Mirela Andronescu

Contact coordinates

Mirela Andronescu

Post-doctoral fellow, Noble Lab
Dept. of Genome Sciences
University of Washington
Seattle, WA, USA
andrones at uw dot edu

Curriculum Vitae

Bio

Mirela Andronescu received her B.Sc. in Computational Economics from the Academy of Economic Studies of Bucharest, Romania, in 1999. In 2001, she joined the Deptartment of Computer Science's bioinformatics group of the BETA lab at the University of British Columbia. She received her M.Sc. degree in 2003 and her Ph.D. degree in 2008. Currently, Mirela is an NSERC post-doctoral fellow in Noble lab at the University of Washington's Deptartment of Genome Sciences.

Research

My main research interests are in developing computational tools, statistical methods, machine learning and other algorithms to analyse biological data, including data from high-throughput genome-wide technologies and mass spectrometry data. Some current areas of research include:

• understanding chromatin structure and relation to genome function;
• analysing large genomic and proteomic data sets in the context of various human diseases, including hearing loss, cancers, asthma and sepsis;
• understanding the role of RNA secondary structure in human disease;
• integrating data from multiple data sources;
• using computational methods to obtain better design of high-throughput technologies.

Articles

1. M. Andronescu, A. Condon, H.H. Hoos, D.H. Mathews and K.P. Murphy, Computational approaches for RNA energy parameter estimation, RNA, in press.
2. Z. Duan*, M. Andronescu*, K. Schutz, S. McIlwain, Y.J. Kim, C. Lee, J. Shendure, S. Fields, C.A. Blau, and W.S. Noble, A three-dimensional model of the yeast genome, Nature 2010, 465:363-7 (* equal contribution). [ pubmed | web page | Nature podcast mp3 | Nature podcast html ]
3. D. Tulpan, M. Andronescu, and S. Leger, Free energy estimation of short DNA duplex hybridizations, BMC Bioinformatics 2010, 11:105. [ pubmed ]
4. M. Andronescu*, C. Pop*, and A. Condon, Improved free energy parameters for RNA pseudoknotted secondary structure prediction, RNA 2010, 16(1):26-42. [ pubmed | web page | run HotKnots online ]
5. M. Andronescu and M. Brodie, Decision tree learning using a Bayesian approach at each node, Proceedings of the 22nd Canadian Conference on Artificial Intelligence 2009, Lecture Notes in Artificial Intelligence 2009, 5549: 4-15. [ Springer link ]
6. M. Andronescu, V. Bereg, H.H. Hoos, and A. Condon, RNA STRAND: The RNA secondary structure and statistical analysis database, BMC Bioinformatics 2008, 9(1): 340. [ pubmed | RNA STRAND database ]
7. M. Andronescu, A. Condon, H.H. Hoos, D.H. Mathews, and K.P. Murphy, Efficient parameter estimation for RNA secondary structure prediction, Bioinformatics 2007, 23(13): i19-i28, ISMB/ECCB 2007 (15\% acceptance rate). [ pubmed | CG software ]
8. M. Andronescu and A. Condon, Finding MFE structures formed by nucleic acid strands in a combinatorial set, Nanotechnology: Science and Computing, J. Chen, N. Jonoska. G. Rozenberg (Eds.), Natural Computing Series 2006, Springer, 121-136. [ pdf ]
9. D. Tulpan, M. Andronescu, S.B. Chang, M.R. Shortreed, A. Condon, H.H. Hoos and L.M. Smith, Thermodynamically based DNA strand design, Nucleic Acids Research 2005, 33(15): 4951-4964. [ pubmed ]
10. M.R. Shortreed, S.B. Chang, D. Hong, M. Phillips, B. Campion, D.C. Tulpan, M. Andronescu, A. Condon, H.H. Hoos and L.M. Smith, A thermodynamic approach to designing structure-free combinatorial DNA word sets, Nucleic Acids Research 2005, 33(15): 4965-4977. [ pubmed ]
11. M. Andronescu, Z.C. Zhang and A. Condon, Secondary structure prediction of interacting RNA molecules, Journal of Molecular Biology 2005, 345(5): 987-1001. [ pubmed | MultiRNAFold download | Pairfold online ]
12. M. Andronescu, A.P. Fejes, F. Hutter, H.H. Hoos and A. Condon, A new algorithm for RNA secondary structure design, Journal of Molecular Biology 2004, 336(3): 607-624. [ pubmed | RNA Designer online ]
13. M. Andronescu, R. Aguirre-Hernandez, A. Condon and H. Hoos,
    RNAsoft: a suite of RNA secondary structure prediction and design software tools, Nucleic Acids Research 2003, 31: 3416-3422. [ pubmed | RNAsoft web site ]
14. M. Andronescu, D. Dees, L. Slaybaugh, Y. Zhao, A. Condon, B. Cohen and S. Skiena, Algorithms for testing that sets of DNA words concatenate without secondary structure, Natural Computing 2003, 2(4): 391-415. Also in the Proceedings of the Eighth International Meeting on DNA Based Computers (DNA 8) 2002, Sapporo, Japan. [ Springer link | CombFold online ]

    Theses

15. Computational approaches for RNA energy parameter estimation, Ph.D. thesis, Dept. of Computer Science, University of British Columbia. [ pdf ]
16. Algorithms for predicting the secondary structure of pairs and combinatorial sets of nucleic acid strands, M.Sc. thesis, Dept. of Computer Science, University of British Columbia. [ pdf ]

Software

1. Constraint Generation (CG), algorithm for RNA free energy parameter estimation
2. MultiRNAFold, software for RNA secondary structure prediction
3. RNAsoft, online access to software for RNA/DNA secondary structure prediction and design
4. RNA STRAND, the online RNA secondary STRucture and statistical ANalysis Database

Collaborators

I've had the pleasure to work with some wonderful people, including:

• Bill Noble, Associate Professor, Depts. of Genome Sciences and Computer Science and Engineering, UW
• Tony Blau, Professor of Medicine, UW
• Stan Fields, Professor of Genome Sciences and Medicine, UW
• Jay Shendure, Assistant Professor of Genome Sciences, UW
• Mike Maccoss, Associate Professor of Genome Sciences, UW
• Ed Rubel, Professor of Otolaryngology, UW
  
  
• Anne Condon, Professor of Computer Science, UBC
• Holger Hoos, Professor of Computer Science, UBC
• Dave Mathews, University of Rochester Medical Center
• Kevin Murphy, Associate Professor of Computer Science and Statistics, UBC

Links

Some non-profit organizations that I like and sometimes support:

• Avaaz, the world in action
• Repower America, a project of Al Gore's Alliance for Climate Protection
• David Suzuki Foundation