Lab pages

Magnasco's current CV

The old page follows.

Employment
 

Aug 2003-		Professor and Head of Lab, Rockefeller University
Jul 2002-           Jul 2003		Research Scientist, Abdus Salam International Centre for Theoretical Physics, UNESCO Trieste, Italy. (On sabbatical leave of absence from RU)
Jan 1999- Jul 2003		Associate Professor and Head of Lab   Rockefeller University
Dec 1993-  Dec 1998		Assistant Professor and Head of Lab, Rockefeller University
Jan 1992- Dec 1993		Postdoctoral Fellow, Rockefeller University (under M. J. Feigenbaum) and Visiting Scientist, NEC Research Institute (under A. J. Libchaber and P. A. Wolff)
1991		William Rayney Harper Dissertation Fellow (best PhD thesis in the Physical Sciences Division) and Sydney Bloomenthal Dissertation Fellow (best PhD thesis in the Physics Department) The University of Chicago
Sep 1988- Dec 1991		Research Assistant, (under L. P. Kadanoff), The James Frank Institute,  Teaching Assistant, Kersten Physics Teaching Center The University of Chicago .

Thesis advised

• Guillermo A. Cecchi. Towards a song code: representations of song in the canary brain. PhD thesis, Rockefeller University, 1999
• Yong Choe, The role of mechanotransduction in osmoreception and auditory amplification Ph. D.  thesis, Rockefeller University, April 2002. (co-advised; principal advisor Jim Hudspeth)
• Mariano Sigman, How the brain learns and constructs the structure of the world. Ph. D. thesis, Rockefeller University, April 2002 (jointly advised with Charles Gilbert)
• Timothy Gardner, Ph. D. Vocal Analysis and Learning Mechanisms for Canary Song. Ph. D. thesis, Rockefeller University, Sept 2002

Lab members

Publications (also - download pdfs - see recent - preprints available - citations )

1. ``A Universal Departure from the Classical Period-Doubling Spectrum", D.L. Gonzalez, M.O. Magnasco, G.B. Mindlin, H. Larrondo and L. Romanelli. Physica D 39 111-123 (1989) [PDF]
2. ``On the Universality Class Dependence of Period Doubling Indices", M. Feingold, D.L. Gonzalez, M.O. Magnasco and O. Piro, Phys. Lett.A 156, 272 (1991) [PDF]
3. ``From disks to hexagons and beyond: a study in two dimensions", J. M. Flesselles, M. Magnasco and A. Libchaber, Phys. Rev. Lett.67.18, 2489-2493 (1991) [PDF]
4. ``Two Dimensional Bubble Rafts", M.O. Magnasco, Phil. Mag. B 65.5 895-920 (1992) [PDF]
5. ``Periodically Kicked Hard Oscillators ", G.A. Cecchi, D.L. Gonzalez, M.O. Magnasco, G.B. Mindlin, O. Piro and A. Santillan. Chaos3.1 51-62 (1993) [PDF]
6. ``Determinism and Stochasticity in Ideal 2-Dimensional Soap Froths", V. Fradkov, M. Magnasco, D. Udler and D. Weaire. Phil. Mag. Lett. 67 203-211 (1993) [PDF]
7. ``Forced Thermal Ratchets'', M. Magnasco. Phys. Rev. Lett. 71.10 1477-1481 (1993) [PDF][clips]
8. ``Measurement of the Persistence Length of Polymerized Actin using Fluorescence Microscopy'', A. Ott, M. Magnasco, A. Simon and A. Libchaber, Phys. Rev. E 48.3 R1642 (1993) [PDF][errata]
9. ``Correlations in Cellular Patterns'', M. Magnasco. Phil. Mag. B 69.3 397 (1994) [PDF]
10. ``Brownian Combustion Engines'', M. Magnasco, in Fluctuations and Order: The New Synthesis (M. Millonas, ed.) Springer-Verlag 1994
11. ``Molecular Combustion Motors'', M. Magnasco. Phys. Rev. Lett. 72.16 2656 (1994) [PDF][clips]
12. ``Actin filaments on myosin beds: The velocity distribution", L. Bourdieu, M. O. Magnasco, D. A. Winkelmann and A. Libchaber, Phys. Rev. E 52.6 (Dec 1995) [PDF]
13. ``Szilard's Heat Engine'', M. Magnasco. Europhys. Lett. 33(8) 583-588 (1996) [PDF]
14. ``Negative Resistance and Rectification in Brownian Transport'', G. A. Cecchi and M. Magnasco, Phys. Rev. Lett. 76.11 1968-1971 (1996) [PDF]
15. ``Changing the Pace of Evolution'', M. Magnasco and D. Thaler, Phys. Lett. A. 221(5):287-292 (1996) [PDF][clips]
16. ``Chemical Kinetics is Turing universal'', M. Magnasco, Phys. Rev. Lett.. 78(6):1190-1193, 1997 Feb 10. [PDF]
17. ``Feynman's Ratchet and Pawl'', M. O. Magnasco and G. Stolovitzky. J. Stat. Phys. 93.3/4 615 (1998) [PDF]
18. ``Towards a song code: evidence for a syllabic representation in the canary brain'', S. Ribeiro, G. A. Cecchi, M. O. Magnasco and C. V. Mello. Neuron 21.2 359 (1998) [PDF][cover][review][clips]
19. ``A model for amplification of hair-bundle motion by cyclical binding of Ca2+ to mechanoelectrical-transduction channels'', Y. Choe, M. Magnasco and A. J. Hudspeth, Proc. Natl. Acad. Sci. USA 95 15321-15326 (1998) [PDF]
20. ``Contingency loci, mutator alleles and their interactions: Synergistic strategies for microbial evolution and adaptation in pathogenesis'', D. Field, M. Magnasco, E. R. Moxon, D. Metzgar, M. M. Tanaka, C. Wills and D. S. Thaler, Ann. NY Acad Sci 870 378-382 (1999) [PDF]
21. ``An automated procedure for the mapping and quantitative analysis of immunocytochemistry of an inducible nuclear protein'', G. A. Cecchi, S. Ribeiro, C. V. Mello and M. O. Magnasco. J. Neurosci. Methods 87 147-158 (1999) [PDF]
22. ``A kinetic proofreading mechanism for disentanglement of DNA by topoisomerases`', Jie Yan, Marcelo Magnasco and John Marko, Nature401932 (1999) [PDF]
23. ``Noise-induced memory in extended excitable systems'', D.R. Chialvo, G. A. Cecchi, M. O. Magnasco, Phys. Rev E 61.5 5654-5657 (2000) [PDF]
24. ``Noise in neurons is message-dependent'', Guillermo Cecchi, Mariano Sigman, Jose Manuel Alonso, Luis Martinez, Dante Chialvo and Marcelo Magnasco, Proc. Natl. Acad. Sci. USA 97.10 5557-5561 (2000) [PDF]
25. ``Essential nonlinearities in hearing'', V. M. Eguiluz , M. Ospeck , Y. Choe , A. J. Hudspeth and M. O. Magnasco, Phys. Rev. Lett. 84.22 5232-5236 (2000) [PDF][clips]
26. ``On a common circle: natural scenes and Gestalt rules'', Mariano Sigman, Guillermo Cecchi, Charles Gilbert and Marcelo Magnasco, Proc. Natl. Acad. Sci. U.S.A. 98 1935 (2001)  [PDF] (was cond-mat/0105097)
27. ``Kinetic Proofreading Can Explain the Supression of Supercoiling of Circular DNAs by Type-II Topoisomerases'', Jie Yan, Marcelo O. Magnasco, and John F. Marko, Phys. Rev. E. 63.2 (2001) [PDF]
28. ``Evidence of a Hopf bifurcation in Frog Hair Cells'', M. Ospeck, V. M. Eguiluz, M. O. Magnasco, Biophys. J. 80.6 2597 (2001) [PDF]
29. ``Unsupervised learning and adaptation in a model of adult neurogenesis'', Guillermo Cecchi, Leooldo Petreanu, Arturo Alvarez-Buylla and Marcelo Magnasco, cond-mat/0105070, J. Comp. Neurosci 11 175-182 (2001) [ PDF ]
30. ``Simple motor gestures for birdsong'', T. Gardner, G. Cecchi, M. Magnasco, R. Laje and G. Mindlin, Phys. Rev. Lett., 87208101 (2001) [ PostScript PDF ] [clips]
31. ``Bailout embeddings, Targetting of KAM orbits, and the Control of Hamiltonian Chaos'', J. H. E. Cartwright, M. O. Magnasco and O. Piro. nlin.CD/0111005  , Phys Rev. E. Rapp Comm 6504.4 043-046 (2002) [ PDF ]
32. ``Characterization of the expression ratio noise structure in high-density oligonucleotide arrays'', F. Naef, C. R. Hacker, N. Patil and M. Magnasco,  Genome Biology (2002) [ PDF ]
33. ``Noise and Inertia-induced inhomogeneity in the distribution of small particles in fluid flows'',  J. H. E. Cartwright, M. O. Magnasco and O. Piro. nlin.CD/0111008., Chaos 12.2 489-495 (2002) [ PDF ]
34. ``DNA hybridization to mismatched templates: a chip study", F. Naef, D. Lim, N. Patil and M. Magnasco, physics/0111199 .  Phys. Rev. E. Rapp. Comm. 6504.4 038-041 (2002) [ PDF ]
35. “Bailout embeddings and neutrally buoyant particles in three-dimensional flows”, J.H.E. Cartwright, M. O. Magnasco, O. Piro and I. Tuval, Phys. Rev. Lett. 89, 264501 (2002) [ PDF ]
    
36. “Hopf bifurcations and hair cells”, M. Ospeck, V. Martinez-Eguiluz and M. Magnasco, Comments on Theoretical Biology, 6, 461-482 (2002) [ PDF ]
    
37. “Noise-induced order out of chaos by bailout embedding”, J.H.E. Cartwright, M. O. Magnasco, O. Piro and I. Tuval, Fluctuation and Noise Letters, 2 (4), R161-R174 (2002) [ PDF ]
    
38. “A study of accuracy and precision in oligonucleotide arrays: extracting more signal at high concentrations”, F. Naef, N. D. Socci, and M. O. Magnasco, Bioinformatics 19: 178-184. (2003) [ PDF ]
    
39. “A wave traveling over a Hopf instability shapes the cochlear tuning curve”, M. Magnasco, physics/0111204, Phys. Rev. Lett. 90.5 058101 (2003)  [ PDF ]
40. “Absolute mRNA concentrations from sequence-specific calibration of oligonucleotide arrays” D.Hekstra, A. Taussig, F. Naef and M. Magnasco, Nucl. Acid  Res. 31(7), 1962-1968 (2003)  [  PDF ]
41. “Solving the riddle of the bright mismatches: Labeling and effective binding in oligonucleotide arrays”, Naef F, Magnasco MO. Phys. Rev. E, 6801(1) 531-534 (2003)  [  PDF ]
42. “Decay rates of human mRNAs: Correlation with functional characteristics and sequence attributes.”, Yang E, van Nimwegen E, Zavolan M, Rajewsky N, Schroeder M, Magnasco M, Darnell JE Jr. Genome Res. 13(8):1863-1872 (2003) [ PDF ]
43. “Bubbling and on-off intermittency in bailout embeddings.” Julyan H. E. Cartwright, Marcelo O. Magnasco, Oreste Piro, and Idan Tuval , Phys. Rev. E 68, 016217 (2003)  [ PDF ]
44. “Production of ribosome components in effector CD4⁺ T cells is accelerated by TCR stimulation and coordinated by ERK-MAPK”, M. Asmal, J. Colgan, F. Naef, Yu B., Lee Y., M. O. Magnasco and J. Luban, Immunity  19.4  535-548 (2003) [ PDF ]
45. “Virtual gating and nuclear transport: the hole picture", Rout MP, Aitchison JD, Magnasco MO, Chait BT, Trends Cell Biol 13.12 622-628   (2003) [ PDF ]
46. "Instantaneous frequency decomposition: An applicatioin to spectrally sparse sounds with fast frequency modulations " T. J. Gardner and M. O. Magnasco , J. Acoust. Soc. Am. 117 2896 (2005) [ PDF ]
47. "Comparing independent microarray studies: the case of human embryonic stem cells" Mayte Suarez-Farinas, Scott Noggle, Michael Heke, Ali Hemmati- Brivanlou and Marcelo O Magnasco, BMC Genomics 6.99 doi:10.1186/1471-2164-6-99 (2005) [ PDF ]
48. "Computational models of adult neurogenesis" Guillermo Cecchi and Marcelo O. Magnasco,Physica A 356 43-47 (2005) [ PDF ]
49. "In vivo transcriptional profile analysis reveals RNA splicing and chromatin remodeling as prominent processes for adult neurogenesis" Daniel A. Lim, Mayte Suarez-Farinas, Felix Naef, Coleen R. Hacker, Benedicte Menn, Hirohide Takebayashi, Marcelo Magnasco, Nila Patil, and Arturo Alvarez-Buylla Molecular and Cellular Neuroscience 31 131-148 (2006) [ PDF ]
50. "Harshlight: a "corrective make-up" program for microarray chips" Mayte Suarez-Farinas, Maurizio Pellegrino, Knut M. Wittkowski2 and Marcelo O. Magnasco, BMC Bioinformatics 6:294 doi:10.1186/1471-2105-6-294 (2006) [ PDF ]
51. "Sparse Time-Frequency Representations",Timothy J. Gardner and Marcelo O. Magnasco Proc. Natl. Acad. Sci. USA103.16 6094-6099 (2006) [ PDF ]

1. ``The thunder of distant Net storms'' M. O. Magnasco, nlin/0010051.
2. ``EGR-1 is over-expressed at the reperesentation of central field in the opposum striate cortex'', R. Pinaud, C.D. Vargas, S. Ribeiro, M. V. Monteiro, G. Cecchi, M. O. Magnasco, P. Delgado, C. V. Mello, C. E. Rocha-Miranda and E. Volchan,  submitted.
3. ``The systematics of Huckel'', M. Magnasco and P. A. Wolff (in preparation).

1. S. Ribeiro, G. Cecchi, M. Magnasco and C. V. Mello. Soc. for Neurosci. Meeting extended abstract, (1996).
2. ``Representation of song-specific features of song in the auditory forebrain of the canary'', S. Ribeiro, G. Cecchi, M. Magnasco and C. V. Mello. Soc. for Neurosci. Meeting extended abstract, (1997).
3. ``Automated mapping of immediate early gene induction patterns at cellular resolution'', G. Cecchi, S. Ribeiro, C. V. Mello and M. O. Magnasco. Soc. for Neurosci. Meeting extended abstract, (1997)
4. ``Analysis of a syllabic representation in the brain of canaries'' G. A. Cecchi, S. Ribeiro, C. V. Mello and M. Magnasco. Soc for Neurosci Meeting extended abstract (1998), and Forum of European Neurosci. extended abstract (1998)
5. ``Ontogenesis of syllabic maps in the caudomedial neostriatum of canaries'', S. Ribeiro, G. A. Cecchi, M. Magnasco and C. V. Mello. Soc for Neurosci. Meeting extended abstract (1998)
6. ''Analysis of a syllabic representation in the brain of canaries'', Cecchi GA, Ribeiro S, Mello CV, Magnasco MO. EUR J NEUROSCI 1998;10:411
7. Ontogenesis of syllabic maps in the caudomedial neostriatum of canaries. Ribeiro S, Cecchi GA, Magnasco MO, Mello CV.  EUR J NEUROSCI 1998 10 408
8. ``The evolution of evolutionary engines'', Marcelo Magnasco, in Complexity from microscopic to macroscopic scales,  A. Skjeltorp, ed., Kluwer (2002) [ PDF ]
9. ``Three lectures on biological networks: enzymatic, genetic and neural", to appear in proc. Les Houches.
10. ``From features to expression: High-density oligonucleotide array analysis revisited'', F. Naef, D. A. Lim, N. Patil, and M. O. Magnasco, physics/0102010 , (which was to appear in the proceedings to the DIMACS Workshop on Analysis of Gene Expression Data that were not published) [ PDF ]
11. Lim DA , Suarez-Farinas M , Naef F , Menn B , Hacker C , Magnasco M , Patil N , Alvarez-Buylla A, Biological insights from the transcriptional profiles of adult mouse subventricular zone (SVZ) stem cell neurogenesis.   NEURO-ONCOLOGY 2004 OCT;6(4):347

1. L. Faucheux, G. Stolovitzky and A. Libchaber, ``Periodic forcing of a Brownian particle'', Phys. Rev. E 51, 5239-5250 (1995).
2. G. Stolovitzky, T. Kapper and L. Sirovich, ``A simple model for chaotic advection and scattering'', Chaos, 5 671-686 (1995).
3. D. Brunner, S. Fairhurst, G. Stolovitzky and J. Gibbon, ``Mnemonics for variability: Remembering food delay'', J. Exp. Psych.: Animal Behavior Processes (in press), (1996).
4. G. Stolovitzky and G. Cecci, ``Efficiency of DNA replication in the Polymarase Chain Reaction'', Proc. Natl. Acad. Sci. U.S.A., 93, 12947-12952, (1996)
5. K. R. Sreenivasan and G. Stolovitzky, ``Statistical dependence of inertial range properties on the large scale in high-Reynolds-number shear flows'', Phys. Rev. Lett., 77 , 2218-2221, (1996).
6. M. Nelkin and G. Stolovitzky, ``Limitations of random multipliers in describing turbulent energy dissipation'', Phys. Rev. E, 54 , 5100-5106 (1996)
7. G. Stolovitzky, ``An exact result concerning the energy balance in turbulent flows'', in preparation (1997) (draft available).
8. G. Stolovitzky, G. Bonet and A. Libchaber ``Probing the elasticity of double-stranded poly(A:T) with molecular beacons'', in preparation (1997).
9. G. Stolovitzky and G. Cecchi ``Quantitative results on the decrease of efficiency of PCR due to competition between primer-template and template-template hybridization'', in preparation (1997).

• Maddox, J. Nature 365203 (Sept 1993)
• Maddox, J. Nature 368287 (March 1994)
• Schewe, F. Physics News Update173 (Apr 1994)
• Council of Engineering Bulletin No. 258, Yale (Apr 1994)
• Leibler, S. Nature 370 412 (Aug 1994)
• Simon, S. Nature 371 103 (Sept 1994)
• Moxon, E. R.  and Thaler, D. Nature 387 (1997)
• G. F. Ball and T. Q. Gentner, Neuron (minireview) 21.2 271 (1998)
• Henry Gee, Nature Japan (bionews) (Sep 24 1998)
• Complexity Digest 18 (May 13 2000)
• Ball, P. Nature Science Update (6 June 2000)
• Cho, A. Science 288(5473) 1954 (2000)
• Ball, P. Nature Science Update, (8 November 2001)

Recent stays

• May 2000 (1mo) Visiting Professor, Universitat delles Illes Balears, Mallorca, Spain (visiting Oreste Piro)
• Feb 2001 (2wks) Visiting Professor, IMPA, Rio de Janeiro (visiting Jacob Palis)
• Apr 2001 (2wks) NATO conference, Geilo, Norway
• May 2001 (1mo) Visiting Professor, Ecole Normale Superieure, Paris (visiting Yves Couder)
• June 2001 (1mo)  Visiting Professor, Universitat delles Illes Balears, Mallorca, Spain (visiting Oreste Piro)
• Aug 2001 (3wks) Aspen Center for Physics Summer School in enzymatic networks.