John Karro
Assistant Professor

EDUCATION:

Ph.D.: University of Virginia (Computer Science, 2000)
M.C.S.: University of Virginia (Computer Science, 1997)
B.S.: College of William and Mary (Mathematics, 1994)

ACADEMIC EXPERIENCE:

Assistant Professor, Miami University (Computer Science and Systems Analysis, Microbiology, 2007 - present)
Research Associate, Pennsylvania State University (Biology, 2004-2007)
Postdoctorial Fellow, Yale University (Molecular Biophysics and Biochemistry, 2003-2004)
Assistant Professor, Oberlin College (Computer Science, 2000-2003)

AWARDS AND HONORS:

Primary Investigator, National Institute of Health K01 Grant (awarded 2004)
Co-investigator, NSF Research Award, Major Research Instrumentation Program (awarded 2004)
NSF AIRE Curriculum Development Grant (Oberlin College, 2002)
Outstanding Teaching Graduate Student (University of Virginia, 1997)
Virginia Space Grant Consortium Aeorspace Graduate Research Fellowship (University of Virginia, 1996-2000)
High Honors in Mathematics (College of William and Mary, 1994)

PUBLICATIONS AND PAPERS:

Peifer, M., Karro, J.E. and von Gruenberg, H.H., "Evidence againt the acceleration of the CpG transition rate during the mammalian radiation", Molecular Biology and Evolution (in review)

Tyekucheva, S., Moakova, K., Karro, J., Hardison, R., Miller, W. and Chiaromonte, F., "Human-macaque comparisons illuminate variation in neutral substitution rates," Genome Research (in preparation)

Karro, J.E., Peifer, M., Hardison, R.C., Hellmann, M. and von Gruenburg, H.H., "Exponential decay of GC-content detected by strand-symmetric substitution rates influences the evolution of isochore structure", Molecular Biology and Evolution (in review)

The Rhesus Macaque Genome Sequencing and Analysis Consortium, “Evolutionary and biomedical insights from the rhesus macaque genome”, Science, v. 316, April 2007, pp. 222-234

Karro, J.E., Yan, Y., Zheng, D., Zhaolei, Z., Carriero, N.,  Cayting, P., Harrison, P. and Gerstein, M., “Pseudogene.org: A comparison platform and comprehensive resource for pseudogene annotations”, Nucleic Acids Research, v.35(Database issue) Jan. 2007,  pp. 55-60

Zheng, Z., Carriero, N., Zhang, D., Karro, J., Harrison, P. and Gerstein, M., “PseudoPipe: an automated pseudogene identification pipeline”, Bioinformatics, v. 22(12), 2006, pp. 1437-9

Bertone, P, Trifonov, V., Rozowsky, J., Schubert, F., Emanuelsson, O., Karro, J., Kao, M.Y., Snyder, M. and Gerstein, M., “Design optimization methods for genomic DNA tiling arrays”, Genome Research, v. 16(2), Feb. 2006, pp. 271-81

Karro, J., Peifer, M., Kollman, M., Timmer, J., Hardison, R., Miller, W., von  Grünberg, H.H., “Time-averaged neutral substitution rate variation over the genomes of modern mammals and the mammalian ancestor”, Biology of Genomes (2006), Cold Spring Harbor Laboratory (poster presentation)

Zheng, D., Zhang, Z., Harrison, P.M., Karro, J., Carriero, N. and Gerstein, M., “Integrated pseudogene annotation for human chromosome 22: evidence for transcription”, Journal of Molecular Biology, v. 349(1), May 2005, pp. 27-45

Karro, J, Haussler, D. and Miller, W, “Removing Duplications for the Reconstructions of the Placental Mammalian Ancestor Genome”, Biology of Genomes (2005), Cold Spring Harbor Laboratory (poster presentation)

Yu, H., Zhu, Xiaowei, Greenbaum, D., Karro, J., and Gerstein, M., “TopNet: a tool for comparing biological sub-networks, correlating protein properties with topological statistics”, Nucleic Acids Research, v. 32(1), 2004, pp. 328-337

J. Cohoon, J. Karro and J. Lienig, "Evolutionary Algorithms for the Physical Design of VLSI Circuits: A Survey," Theory and Applications of Evolutionary Computation: Recent Trends, Ghosh, A. and Tsturi, S., Springer-Verlag, to be published.

J. Karro and J. Cohoon, "Gambit: A Tool for the Simultaneous Placement and Detailed Routing of Gate-Arrays," 11th International Conference on Field Programmable Logic and Applications, Belfast, Northern Ireland, Aug. 2001, pp. 243-253.

J. Karro and J. Cohoon., An Approach to the Physical Design Problems of 3D-FPGAs," International Symposium on Circuits and Systems, Iasi, Rumania, July 1999, pp. 69-72.

J. Karro and J. Cohoon, "A Spiffy Tool for the Simultaneous Placement and Global Routing for Three-Dimensional Field Programmable Gate Arrays," Ninth Great Lakes Symposium on VLSI, Ann Arbor, Michigan, March 1999, pp. 226-227

J. Cohoon, J. Karro, W. Martin, K. Nagel, and W. Neible, "Perturbation method for probabilistic search for the Traveling Salesperson Problem," (invited paper) Application and Science of Neural Networks, SPIE 1998, pp. 118-127.

J.L. Pfaltz, J. Karro and S. McCulloch, "Distance in Anti-Matroids," Congressus Numerantium, 1997, pp. 5-22.

J. Karro and C.K. Li," A Unified Elementary Approach to Cononical Forms of Matricies," SIAM Review, 39:2, June 1997, pp. 305-309.

M. Alexander, J.P. Cohoon, J. Karro, E.L. Peters, and G. Robins, "Placement and Routing for Three-Dimensional FPGAs", Fourth Canadian Workshop on Field-Programmable Devices, Toronto, Canada, May 1996, pp. 11-18.

M. Alexander, J.P. Cohoon, J. Karro, E.L. Peters, and G. Robins, "Physical Layout for Three-Dimensional FPGAs," ACM/SIGDA Physical Design Workshop, Reston, VA, April 1996, pp. 142-149. M. Alexander, J. P. Cohoon, J. L. Colflesh, J. E. Karro, and G. Robins, "Three-Dimensional Field-Programmable Gate Arrays," Proceedings of the IEEE International ASIC Conference, Austin, TX, September 1995, pp. 253-256.

MAJOR INTEREST AREAS:

• Computational Biology
  • Comparative Genomics
  • Molecular Evolution
  • Population Genetics
• Algorithms and design automation
• Closure spaces and anti-matroids
• Computational geometry
• Probabilistic search methods and evolutionary computation
• Complexity theory