John E. Karro

"Marching to a different kettle of fish."
John Karro
Research Associate

Center for Comparitive Genomics and Bioinformatics
Pennsylvania State University
University Park, PA 16802

Phone: (814) 466-2049

Email: jkarro at acm dot org
Office: 506B Wartik

Profession Experience and Degrees

Assistant Professor, Miami University (Computer Science and Systems Analysis, Microbiology (affiliate), 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)
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)

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)

Areas of Research Interest

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

Biographical Sketch

I received a BS degree in Mathematics and Computer Science from the College of William and Mary in 1994, my masters in Computer Science from the University of Virginia in 1997, and my Ph.D. in 2000 (also at the University of Virginia). From 2000 to 2003 I taught in the Computer Science program at Oberlin College, as position which I left to take a position at in the Molecular Biophysics and Biochemistry at Yale University to re-focus my research into bioinformatics. In 2004 I received an NIH fellowship to support this research at the Pennsylvania State University Center for Computational Genomics and Bioinformatics, where I will remain through June, 2007. For further information, see my vitae.

Research

Current research projects:

Neutral substitution rate variation at the genomic level.
Identification of genomic regions under selective pressure.
Identification and dating of large-scale genomic duplications.
Reconstruction of the mammalian ancestral genome.
Investigation of the phylogenetic history of the Calpain protein family.
Collaboration on the Macaque project -- an analysis of the first published sequence of the Rhesus monkey.

Family

Wife: Laura
Daughter: Alexandra Constance (16 months old)
Daughter: Samantha Eleanor (0.25 months old)
Dogs: Loki (German Shepard), Finnegan and Delilah (Chesapeake Bay Retrievers)

Other Interests and Hobbies

Travel
Dancing (East Coast and West Coast Swing)
Cooking
Bridge and Chess
Oceanic Air, Flight 815
Dogs

Publications

Peifer, M., Karro, J.E. and von Gruenberg, H.H., "Evidence againt the acceleration of the CpG transition rate during the mammalian radiaton", 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 review)

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

The Rhesus Macaque Genome Sequence and Analysis Consortium, "The Thesus Macaque Genome Sequence Informs Biomedical and Evolutionary Analysis", Science, v. 316, April 2007, pp. 222-234

Karro, J., Yan, Y., Zheng, D., Zhaolei, Z., Carriero, N., Harrison, P. and Gerstein, M., " Pseudogene.org: A comparison platform and comprehensive resource for pseudogene annorations", Nucleic Acids Research, v. 35(Database issue), Jan. 2007, pp.D55-60
Zheng, Z., Carriero, N., Zhang, D., Karro, J., Harrison, P. and Gerstein, M., "PseudoPipe: an automated pseudogene identification pipeline", Bioinformatics , v. 22(1), June 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
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
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.

"The goal of Computer Science is to build something that will last at least until we have finished building it."

Last modified Nov. 3, 2006