Papers    &    Presentations

High sensitivity to aligner and high rate of false positives in the estimates of positive selection in the 12 Drosophila genomes. Markova-Raina P, Petrov D. 2011. Genome Research (in press).

Regions lacking stable 3D structure are the primary source of alignment ambiguities and indels in Drosophila proteins. Markova-Raina P, Petrov D. In submission.

Fast and furious evolution of the unstructured protein regions in Drosophila. Markova-Raina P, Petrov D. In submission.

Evidence that selection on synonymous sites is non-uniform and sometimes strong. Hershberg R, Markova-Raina P, Zhu Y, Petrov D. In preparation.

Inferred positive selection, alignment quality and intrinsically disordered protein regions. Markova-Raina P, Petrov D. Contributed poster, SMBE 2010.

Robust genome-wide evolutionary analysis in the presence of misalignments, and scaling evolutionary analysis with graphics processors. Markova-Raina P, Petrov D. Contributed poster, SMBE 2009.

The choice of aligner significantly impacts the estimates of positive selection in the 12 Drosophila genomes genes. Markova-Raina P, Petrov D. Contributed talk, SMBE 2008.

Protein evolution in the context of Drosophila. Davis J, Brandman O, Markova P, Petrov D. Contributed talk, SMBE 2005.

The Leaf Projection Path View of Parse Trees: Exploring String Kernels for HPSG Parse Selection. Toutanova K, Markova P, Manning C. In proceedings of EMNLP 2004.

Incremental methods for computing word pair similarity. Farahat A, Pirolli P, Markova P. TR-04-6-2004, Palo Alto Research Center.

Increasing Realized Revenue Via Profit Redistribution: A Variant of Online Dutch Auction. Markov M, Markova P, Mohania M, Kambayashi Y. EC-WEB September 2003. Lecture Notes in Computer Science, Vol. 2738, 2003.

iROS: A Meta-operating System for Interactive Workspaces. Johanson B, Ponnekanti S, Kiciman S, Markova P, Fox A. Contributed poster, ACM Symposium on Operating Systems Principles 2001.