Ariel Fernandez
Contact Information
ariel AT uchicago.edu
258 Ryerson Hall
608 609 4836
Honorary member, Collegium Basilea, Institute for Advanced Study, Basel, Switzerland (2006-)
Karl F. Hasselmann Chair in Engineering, Professor of Bioengineering (2005-2010)
Rice Research Professor (2011-)
Department of Bioengineering
Rice University
Houston, TX 77005
Principal Investigator, Instituto Argentino de Matematica (IAM), Buenos Aires, Argentina
Ariel Fernandez' Homepage at IAM
Distinguished Investigator, Morgridge Institute for Research at the University of Wisconsin-Madison (2011-2012)
Visiting Professor, Department of Mathematics, Tsing-Hua University, Republic of China
Adjunct Professor (2005-2009), Visiting Scholar (2011-), The University of Chicago
Adjunct Professor of Molecular Therapy, M. D. Anderson Cancer Center
Pharmaceutical Consultancy
Biographical sketch
Office: 258 Ryerson Hall
Phone: 608 609 4836
Fax: 317 278 9217
ariel@uchicago.edu
Personal Homepage
http://people.cs.uchicago.edu/~arifer/
Research
Prof. Ariel Fernández is interested in cooperativity and many-body problems associated with biomolecular folding and interactions. These themes led him to introduce the concept of structural wrapping and establish its importance in the realms of network centrality, molecular disease, molecular evolution and drug discovery. A singularity in the wrapping of a protein is known as dehydron. It consists of a solvent-exposed backbone hydrogen bond that is inherently sticky and not conserved across proteins of common ancestry. Dehydrons possess unique properties that can only be captured equipped with a good nanoscale model of water. Illustrative contributions on dehydrons are listed below.
Ariel Fernández and Michael Lynch: "Nonadaptive origins of interactome complexity". Nature 474, 502-505 (2011).
News and Views on the Nature paper on dehydrons in molecular evolution by Ariel Fernández and Michael Lynch: The Achilles' Heel of Biological Complexity
Ariel Fernández: Recent publications listed in the NIH/National Library of Medicine (PubMed)
Ariel Fernández: Recent Physics/Chemistry Publications (SCIRUS information resource)
Ariel Fernández's lecture Evolutionary insights into the control of drug specificity " at the Distinguished Scientific Leader Series, Georgia Institute of Technology (11/10/2010), describes current research efforts to control drug specificity by targeting protein dehydrons (click on the title and watch).
The wrapping concept and its enabled biotechnology are described in the following contributions:
Ariel Fernández: "Keeping Dry and Crossing Membranes". Nature Biotechnology 22, 1081-1084 (2004).
Ariel Fernández and Michael Lynch: "Nonadaptive origins of interactome complexity". Nature 474, 502-505(2011).
Ariel Fernández "Transformative concepts in drug design: Target wrapping" (Book), Springer, Heidelberg (2010).
Ariel Fernandez's Transformative Concepts... Preview in Google Books
Ariel Fernández et al.:"An anticancer C-Kit inhibitor is re-engineered to make it more active and less cardiotoxic". Journal of Clinical Investigation 117, 4044-4054 (2007).
His current research interests are centered in understanding how proteins may enhance their interactive versatility while their fold remains essentially conserved across evolutionary change. In this regard, his contributions to systems biology stem from a physico-chemical background. His most recent publications along these lines are:
Ariel Fernández, L. Ridgway Scott and R. Stephen Berry:The nonconserved wrapping of conserved folds reveals a trend towards increasing connectivity in proteomic networks". Proceedings of the National Academy of Sciences, USA 101, 2823-2827 (2004)
Ariel Fernández and R. Stephen Berry: "Molecular dimension explored in evolution to promote proteomic complexity". Proceedings of the National Academy of Sciences, USA 101, 13460-13465 (2004)
Florin Despa, Ariel Fernández and R. Stephen Berry: “Dielectric modulation of biological water”. Physical Review Letters 93, 228104 (4 pages) (2004); Featured in Nature (News and Views) 432, 688 (2004)
Within the realm of drug discovery, Ariel Fernández introduced the paradigm of "inhibitor as a wrapper of structural defects in proteins", a concept of paramount importance to control specificity and personalize molecular therapy. One of his recent contributions in this realm is:
Ariel Fernández, Kristina Rogale, Ridgway Scott and Harold A. Scheraga: "Inhibitor design by wrapping packing defects in HIV-1 proteins", Proceedings of the National Academy of Sciences USA 101, 11640-11645 (2004).
Grant support
NIH Grant Award 1R01 GM072614 from the National Institute of General Medical Sciences (NIGMS).
PI: Ariel Fernandez.
Title: “Protein packing defects as functional markers and drug targets”.
Total amount of Award: $1.7 million.
Education
M. Sc., M. Phil., Ph. D., Yale University, 1982-1984 (fastest awarded Ph. D. in Yale history).
Sr. Research Scientist, Max-Planck-Institut fuer biophysikalische Chemie, Abteilung Manfred Eigen, Goettingen, Germany, 1986-1989.
Research Associate (1985-1987), Visiting Senior Research Scientist (1994-1996), Princeton University.
Licenciado en Matematica (1980), Quimico (1979), Universidad Nacional del Sur, Argentina.
Ariel Fernández has contributed to a wide spectrum of research areas: Algebra, Representation Theory, Statistical Mechanics, Chemical Physics, Polymer Physics, Dissipative Systems, Molecular Biophysics, Interactive Proteomics and Integrative Biology. He has also perfomed and reported experimental work.
Awards and Previous Appointments
• Camille and Henry Dreyfus Teacher-Scholar Awardee, 1991
• Camille and Henry Dreyfus Distinguished New Faculty Awardee, 1989
• John S. Guggenheim Memorial Foundation Fellow, 1995-1996
• Consultant to U.S. Federal Government, NIH, Special Panel on Centers of Excellence in Systems Biology, 2003-
• National Cancer Institute (NCI) Reviewer. NIH Study Section RFA-07-005 "Advanced Proteomic Platforms and Computational Sciences for NCI Clinical Proteomic Technologies Initiative", 2006-
• Guest Professor, Institute for Protein Research, Osaka University, Japan, 2003
• Visiting Senior Researcher, Max-Planck-Institut fuer Biochemie, Abteilung Robert Huber, Martinsried, Germany, 2000-
• Visiting Senior Scientist, Institute for Nonlinear Science, University of California at San Diego, 1989
• Managing Editor, Frontiers in Bioscience, Encyclopedia of Bioscience, 2006-
• Editor, Journal of Biological Physics and Chemistry, Basel, Switzerland, 2000-
• Fulbright Scholar, US Information Agency, 1999 and Fulbright Fellow, 1981
• Alexander von Humboldt Foundation Awardee (1995)
• Max Planck Society Scholar, Goettingen, Germany (1987-1989)
• Feinberg Fellow, Israel, 1984-1985
• Full Professor, Indiana University School of Informatics, 2003-2005.
• Full Professor, Center for Computational Biology and Bioinformatics, Indiana University School of Medicine, 2003-2005.
• Elected Fellow, American Institute for Medical and Biological Engineering, 2006
• Full Professor and Principal Investigator, UNS and Natl. Res. Council of Argentina, 1994-2003.
• Medal "State of Buenos Aires" to the best graduate, Argentina, 1980
• Deputy Governor, American Biographical Institute, 1998-
• Co-organizer and Proceedings Editor of the Miami Bio/Technology Winter Symposium, Nature-sponsored, 1993.
• Chair, “Resistance and Safety”, Discovery on Target: Cambridge Healthtech Institute’s Second Annual KINASE INHIBITORS; October 20-23, Boston, MA, USA, 2008.
• Honorary Member, Collegium Basilea, Institute for Advanced Study, Basel, Switzerland, 2006-
• Adjunct Professor of Computer Science, The University of Chicago (2005-2008).
• Editorial Board Member, Journal of Postgenomics: Drug & Biomarker Development - Open Access, OMICS Publishing Group, 2010-
• Editorial Board Member, Journal of Bioengineering & Biomedical Science, OMICS Publishing Group, 2010-
Consultancy / IP Litigation
• Schiff/Hardin, LLP (Chicago-based Law Firm). Expert consultancy for pharmaceutical patent litigations.
Additional
Selected recent publicationsAriel Fernandez has published 325 research articles and one book.
1. Ariel Fernandez and Michael Lynch: "Nonadaptive origin of interactome complexity". Nature, in press (2011).
2.Ariel Fernandez: "Keeping Dry and Crossing Membranes". Nature Biotechnology 22, 1081-1084 (2004).
3.Ariel Fernandez, L. Ridgway Scott and R. Stephen Berry: "The nonconserved wrapping of conserved folds reveals a trend towards increasing connectivity in proteomic networks". Proceedings of the National Academy of Sciences, USA 101, 2823-2827 (2004).
4.Ariel Fernandez, Kristina Rogale, L. Ridgway Scott and Harold A. Scheraga: "Inhibitor design by wrapping packing defects in HIV-1 proteins". Proceedings of the National Academy of Sciences, USA 101, 11640-11645 (2004).
5.Ariel Fernandez and Harold A. Scheraga: "Insufficiently dehydrated hydrogen bonds as determinants for protein interactions", Proceedings of the National Academy of Sciences, USA 100, 113-118 (2003).
6.Ariel Fernandez and R. Stephen Berry: "Proteins with hydrogen-bond packing defects are highly interactive with lipid bilayers: Implications for amyloidogenesis", Proceedings of the National Academy of Sciences, USA 100, 2391-2396 (2003).
7.Ariel Fernandez and Ridgway Scott: "Adherence of packing defects in soluble proteins", Physical Review Letters 91, 018102, 4 pages (2003).
8.Ariel Fernandez, Jozsef Kardos, Ridgway Scott, Yuji Goto and R. Stephen Berry: "Structural defects and the diagnosis of amyloidogenic propensity", Proceedings of the National Academy of Sciences,USA 100, 6446-6451 (2003).
Past Lectures
Ariel Fernández has been an invited speaker at numerous leading institutions of learning and research: Yale U. (1988); U. of Chicago (2001); Cornell U. (2002); Burroughs-Wellcome Lecturer, Univ. of Chicago (2002); Argonne Natl. Labs. (2001); Max-Planck-Institut fuer Biochemie (1999-) MPI biophysikalische Chemie (1988); Universitaet Zurich (1988); Universitaet Goettingen, Germany (1988); Universities of Tokyo, Kobe and Osaka, Japan (June-August, 2002); Japan Atomic Energy Research Institute (Kizu-Minami/Nara, July, 2002); Physics Department/Computations in Science Seminar, University of Chicago (August 20, 2003), etc.
Osaka University, Institute for Protein Research, August, 2002; Unilever lecture at the University of Cambridge (UK), Chemical Laboratory, Biophysics Colloquia, December 10, 2003; lecture seminar at Eli Lilly Corporation, on January 27, 2004; presentation at the Dean’s Council meeting, IUPUI/Interactive Intelligence Co., Indianapolis, April 30, 2004; lecture at the Center for Genomics and Bioinformatics, Indiana University/Bloomington, on May 19, 2004; Charles University, Prague, Czech Republic, June, 2004; NIH / National Cancer Institute, Frederick, Maryland, June, 2004; Indiana University, Bloomington, Indiana, Chemistry Department, September, 2004; State University of New York, Chemistry and Biological Sciences; Albany, 2005, 14th Conversation (6/05).
Recent Lectures, Chairmanships
• Seminar lecture: “Curbing drug side effects by exploiting integrative ideas in molecular biophysics”, Computations in Science Seminars, Kersten Physics Teaching Center, The University of Chicago, November 28 (2007). • Keynote speaker: “Curbing the Cardiotoxicity of Kinase Inhibitors: The Methyl that Saved the Heart”, Discovery on Target 2007, Cambridge Healthtech Institute Fifth Annual, “Developing inhibitors for Promising Drug Targets”, World Trade Center, Boston, MA, October 15-18 (2007). • "7th International Workshop on Pharmacodynamics of Anticancer Agents”, organized by the University of Chicago, Guanacaste, Costa Rica, September 16-20 (2007). • “Re-engineering of Imatinib to Decrease Cardiac Risk: Translational Ideas in Drug Discovery”, World Pharmaceutical Congress, Cambridge Healthtech Institute Second Annual “Cardiotoxicity and Drug Safety”, Philadelphia, PA, May 12-13 (2008). • “Curbing side effects in anticancer drugs”, in “Science for Health with a Human Face”, International Symposium (4 Nobel laureates in attendance), Madrid, Spain, November 4-7 (2008). • “Translational ideas in drug discovery”, Guest lecturer, Genomics Research Center, Academia Sinica, Taipei, Taiwan, June 14-21 (2008). • Lecturer and Chair, “Resistance and Safety”. Lecture title: “Translational ideas to curb side effects in anticancer kinase-targeting therapy: Reducing cardiotoxicity through inhibitor redesign”. Discovery on Target: Cambridge Healthtech Institute’s Second Annual KINASE INHIBITORS; October 20-23, 2008, Boston, MA, USA. • Lecturer, 238th American Chemical Society National Meeting & Exposition. ACS paper 251: “Translational ideas in molecular therapy: Re-engineering anticancer drugs to curb side effects”; section “Novel Approaches to fine tune anticancer drugs to achieve acceptable clinical outcomes, Walter E. Washington Convention Center, August 16-20, 2009, Washington DC, USA. • Lecturer, “Frontiers in Pharmacology” Seminar Series, University of California at Davis, Department of Pharmacology, GBSF Auditorium, October 23, 2009, UC Davis, Davis CA, USA. • Keynote speaker, “Origin of Life: Molecular origins, Extinction, Life in Extremes, Species Diversification”, Vienna Biocenter, Noviembre 18, 2010, Vienna, Austria, sitio web: www.originoflife2010.com • Lecturer and Chair of Session: Kinase Inhibitors in Cancer (5-8), BIT Life Sciences 4th Annual Protein and Peptide Conference- PepCon 2011, March 23-25, 2011, Beijing, China.
Popular Press (Al-Jazeera): "Human Evolution: No Easy Fix"
Projects
Laboratories
List of Publications
Available in PDF.
Technical Reports
- TR-2011-05
- WRAPPA: A Screening Tool for Candidate Dehydron Identification. Christopher M. Fraser; Ariel Fernandez; L. Ridgway Scott. 4 December, 2011. Communicated by L. Ridgway Scott.