysical students in the Chemistry and Molecular Biophysics and Biochemistry Departments at Yale University voted an invitation as a “Student Invited Speaker to help keep this continuing BPTG tradition of prestigious speakers.” 2014• Theodore von Kármán Fellow Internationally recognized scientist, RWTH Aachen University, Institute for Advanced Simulation and Institute for Neuroscience and Medicine, Forschungszentrum Jülich, and German Research School for Simulation Sciences, 2015Committees and Boards:Advisory committee reviewing the Department of Bioinformatics in Bergen, Norway; Site visit committee of DCRT (Division of Computing Resources and Technology, NIH); Site visit committee GMD Institute of Algorithms, Bonn, Germany; NCI Steering Committee for Bioinformatics and Computational Biology NCI; NCI Steering Committee for Systems Biology; NCI Immunology Center of Excellence; Program Committee, Intelligent Systems in Molecular Biology Brazil, 2006; Program Committee, Intelligent Systems in Molecular Biology-ECCB, Vienna, 2007; Advisory Committee Modeling Protein Interactions; Numerous tenure andNussinov-5promotion committees and evaluations; Chair, Graduate Studies in Bioinformatics; Organized the NIH-INRIA (France) Workshop; Program Committee, Intelligent Systems in Molecular Biology; External Review Committee for the Science Focus Area for Basic Energy Research, Los Alamos National Laboratory to assess LANL capability to address Gene Function Discovery; PC Member of Bioinformatics Track, 2008; Tenure/Tenure Track Committee at the NIH, 2008; Site Visitor, Biomolecular Modeling Laboratory, Cancer Research UK London Research Institute, 2009; Chair, NIH-wide Earl Stadtman Investigator in Computational Biology, 2009/2010; Program Committee, ECCB, Protein and Nucleotide Structure, 2010; Member, Earl Stadtman NIH-wide tenure-track Investigator Search Committee, 2010, 2011; Invitation, Earl Stadtman NIH-wide tenure-track Investigator Search Committee, 2011, 2012; NSF external advisory board of the University of Chicago, multiscale theory and simulation for bimolecular systems, 2011-2013; Assisted in many other meeting organizations;Organizing Committee, Modeling of Protein Interactions, November 2012; Faculty Committee, Uppsala University, February 2013; National Academy of Sciences, Molecular Dynamics ANTON Award Committee (2013); The NIH Stadtman Investigator Search Committee in Computational Biology, 2013/2014; Review Committee, Universite' de Toulouse, LAAS, CNRS, Toulouse, France, April, 2014; Site Visit Committee, Quinquennial Review, London Cancer Research Institute, London, UK, 2009; Invited to Site Visit the theory group, Los Alamos, 2010; Invited by AERES (Agence d’Evaluation de la Recherche et des etablissements d’Enseignement Superieur) to Site Visit CEA Saclay in Paris, 2010; Site Visit Committee, RWTH Aachen University and the Forschungszentrum Julich, German Research School, responsible for the Laboratory of Computational Biophysics, 2011; Site Visit Committee, Chair, Site visit of the German Research School for Simulation Science, FZ-Julich and RWTH Aachen, 2011; NSF Advisory Board, University of Chicago, 2013; Advisory Board, responding to the recommendation "Thought Leaders from the Various Structural Biology Disciplines..." to overview "the future of structural biology is hybrid" in the Protein Data Bank (PDB). UK, 2014;Numerous various other Committees and Boards (also listed below)Community Activities:• Advisory Committee to Modeling of Protein Interactions since its inception in 2001• IEEE Computer Soc. Bioinformatics, Stanford Program Committee, 2003• Elected Member to the Council of the Biophysical Society• IEEE Computer Soc. Stanford, Program Committee, 2005• Elected Council Member, Biophysical Society (2005-2008)• Biophysical Society, Abstract Sort and Speaker Assignment, many times• INRIA-NIH; Organized on behalf of NIH together with French Embassy, 2007• NCI Steering Committee in Bioinformatics and Computational Biology• NCI Steering Committee in Systems Biology• NCI Faculty of Structural and Chemical Biology• Supervisor, SAIC, NCI-Frederick• Organizer in Gordon Research Conference on Protein Interaction Dynamics: Theory, Methods, and Practice, January 2008• Search Committee for the Editor of Proteins• Serves on the NCI/CCR Site Visit Team to UMD to Foster CollaborationsNussinov-6• Ad hoc Member of the CSR Molecular Structure and Function Study Section (Computational Biophysics Panel)• Program Committee ECCB08• Co-Chair: Protein Structure and Allosteric Communication, 52nd Biophysical Society Meeting & 16th IUPAB Biophysics Congress• Invited to Serve as a Member of the Macromolecular Structure and Function D Study Section for the Center for Scientific Review, NIH• External Review Committee for the Science Focus Area for Basic Energy Research, Los Alamos National Laboratory, to assess LANL capability to address Gene Function Discovery• Evaluation panel Ghent University, 2008• Reviewer for the GRC Board of Trustees, 2009, 2009• Site Visit Committee, Quinquennial Review, London Research Institute, London, UK, 2009• Responded to the request to assist in the review of the NIH American Recovery and Reinvestment Act (ARRA) Challenge Grant RFA, 2009• Assisted the NIGMS Grant Opportunity (GO grants, RC2 mechanism) Award Program, 2009• MSFD NIH Study Section, 2009• Committee Chair for Trans-NIH Tenured or Tenure Track Recruitment in Systems Biology, and Earl Stadtman Investigators, for top-tier tenure-track candidates to become “NIH Earl Stadtman Investigators” in Computational Biology.• MSFD NIH Study Section, Long Term Member, 2009-2015• Member of the Center for Cancer Research, National Cancer Institute Advisory Board• Invited to serve on the reviewing committee in CEA Saclay, Agence d’Evaluation de la Recherche et des etablissement d’Enseignement Superieur, Paris, France, March 2010• Graduate School Committee, Computational Biophysics, German Research School for Simulation Sciences GmbH, GmbH, Aachen, Germany, January 2011• External Reviewer of Computational, Genomics and Systems Biology in GmbH, Aachen, Germany, 2011• NSF external advisory board of the University of Chicago, multiscale theory and simulation for biomolecular systems, 2011• NSF-Structural Biochemistry Review Panel, 2011• NSF external advisory board of the University of Chicago, multiscale theory and simulation for bimolecular systems, 2011- to date• Editor-in-Chief, PLoS Computational Biology• Editor/Editorial Boards: Physical Biology; Proteins; JBC; BMC Bioinformatics; Intrinsically disordered proteins; Critical Opinion in Structural Biology, and more• Review Committee, Universite' de Toulouse, LAAS, CNRS, Toulouse, France, April, 2014• Advisory Board, responding to the recommendation "Thought Leaders from the Various Structural Biology Disciplines..." to overview "the future of structural biology is hybrid" in the Protein Data Bank (PDB). UK, 2014Reviews:Nussinov-7Journals:• Reviewer for Biochemistry, J. Molecular Biology, TIBS, Proceedings National Academy of Science (USA), Protein Science, Protein Engineering, JACS, Biopolymers, J. Biomolecular Structure and Dynamics, Structure, J. Theoretical Biology, Biophysical J., Proteins, Nucleic Acids Research, Bioinformatics, PLoS, J. Med. Chem., J. Physical Chemistry, J. Chemical Physics, Physical Biology, Trends in Biotechnology, FEBS Lett., PEDS, BMC Series Journals, Nature journals, and many others.Grants:• Welcome Trust Funds (Britain), Australian Grant system, Austria, Canadian grants (Research Council of Canada), NSF, Israel Academy of Science, Special advisor to GIF (German - Israel Funds); BSF (US-Israel Binational Science Foundation); CPA II, Center of Excellence Academy of Science; U.S. Army; NSF; NIH Project Grants; NSF Cancer Development Award; DOE; Netherland Science Foundation; Petroleum Research Fund; NIAID; Science Center Programs of the U.S. Department of State; Cyprus Grant System, and numerous others.Students:• About 70 current and past advised and co-advised graduate students since 1990Grants - at Tel Aviv University, and at the NCI:• Center of Excellence (funded by the Israel Academy of Science)• U.S. Army• Tel Aviv Research Foundation• Da’at Consortium – Industry Development Grant• Adams Brain Center• U.S. Army (to Tel Aviv Univ.)• Binational Science Foundation• Israel Academy of Science• Ministry of Science• ADMET Consortium for Drug Design Joint with Industry• NIAID (Renewed July 2007 for 3 years)• U.S. Army (to the NCI)• PI NCI – Nano Alliance (with Barcelona; extended 2009)• NCI Nanotechnology Alliance for Cancer (2006-2008). Collaboration with Polytechnic University of CataloniaInvited Talks (Last 10 year):Nussinov-826. Invited Speaker, Special Symposium in Quantum Bioinformatics in Kyoto Hall, Kyoto, Japan, 2004.27. Invited Speaker, University of Tokyo, Japan, 2004.28. Invited Speaker, Kyushu Technical University, Kyushu, Japan, 2004.29. Invited Speaker, Biophysical Society Meeting, Baltimore, MD, 2004.30. Organizer and Invited Speaker, Protein Interactions, Philadelphia, PA, 2004.31. Invited Speaker, Program Committee of the Third IEEE Computer Society Bioinformatics Conference, Stanford, CA, 2004.32. Invited Speaker, From Structural Genomics to Drug Design, Palma, Italy, 2004.33. Invited Speaker, Frontiers in Computational Biophysics and Drug Design, organized by the U.S. Army, Frederick, MD, 2004.34. Invited Speaker, DARPA Workshop on Protein Stability and Preservation, Fairfax, VA, 2005.35. Invited Speaker, Biophysical Society Meeting, Long Beach, CA, 2005.36. Invited Speaker, Bolognia Winter School, Bologna, Italy, 2005.37. Invited Speaker, ACS Meeting, San Diego, CA, 2005.38. Invited Speaker, Biodefense Workshop, Frederick, MD, 2005.39. Invited Speaker, DIMACS Workshop on Systems Biology, 2005.40. Organizer and Invited Speaker, Protein Society Meeting, Barcelona, Spain, 2005.41. Invited Speaker and Organizer, Protein Flexibility, Tempe, AZ, 2005.42. Invited Speaker 14th Conversation Biomolecular Stereodynamics, Albany, NY, 2005.43. Invited Speaker and on Organizing Committee, Protein Interactions, Lawrence, KS, 2005.44. Invited Speaker, IEEE Computer Society Bioinformatics Conference, Program Committee, Stanford, Palo Alto, CA, 2005.45. Featured Speaker, JCIS Meeting, Salt Lake City, UT, 2005.Nussinov-946. Invited Speaker, Biophysics Program, Opening the Seminar Year, University of Wisconsin, Madison, WI, 2005.47. Invited Talk, Laboratory of Structural Biology Research, NIH, Bethesda, MD, 2005.48. Invited Speaker, Hebrew University, Jerusalem, Israel, 2005.49. Featured Speaker, Annual Molecular Biophysics Symposium, University of Michigan, Ann Arbor, MI, 2006.50. Invited Speaker, CCP4 (Collaborative Computational Project 4) Synchrotron Radiation Department, Leeds, United Kingdom, 2006.51. Invited Speaker, Biochemistry and Molecular Biophysics, Washington University, St. Louis, MO, 2006.52. Chair and Invited Speaker, Biophysical Society Meeting, Symposium on Nanobiology, Salt Lake City, UT, 2006.53. Invited Speaker, CECAM Workshop on Self Assembly and Aggregation, Lyon, France, 2006.54. Invited Speaker, Nanobiology, Barcelona, Spain, 2006.55. Invited Speaker, Joint SIAM Conference on the Life Sciences, Raleigh, NC, 2006.56. Invited Speaker, Gordon Conference on Cellular Systems Biology, Mt. Holyoke College, South Hadley, MA, 2006.57. Invited Speaker, Virginia Tech, Blacksburg, VA, 2006.58. Invited Speaker, Purdue University, Washington, DC, 2006.59. Invited Featured Keynote Speaker, Keck Center, Houston, TX, 2006.60. Invited Speaker, Polytechnique de Catalonia, Barcelona, Spain, 2006.61. Invited Speaker, Koc University, Istanbul, Turkey, 2007.62. Invited Speaker, Department of Structural Biology, Weizmann Institute of Science, Rehovot, Israel, 2007.63. Invited Speaker, Center for Non-Linear Studies: Biosystems, Biophysics and Soft Matter Seminar Series, Los Alamos, 2007.64. Chair and Speaker, Biophysical Society, Baltimore, MD, 2007.Nussinov-1065. Invited Speaker, Two Decades to the Launching of the Human Genome Project, Boston, MA, 2007.66. Organizer and Chair, INRIA (French Institute for Computational Sciences)/NIH Workshop on Biomedical and Life Science Computing, Bethesda, MD, 2007.67. Invited Speaker, EMBO Workshop on Disordered Proteins, Budapest, Hungary, 2007.68. Invited Speaker, Workshop on Structure and Dynamics in Soft Matter and Macromolecules: From Single Molecules to Ensembles, the International Center for Theoretical Physics, Trieste, Italy, 2007.69. Invited Speaker, 234th ACS Meeting, Boston, MA, 2007.70. Invited Speaker, GTCbio First Protein Discovery and Development Summit, Washington, DC, 2007.71. Invited Speaker, NIH Systems Biology Interest Group, NIH, Bethesda, MD, 2007.72. Invited Speaker, Program in Structural and Computational Biology and Molecular Biophysics, Baylor College of Medicine, Houston, TX, 2007.73. Invited Speaker, Modeling Protein Interactions, Kansas City, MO, 2007.74. Invited Speaker, Workshop on RNA in Biology, Bioengineering and Nanotechnology, Minneapolis, MN, 2007.75. Invited Participant, Nanotechnology Alliance Meeting, Chapel Hill, NC, 2007.76. Invited to Serve on the NCI/CCR Site Visit Team to UMD and Present Open Collaborative Areas, 2007.77. Invited Talk, Dahlem Colloquia in Molecular Genetics, Berlin, Germany, 2007.78. Invited Speaker, Polymer Research Center and Chemical Engineering Department, Bogazici University, Istanbul, Turkey, 2007.79. Invited Speaker, Sabanci University, Istanbul, Turkey, 2007.80. Chair and Session Organizer, Gordon Research Conference, Protein Interaction Dynamics: Theory, Methods, Practice, Ventura, CA, 2008.81. Invited Talk, Albert Einstein College of Medicine, Bronx, NY, 2008.82. Invited to Chair a Session in the Biophysical Society Meeting, Long Beach, CA, 2008.Nussinov-1183. Invited Keynote Speaker, International Symposium on Health Informatics and Bioinformatics, Istanbul, Turkey, 2008.84. Invited Panelist, Bio-Geometry and Computational Chemistry, ACM Symposium (Association for Computing Machinery, Solid and Physical Modeling, Stonybrook, NY, 2008.85. Invited Speaker, 2nd International Conference on Molecular Perspectives on Protein-protein Interactions, Dubrovnic, Croatia, 2008.86. Invited Plenary Talk, 2008 President’s Meeting of the International Society of Quantum Biology and Pharmacology (ISQBP). Pushing the Boundaries of Biomolecular Simulation. Centro Stefano Franscini, Ascona, Switzerland, 2008.87. Invited Speaker, Telluride Workshop on Characterizing Landscape: From Biomolecules to Cellular Networks, Telluride, CO, 2008.88. Chair, Organizer and Invited Speaker, Gordon Conference on Macromolecular Organisation and Cell Function, Oxford, England, 2008.89. Invited Speaker, American Chemical Society, Protein Folding Session, Philadelphia, PA, 2008.90. Invited Talk, American Chemical Society Meeting, Symposium Combining Computational Chemistry with Sequence-based Bioinformatics for Structure-Function-Activity Relationships, Philadelphia, PA, 2008.91. Invited Talk, GTBio, Protein-Protein Interactions, San Diego, CA, 2008.92. Invited Talk, Protein Structure and Mechanics Symposium, Shanghai, China, 2008.93. Invited Talk, Department of Chemistry, University of Miami, Miami, FL, 2008.94. Invited Distinguished Lecturer, Molecular Basis of Disease Program, Georgia State University, Atlanta, GA, 2008.95. Invited Talk, Gibbs Conference, Carbondale, IL, 2008.96. Invited Talk, University of Missouri-Columbia, Columbia, MO, 2008.97. Invited to give Lectures, International Course on Computational Structural Biology, Brno, Czech Republic, 2008.98. Plenary BigRoc* Lecture, Weizmann Institute, Israel, 2008.99. Invited Talk, Indiana University School of Medicine, Indianapolis, IN, 2008.Nussinov-12100. Invited Talk, Biowulf Symposium, Bethesda, MD, 2009.101. Invited Talk, Johns Hopkins, Baltimore, MD, 2009.102. Invited Talk, Symposium, Biophysical Society Meeting, Boston, MA, 2009.103. Invited Keynote Speaker, 9th Swedish Bioinformatics Workshop, Umea, Sweden, 2009.104. Invited Talk, Technion, A Workshop on RNA, DNA, and Protein Structure Prediction, Haifa, Israel, 2009.105. Invited Talk, Chemistry Department, Penn State, University Park, PA, April 2009.106. Invited Speaker, International Jacques Monod Conference, Centre Paul Langevin in Aussois (Savoie), France, 2009.107. Invited Lecturer (three 2-hr lectures), The International School for Advanced Studies SISSA, Trieste, Italy, 2009.108. Invited Talk, CECAM Workshop, Frontiers in Bio-molecular Aggregation, Dublin, Ireland, 2009.109. Organizer and Chair, Biomolecular Structure and Dynamics, Albany, NY, 2009.110. Organizer, NIH-INRIA Meeting on Biomedical Computing, Paris, France, 2009.111. Invited Talk, Hebrew University, Jerusalem, Israel, 2009.112. Invited Talk, 2nd Conference on Drug Development for the Third World: From Computational Molecular Biology to Experimental Approaches ICTP, Trieste, Italy, 2009.113. Invited Talk, Telluride Workshop on Method Development for Protein Structure Prediction, Telluride, CO, 2009.114. Invited Talk, Kavli Institute of Theoretical Physics in China (KITPC), a sister site to the KITP in Santa Barbara, CA, Beijing, China, 2009.115. Invited Talk, International Symposium on Multi-Scale Dynamics of Protein Complex Formation, Tokyo, 2009.116. Invited Talk, ACS Meeting, Washington, DC, 2009.117. Invited Talk, CECAM Workshop, Coarse-Graining Biological Systems: Towards Large-Scale Interactions and Assembly, Lausanne, Switzerland, 2009.Nussinov-13118. Invited Talk, University of Akron, Chemical and Biomolecular Engineering, Akron, OH, 2009.119. Invited Talk, Hebrew University, Jerusalem, Israel, 2009.120. Invited Talk, Integrative Genomics and Department of Chemical Engineering, Princeton University, Washington, DC, 2009.121. Invited Talk and Session Chair, Keystone Symposia on Biomolecular Interaction Networks: Function and Disease, Quebec, Canada, 2010.122. Invited Talk, National Natural Science Foundation of China (NSFC), Theoretical and Experimental Approaches to Drug Design, Changzhou, China, 2010.123. Invited Speaker, Biological Interfaces: A TYC Computational Modelling Workshop, King’s College London, London, UK, 2010.124. Invited Speaker, Proteins: Dynamics, Folding and Function Symposium, University of Maryland, MD, 2010.125. Invited to give main lecture, First International Conference on Molecular Recognition under the auspices of Aegean Conferences, Crete, 2010.126. Distinguished Speaker, Inaugural Annual Biophysics Symposium, Molecular Biophysics Training Program at Northwestern University, Evanston, IL, 2010.127. Invited Speaker, Telluride, CO, 2010.128. Invited Talk, CIPSM Lecture (Center of Integrated Protein Science Munich) and Physical Chemistry Series, Munich, Germany, 2010.129. Invited Talk, 240th American Chemical Society National Meeting and Exposition, Boston, MA, 2010.130. Invited Speaker, Department of Computational Biology, University of Pittsburgh, Pittsburgh, PA, 2010.131. Invited Talk, Korean Protein Society, 10th International Conference on Protein Structure, Dynamics and Function, Seoul, Korea, 2010.132. Invited Talks (two) & Keynote Speaker, Conference on Molecular Aspects of Cell Biology: A Perspective from Computational Physics, ICTP. Trieste, Italy, 2010133. Invited Speaker, Modeling Protein Interactions, Lawrence, KS, 2010.Nussinov-14134. Invited Talk, Faculty of Agriculture, Hebrew University, Rehovoth, Israel, 2010.135. Invited Speaker, Southeast/Southwest Regional ACS Meeting, New Orleans, 2010.136. Invited Keynote Speaker, 2010 IEEE International Conference on Bioinformatics & Biomedicine (BIBM2010), Hong Kong, 2010.137. Invited talk, Computational Biophysics, German Research School for Simulation Sciences GmbH, GmbH, Aachen, Germany, 2011.138. Invited Speaker, Macromolecular Complexes & Interactions, ILANIT Conference, Eilat, 2011.139. Invited talk, George Washington University, Biochemistry and Molecular Biology Department, Washington, DC, 2011.140. Invited Speaker, Program Frontiers in Genomics 2011 of the National University of Mexico, the Center for Genomic Sciences (CCG), the Institute of Biotechnology (IBT) and the Undergraduate Program of Genomic Sciences of the National University of Mexico and the Mexican Society of Genomic Sciences, 2011.141. Invited committee member and talk in the Department of Biology, University of Copenhagen, 2011.142. Invited talk, Howard Hughes Medical Institute, Department of Biochemistry, University of Texas Southwestern Medical Center, 2011.143. Invited talk, ACS Meeting, Anaheim, CA, 2011.144. Invited talk, Mini Workshop on Modeling Electrostatics in Molecular Biology, Clemson, SC, 2011.145. Invited Teacher, University of Copenhagen Summer School on Protein Science, Spetses Island, Greece, 2011.146. Invited talk, FASEB 2011 Summer Research Conference entitled: "The Basic Origins and Medical Consequences of Protein Aggregation", Snowmass, CO, 2011.147. Invited Keynote Lecture at 3DSig, Vienna, ISMB, 2011.148. Invited Speaker, Semmelweis University, School of Medicine, Department of Medical Chemistry, Budapest, Hungary, 2011.149. Invited talk, International Conference on Mathematical Biology, Bangalore, India, 2011.Nussinov-15150. Invited talk, Biological & Soft Matter Physics Seminar, Arizona State University, Phoenix, AZ, 2011.151. Invited talk, Biochemistry and Biomedical Sciences’ Seminar Series, McMaster University, Hamilton, Ontario, Canada, 2011.152. Invited talk, Barcelona Biomed Conference on Macromolecular Dynamics (BBCMD), Barcelona, Spain, 2011.153. Invited talk, University of Massachusetts at Boston, 2011.154. Session Chair, Macromolecular Dynamics Conference, Barcelona, 2011.155. Invited Plenary speaker, Protein and RNA Structure Prediction Conference, Mexico, 2011.156. Invited talk, Gordon Research Conference, Ventura, CA, 2012.157. Invited talk, University of Colorado at Boulder, Boulder, CO, 2012.158. Invited talk, Department of Chemistry and Biochemistry, University of Arizona, Tucson, AZ, 2012.159. Invited talk, Symposium in American Physical Society (APS) Meeting, 2012.160. Invited talk, Iowa State University, 2012.161. Invited talk, Addex, Geneva, Switzerland, 2012.162. Invited Distinguished J. Clarence Karcher (Rosetta Barton) Lecturer in "Frontiers in Chemical Research", University of Oklahoma, 2012.163. Invited talk, Anchoring simulations to experiments: challenges for understanding and treating Alzheimer's disease, Cecam Meeting, Paris, 2012.164. Invited talk, the Department of Experimental Therapeutics and the Center for Targeted Therapy, Univ. Texas M.D. Anderson Cancer Center, 2012.165. Invited talk at the ACS Mid-Atlantic Regional Meeting, Frontiers in the Application of Computational Chemistry to Biological Systems, Maryland, 2012.166. Invited talk, Gordon Research Conference, Biopolymers, 2012.167. Session Chair, Gordon Research Conference, Biopolymers, 2012.168. Invited speaker, international conference on Molecular Crowding: Chemistry and Physics Nussinov-16meet Biology, ETHZ Monte Verita Congress center at Ascona, Switzerland, 2012.169. Colloquium, Distinguished Ulam Scholar, The Center for Nonlinear Studies (CNLS), Los Alamos National Labs, 2012.170. Invited talk, Conference on protein plasticity in allostery, evolution, and self-assembly, Dresden, 2012.171. Invited Plenary Speaker and Special Max Planck Institute for the Physics of Complex Systems, Institute Colloquium Speaker Conference on protein plasticity in allostery, evolution, and self-assembly, Dresden, 2012.172. Invited talk, q-bio seminar, Los Alamos, 2012.173. Organizer, Coarse-Grained Modeling of Structure and Dynamics of Biomacromolecules,Telluride, 2012.174. Invited talk, ACS Symposium on "Continuum Solvation Modeling in Biological Systems: Developments and Applications", Philadelphia, 2012.175. Invited talk, ACS Symposium on "multi-scale modeling of biological systems", Philadelphia, 2012.176. Invited Speaker, CNIO Frontiers Meetings: Allosteric Regulation of Cell Signaling, Madrid, 2012.177. Invited Keynote Speaker in the German Conference on Bioinformatics, Jena, Germany, 2012.178. Invited talk, Exploring Protein Interactions through Theory and Experiments, Cecam, Lausanne, Switzerland, 2012.179. Invited Speaker, Cecam, "Signalling pathways: interplay between microscopic changes and global behaviour of biological systems", Ecole Normale Superieure de Cachan, France, 2012.180. Invited lectures (2), at the School in Biological Physics of Protein Folding and Conformational Diseases, Rio de Janeiro, Brazil, 2012.181. Invited talk, Department of Chemistry and Biochemistry, University of Notre Dame, Indiana, 2012.182. Invited talk, Department of Computational Medicine and Bioinformatics seminar, University of Michigan, Ann Arbor, 2012.183. Invited speaker, Biophysics seminar, University of Michigan, Ann Arbor, 2012.Nussinov-17184. Invited talk, Modeling of Protein Interactions, Lawrence, Kansas, 2012.185. Invited Colloquium speaker, Chemistry Graduate Students Association, Northeastern University, 2012.186. Invited speaker, Department of Bioengineering, University of Maryland, 2012.187. Invited Plenary Speaker, Mathematical and Computational Medicine Conference, Zing Conference, Occidental Grand Xcaret, Mexico, 2012.188. Invited speaker, King’s College London, London, UK, 2013.189. Invited talk, Biological Sector, Department of Chemistry, University of Cambridge, Cambridge, UK, 2013.190. Invited Plenary talk, Royal Society of Chemistry, Protein-protein Interaction Meeting,London, UK, 2013.191. Invited speaker, Department of Biology, Copenhagen Biocenter, University ofCopenhagen, Copenhagen, Denmark, 2013192. Invited seminar speaker, Chemistry Department, Drexel University, Philadelphia, PA, 2013.193. Invited Distinguished Speaker, College of Medicine, University of South Florida, Tampa, 2013.194. Invited speaker, Uppsala University, Sweden, 2013.195. Invited Talk, CSIR-Indian Institute of Chemical Biology, Transcription and Chromatin Conference, 2013.196. Invited to participate in a Speaker panel at the American Physical Societymeeting, Baltimore, MD, 2013197. Invited seminar speaker, Department of Bioinformatics and Genomics, University of North Carolina at Charlotte, Charlotte, NC, 2013.198. Plenary speaker at the CCP-BioSim Conference: Frontiers of Biomolecular Simulation 2013, the University of Nottingham, UK, 2013.199. Invited seminar speaker, Chemistry Department, University of Cincinnati, 2013.200. Invited speaker, Protein Dynamics Conference, Durham, UK, 2013.Nussinov-18201. Invited speaker, Department of Chemistry at Bowling Green State University in Ohio,2013.202. Invited Speaker, "Computational Biology: Then and Now" Weizmann Institute of Science, Rehovoth, Israel, 2013.203. Invited talk, Department of Pharmaceutical Sciences at the University ofMaryland, Baltimore, 2013.204. Invited talk, Cancer and Inflammation Symposium, National Cancer Institute, Bethesda, 2013.205. Invited talk, Clinical Genomics Unit, Head and Neck Surgery Branch, NIDCD, National Cancer Institute, Bethesda, MD, 2013.206. Invited Keynote Speaker, SNP-SIG: Identification and annotation of SNPs inthe context of structure, function, and disease, ISMB, Berlin, Germany, 2013.207. Invited talk, American Chemical Society (ACS) Symposium, Indianapolis, IN, 2013.208. Invited keynote lecture, the 2013 ACM Conference on Bioinformatics,Computational Biology, and Biomedicine (ACM BCB 2013), Washington, DC2013.209. Key note speaker, Computational Structural Bioinformatics Workshop, ACM Conference On Bioinformatics, Computational Biology and Biomedical Informatics, Bethesda, MD, 2013.210. Invited colloquium in the Center for Structural Biology, University of Florida, Gainesville, FL, 2013.211. Invited speaker, Annual Anbar Lecture, honoring and endowed by the Chair of Biophysics, Neuroscience Program, University at Buffalo, NY, 2013.212. Keynote talk, PLOS Computational Biology Board meeting, Washington, DC, 2013.213. Invited Speaker, International Structure Biology and Functional Genomics(SBFG) Conference: Five Facets of Human Genome Function, NationalUniversity of Singapore, Singapore, 2013.214. Invited Keynote speaker, Basel Chemical Society, Symposium on Targeting Protein-Protein Interactions, Basel, Switzerland, 2013.215. Invited keynote speaker, Special Symposium on Protein-DNA Modeling, Bioscience andBioinformatics, Graduate School of Computer Science and Systems Engineering, KyushuInstitute of Technology, Iizuka, Fukuoka, Japan, 2014.Nussinov-19216. Invited speaker, Molecular Modeling and Simulation, Quantum Beam ScienceDirectorate, Japan Atomic Energy Agency, Kyoto, Japan, 2014.217. Invited speaker, Laboratory for Integrated Cellular Systems, RIKEN Center for Integrated Medical Sciences, Yokohama, Japan, , 2014.218. Invited speaker, Molecular Biology and Genetics, Virginia Commonwealth UniversityVCU, Richmond, VA, 2014.219. The Michael and Ada Anbar Award Lecture in the Biophysical Sciences, Buffalo University, 2014.220. Invited speaker, Ras Symposium, NCI, Shady Grove, MD, 2014.221. Invited Speaker, EMBO Workshop on Magnetic Resonance for Cellular Structural Biology, Fattoria La Principina, Principina Terra, Grosseto, Italy, 2014.222. Invited Speaker, The Nobel Swedish Structural Biology Meeting, Tallberg, Sweden, 2014.223. Invited Speaker, Protein Folding, Misfolding, Aggregation & Diseases, 8th IUPAP International Conference on Biological Physics, Beijing, China, 2014.224. Invited lecturer, FEBS advanced course, Ligand-binding theory and practice, Nove'Hrady, the South Bohemian Region of the Czech Republic, 2014.225. Invited Keynote Speaker, Gordon Research Conference on Intrinsically Disordered Proteins, 2014.226. Discussion Leader, Gordon Research Conference Human Single NucleotidePolymorphisms & Disease. Stonehill College, Easton, MA, 2014.227. Invited Speaker, ACS Symposium, Modeling the Effects of Water and Solvation in Biological Systems: Developments and Applications, San Francisco, CA, 2014.228. Invited Speaker, Special Symposium on Modeling of Protein Kinases and Phosphorylation: Protein Dynamics, Regulation, Function and Signal Transduction, San Francisco, CA, 2014.229. Invited Speaker, the Biophysical Society Thematic Meeting "Modeling of Biomolecular Systems Dynamics, Allostery and regulation: Bridging Experiment and Computations", Istanbul, Turkey, 2014.230. Invited wwPDB "The future of structural biology is hybrid", European Bioinformatics Institute (EBI), Hinxton, UK, 2014.Nussinov-20231. Invited Speaker, Modeling of Protein Interactions. Lawrence, Kansas, 2014.232. Chair, 40+ Years of Protein Structure Analysis. Symposium. NIH, Bethesda, MD, 2014.233. Invited Speaker, University of Maryland Department of Chemistry, 2014.234. Invited Speaker, the Cancer: Research, Discovery and Therapeutics BioConference Live, 2014.235. Invited Speaker, Koc University, Istanbul, 2014236. Invited Speaker, Biophysical Properties and Biological Significance of Amyloid-β Assemblies, Cold Spring Harbor Laboratory symposium, Banbury Center, Cold Spring Harbor Laboratory, 2015237. Invited Speaker, University of Florida, 2015.238. Invited Speaker, ACS Symposium on Membranes and Amyloids, Denver, Colorado, 2015.239. Invited Speaker, ACS Symposium on Progress and Challenges in Molecular Simulations of Biomolecules, Denver, Colorado, 2015.240. Invited Speaker, Physics of Proteins Focus Session, the American Physical Society meeting, San Antonio, Texas, 2015.241. Invited Speaker, The CCB (Chemistry and Chemical Biology Graduate Program)/iPQB(Integrative Program in Quantitative Biology, encompassing Biophysics, Bioinformaticsand Systems Biology) Seminar, University of California San Francisco, 2015242. Invited Speaker, Dept. of Chemistry and Biochemistry, University of Maryland, 2015243. Yale University, The Biophysical Students in the Chemistry and Molecular Biophysics and Biochemistry Departments voted invitation as the “Student Invited Speaker to help keep this continuing BPTG tradition of prestigious speakers”, 2015.244. The 2015 Sarkar Lecturer, Molecular Structure & Function Program at The Hospital for Sick Children (SickKids). The invitation for “Distinguished Research” is decided by the students and post-doctoral fellows committee, Toronto, Canada, 2015.245. Invited Speaker, The Israeli Society for Bioinformatics and Computational Biology (ISBCB), Tel Aviv University, Tel Aviv 2015246. Invited keynote speaker, symposium on Structural Bioinformatics, 98th CanadianChemistry Conference, Ottawa, 2015Nussinov-21247. Invited Speaker, Shanghai International Symposium on Computational Chemistry, sponsored by the NYU-ECNU Center for Computational Chemistry at NYU Shanghai, Shanghai, 2015248. Invited Speaker, Queenstown Molecular Biology Meeting, Computational Genomics satellite, Queenstown, New Zealand, 2015249. Invited Speaker, ComBio 2015, Australian Society for Biochemistry and MolecularBiology, Australia and New Zealand Society for Cell and Developmental Biology, NewZealand Society for Biochemistry and Molecular Biology and New Zealand Society ofPlant Biologists. Melbourne, Victoria, 2015250. Invited Speaker, American Society for Biochemistry & Molecular Biology (ASBMB), special Symposium “Small Molecule Modulators in Genomic Reprogramming”, Khajuraho, Madhya Pradesh, India, 2015251. Invited Speaker, Workshop 4: Mathematical Challenges in Drug and Protein Design. The Mathematical Biosciences Institute (MBI). Columbus, Ohio, 2015.252. Invited Speaker, American Chemical Society Pacifichem Symposium “Metal ions and protein function: theoretical models and applications”. Hawai, 2015253. Invited talk, FEBS advanced course "Ligand-binding theory and practice”, South Bohemia, Czech Republic, 2016Nussinov-22BIBLIOGRAPHYPublished:1. Nussinov, R.: Secondary structure analysis of nucleic acids. Ph.D. thesis, Rutgers University. 374, 1977.2. Nussinov, R., Pieczenik, G., Griggs, J., and Kleitman, D.: Algorithms for loop matchings, Soc. Ind. Appl. Math. (C). J. Appl. Math. 35: 68-82, 1978.3. Nussinov, R.: Some rules in the ordering of nucleotides in the DNA. Nucleic Acids Res. 8: 4545-4562, 1980.4. Nussinov, R.: Strong adenine clustering in nucleotide sequences. J. Theor. Biol. 85: 285-291, 1980.5. Nussinov, R.: Three dimensional structure and sequence homology determine splicing sites in eukaryotic precursor RNA. J. Theor. Biol. 83: 647-662, 1980.6. Nussinov, R. and Jacobson, A. B.: Fast algorithm for predicting the secondary structure of single stranded RNA. Proc. Natl. Acad. Sci. USA 77: 6309-6313, 1980.7. Nussinov, R., Sussman, J. L., and Trifonov, E. N.: MS2 RNA has a potential to form an unusually large number of stable hairpins. J. Theor. Biol. 85: 481-486, 1980.8. Nussinov, R.: Nearest neighbor nucleotide patterns: Structural and biological implications. J. Biol. Chem. 256: 8458-8462, 1981.9. Nussinov, R.: The eukaryotic dinucleotide preference rules and their implications on degenerate codon choice. J. Mol. Biol. 149: 125-131, 1981.10. Nussinov, R.: The universal dinucleotide asymmetry rules in DNA and the amino acid codon choice. J. Mol. Evol. 17: 237-244, 1981.11. Nussinov, R. and Tinoco, I., Jr.: Sequential folding of a messenger RNA molecule. J. Mol. Biol. 151: 519-533, 1981.12. Wain-Hobson, S., Nussinov, R., Brown, R. J., and Sussman, J. L.: Preferential codon usage in genes. Gene 13: 355-364, 1981.13. Nussinov, R.: Some indications for inverse DNA duplication. J. Theor. Biol. 95: 783-791, 1982.Nussinov-2314. Nussinov, R.: Splicing and transport of eukaryotic mRNAs: A theoretical model. J. Theor. Biol. 97: 129-140, 1982.15. Nussinov, R.: RNA folding is unaffected by the nonrandom degenerate codon choice. Biochim. Biophys. Acta 698: 111-115, 1982.16. Nussinov, R., Tinoco, I., Jr., and Jacobson, A. B.: Secondary structure model for the complete simian virus 40 late precursor RNA. Nucleic Acids Res. 10: 351-364, 1982.17. Nussinov, R., Tinoco, I., Jr., and Jacobson, A. B.: Small changes in free energy assignments for unpaired bases do not affect predicted structures in single stranded RNA. Nucleic Acids Res. 10: 341-350, 1982.18. Nussinov, R.: An efficient code searching for sequence homology and DNA duplication. J. Theor. Biol. 100: 319-238, 1983.19. Nussinov, R.: Efficient algorithms for searching for exact repetition of nucleotide sequence. J. Mol. Evol. 19: 283-285, 1983.20. Comay, E., Nussinov, R., and Comay, O.: An extremely accelerated algorithm for calculating the secondary structure of single stranded RNA. Nucleic Acids Res. 12: 53-66, 1984.21. Lennon, G. G., and Nussinov, R.: Homonyms, synonyms and mutations of the sequence/structure vocabulary. J. Mol. Biol. 175: 425-430, 1984.22. Nussinov, R.: Doublet frequencies in evolutionary distinct groups. Nucleic Acids Res. 12: 1749-1763, 1984.23. Nussinov, R.: Effects of secondary structure in RNA on interlocking probabilities. J. Math. Biol. 19: 95-107, 1984.24. Nussinov, R.: Promoter helical structure variation at the E. Coli polymerase interaction sites. J. Biol. Chem. 259: 6798-6805, 1984.25. Nussinov, R.: Strong doublet preferences in nucleotide sequences and DNA geometry. J. Mol. Evol. 20: 111-119, 1984.26. Nussinov, R. and Lennon, G. G.: Periodic structurally similar oligomers are found on one side of the axes of symmetry in the lac, trp and gal operators. J. Biomol. Struct. Dyn. 2: 387-396, 1984.27. Nussinov, R. and Lennon, G. G.: Structural features are as important as sequence homologies in Drosophila heat shock gene upstream regions. J. Mol. Evol. 20: 106-110, 1984.Nussinov-2428. Nussinov, R. and Pieczenik, G.: Folding two large polynucleotide chains. J. Theor. Biol. 106: 261-273, 1984.29. Nussinov, R. and Pieczenik, G.: Structural and combinatorial constraints on base pairing in large nucleotide sequences. J. Theor. Biol. 106: 245-259, 1984.30. Nussinov, R., Shapiro, B., Lipkin, L. E., and Maizel, J. V., Jr.: DNAase I hypersensitive sites may be correlated with genomic regions of large structural variation. J. Mol. Biol. 177: 591-608, 1984.31. Nussinov, R., Shapiro, B., Lipkin, L. E., and Maizel, J. V., Jr.: Enhancer elements share local homologous twist angle variations with a helical periodicity. Biochim. Biophys. Acta 783: 246-257, 1984.32. Nussinov, R.: Large helical conformational deviation from ideal B-DNA and prokaryotic regulatory sites. J. Theor. Biol. 115: 179-189, 1985.33. Greif, P. C., Nussinov, R., Kanehisa, M., and DeLisi, C.: Highly nonrandom recurrence of consecutive repeats in non-coding mammalian sequences. Journal of Mathematical Bioscience 81: 43-52, 1986.34. Jernigan, R. L., Sarai, A., Ting, K. -L., and Nussinov, R.: Hydrophobic interactions in the major groove can influence DNA local structure. J. Biomol. Struct. Dyn. 4: 41-48, 1986.35. Landau, G., Vishkin, U., and Nussinov, R.: An efficient string matching algorithm with k differences for nucleotide and amino acid sequences. Nucleic Acids Res. 14: 31-46, 1986.36. Lennon, G. G. and Nussinov, R.: Eukaryotic oligomer frequencies are correlated with certain DNA helical parameters. J. Theor. Biol. 116: 427-434, 1986.37. Nussinov, R.: Compilation of eukaryotic sequences around transcription initiation sites. J. Theor. Biol. 120: 479-487, 1986.38. Nussinov, R.: Presence of large helical structure variation in yeast His-4 upstream region is correlated with general amino acid control on the CYC-1 gene. J. Biomol. Struct. Dyn. 3: 349-362, 1986.39. Nussinov, R.: Sequence signals which may be required for efficient formation of mRNA 3' termini. Nucleic Acids Res. 14: 3557-3572, 1986.40. Nussinov, R.: Some guidelines for identification of recognition sequences: Regulatory sequences frequently contain (T)GTG/CAC(A), TGA/TCA and (T)CTC/GAG(A). Biochim. Biophys. Acta 866: 93-108, 1986.Nussinov-2541. Nussinov, R.: Structural wrinkles and eukaryotes genomic regulatory sites. J. Mol. Evol. 22: 150-159, 1986.42. Nussinov, R.: TGTG, G clustering and other signals near non-mammalian vertebrate mRNA 3' termini: Some implications. J. Biomol. Struct. Dyn. 3: 1145-1154, 1986.43. Nussinov, R., Owens, J., and Maizel, J. V., Jr.: Sequence signals in eukaryotic upstream regions. Biochim. Biophys. Acta 866: 109-119, 1986.44. Nussinov, R. and Weisberg, R. A.: Bacteriophage lambda into protein may recognize structural features of the attachment sites. J. Biomol. Struct. Dyn. 3: 1133-1144, 1986.45. Shapiro, B., Nussinov, R., Lipkin, L., and Maizel, J. V., Jr.: A sequence analysis system encompassing rules for DNA helical distortion. Nucleic Acids Res. 14: 75-85, 1986.46. Jernigan, R. L., Sarai, A., Shapiro, B., and Nussinov, R.: Relationship between curved DNA conformations and slow gel migration. J. Biomol. Struct. Dyn. 4: 561-567, 1987.47. Landau, G., Vishkin, U., and Nussinov, R.: An efficient string matching algorithm with k mismatches for nucleotide and amino acid sequences. J. Theor. Biol. 126: 483-490, 1987.48. Le, S., Currey, K. M., Nussinov, R., and Maizel, J. V., Jr.: Studies of frequently recurring substructures in human alpha-like globin mRNA precursors. Comput. Biomed. Res. 20: 563-582, 1987.49. Nussinov, R.: (A)GGG(A), (A)CCC(A) and other potential 3' splice signals in primate pre-mRNA sequences. Biochim. Biophys. Acta 910: 261-270, 1987.50. Nussinov, R.: Asymmetry and sharp differences in the distribution of the four nucleotides at mRNA initiation and 3' termini: Some implications. Biochim. Biophys. Acta 908: 143-149, 1987.51. Nussinov, R.: Conserved putative signals in 3' intron junctions in rodents. J. Biomol. Struct. Dyn. 4: 1051-1064, 1987.52. Nussinov, R.: Nucleotide quartets in the vicinity of transcription initiation sites: Some DNA and chromatin structural implications. DNA 6: 13-22, 1987.53. Nussinov, R.: Theoretical molecular biology: Prospectives and perspectives. J. Theor. Biol. 125: 219-235, 1987.54. Nussinov, R., Barber, A., and Maizel, J. V., Jr.: The distribution of nucleotides near bacterial transcription initiation and termination sites show distinct signals that may affect DNA geometry. J. Mol. Evol. 26: 187-197, 1987.Nussinov-2655. Shapiro, B., Nussinov, R., Lipkin, L., and Maizel, J. V., Jr.: An interactive dot matrix system for locating significant features in nucleic acids molecules. J. Biomol. Struct. Dyn. 4: 697-706, 1987.56. Landau, G., Vishkin, V., and Nussinov, R.: Locating alignments with k differences for nucleotide and amino acid sequences. Comput. Appl. Biosci. 4: 19-25, 1988.57. Le, S., Chen, K-H., Nussinov, R., and Maizel, J. V., Jr.: An improved secondary structure computation method and its application to intervening sequences in the human alpha-like globin mRNA precursors. Comput. Appl. Biosci. 4: 337-344, 1988.58. Margalit, H., Shapiro, B. A., Nussinov, R., Owens, J., and Jernigan, R. L.: Helix stability in prokaryotic promoter regions. Biochemistry 27: 5179-5188, 1988.59. Nussinov, R.: Conserved quartets near 5' intron junctions in primate nuclear pre-mRNAs. J. Theor. Biol. 133: 73-84, 1988.60. Nussinov, R.: Putative viral elements in the vicinity of transcription initiation sites. Int. J. Biochem. 20: 721-730, 1988.61. Nussinov, R., Sarai, A., Smythers, G. W., and Jernigan, R. L.: Sequence context of oligomer tracts in eukaryotic DNA: Biological and conformational implications. J. Biomol. Struct. Dyn. 6: 543-562, 1988.62. Nussinov, R., Sarai, A., Wang, D., and Jernigan, R. L.: Sequence context of homooligomer tracts in eukaryotic genomes: Some DNA conformational implications. In Olson, W. K., Sarma, M. H., Sarma, R. H., and Sundaralingam, M. (Eds.): Proceedings of the 6th Conversation of Stereodynamics. DNA Bending and Curvature. Albany, Adenine Press, 1988, (3) pp. 129-138.63. Owens, J., Chatterjee, D., Nussinov, R., Konopka, A. K., and Maizel, J. V., Jr.: A fixed-point alignment technique for detection of recurrent and common sequence motifs associated with biological features. Comput. Appli. Biosci. 4: 73-77, 1988.64. Sarai, A., Mazur, J., Nussinov, R., and Jernigan, R. L.: Origin of DNA helical structure and its sequence dependence. Biochemistry 27: 8498-8502, 1988.65. Sarai, A., Mazur, J., Nussinov, R., and Jernigan, R. L.: Sequence dependence of DNA conformations: Means and fluctuations. In Olson, W. K., Sarma, M. H., Sarma, R. H., and Sundaralingam, M. (Eds.): Proceedings of the 6th Conversation of Stereodynamics. DNA Bending and Curvature. Albany, Adenine Press, 1988, (3) pp. 213-223.66. Le, S. -Y., Nussinov, R., and Maizel, J. V., Jr.: Tree graphs of RNA secondary structures and their comparisons. Comput. Biomed. Res. 22: 461-473, 1989.Nussinov-2767. Le, S. -Y., Owens, J., Nussinov, R., Chen, J-H., Shapiro, B., and Maizel, J. V., Jr.: RNA secondary structures: Comparison and determination of frequently recurring substructures. Comput. Appl. Biosci. 5: 205-210, 1989.68. Nussinov, R.: Conserved signals around the 5' splice sites in eukaryotic nuclear precursor mRNAs: G-runs are frequent in the introns and C in the exons near both 5' and 3' splice sites. J. Biomol. Struct. Dyn. 6: 985-1000, 1989.69. Nussinov, R.: The ordering of the nucleotides in the DNA: Computational problems in molecular biology. Computers in Biology and Medicine 19: 269-281, 1989.70. Nussinov, R., Sarai, A., Smythers, G. W., and Jernigan, R. L.: Distinct patterns in homooligomer tract sequence context in prokaryotic and eukaryotic DNA. Biochim. Biophy. Acta 1008: 329-338, 1989.71. Nussinov, R., Sarai, A., Smythers, G., Wang, D., and Jernigan, R. L.: Strong patterns in homooligomer tracts occurrences in non-coding and in potential regulatory sites in eukaryotic genomes. J. Biomol. Struct. Dyn. 7: 707-722, 1989.72. Sarai, A., Mazur, J., Nussinov, R., and Jernigan, R. L.: Sequence dependence of DNA conformation flexibility. Biochemistry 28: 7842-7849, 1989.73. Landau, G. M., Vishkin, V., and Nussinov, R.: Fast alignment of DNA and protein sequences. Methods Enzymol. 183: 487-502, 1990.74. Le, S. -Y., Nussinov, R., and Maizel, J. V., Jr.: Studies of local stability in histone, U-snRNA and globin precursor mRNA around transcription termination sites. Computers and Mathematics with Applications 20: 49-56, 1990.75. Nussinov, R.: General nearest neighbor preferences in G/C oligomers interrupted by A/T Correlation with DNA structure. J. Biomol. Struct. Dyn. 8: 399-412, 1990.76. Nussinov, R.: Sequence signals in eukaryotic upstream regions. Crit. Rev. Biochem. Mol. 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BMC Bioinformatics 12: 167, 2011.430. Ma, B. and Nussinov, R. Polymorphic Triple β-Sheet Structures Contribute to Amide H/D Exchange Protection in Alzheimer’s Amyloid β42. J. Biol. Chem. 286: 34244-34253, 2011.431. Ma, B., Tsai, C-J., HaliloAlu, T., and Nussinov, R. Dynamic Allostery: Linkers are not Merely Flexible. Structure 19: 907-917, 2011.432. Mashiach-Farkash, E., Nussinov, R., and Wolfson, H. J. SymmRef: A Flexible Refinement Method for Symmetric Multimers. Proteins 79: 2607-2623, 2011.433. Miller, Y., Ma, B., and Nussinov, R. The Unique Alzheimer’s β-Amyloid Triangular Fibril has a Cavity Along the Fibril Axis Under Physiological Conditions. J. Am. Chem. Soc. 133: 2742-2748, 2011.434. Miller, Y., Ma, B., and Nussinov, R. Synergistic Interactions Between Repeats in tau Protein and Aβ Amyloids may be Responsible for Accelerated Aggregation Via Polymorphic States. Biochemistry 50: 5172-5181, 2011.Nussinov-57435. Nussinov, R., Panchenko, A. R., and Przytycka, T. Physics Approaches to Protein Interactions and Gene Regulation. Phys. Biol. 8: 030301, 2011.436. Nussinov, R., Tsai, C-J., and Csermely, P. Allo-Network Drugs: Harnessing Allostery in Cellular Networks. Trends Pharmacol. Sci. 32: 686-693, 2011.437. Pan, Y. and Nussinov, R. The Role of Response Elements Organization in Transcription Factor Selectivity: The IFN-β Enhanceosome Example. PLoS Comput. Biol. 7: e1002077, 2011.438. Parthasarathy, S., Long, F., Miller, Y., Xiao, Y., McElheny, D., Thurber, K., Ma, B., Nussinov, R., and Ishii, Y. Molecular-Level Examination of Cu2+ Binding Structure for Amyloid Fibrils of 40-Residue Alzheimer’s β by Solid-State NMR Spectroscopy. J. Am. Chem. Soc. 133: 3390-3400, 2011.439. Puri, A., Jang, H., Yavlovich, A., Masgood, A., Veenstra, T., Luna, C., Aranda-Espinoza, H., Nussinov, R., and Blumenthal, R. Material Properties of Matrix Lipids Determine Conformation and Intermolecular Reactivity of a Diacetylenic Phosphatidylcholine in the Lipid Layer. Langmuir 27: 15120-15128, 2011.440. Revilla-Lopez, G., Rodriguez-Ropero, F., Curco, D., Torras, J. Calaza, M. I., Zanuy, D., Jimenez, A. I., Cativiela, C., Nussinov, R., and Aleman, C. Integrating the Intrinsic Conformational Preferences of Noncoded α-Amino Acids Modified at the Peptide Bond into the Noncoded Amino Acids Database. Proteins 79: 1841-1852, 2011.441. Revilla-Lopez, G., Torras, J., Nussinov, R., Aleman, C., and Zanuy, D. Exploring the Energy Landscape of a Molecular Engineered Analog of a Tumor–Homing Peptide. Phys. Chem. Chem. Phys. 13: 9986-1894, 2011.442. Tsai, C-J. and Nussinov, R. Gene-Specific Transcription Activation Via LongRrange Allosteric Shape-Shifting. Biochem. J. 439: 15-25, 2011.443. Tsai, C-J. and Nussinov, R. A Unified Convention for Biological Assemblies with Helical Symmetry. Acta Crystallogr. D. Biol Crystallogr. 67: 716-728, 2011.444. Tuncbag, N., Gursoy, A., Nussinov, R., and Keskin, O. Predicting Protein-Protein Interactions on a Proteome Scale by Matching Evolutionary and Structural Similarities at Interfaces using PRISM. Nat. Proc. 6: 1341-1354, 2011.445. Yuan, P., Liang, K., Ma, B., Zhang, N., Nussinov, R., and Huang, J. Multiple-Targeting and Conformational Selection in the Estrogen Receptor: Computation and Experiment. Chem. Biol. Drug Des. 78: 1137-1149, 2011.Nussinov-58446. Acuner Ozbabacan, S. E., Keskin, O., Nussinov, R., and Gursoy, A. Enriching the Human Apoptosis Pathway by Predicting the Structures of Protein-Protein Complexes. J. Struct. Biol. 179: 338-346, 2012.447. Capone, R., Jang, H., Kotler, S. A., Connelly, L., Teran, Arce C., Ramachandran, S., Kagan, B. L., Nussinov, R., and Lal, R. All-d-enantiomer of β-Amyloid Peptide Forms Ion Channels in Lipid Bilayers. J. Chem. Therory Comput. 8: 1143-1152, 2012.448. Capone, R., Jang, H., Kotler, S.A., Kagan, B.L., Nussinov, R., and Lal, R. Probing Structural Features of Alzheimer’s Amyloid-β Pores in Bilayers using Site-Specific Amino Acid Substitutions. Biochemistry 51: 776-785, 2012.449. Connelly, L., Jang, H., Ramachandran, S., Kagan, B., Nussinov, R., and Lal, R. Effects of Point Substitutions on the Structure of Toxic Alzheimer’s β-Amyloid Channels: Atomic Force Microscopy and Molecular Dynamics Simulations. Biochemistry 51: 3031-3038, 2012.450. Connelly, L.S., Teran Arce, F., Jang, H., Capone, R., Kotler, S.A., Ramachandran, S., Kagan, B.L., Nussinov, R., and Lal, R. Atomic Force Microscopy and MD Simulations Reveal Pore-Like Structures of All-d-Enantiomer of Alzheimer’s β-Amyloid Peptide: Relevance to the Ion Channel Mechanism of AD Pathology. J. Phys. Chem. B. 116: 1728-1735, 2012.451. Csermely, P., Sandhu, K. S., Hazai, E., Hoksza, Z., Kiss, H. J. M., Miozzo, F., Veres, D. V., Piazza, F., and Nussinov, R. Disordered Proteins and Network Disorder in Network Descriptions of Protein Structure, Dynamics and Function. Hypotheses and a Comprehensive Review. Curr. Protein Pept. Sci. 13: 19-33, 2012.452. Dickin, R., Hall, C.J., Taylor, L.K., Collings, A.M., Nussinov, R., and Bourne, P.E. A Review of 2011 for PLoS Computational Biology. PLoS Comput Biol. 8: e1002387, 2012.453. Engin, H. B., Keskin, O., Nussinov, R., and Gursoy, A. A Strategy Based on Protein-Protein Interface Motifs may Help in Identifying Drug Off-Targets. J. Chemical Information and Modeling. 52: 2273-2286, 2012.454. Kagan, B. L., Jang, H., Capone, R., Teran Arce, F., Ramachandran, S., Lal, R., and Nussinov, R. Antimicrobial Properties of Amyloid Peptides. Mol. Pharm. 9: 708-717, 2012.455. Kar, G., Keskin, O., Nussinov, R., and Gursoy, A. Human Proteome-Scale Structural Modelling of E2-E3 Interactions Exploiting Interface Motifs. J. Proteome Res. 11: 1196-1207, 2012.Nussinov-59456. Korkmaz, E. N., Nussinov, R., and Haliloglu, T. Conformational Control of the Binding of the Transactivation Domain of the MLL Protein and c-Myb to the KIX Domain of CREB. PloS Comput. Biol. 8: e1002420, 2012.457. Kuzu, G., Keskin, O., Gursoy, A., and Nussinov, R. Constructing Structural Networks ofSignaling Pathways on the Proteome Scale. Curr. Opin. Struct. Biol. 22: 367-377, 2012.458. Kuzu, G., Keskin, O., Gursoy, A., and Nussinov, R. Expanding the Conformational Selection Paradigm in Protein-Ligand Docking. Methods Mol. Biol. 819: 59-74, 2012.459. Ma, B. and Nussinov, R. Selective Molecular Recognition in Amyloid Growth andTransmission and Cross-Species Barriers. J. Mol. Biol. 421: 172-184, 2012.460. Miller, Y., Ma, B., and Nussinov, R. Metal Binding Sites in Amyloid Oligomers:Complexes and Mechanisms. Coord. Chem. Rev. 19-20: 2245-2252, 2012.461. Nussinov, R. Allosteric Modulators can Cestore Function in an Amino AcidNeurotransmitter Receptor by Slightly Altering Intra-Molecular Communication Pathways. Br. J. Pharmacol. 165: 2110-2112, 2012.462. Nussinov, R. A Future Vision for PLoS Computational Biology. PLoS Comput Biol8: e1002727, 2012.463. Nussinov, R. How do Cellular Signals Travel Long Distances? Mol. Biosyst. 8(1): 22-26, 2012.464. Nussinov, R. and Ma, B. Protein Dynamics and Conformational Selection in Bidirectional Signal Transduction. BMC Biol. 10: 2, 2012.465. Nussinov, R., and Tsai, C. J. The Different Ways Through which Specificity Works inOrthosteric and Allosteric Drugs. Curr. Pharm. Des. 18: 1311-1316, 2012.466. Nussinov, R., Tsai, C-J., Xin, F., and Radivojac, P. Allosteric Post-TranslationalModification Dodes. Trends Biochem. Sci. 37: 447-455, 2012.467. Papp, D., Lenti, K., Modos, D., Fazekas, D., Dul, Z., Turei, D., Foldvari-Nagy, L.,Nussinov, R., Csermely, P., and Korcsmaros, T. The NRF2-Related Interactome and Regulome Contain Multifunctional Proteins and Fine-Tuned Autoregulatory Loops. FEBS Lett. 586: 1795-802, 2012.468. Siddiqua, A., Luo, Y., Meyer, V., Swanson, M.A., Yu, X., Wei, G., Zheng, J., Eaton,G.R., Ma, B., Nussinov, R., Eaton, S.S., and Margittai, M. Conformational Basis for Asymmetric Seeing Barrier in Filaments of Three- and Four-Repeat Tau. J. Am. Chem. Soc. 134: 10271-10278, 2012.469. Tuncbag, N., Keskin, O., Nussinov, R., and Gursoy, A. Fast and Accurate Modelling ofNussinov-60Protein-Protein Interactions by Combining Template-Interface-Based Docking with Flexible Fefinement. Proteins 80: 1239-1249, 2012.470. Xu, Y., Ma, B., Nussinov, R. Structural and Functional Consequences of Phosphate-Arsenate Substitutions in Selected Nucleotides: DNA, RNA and ATP. J. Phys. Chem. B.116: 4801-4811, 2012.471. Yu, X., Luo, Y., Dinkel, P., Zheng, J., Wei, G., Margittai, M., Nussinov, R., and Ma, B.Cross-Seeding and Conformational Selection Between Three- and Four-Repeat Human tau Proteins. J. Biol. Chem. 287: 14950-14959, 2012.472. Zhao, J., Luo, Y., Jang, H., Yu, X., Wei, G., Nussinov, R., and Zheng, J. Probing IonChannel Activity of Human Islet Amyloid Polypeptide (Amylin). Biochim Biophys Acta(Membranes) 1818: 3121-3130, 2012.473. Csermely, P., Korcsmaros, T., Kiss, H. J. M., London, G., and Nussinov, R. Structureand Dynamics of Molecular Networks: A Novel Paradigm of Drug Discovery. Pharmacology and Therapeutics. 138: 333-408, 2013.474. Csermely, P., Nussinov, R., and Szilagyi, A. From Allosteric Drugs to Allo-NetworkDrugs: State of the Art and Trends of Design, Synthesis, and Computational Methods. Curr. Top. Med. Chem. 13: 2-4, 2013.475. Gupta, K., Jang, H., Harlen, K., Puri, A., Nussinov, R., Schneider, J., Blumenthal, R.,Mechanism of Membrane Permeation Induced by Synthetic β-Hairpin Peptides. J.Biophysical Chemistry, 105: 2093-2103, 2013.476. Guven Maiorov, E., Keskin, O., Gursoy, A., and Nussinov, R. The Structural Networkof Inflammation and Cancer: Merits and Challenges. Semin. Cancer Biol. 23: 243-251, 2013.477. Haspel, N., Laurent, A. D., Zanuy, D., Nussinov, R., Aleman, C., Puiggali, J., andRevilla-Lopez, G. Conformational Exploration of Two Peptides and Their HybridPolymer Conjugates: Potentialities as Self-Aggregating Materials. J. Phys. Chem. B. 116: 13941-13952, 2013.478. Huang, Q., Yu, L., Levine, A. J., Nussinov, R., and Ma, B. Dipeptide Analysis of p53Mutations and Evolution of p53 Family Proteins. Biochim. Biophys. Acta. 844: 198-206, 2013.479. Jang, H., Connelly, L., Arce, F. T., Ramachandran, S., Kagan, B. L., Lal, R., andNussinov, R. Mechanisms for the Insertion of Toxic, Fibril-like β-Amyloid Oligomers into the Membrane. J. Chemical Theory Comput. 9: 822-833, 2013.480. Jang, H., Connelly, L., Teran Arce, F., Ramachandran, S., Lal, R., Kagan, B. L., andNussinov, R. Alzheimer’s Disease: Which Type of Amyloid-Preventing Drug Agents toNussinov-61Employ? Physical Chemistry Chemical Physics. 15: 8868-8877, 2013.481. Jang, H., Teran Arce, F., Ramachandran, S., Kagan, B. L., Lal, R., and Nussinov, R. Familial Alzheimer’s Disease Osaka Mutant (ΔE22) β-Barrels Suggest an Explanation for the Different Aβ1-40/42 Preferred Conformational States Observed by Experiment. J. Physical Chemistry. 117:11518-11529, 2013.482. Kuzu, G., Gursoy, A., Nussinov, R., and Keskin, O. Exploiting ConformationalEnsembles in Modelling Protein-Protein Interactions on the Proteome Scale. J. ProteomeResearch 12: 2641-4653, 2013.483. Lengauer, T. and Nussinov, R. New Methods Section in PLoS Computational Biology.PLoS Comput Biol 9: e1002972, 2013.484. Liu, J. and Nussinov, R. The Role of Allostery in the Ubiquitin-Proteasome System. Crit.Rev. Biochem. Mol. Biol. 48: 89-97, 2013.485. Luo, Y., Dinkel, P., Yu, X., Margittai, M., Zheng, J., Nussinov, R., Wei, G., and Ma, B.Molecular Insights into the Reversible Formation of Tau Protein Fibrils. Chemical Communications 49: 3582-3584, 2013.486. Ma, B. and Nussinov, R. Structured Crowding and its Effects on Enzyme Catalysis.Topics in Current Chemistry. 337: 123-137, 2013.487. Nussinov, R. The Spatial Structure of Cell Signaling Systems. Physical Biology 10:045004, 2013.488. Nussinov R. How Can PLoS Computational Biology Help the Biological Sciences?PLOS Computational Biology 9: e1003262, 2013.489. Nussinov, R., Ma, B., and Tsai, C.-J. A Broad View of Scaffolding Suggests thatScaffolding Proteins can Actively Control Regulation and Signalling of MultienzymeComplexes through Allostery. BBA-Proteomics 1834: 820-829, 2013.490. Nussinov, R., Ma, B., Tsai, C.J., and Csermely, P. Allosteric Conformational BarcodesDirect Signaling in the Cell. Structure 21: 1509-1521, 2013.491. Nussinov, R. and Tsai, C.-J. Allostery in Disease and in Drug Discovery. Cell 153:293-305, 2013.492. Nussinov, R., Tsai, C.-J., and Ma, B. The Underappreciated Role of Allostery in theCellular Network. Annual Reviews in Biophysics 642: 169-189, 2013.493. Nussinov R, Tsai CJ, Mattos C. Pathway Drug Cocktail': Targeting Ras Signaling Based on Structural Pathways. Trends Mol Med. 19: 695-704, 2013.Nussinov-62494. Nussinov, R., Ma, B., Tsai, C.-J., and Csermely P. Allosteric Conformational BarcodesCirect Signaling in the Cell. Structure 21:1509-1521, 2013.495. Szilagyi, A., Nussinov, R., and Csermely, P. Allo-Network Drugs: Extension of theAllosteric Drug Concept to Protein-Protein Interaction and Signaling Networks. Curr. Top. Med. Chem. 13: 64-77, 2013.496. Tsai, C. J. and Nussinov, R. The Molecular Basis of Targeting Protein Kinases inCancer Therapeutics. Semin. Cancer Biol. 23: 235-242, 2013.497. Xu, Y., Wang, H., Nussinov, R., and Ma, B. Protein Charge and Mass Contribute to theSpatio-Temporal Dynamics of Protein-Protein Interactions in a Minimal Proteome. Proteomics 13: 1339-1351, 2013.498. Zanuy, D. Kotla, R., Nussinov, R., Teesalu, T., Sugahara, K. N., Aleman, C., and Haspel,N. Sequence Dependence of C-End Rule Peptides in Binding and Activation of Neuropilin-1 Receptor. J. Strut. Biol. 182: 78-86, 2013.499. Zanuy, D., Sayago, F. J., Revilla-Lopez, G., Ballano, G., Agemy, L., Kotamraju, V. R.,Jimenez, A. I., Cativiela, C., Nussinov, R., Sawvel, A. M., Stucky, G., Ruoslahti, E., and Alman, C. Engineering Strategy to Improve Peptide Analogs: From Structure-Based Computational Design to Tumor Homing. J. Computer Aided Mol. Design 27: 31-43, 2013.500. Acuner-Ozbabacan, E.S., Engin, H.B., Guven-Maiorov, E., Kuzu, G., Muratcioglu, S., Baspinar, A., Chen, Z., Van Waes, C., Gursoy, A., Keskin, O., and Nussinov, R. The Structural Network of Interleukin-10 and its Implications in Inflammation and Cancer. BMC Genomics. 15: S2, 2014.501. Acuner Ozbabacan, S.E., Gursoy, A., Nussinov, R., and Keskin, O. The Structural Pathway of Interleukin 1 (IL-1) Initiated Signaling Reveals Mechanisms of Oncogenic Mutations and SNPs in Inflammation and Cancer. PLoS Comput Biol. 10: e1003470, 2014.502. Baspinar, A., Cukuroglu, E., Nussinov, R., Keskin, O. and Gursoy, A. PRISM: A Web Server and Repository for Prediction of Protein-Protein Interactions and Modelling their 3D Complexes. Nucleic Acids Research 42 (Web Server issue): W285-289, 2014.503. Cui, Q. and Nussinov R.Making Biomolecular Simulations Accessible in the Post-Nobel Prize Era. PLoS Comput. Biol. 10: e1003786, 2014.504. Cukuroglu, E., Gursoy, A., Nussinov, R. and Keskin, O. Non-Redundant Unique Interface Structures as Templates for Modelling Protein Interactions. PLoS ONE 9: e86738, 2014Nussinov-63505. Dai, D., Huang, Q., Nussinov, R., and Ma, B. Promiscuous and Specific Recognition Among Ephrins and Eph Receptors. Biochim. Biophys. Acta. 1844: 1729-1740, 2014.506. Engin, H. B., Gursoy, A., Nussinov, R., and Keskin, O. Network-Based Strategies can help Mono- and Poly-Pharmacology Drug Discovery: A Systems Biology View. Current Pharmaceutical Design 20: 1201-1207, 2014.507. Gillman. A.L., Jang, H., Lee, J., Ramachandran, S., Kagan, B.L., Nussinov, R., Teran Arce, F. Activity and Architecture of Pyroglutamate-Modified Amyloid-β (AβpE3-42) Pores. J Phys Chem B. 118(26):7335-44. 2014.508. Guven-Maiorov, E., Acuner-Ozbabacan, S. E., Keskin, O., Gursoy, A. and Nussinov, R.Structural Pathways of Cytokins May Illuminate their Roles in Regulation of Cancer Development and Immunotherapy. Cancers (Basel) 6: 663-683, 2014.509. Jang, H., Teran Arce, F., Ramachandran, S., Kagan, B.L., Lal, R., and Nussinov, R. Disordered Amyloidogenic Peptides May Insert into the Membrane and Assemble into Common Cyclic Structural Motifs. Chem. Soc. Rev. 43(19):6750-64, 2014.510. Ji, X., Huang, Q., Yu, L., Nussinov, R., and Ma, B. Bioinformatics Study of Cancer-Related Mutations Within p53 Phosphorylation Site Motifs. Int. J. Mol. Sci. 15: 13275-13298, 2014.511. Kuzu, G., Keskin, O., Nussinov, R., and Gursoy, A. Modeling Protein Assemblies in the Proteome. Mol. Cell Proteomics 13:887-96, 2014.512. Lee, J., Gillman, A.L., Jang, H., Ramachandran, S., Kagan, B.L., Nussinov, R., and Teran Arce, F. Role of the Fast Kinetics of Pyroglutamate-Modified Amyloid-β Oligomers in Membrane Binding and Membrane Permeability. Biochemistry 53: 4704-4714, 2014.513. Lu, S., Huang, W., Wang, Q., Shen, Q., Li, S., Nussinov, R., and Zhang, J. The structural basis of ATP as an allosteric modulator. PLoS Comput Biol. 10(9):e1003831, 2014.514. Luo, Y., Ma B, Nussinov, R., and Wei, G. Structural Insight into Tau Protein's Paradox of Intrinsically Disordered Behavior, Self-Acetylation Activity, and Aggregation. J Phys Chem Lett. 5(17):3026-3031, 2014.515. Lu, S., Huang, W., Wang, Q., Shen, Q., Li, S., Nussinov, R. and Zhang, J. The structural basis of ATP as an allosteric modulator. PLoS Comput Biol. 10(9):e1003831, 2014.516. Ma, B., Kolb, S., Diprima, M., Karna, M., Tosato, G., Yang, Q., Huang, Q. and Nussinov, R. Investigation of the interactions between the EphB2 receptor and SNEW peptide variants. Growth Factors. 32(6):236-46, 2014.517. Ma, B., and Nussinov, R. Druggable Orthosteric and Allosteric Hot Spots to Target Protein-Protein Interactions. Current Pharmaceutical Design 20: 1293-1301, 2014.Nussinov-64518. Meyer, V., Dinkel, P. D., Luo, Y., Yu, X., Wei, G., Zheng, J., Eaton, G. R., Ma, B., Nussinov, R., Eaton, S. S., and Margittai, M. Single Mutations in Tau Modulate the Populations of Fibril Conformers through Seed Selection. Angewandte Chemie 53: 1590-1593, 2014.519. Murase, S.K., Haspel, N., del Valle, L., Perpete, E.A., Michaux, C., Nussinov, R., Puiggali, J. and Aleman, C. Molecular characterization of L-phenylalanine terminated poly(L-lactide) conjugates RSC Advances 4(44):23231-23241, 2014.520. Nussinov, R. The Significance of the 2013 Nobel Prize in Chemistry and the ChallengesAhead. PLoS Comput Biol. 10: e1003423, 2014.521. Nussinov R, Jang H. Dynamic Multiprotein Assemblies Shape the Spatial Structure ofCell Signaling. Prog. Biophys. Mol. Biol., 116(2-3):158-64, 2014.522. Nussinov, R. Jang, H. and Tsai, C.-J. The Structural Basis for Cancer Treatment Decisions. Oncotarget, 15(17): 7285-7302, 2014.523. Nussinov, R., Ma, B., and Tsai, C.-J. Multiple Conformational Selection and Induced Fit Events Take Place in Allosteric Propagation. Biophys. Chem. 86: 22-30, 2014.524. Nussinov, R. and Tsai, C,-J. Unraveling Structural Mechanisms of Allosteric Drug Action. Trends Pharmacol. Sci. 35(5): 256-264, 2014.525. Nussinov, R. and Tsai, C.-J. Free Energy Diagrams for Protein Function. Chemistry and Biology 21: 311-318, 2014.526. Nussinov, R., Tsai, C.-J. and Liu, J. Principles of allosteric interactions in cell signaling. J Am Chem Soc. 136(51):17692-701, 2014527. Nussinov, R. and Wolynes, P.G. A Second Molecular Biology Revolution? The EnergyLandscapes of Biomolecular Function. Phys. Chem. Chem. Phys. 16: 6321-6322, 2014.528. Qi, R., Luo, Y., Ma, B., Nussinov, R. and Wei, G. Conformational Distribution and α- Helix to β-Sheet Transition of Human Amylin Fragment Dimer. Biomacromolecules 15: 122-131, 2014.529. Ozbabacan, S. E. A., Gursoy, A., Nussinov, R., and Keskin, O. The Structural Pathwayof Interleukin 1 (IL-1) Initiated Signalling Reveals Mechanisms of Oncogenic Mutations and SNPs in Inflammation and Cancer. PLoS Computational Biology 10: e1003470, 2014.530. Sudha, G., Nussinov, R., and Srinivasan, N. An Overview of Recent Advances inStructural Bioinformatics of Protein-Protein Interactions and a Guide to their Principles.Prog. Biophys. Mol. Biol. 116(2-3):141-50, 2014.Nussinov-65531. Szalay, K.Z., Nussinov, R., and Csermely, P. Attractor Structures of Signaling Networks: Consequences of Different Conformational Barcode Dynamics and their Relations to Network-Based Drug Design. Molecular Informatics 33(6-7): 463-468, 2014.532. Tsai, C.-J. and Nussinov, R. A Unified View of ‘How Allostery Works’. PLoSComputational Biology 10: e1003394, 2014.533. Tsai, C.-J. and Nussinov, R. The Free Energy Landscape in Translational Science: How can Somatic Mutations Result in Constitutive Oncogenic Activation? Physical Chemistry Chemical Physics 16: 6332-6341, 2014.534. Miller, Y., Ma, B., and Nussinov R. Polymorphism in Self-Assembly of Peptide-Based β-Hairpin Contributes to Network Morphology and Hydrogel Mechanical Rigidity. J Phys Chem B. 119(2):482-90, 2015.535. Nussinov R. Advancements and challenges in computational biology. PLoS Comput Biol. 8;11(1):e1004053 2015.536. Nussinov, R. and Tsai, C.-J. The Design of Covalent Allosteric Drugs. Ann. Review ofPharmacology and Toxicology, 55:249-67, 2015.In Press:1. Cronin, M., Coolbaugh, M.J., Nellis, D., Zhu, J., Wood, D.W., Nussinov, R., and Ma, B. Dynamics Differentiate Between Active and Inactive Inteins. Eur. J. Med. Chem. July, 2014.2. Nussinov, R., Jang, H. and Tsai, C.-J. Oligomerization and Nanocluster Organization Render Specificity. Biological Reviews Camb. Philos. Soc., June, 2014.3. Nussinov, R. and Tsai, C. Allostery without a conformational change? Revisiting the paradigm. Curr Opin Struct Biol. 2014 Dec 11Books/Book Chapters (Last 10 years):11. Benyamini, H., Gunasekaran, K., Wolfson, H., and Nussinov, R. Gelsolin Amyloidosis. In: Amyloid Proteins: The Beta Pleated Sheet Conformation and Disease, Sipe, J. (Ed.), Wiley-VCH Verlag GmbH & Co., Weinheim, Germany, 2005, pp. 625-634.Nussinov-6612. Haspel, N., Zanuy, D., Tsai, H-H., Ma, B., Wolfson, H., and Nussinov, R. Computational Approaches and Tools for Establishing Structural Models for Short Amyloid-Forming Peptides. In: Amyloid Proteins: The Beta Pleated Sheet Conformation and Disease, Sipe, J. (Ed.), Wiley-VCH Verlag GmbH & Co., Weinheim, Germany, 2005, pp. 301-318.13. Dror, O., Shulman-Peleg, A., Nussinov, R., and Wolfson, H.J. Predicting Molecular Interactions In: Silico: I. A Updated Guide to Pharmacophore Identification and its Applications to Drug Design. Frontiers in Medicinal Chemistry, 2006, pp. 551-584.14. Bai, Y. and Nussinov, R. Protocols for Protein Folding. Methods in Molecular Biology, Humana Press, Totowa, NJ, 2007, pp. 69-81.15. Haspel, N., Wainreb, G., Inbar, Y., Tsai, H-H., Tsai, C-J., Wolfson, H. J., and Nussinov, R. A Hierarchical Protein Folding Scheme Based on the Building Block Model. In: Methods in Molecular Biology, Nussinov R. and Bai, Y. (Eds.), Humana Press, U.S.A., Totowa, NJ, 2007, Vol. 350, pp. 189-204.16. Inbar, Y., Schneidman-Duhovny, D., Dror, O., Nussinov, R., and Wolfson, H.J. Deterministic Pharmacophore Detection Via Multiple Flexible Alignment of Drug-Like Molecules. In: Research in Computational Molecular Biology, Speed, T. (Ed.), Springer, San Francisco, CA, Volume LNBI 4453, 2007, Vol. 412, pp. 412-429.17. Kumar, S., Arya, S., and Nussinov, R. Temperature-Dependent Molecular Adaptation Features in Proteins. In: Physiology and Biochemistry of Extremophiles, Glansdorff, N. and Gerday, C. (Eds.) American Society for Microbiology, 2007, pp. 75-85.18. Gazit, E. and Nussinov, R. Nanostructure Design: Methods and Protocols. Methods in Molecular Biology. Humana Press, U.S.A, 2008, Vol. 474, pp. v-vii.19. Shatsky, M., Nussinov, R., and Wolfson, H. Algorithms for Multiple Protein Structure Alignment and Structure-Derived Multiple Sequence Alignment. In: Methods in Molecular Biology, Zaki, M.J. and Bystroff, C. (Eds.), Humana Press, U.S.A., 2008, Vol. 413, pp. 125-146.Invited NCI Publications:1. Ma, B., Elkayam, T., Wolfson, H., and Nussinov, R. Protein-Protein Interactions: What are the Preferred Ways in Which Proteins Interact? Center for Cancer Research Frontiers in Science, Structural Biology, Vol. 4, November 2005.2. Keskin, O., Ma, B., Rogale, K., Gunasekaran, K., and Nussinov, R. Protein-Protein Interactions in a Bottom-Up Systems Biology Approach. Center for Cancer Research Frontiers in Science, Molecular Biology, Vol. 5, November 2006.Nussinov-673. Zheng, J., Ma, B., Tsai, C J., and Nussinov, R. A Catalogue of Structural Motifs in Amyloid Fibril Organization. Center for Cancer Research Frontiers in Science, Molecular Biology, Vol. 8, April 2007.Nussinov-68
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