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José Onuchic

Harry C. and Olga K. Wiess Chair of Physics; Professor of Chemistry; Professor of BioSciences


E. Haglund, A. Pilko, R. Wollman, P.A. Jennings and J.N. Onuchic Pierced Lasso Topology Controls Function in Leptin.  j. Phy. Chem. B 2017: 706–718

M. Di Pierro, B. Zhang , E.L. Aiden , P.G. Wolynes and J.N. Onuchic A Transferable Model For Chromosome Architecture.  Proc. Natl. Acad. Sci. USA, 113 2016: 12168-12173

S. Holt, M. Darash-Yahana, Y.S. Sohn, L. Song, O. Karmi, S. Tamir, D. Michaeli, Y. Luo, M. Paddock, P.Jennings, J. Onuchic, R. Azad, E. Pikarsky, I. Cabantchik, R. Nechushtai, and R. Mittler Activation of Apoptosis in NAF-1-Deficient Human Epithelial Breast Cancer Cells.  J. Cell Sci., 129 2016: 155-165

M. Darash-Yahana , Y. Pozniak , M. Lu , Y.-S. Sohn , O. Karmi , S. Tamir , F. Bai , L. Song , P.A. Jennings , E. Pikarsky , T. Geiger , J.N. Onuchic, R. Mittler and R. Nechushtai Breast cancer tumorigenicity is dependent on high expression levels of NAF-1 and the lability of its Fe-S clusters.  Proc. Natl. Acad. Sci. USA, 113 2016: 10890–10895

R.R. Cheng, O. Nordesjo, R.L. Hayes, H. Levine, S.C. Flores, J.N. Onuchic and F. Morcos Connecting the sequence-space of bacterial signaling proteins to phenotypes using coevolutionary landscapes.  Mol. Biol. Evol., 33 2016: 3054-3064

R.R. Cheng, M. Raghunathan, J.K. Noel, and J.N. Onuchic Constructing sequence-dependent protein models using coevolutionary information.  Prot. Sci., 25 2016: 111-122

F. Bai, F. Morcos, R.R. Cheng, H. Jiang, and J.N. Onuchic Elucidating the druggable interface of protein?protein interactions using fragment docking and coevolutionary analysis.  Proc. Natl. Acad. Sci. USA, 113 2016: E8051-E8058

K. Yim, T.L. Prince, S. Qu F. Bai, P.A. Jennings, J.N. Onuchic, E.A. Theodorakis and L. Neckers Gambogic acid identifies a novel isoform-specific druggable pocket in the middle domain of Hsp90 beta.  Proc. Natl. Acad. Sci. USA, 113 2016: E4801-E4809

X. Lin, J.K. Noel, Q. Wang, J. Ma and J.N. Onuchic Lowered PH Leads to Fusion Peptide Release and a Highly-Dynamic Intermediate of Influenza Hemagglutinin.  J. Phys. Chem. B, 120 2016: 9654–9660

M. Boareto, M. K.Jolly, M.Goldman, M. Pietila, S. A.. Mani, S. Sengupta, E. Ben-Jacob, H. Levine and J. N. Onuchic Notch-Jagged signalling can give rise to clusters of cells exhibiting a hybrid epithelial/mesenchymal phenotype.  J. R. Soc. Interface, 13 2016: art. no. 20151106

Y. Suzuki, M. Lu, E. Ben-Jacob and J.N. Onuchic Periodic, Quasi-periodic and Chaotic Dynamics in Simple Gene Elements with Time Delays.  Scientific Reports, 6 2016: art. no. 21037

G.N. Phillips and J.N. Onuchic Preface to Special Topic on Protein Dynamics: Beyond Static Snapshots in Structural Biology.  Struct. Dyn., 3 2016: art. no. 011901

J.K. Noel, F. Morcos and J.N. Onuchic Sequence co-evolutionary information is a natural partner to minimally-frustrated models of biomolecular dynamics.  F1000Res., 5 2016: art. no. Faculty Rev-106

B. Jana and J.N. Onuchic Strain mediated adaptation is key for myosin mechanochemistry: Discovering general rules for motor activity.   PLoS Comput. Biol., 16 2016: art. no. e1005035

D.C. Ferreira, M.G. van der Linden, L.C. de Oliveira, J.N. Onuchic, A.F.P. de Araujo `Information and redundancy in the burial folding code of globular proteins within a wide range of shapes and sizes.  Prot. Struct. Func. Bioinf., 84 2016: 515-531

M. Chen, X. Lin, W. Zheng, J.N. Onuchic and P.G. Wolynes `Protein Folding and Structure Prediction from the Ground Up: The Atomistic Associative Memory, Water Mediated, Structure and Energy Model (AAWSEM).  J. Phys. Chem. B, 120 2016: 8557–8565

J.K. Noel, M. Levi, M. Raghunathan, H. Lammert, R.L. Hayes, J.N. Onuchic and P.C. Whitford `SMOG 2: A Versatile Software Package for Generating Structure-Based Models.  PLoS Comput. Biol., 12 2016: art. no. e1004794

C.H. Lipper, M.L. Paddock, R. Nechushtai, and P.A. Jennings Cancer-Related NEET Proteins Transfer 2Fe-2S Clusters to Anamorsin, a Protein Required for Cytosolic Iron-Sulfur Cluster Biogenesis.  PLoS One, 10 2015: art. no e0139699

H. Lammert, J. Noel, E. Haglund, A. Schug, and J. Onuchic Constructing a folding model for protein S6 guided by native fluctuations deduced from NMR structures.  J. Chem. Phys., 143 2015: art. no. 243141

R.N. dos Santos, F. Morcos, A.D. Andricopulo, and J.N. Onuchic. J.N. Onuchic Dimeric interactions and complex formation using direct coevolutionary couplings.  Scientific Reports, 5 2015: art. no.13653

R. Hayes, J.K. Noel, A. Mandic, P.C. Whitford, K.Y. Sanbonmatsu, U. Mohanti, and J.N. Onuchic Generalized Manning Condensation Model Captures the RNA Ion Atmosphere.  Phys. Rev. Let., 114 2015: art. no. 258105

K.M. Fisher, E, Haglund, J.K. Noel, K.L. Hailey, J.N. Onuchic, P.A. Jennings Geometrical frustration in Interleukin-33 decouples the dynamics of the functional element from the folding transition state ensemble.  PLoS One, 10 2015: art. no. e0144067

M.K. Jolly, M. Boareto, B. Huang, D. Jia, MY. Lu, E. Ben-Jacob, J.N. Onuchic, and H. Levine Implications of the Hybrid Epithelial/Mesenchymal Phenotype in Metastasis.  Front. Oncol., 5 2015: art. no. 155

M. Boareto, M.K. Jolly, E. Ben-Jacob, and J.N. Onuchic Jagged mediates differences in normal and tumor angiogenesis by affecting tip-stalk fate decision.  Proc. Natl. Acad. Sci. USA, 112 2015: E3836-E3844

M. Boareto, M.K. Jolly, M. Lu, J.N. Onuchic, C. Clementi, E. Ben-Jacob Jagged-Delta Asymmetry in Notch Signaling Can Give Rise to a Sender/Receiver Hybrid Phenotype.  Proc. Natl. Acad. Sci. USA, 112 2015: E402-E409

B. Huang, M. Kumar Jolly, M. Lu1, Ilan Tsarfaty, E. Ben-Jacob, and J.N. Onuchic Modeling the Transitions between Collective and Solitary Migration Phenotypes in Cancer Metastasis.  Scientific Reports, 5 2015: art. no. 17379

M.K. Jolly, M. Boareto, MY. Lu, J.N. Onuchic, C. Clementi and E. Ben-Jacob Operating principles of Notch-Delta-Jagged module of cell-cell communication.  New J. Phys., 17 2015: art. no. 055021

S. Tamir, M.L. Paddock, M. Darash-Yahana-Baram, S.H. Holt, Y.S. Sohn, L. Agranat, D. Michaeli, J.T. Stofleth, C.H. Lipper, F. Morcos, I.Z. Cabantchik, J.N. Onuchic, P.A. Jennings, R. Mittler, and R. Nechushtai Structure-function analysis of NEET proteins uncovers their role as key regulators of iron and ROS homeostasis in health and disease.  BBA Mol. Cell Res., 1853 2015: 1294-1315

F. Bai, F. Morcos, Y.-S. Sohn, M. Darash-Yahana, C.O. Rezende, C.H. Lipper, M.L.Paddock, L Song, Y. Luo, S.H. Holt, S. Tamir, E.A. Theodorakis, P.A. Jennings, J.N. Onuchic, R. Mittler and R.Nechushtai The Fe-S cluster-containing NEET proteins mitoNEET and NAF-1 as chemotherapeutic targets in breast cancer.  Proc. Natl. Acad. Sci. USA, 112 2015: 3698-3703

P.C. Whitford and J.N. Onuchic What protein folding teaches us about biological function and molecular machines.  Curr. Opin. Struct. Biol., 30 2015: 57-62

S. Kirmizialtin, S.P. Hennelly, A. Schug, J.N. Onuchic, and K.Y. Sanbonmatsu ntegrating Molecular Dynamics Simulations with Chemical Probing Experiments Using SHAPE-FIT.  Method. Enzymol., 553 2015: 215-234

M. G. van der Linden, D. C. Ferreira, L. C. de Oliveira, J.N. Onuchic and A. F. P. de Araujo. Ab initio protein folding simulations using atomic burials as informational intermediates between sequence and structure.  Prot. Struct. Func. Bioinf., 82 2014: 1186-1199

M. G. van der Linden, D. C. Ferreira, L. C. de Oliveira, J.N. Onuchic and A. F. P. de Araujo Ab initio protein folding simulations using atomic burials as informational intermediates betweensequence and structure,.  Prot.: Struct. Func. Bioinf.,, 82 2014: 1186-1199

F. Morcos, N.P. Schafer, R.R. Cheng, J.N. Onuchic, and P.G. Wolynes Coevolutionary information, protein folding landscapes, and the thermodynamics of natural selection.  Proc. Natl. Acad. Sci. USA, 111 2014: 12408-12413

L. Sun, J.K. Noel, J.I.Sulkowska, H. Levine and J.N. Onuchic Connecting thermal and mechanical protein (un)folding landscapes.  Biophys. J., 107 2014: 2941-2952

M. Lu, J.N. Onuchic and E. Ben-Jacob Construction of an effective landscape for multistate genetic switches.  Phys. Rev. Lett., 113 2014: art. no. 078102

B. Jana, F. Morcos and J.N. Onuchic From structure to function: the convergence of structure based models and co-evolutionary information.  Phys. Chem. Chem. Phys., 16 2014: 6496-6507

S. Tamir, S. Rotem-Bamberger, C. Katz, F. Morcos, K.L. Hailey, J.A. Zuris, C. Wang, A.R. Conlan, C.H. LIpper, M.L. Paddock, R. Mittler, J.N. Onuchic, P.A. Jennings, A. Friedler and R. Nechushtai Integrated strategy reveals the protein interface between cancer targets Bcl-2 and NAF-1.  Proc. Natl. Acad. Sci. USA, 111 2014: 5177-5182

J. Zimmermann, R.L. Hayes, M. Basan, J.N. Onuchic, W.-J. Rappel and H. Levine Intercellular Stress Reconstitution from Traction Force Data,.  Biophys. J., 107 2014: 548-554

M. Lu, B. Huang, S.M. Hanash, J.N. Onuchic and E. Ben-Jacob Modeling putative therapeutic implications of exosome exchange between tumor and immune cells.  Proc. Natl. Acad. Sci. USA, 111 2014: E4165–E4174

X.C. Lin, N.R. Eddy, J.K.Noel, P.C. Whitford, Q.H. Wang, J. Ma, and J.N. Onuchic Order and disorder control the functional rearrangement of influenza hemagglutinin.  Proc. Natl. Acad. Sci. USA, 111 2014: 12049-12054

J.N. Onuchic Physics transforming the Life Sciences.  Phys. Biol., 11 2014: art. no. 053006

E. Haglund, J.I. Sulkowska, J.K. Noel, H. Lammert, J.N. Onuchic and P.A. Jennings Pierced lasso bundles are a new class of knot-like motifs.  PLoS Comp. Biol., 10(6) 2014: e1003613

R.L. Hayes,, J.K. Noel, P.C. Whitford, U. Mohanty, K.Y. Sanbonmatsu and J.N. Onuchic Reduced Model Captures Mg2+-RNA Interaction Free Energy of Riboswitches.  Biophys. J., 106 2014: 1508-1519

E. Ben-Jacob, M. Lu, D. Schultz, and J.N. Onuchic The physics of bacterial decision making.  Front. Cell. Infec. Microb., 4 2014: art. no. 154

B. Huang, M. Lu, M.K. Jolly, I. Tsarfaty, J. Onuchic and E. Ben-Jacob The three-way switch operation of Rac1/RhoA GTPase-based circuit controlling amoeboid-hybrid-mesenchymal transition.  Scientific Reports (Nature), 4 2014: art. no. 06449

R.R. Cheng, F. Morcos, H. Levine and J.N. Onuchic Toward rationally redesigning bacterial two-component signaling systems using coevolutionary information.  Proc. Natl. Acad. Sci. USA, 111 2014: E563-E571

M. Lu, M.K. Jolly, J. Onuchic and E. Ben-Jacob Towards decoding the principles of cancer metastasis circuits.  Cancer Res., 74 2014: 4574-4587

E.L. Baxter , J.A. Zuris , Charles Wang , H.L Axelrod , A.E Cohen , M.L. Paddock , R. Nechushtai , J.N. Onuchic, and P.A. Jennings Allosteric control in a metalloprotein dramatically alters function.  Proc. Natl. Acad. Sci. USA, 110 2013: 948-953

D.T. Capraro, H. Lammert, D.K. Heidary,, M. Roy, L.A. Gross, J.N. Onuchic, and P.A. Jennings Altered Backbone and Side-Chain Interactions Result in Route Heterogeneity during the Folding of Interleukin-1beta (IL-1beta ).  Biophys. J., 105 2013: 975-983

F. Morcos, B. Jana, T. Hwa, and J.N. Onuchic. Evolutionary footprints across protein lineages help capture multiple protein conformations.  Proc. Natl. Acad. Sci. USA, 110 2013: 20533-20538

B.T. Andrews, D.T. Capraro, J.I. Sulkowska, J.N. Onuchic, and P.A. Jennings Hysteresis as a Marker for Complex, Overlapping Landscapes in Proteins.  J. Phys. Chem. Let., 4 2013: 180-188

J.K. Noel, J.N. Onuchic and J.I. Sulkowska Knotting a protein in explicit solvent.  J. Phys. Chem. Let., 4 2013: 3570-3573

J.I. Sulkowska, J.K. Noel, C.A. Ramirez-Sarmiento, E.J. Rawdon, K.C. Millett, and J.N. Onuchic. Knotting pathways in proteins.  Biochem. Soc. Trans., 41 2013: 523-527

J.N. Onuchic, P.A. Jennings, and E. Ben-Jacob Learning from Cancer how to Defeat Bacteria.  Proc. Natl. Acad. Sci. USA, 110 2013: 3212

M. Lu, M.K. Jolly, H. Levine, J.N. Onuchic and E. Ben-Jacob MicroRNA-based regulation of epithelialhybridmesenchymal fate determination.  Proc. Natl. Acad. Sci. USA, 110 2013: 18144-18149

Y.-S. Sohn, S. Tamir, L. Song, D. Michaeli, I. Matouk, A.R. Conlan, Y. Harir, S.H. Holt, Vladimir S., M.L. Paddock, A. Hochberg, I.Z. Cabanchick, J.N. Onuchic, P.A. Jennings and R.Nechushtai NAF-1 and mitoNEET are central to human breast cancer proliferation by maintaining mitochondrial homeostasis and promoting tumor growth.  Proc. Natl. Acad. Sci. USA, 110 2013: 14676-14681

F. Bai , Y. Xu , J. Chen , Q. Liu , J. Gu , X. Wang , J. Ma , H. Li , J.N. Onuchic, and H. Jiang The free energy landscape of the binding process of HupA to TcAChE.  Proc. Natl. Acad. Sci. USA, 110 2013: 4273-4278

W.A. Eaton, M. Gruebele, V. Lubchenko and J.N. Onuchic Tribute to Peter G. Wolynes.  J. Phys. Chem. B, 117 2013: 12669-12671

M. Lu, M. Jolly, R. Gomoto, B. Huang, J. Onuchic and E. Ben-Jacob Tristability in Cancer Associated miRNA-TF Chimera Toggle Switch.  J. Phys. Chem. B, 117 2013: 13164-13174

D. Schultz, M. Lu, T. Stavropoulos, J. Onuchic, and E. Ben-Jacob Turning Oscillations into Opportunities: Lessons from a Bacterial Decision Gate.  Scientific Reports (Nature), 3 2013: art. no.1668

D.T. Capraro, M. Roy, J.N. Onuchic, S. Gosavi, and P.A. Jennings Beta-Bulge triggers route-switching on the functional landscape of interleukin-1 beta.  Proc. Natl. Acad. Sci. USA, 109 2012: 1490-1493

P.C. Whitford, K.Y. Sanbonmatsu, and J.N. Onuchic Biomolecular dynamics: order-disorder transitions and energy landscapes.  Rep. Prog. Phys., 75 2012: 076601

J.I. Sulkowska , E.J. Rawdon , K.C. Millett , J.N. Onuchic, and A. Stasiak Conservation of complex knotting and slipknotting patterns in proteins.  Proc. Natl. Acad. Sci. USA, 109 2012: E1715-E1723

J.I. Sulkowska, J.K. Noel, and J.N. Onuchic Energy landscape of knotted protein folding.  Proc. Natl. Acad. Sci. USA, 109 2012: 17783-17788

D. T. Capraro, S. Gosavi, M. Roy, J.N. Onuchic, and P.A. Jennings Folding Circular Permutants of IL-1 beta: Route Selection Driven by Functional Frustration.  PLoS ONE, 7(6) 2012: e38512

J.I. Sulkowska, F. Morcos, M. Weigt, T. Hwa and J.N. Onuchic Genomics-aided structure prediction.  Proc. Natl. Acad. Sci. USA, 109 2012: 10340-10345

J. Singh, P. Whitford, N. Hayre, J.N. Onuchic, and D. Cox Large-Scale Conformational Change in the Mammalian Prion Protein.  Prot.: Struct. Func. Bioinf., 80 2012: 1299-1307

R. Hayes, J. Noel, U. Mohanty, P. Whitford, S. Hennelly, J. Onuchic and K. Sanbonmatsu Magnesium Fluctuations Modulate RNA Dynamics in the SAM-I Riboswitch.  J. Am. Chem. Soc., 134 2012: 12043-12053

J.K. Noel, A. Schug, A. Verma, W. Wenzel, A.E. Garcia, and J.N. Onuchic Mirror Images as Naturally Competing Conformations in Protein Folding.  J. Phys. Chem. B, 116 2012: 6880-6888

D.N. Beratan and J.N. Onuchic Redox redux.  PHYSICAL CHEMISTRY CHEMICAL PHYSICS , 40 2012: 13728-13728

E.L. Baxter, P.A. Jennings and J.N. Onuchic Strand swapping regulates the iron-sulfur cluster in the diabetes drug target mitoNEET.  Proc. Natl. Acad. Sci. USA, 109 2012: 1955-1960

M.A. Jamros, L.C. Oliveira, P.C. Whitford, J.N. Onuchic, J.A. Adams, P. Jennings Substrate-Specific Reorganization of the Conformational Ensemble of CSK Implicates Novel Modes of Kinase Function.  PLoS Comp. Biol., 8(9) 2012: e1002695

H. Lammert, P.G. Wolynes, and J.N. Onuchic. The Role of Atomic Level Steric Effects and Attractive Forces in Protein Folding.  Prot.: Struct. Func. Bioinf., 80 2012: 362-373

J.K. Noel, P.C. Whitford and J.N. Onuchic. The Shadow Map: A General Contact Definition for Capturing the Dynamics of Biomolecular Folding and Function.  J. Phys. Chem. B, 116 2012: 8692-8702

E. Haglund, J.I. Sulkowska , Z. He, G.-S. Feng, J.N. Onuchic and P. Jennings The Unique Cysteine Knot Regulates the Pleotropic Hormone Leptin.  PLoS ONE, 7(9) 2012: e45654

H. Lammert, J.K. Noel and J.N. Onuchic The dominant folding route minimizes backbone distortion in SH3.  PLoS Comp. Biol., 8(11) 2012: e1002776

J.K. Noel and J.N. Onuchic The many faces of structure-based potentials: from protein folding landscapes to structural characterization of complex biomolecules.  Computational Modeling of Biological Systems: From Molecules to Pathways 2012: 31-54

B. Jana, C. Hyeon and J.N. Onuchic The origin of minus-end directionality and mechanochemistry of Ncd motors.  PLoS Comp. Biol., 8(11) 2012: e1002783

J. Wang, R.J. Oliveira, X. Chua, P.C. Whitford, J. Chahine, W. Han, E. Wang, J.N. Onuchic and V.B.P. Leite Topography of funneled landscapes determines the thermodynamics and kinetics of protein folding.  Proc. Natl. Acad. Sci. USA, 109 2012: 15763-15768

D. Schultz, J.N. Onuchic, and E. Ben-Jacob Turning death into creative force during biofilm engineering.  Proc. Natl. Acad. Sci. USA, 109 2012: 18633-18634

C. Hyeon and J.N.Onuchic A Structural Perspective on the Dynamics of Kinesin Motors.  Biophys. J., 101 2011: 2749-2759

Y. Suzuki, J.K. Noel, and J.N. Onuchic A semi-analytical description of protein folding that incorporates detailed geometrical information.  J. Chem. Phys., 134 2011: 245101

R. Nechushtai , H. Lammert , D. Michaeli , Y. Eisenberg-Domovich , J. Zuris , M. Luca , D. Capraro , A. Fish , O. Shimshon , M. Roy , A. Schug , P. Whitford , O. Livnah , J.N. Onuchic, and P.A. Jennings Allostery in the ferredoxin protein motif does not involve a conformational switch.  Proc. Natl. Acad. Sci., 108 2011: 2240-2245

F. Morcos , A. Pagnani , Br. Lunt , A. Bertolino , D. Marks , C. Sander, R. Zecchina , J.N. Onuchic, T. Hwa and Ma. Weigt Direct-coupling analysis of residue co-evolution captures native contacts across many protein families.  Proc. Natl. Acad. Sci., 108 2011: E1293-E1301

P. C. Whitford, Y. Yu, S. Hennely, A. Ahmed, F. Tama, C. Spahn, J. N. Onuchic, and K. Y. Sanbonmatsu Excited states of ribosome translocation revealed through integrative molecular modeling.  Proc. Natl. Acad. Sci., 108 2011: 18943-18948

J.A. Zuris, Y. Harir, A.R. Conlan, M. Shvartsman, S. Tamir, M.L. Paddock, J.N. Onuchic, R. Mittler, Z.I. Cabantchik, P.A. Jennings, and R. Nechushtai Facile transfer of [2Fe-2S] clusters from the diabetes drug target, MitoNEET, to an apoacceptor protein.  Proc. Natl. Acad. Sci., 108 2011: 13047-13052

E.B. Baxter, P.A. Jennings, and J.N. Onuchic Interdomain communication revealed in the diabetes drug target mitoNEET.  Proc. Natl. Acad. Sci., 108 2011: 5266-5271

F.M. Ferreira, L.C. Oliveira, G.G. Germino, J.N. Onuchic, and L.F.Onuchic The Macromolecular Assembly of Polycystin-2 Intracytosolic C-Terminal Domain.  Proc. Natl. Acad. Sci., 108 2011: 9833-9828

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  • B.S. Electrical Engineering (1980) Universidade de Sao Paulo
  • B.S. Physics (1981) Universidade de Sao Paulo
  • M.S. Applied Physics (1982) Universidade de Sao Paulo
  • Ph.D. Chemistry (1987) California Institute of Technology
  • Department of BioSciences
  • Department of Chemistry
  • Department of Physics and Astronomy
  • JOSE ONUCHIC has led the biological physics community to devise an integrated picture of a variety of model biochemical and biological systems. His research has expanded across the scales of molecular-level interactions to cellular systems and multi-cellular structures. At Rice he has moved towards medical applications focusing on cancer. In protein folding, he introduced the concept of protein folding funnels. Convergent kinetic pathways, or folding funnels, guide folding to a unique, stable, native conformation. Energy landscape theory and the funnel concept provide the theoretical framework needed to pose and to address the questions of protein folding and function mechanisms. He also works on theory of chemical reactions in condensed matter with emphasis on biological electron transfer. He is also interested in stochastic effects in gene networks with connections to bacteria decision-making and cancer. Currently his group is also focusing on chromatin folding and function.
Email: jonuchic@rice.edu
Phone: (713) 348-4197
Office: BioScience Research Collaborative , 1005F