I have defended my thesis in July, finished some projects at the lab, and now moved to California to join the Sequencing Unit as a principal scientist at Roche Molecular Diagnostics.

I am a fifth-year PhD student in computer science at Carnegie Mellon University, I am interested in algorithms for processing and modeling using high-throughput biological data as well as information visualization. My advisor is Carl Kingsford. I started my undergraduate career in Computational Mathematics and Cybernetics (CMC) at Lomonosov Moscow State University and transferred to University of Maryland in my 3rd year. I received a B.S. in Mathematics and Computer Science in 2007 and M.S. in Computer Science in 2009. After a short break, I joined Maryland's computer science PhD program in the Fall of 2010. I transferred to CMU's computer science program with my advisor in 2012 and defended my thesis in 2015.

Here [pdf].

Try SHARQ - a tool that groups public sequencing experiments by tissue and cell type for easy data access! Have other ideas on how to improve search in Sequence Read Archive? Shoot me an email!

TechNights@CMU session on genome assembly: slides & handouts, some photos.
Slides on preparing your grad school application. Here is another useful resource from Mor Harchol-Balter.
TA, CMSC423, Fall 2011: Bioinformatic Algorithms, Databases, and Tools
TA, CMSC122, Summer 2009: Web Programming

Authors list to Bibtex

1. Rapid Separable Compression Enables Fast Analyses of Sequence Alignments
   D. Filippova, C. Kingsford. ACM BCB. 2015.
   [pdf][webpage]
2. Identification of alternative topological domains in chromatin
   D. Filippova, R. Patro, G. Duggal, C. Kingsford. Algorithms for Molecular Biology. 9:14. 2014.
   [pdf][webpage]
3. Multiscale Identification of Topological Domains in Chromatin
   D. Filippova, R. Patro, G. Duggal, C. Kingsford. WABI 2013.
   [pdf][webpage]
4. ChromoVis: Feature-Rich Layouts of Chromosome Conformation Graphs
   D. Filippova, G. Duggal, R. Patro, and C. Kingsford. Unpublished manuscript.
   [pdf]
5. Resolving Spatial Inconsistencies in Chromosome Conformation Measurements (journal version)
   G. Duggal, R. Patro, E. Sefer, H. Wang, D. Filippova, S. Khuller, and C. Kingsford. Algorithms for Molecular Biology. 8(8):10. 2013.
   [pdf] [webpage]
6. Resolving Spatial Inconsistencies in Chromosome Conformation Data
   G. Duggal, R. Patro, E. Sefer, H. Wang, D. Filippova, S. Khuller, and C. Kingsford. WABI 2012.2
   [pdf] [webpage]
7. Coral: an integrated suite of visualizations for comparing clusterings
   D. Filippova, A. Gadani, C. Kingsford. BMC Bioinformatics. 13(1):276. 2012.
   [pdf] [webpage] [ISMB poster]
8. Dynamic exploration of recording sessions between jazz musicians over time.
   D. Filippova, C. Kingsford, M. Fitzgerald, and F. Benadon. SocialCom 2012.
   [pdf] [website]
9. The Missing Models: a Data-Driven Approach for Learning How Networks Grow.
   R. Patro, G. Duggal, E. Sefer, H. Wang, D. Filippova, and C. Kingsford. In KDD, 2012. Best video.
   [pdf] [website] [video] [KDD poster]
10. Mining Multivariate Accident Data.
    D. Filippova and M. L. Pack. In Transportation Research Board 88th Annual Meeting, pages 1-18, Washington, DC, 2009.
    [pdf] [website]
11. ICE -- Visual Analytics for Transportation Incident Datasets.
    M. L. Pack, K. Wongsuphasawat, M. VanDaniker, and D. Filippova. In IEEE Internation Conference on Information Reuse and Integration, pages 200-205, LasVegas, USA, 2009.
    [pdf] [website]
12. Visual Analytics for Transportation Incident Data Sets.
    K. Wongsuphasawat, M. L. Pack, D. Filippova, M. VanDaniker, and A. Olea. Journal of Transportation Research Board, 2138:135-145, 2009. Best Paper.
    [pdf] [website]
13. Interactive Exploration of Multivariate Categorical Data: Exploiting Ranking Criteria to Reveal Patterns and Outliers.
    D. Filippova and B. Shneiderman. Technical Report HCIL-2009-38, University of Maryland, College Park, 2008.
    [pdf] [website] [software]

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