Some Papers and Preprints

Fluids papers


John Harlim, Mike Oczkowski, James A. Yorke, Eugenia Kalnay, and Brian R. Hunt,

Convex Error Growth Patterns in a Global Weather Model,

PRL (accepted 5/05)


Joseph D. Skufca, James A. Yorke, and Bruno Eckhardt,

The edge of chaos in a parallel shear flow,

Phys Rev Letters 2006







H. W. Hethcote and J. A. Yorke,

Gonorrhea Transmission Dynamics and Control,

Springer-Verlag Lecture Notes in Biomathematics #56, 1984.

(Out of print; copyright now retained by the authors)


Brandy L. Rapatski, Frederick Suppe, and James A. Yorke,

HIV Epidemics Driven by Late Disease-Stage Transmission,

J. AIDS, 38, 2005, 241-253.


Genome papers


Steven L. Salzberg and James A Yorke

Beware of Mis-assembled Genomes

Letter to the editor, (2005) V 21 (no. 24): 4320-4321 Bioinformatics

Michael Roberts, Wayne Hayes, Brian R. Hunt, Stephen M. Mount, James A. Yorke,

Reducing storage requirements for biological sequence comparison [Minimizers],

Bioinformatics, Dec 2004; 20: 3363 - 3369.


Michael Roberts, Brian R. Hunt, and James A. Yorke, Randall Bolanos, and Art Delcher,

A Preprocessor for Shotgun Assembly of Large Genomes,

J Comput Biol. 2004; 11(4), 734-752


Cevat Ustun, Wayne Hayes, Brian Hunt, Michael Roberts, James Yorke, Aleksey V. Zimin and Paul Havlak.

Improving Sequence Assembly of the Rat Genome Using Reliable Overlaps and Extended Reads,



Chaos papers

H. E. Nusse and J. A. Yorke,

Characterizing the basins with the most entangled boundaries,

Ergodic Theory and Dyn. Sys., 2003 23 895-906.


William Ott and J. A. Yorke,


Bull. Amer. Math. Soc. 42, 2005, 263-290.


Joshua A. Tempkin & J. A.Yorke,

Spurious Lyapunov Exponents Computed from Data,



G.-C. Yuan, J.A. Yorke, T.L. Caroll, E. Ott, L.M. Pecora,

Testing whether two chaotic one dimensional processes are dynamically identical,

Phys. Rev. Lett 85, 2000, 4265-4268.


C.M. Danforth and J.A. Yorke

Making Forecasts for Chaotic Physical Processes

Physical Review Letters, 96, 144102 (2006)


Chaotic n-dimensional Euclidean and Hyperbolic Open

Billiards and Chaotic Spinning Planar Billiards

Ali Deniz, Judy Kennedy, Sahin Kocak

Andrei V. Ratiu, Cevat Ustun, James A. Yorke


M. Brin, W. Ott, and J. A. Yorke,

Enveloping manifolds,

Topology and its Applications, 145, 233-239


J. T. Halbert and J. A. Yorke

Taffy Machine

A draft paper for an e-journal