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Publications

Extended Kalman filter estimates the contour length of a protein in single molecule atomic force microscopy experiments
Vicente I. Fernandez
Pallav Kosuri
Vicente Parot
Julio M. Fernandez
Review of Scientific Instruments
November, 2009
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Fernandez Rev Sci Inst 2009.pdf
Modulation of Titin-Based Stiffness by Disulfide Bonding in the Cardiac Titin N2-B Unique Sequence
Anika Grützner
Sergi Garcia-Manyes
Sebastian Kötter
Carmen L. Badilla
Julio M. Fernandez
Wolfgang A. Linke
Biophysical Journal
August, 2009
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Grutzner Biophys J 2009.pdf
Diversity of chemical mechanisms in thioredoxin catalysis revealed by single-molecule force spectroscopy
Raul Perez-Jimenez
Jingyuan Li
Pallav Kosuri
Julio M. Fernandez
et al.
Nature Structural & Molecular Biology
July, 2009
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Perez-Jimenez NSMB 2009.pdf
Mechanochemistry: One Bond at a Time
Jian Liang
Julio M. Fernandez
ACS Nano
July, 2009
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Liang ACS Nano 2009.pdf
Direct observation of an ensemble of stable collapsed states in the mechanical folding of ubiquitin
Sergi Garcia-Manyes
Lorna Dougan
Carmen L. Badilla
Jasna Brujic
Julio M. Fernandez
Proceedings of the National Academy of Sciences
June, 2009
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Garcia-ManyesPNAS2009a.pdf
Osmolyte-induced separation of the mechanical folding phases of ubiquitin
Sergi Garcia-Manyes
Lorna Dougan
Julio M. Fernandez
Proceedings of the National Academy of Sciences
June, 2009
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Garcia-ManyesPNAS2009b.pdf
Single homopolypeptide chains collapse into mechanically rigid conformations
Lorna Dougan
Jingyuan Li
Carmen L. Badilla
Bruce J. Berne
Julio M. Fernandez
Proceedings of the National Academy of Sciences
June, 2009
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Dougan PNAS 2009.pdf
Force-activated reactivity switch in a bimolecular chemical reaction
Sergi Garcia-Manyes
Liang J
Szoszkiewicz R
Kuo T
Fernandez JM
Nature Chemistry
May, 2009
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Garcia-Manyes Nature Chemistry 2009.pdf
Mechanical characterization of protein L in the low-force regime by electromagnetic tweezers/evanescent nanometry
Ruchuan Liu
Garcia-Manyes S
Sarkar A
Badilla CL
Fernandez JM
Biophysical Journal
April, 2009
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Liu Biophysical Journal 2009.pdf
Stretching single talin rod molecules activates vinculin binding
Armando del Rio
Perez-Jimenez R
Liu R
Roca-Cusachs P
Fernandez JM
Sheetz MP
Science
January, 2009
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del_Rio_Science_2009.pdf
A Single-Molecule Perspective on the Role of Solvent Hydrogen Bonds in Protein Folding and Chemical Reactions
Lorna Dougan
Ainavarapu Sri Rama Koti
Georgi Genchev
Hui Lu
Julio M. Fernandez
ChemPhysChem
December, 2008
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CPC_Dougan.pdf
Force-clamp spectroscopy detects residue co-evolution in enzyme catalysis
Raul Perez-Jimenez
Arun Wiita
Rodriguez-Larrea D
Kosuri P
Gavira JA
Sanchez-Ruiz JM
Fernandez JM
J Biol Chem
August, 2008
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Perez-Jimenez JBC 2008.pdf
Single-molecule force spectroscopy measurements of bond elongation during a bimolecular reaction.
Ainavarapu Sri Rama Koti
Wiita AP
Dougan L
Uggerud E
Fernandez JM.
J Am Chem Soc
May, 2008
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ainavarapu_jacs1008.pdf
Solvent molecules bridge the mechanical unfolding transition state of a protein.
Lorna Dougan
Feng G
Lu H
Fernandez JM
Proc Natl Acad Sci U S A
March, 2008
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dougan_PNAS2008.pdf
Dwell time analysis of a single-molecule mechanochemical reaction.
Robert Szoszkiewicz
Ainavarapu SR
Wiita AP
Perez-Jimenez R
Sanchez-Ruiz JM
Fernandez JM
Langmuir
February, 2008
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szoszkiewicz_langmuir.pdf
A single-molecule assay to directly identify solvent-accessible disulfide bonds and probe their effect on protein folding.
Ainavarapu Sri Rama Koti
Wiita AP
Huang HH
Fernandez JM
J Am Chem Soc
January, 2008
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ainavarapu_jacs.pdf
Tandem repeating modular proteins avoid aggregation in single molecule force spectroscopy experiments.
Lorna Dougan
Fernandez JM
J Phys Chem A
December, 2007
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dougan_jpc.pdf
Probing the chemistry of thioredoxin catalysis with force.
Arun Wiita
Perej-Jiminez R
Walther KA
Gräter F
Berne BJ
Holmgren A
Sanchez-Ruiz JM
Fernandez JM
Nature
November, 2007
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wiita_nature06231.pdf
Force-clamp spectroscopy of single protein monomers reveals the individual unfolding and folding pathways of I27 and ubiquitin
Sergi Garcia-Manyes
Jasna Brujić
Carmen L. Badilla
J.M Fernández
Biophys J
June, 2007
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Garcia-Manyes_BiophysicalJournalJune2007.pdf
Dwell-Time Distribution Analysis of Polyprotein Unfolding Using Force-Clamp Spectroscopy
Jasna Brujic
Rodolfo I. Z. Hermans
Sergi Garcia-Manyes
Kirstin A. Walther
Julio M. Fernandez
Biophys J
April, 2007
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Brujic_BiophysicalJournal92Apr2007.pdf
The Mechanical Fingerprint of a Parallel Polyprotein Dimer
Atom Sarkar
Sofia Caamano
Julio M. Fernandez
Biophys J
February, 2007
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Sarkar_BiophysicalLettersNov2006.pdf
Contour Length and Refolding Rate of a Small Protein Controlled by Engineered Disulfide Bonds
Ainavarapu Sri Rama Koti
Jasna Brujic
Hector H Huang
Arun P Wiita
Hui LU
Lewyn Li
Kirstin A Walther
Mariano Carrion-Vazquez
Hongbin Li
Julio M Fernandez
Biophysical Journal
January, 2007
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Ainavarapu2007b.pdf
Mechanical Unfolding Pathways of the Enhanced Yellow Fluorescent Protein Revealed by Single Molecule Force Spectroscopy
Raul Perez-Jimenez
Sergi Garcia-Manyes
Sri Rama Koti Ainavarapu
Julio M. Fernandez
J Biol Chem
December, 2006
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Perez-Jimenez_JBC52Dec2006.pdf
Force-dependent chemical kinetics of disulfide bond reduction observed with single-molecule techniques
Arun Wiita
Sri Rama Koti Ainavarapu
Hector H. Huang
Julio M. Fernandez
Proc Natl Acad Sci U S A
May, 2006
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ForceDependentKinetics2006.pdf
Sub-Angstrom Conformational Changes of a Single Molecule Captured by AFM Variance Analysis
Kirstin Walther
Jasna Brujic
Hongbin Li
Julio M. Ferna´ndez
Biophys J
May, 2006
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2006_BiophysJ_Walther.pdf
Single-molecule force spectroscopy reveals signatures of glassy dynamics in the energy landscape of ubiquitin
Jasna Brujic
RODOLFO I. HERMANS Z.
KIRSTIN A. WALTHER
JULIO M. FERNANDEZ
Nature Phys
April, 2006
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2006_NatPhys_Brujic_Fernandez.pdf
Stepwise Unfolding of Ankyrin Repeats in a Single Protein Revealed by Atomic Force Microscopy
Lewyn Li
Svava Wetzel
Andreas Plu¨ckthun
Julio M. Fernandez
Biophys J
February, 2006
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2006_BiophysJ_Li_Fernandez.pdf
Ligand Binding Modulates the Mechanical Stability of Dihydrofolate Reductase
Ainavarapu Sri Rama Koti
Lewyn Li
Carmen L. Badilla
Julio M. Fernandez
Biophys J
November, 2005
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2005_BiophysJ_Koti.pdf
Mechanical Unfolding Intermediates Observed by Single-molecule Force Spectroscopy in a Fibronectin Type III Module
Lewyn Li
Hector Han-Li Huang
Carmen L. Badilla
Julio M. Fernandez
J Mol Biol
January, 2005
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2005-JMB-lewyn_li.pdf
The Elasticity of Individual Titin PEVK Exons Measured by Single Molecule Atomic Force Microscopy
Atom Sarkar
Sofia Caamano
Julio M. Fernandez
J Biol Chem
January, 2005
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caamano_sarkar_jbc_2005_6261.pdf
Response to Comment on ‘‘Force-Clamp Spectroscopy Monitors the Folding Trajectory of a Single Protein’’
Julio M. Fernandez
Hongbin Li
Jasna Brujic
Science
October, 2004
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brujic_fernandez_li_science_2004.pdf
Simultaneous atomic force microscope and fluorescence measurements of protein unfolding using a calibrated evanescent wave
Atom Sarkar
Ragan B. Robertson
Julio M. Fernandez
Proc Natl Acad Sci U S A
August, 2004
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sarkar_pnas_2004.pdf
The unfolding kinetics of ubiquitin captured with single-molecule force-clamp techniques
Schlierf M
Li H
Fernandez JM
Proc Natl Acad Sci U S A
May, 2004
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Schlierf2004.pdf
Force-clamp spectroscopy monitors the folding trajectory of a single protein
Julio M. Fernandez
Li H
Science
March, 2004
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Fernandez2004.pdf
Mechanical design of the first proximal Ig domain of human cardiac titin revealed by single molecule force spectroscopy
Hongbin Li
Fernandez JM
J Mol Biol
November, 2003
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Li2003.pdf
The force-driven conformations of heparin studied with single molecule force spectroscopy
Piotr Marszalek
Oberhauser AF
Li H
Fernandez JM
Biophys J
October, 2003
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Marszalek2003.pdf
The mechanical stability of ubiquitin is linkage dependent
Mariano Carrion-Vazquez
Li H
Lu H
Marszalek PE
Oberhauser AF
Fernandez JM
Nat Struct Biol
September, 2003
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CarrionVazquez2003.pdf
Linkage between ATP consumption and mechanical unfolding during the protein processing reactions of an AAA+ degradation machine
Kenniston JA
Baker TA
Fernandez JM
Sauer RT
Cell
August, 2003
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Kenniston2003.pdf
Reverse engineering of the giant muscle protein titin
Hongbin Li
Linke WA
Oberhauser AF
Carrion-Vazquez M
Kerkvliet JG
Lu H
Marszalek PE
Fernandez JM
Nature
August, 2002
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Li2002.pdf
The mechanical hierarchies of fibronectin observed with single-molecule AFM
Andres Oberhauser
Badilla-Fernandez C
Carrion-Vazquez M
Fernandez JM
J Mol Biol
May, 2002
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Overhauser2002.pdf
Chair-boat transitions in single polysaccharide molecules observed with force-clamp AFM
Piotr Marszalek
Li H
Oberhauser AF
Fernandez JM
Proc Natl Acad Sci U S A
April, 2002
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Marszalek2002.pdf
PEVK domain of titin: an entropic spring with actin-binding properties
Linke WA
Kulke M
Li H
Fujita-Becker S
Neagoe C
Manstein DJ
Gautel M
Fernandez JM
J Struct Biol
January, 2002
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Linke2002.pdf
Multiple conformations of PEVK proteins detected by single molecule techniques
Hongbin Li
Oberhauser, A. F.
Redick, S. D.
Carrion-Vazquez, M.
Erickson, H. P.
Fernandez, J. M.
Proc Natl Acad Sci U S A
October, 2001
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Li_PNAS_2001.pdf
Single molecules
Basche T
Nie S
Fernandez JM
Proc Natl Acad Sci U S A
September, 2001
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Basche2001.pdf
RNA structure: pulling on hair(pins) (perspective)
Julio M. Fernandez
Chu S
Oberhauser AF
Science
April, 2001
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Unfolding of titin domains explains the viscoelastic behavior of skeletal myofibrils
Minajeva, A.
Ivemeyer, M.
Fernandez, J. M.
Linke, W. A.
Biophys J
March, 2001
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Minajeva_BJ_2001.pdf
Fingerprinting polysaccharides with single-molecule atomic force microscopy
Piotr Marszalek
Li H
Fernandez JM
Nat Biotechnol
March, 2001
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Marszalek2001.pdf
Stepwise unfolding of titin under force-clamp AFM
Andres Oberhauser
Hansma, P.K.
Carrion-Vazquez, M.
Fernandez, J. M.
Proc Natl Acad Sci U S A
January, 2001
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Oberhauser_PNAS_2001.pdf
Point mutations alter the mechanical stability of immunoglobulin modules
Hongbin Li
Carrion-Vazquez, M.
Oberhauser, A. F.
Marszalek, P. E.
Fernandez, J. M.
Nat Struct Biol
December, 2000
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Li_NSB_2000.pdf
Single molecule force spectroscopy of modular proteins in the nervous system
Fisher T. E.
Carrion-Vazquez, M.
Oberhauser, A.F.
Hongbin Li
Marszalek, P.E.
Fernandez, J.M.
Neuron
September, 2000
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Fisher_Neuron_2000.pdf
Stretching single molecules into novel conformations using the atomic force microscope
Fisher T. E.
Marszalek, P. E.
Fernandez, J. M.
Nat Struct Biol
September, 2000
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Fisher_NSB_2000.pdf
Intracellular Ca++ channel immunoreactivity in neuroendocrine axon terminals
Fisher T. E.
Carrion-Vazquez, M
Fernandez, J.M.
FEBS Lett
September, 2000
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Fisher_FEBSLetters_2000.pdf
Mechanical design of proteins studied by single-molecule force spectroscopy and protein engineering
Carrion-Vazquez, M.
Oberhauser, A. F.
Fisher, T. E.
Marszalek, P. M.
Li, H.
Fernandez, J. M.
Prog Biophys Mol Biol
July, 2000
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Carrion-Vazquez_PBMB_2000.pdf
Atomic force microscopy captures quantized plastic deformation in gold nanowires
Piotr Marszalek
Greenleaf, W. J.
Li, H.
Oberhauser, A. F.
Fernandez, J. M.
Proc Natl Acad Sci U S A
June, 2000
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Marszalek_PNAS_2000.pdf
Atomic force microscopy reveals the mechanical design of a modular protein
Hongbin Li
Oberhauser, A. F.
Fowler, S. B.
Clarke, J.
Fernandez, J. M.
Proc Natl Acad Sci U S A
June, 2000
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Li_PNAS_2000.pdf
Mechanical unfolding intermediates in titin modules
Piotr E. Marszalek
Hui Lu
Mariano Carrion-Vazquez
Andres F. Oberhauser
Klaus Schulten
Julio M. Fernandez
Nature
November, 1999
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marszalek_1999.pdf
Single protein misfolding events captured by atomic force microscopy
Andres Oberhauser
Piotr E. Marszalek
Mariano Carrion-Vazquez
Julio M. Fernandez
Nature Structural Biology
November, 1999
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oberhauser_1999.pdf
The study of protein mechanics with the atomic force microscope
Thomas E. Fisher
Andres F. Oberhauser
Mariano Carrion-Vazquez
Piotr E. Marszalek
Julio M. Fernandez
Trends Biochem Sci
October, 1999
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fisher_1999.pdf
Pulsed laser imaging of Ca2+ influx in a neuroendocrine terminal
Fisher, T. E.
Fernandez, J. M.
J Neurosci
September, 1999
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Fisher_JNeurosci_1999.pdf
Atomic force microscopy captures length phenotypes in single proteins.
Mariano Carrion-Vazquez
Piotr E. Marszalek
Andres F. Oberhauser
Julio M. Fernandez
Proc Natl Acad Sci U S A
September, 1999
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carrion-vazquez_1999.pdf
Atomic levers control pyranose ring conformations
Piotr Marszalek
Pang, Y. P.
Li, H.
Yazal, J. E.
Oberhauser, A. F.
Fernandez, J. M.
Proc Natl Acad Sci U S A
July, 1999
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Marszalek_PNAS_1999.pdf
The micro-mechanics of single molecules studied with atomic force microscopy
Fisher, T.E.
Marszalek, P. E.
Oberhauser, A. F.
Carrion-Vazquez, M.
Fernandez, J. M.
J Physiol
April, 1999
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Fisher_JPhysiology_1999.pdf
Mechanical and chemical unfolding of a single protein: A comparison
Mariano Carrion-Vazquez
Andres F. Oberhauser
Susan B. Fowler
Piotr E. Marszalek
Sheldon E. Broedel
Jane Clarke
Julio M. Fernandez
Proc Natl Acad Sci U S A
March, 1999
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carrion-vazquez_1999b.pdf
Polysaccharide elasticity governed by chair-boat transition of the glucopyranose ring
Piotr E. Marszalek
Andres F. Oberhauser
Yuan-Ping Pang
Julio M. Fernandez
Nature
December, 1998
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marszalek_1998.pdf
Elastically Coupled Two-Level Systems as a Model for Biopolymer Extensibility
Matthias Rief
Julio M. Fernandez
Hermann E. Gaub
Physical Review Letters
November, 1998
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rief_1998.pdf
Themolecular elasticity of the extracellular matrix protein tenascin
Andres Oberhauser
Piotr E. Marszalek
Harold P. Erickson
Julio M. Fernandez
Nature
May, 1998
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oberhauser_1998.pdf
Regulation of Exocytotic Fusion by Cell Inflation
Carles Solsona
Barbara Innocenti
Julio M. Fernandez
Biophysical Journal
February, 1998
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solsona_1998.pdf
Reversible Unfolding of Individual Titin Immunoglobulin Domains by AFM
Matthias Rief
Mathias Gautel
Julio M. Fernandez
Hermann E. Gaub
Science
May, 1997
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rief_1997.pdf
Cellular and molecular mechanics by atomic force microscopy: Capturing the exocytotic fusion pore in vivo?
Julio M. Fernandez
Proc Natl Acad Sci USA
January, 1997
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fernandez_1997.pdf

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Julio Fernandez Lab, Phd Columbia University Biological Sciences MC 2449  1011A Fairchild Center  1212 Amsterdam Avenue  New York, N.Y. 10027  Phone: (212) 854 9474 ©2008 A Pannonica Production