Uwe Ohler's Research Group

Molly Megraw, PhD

Molly Megraw, PhD

Postdoctoral Associate

Location: 2149 CIEMAS
Hometown: Seattle, WA

Research Interests

  • Bioinformatic-experimental approaches to promoter element identification
  • Machine learning approaches to eukaryotic microRNA gene identification
  • Computational analysis of microRNA genomic organization and function

Education

University of Pennsylvania
Ph.D. Genomics and Computational Biology, 2007

Johns Hopkins University
M.S.E. Mathematical Sciences, 1999

University of Washington
B.S. Mathematics, 1996
B.S.E. Interdisciplinary Engineering, Focus: Control Systems, Mechanical Engineering, 1996

Publications

Research Articles

Petricka JJ, Schauer MA, Megraw M, Breakfield NW, Thompson JW, Georgiev S, Soderblom EJ, Ohler U, Moseley MA, Grossniklaus U, Benfey PN (2012). The protein expression landscape of the Arabidopsis root. PNAS, 109:6811-8.

Brady SM, Zhang L, Megraw M, Martinez NJ, Jiang E, Yi CS, Liu W, Zeng A, Taylor-Teeples M, Kim D, Ahnert S, Ohler U, Ware D, Walhout AJM, Benfey P (2011). A Stele-Enriched Gene Regulatory Network in the Arabidopsis Root. Molecular Systems Biology, 7:459.

Iizasa H, Wulff BE, Alla NR, Maragkakis M, Megraw M, Hatzigeorgiou A, Iwakiri D, Takada K, Wiedmer A, Showe L, Lieberman P, Nishikura K (2010). Editing of Epstein-Barr virus-encoded BART6 microRNAs controls their dicer targeting and consequently affects viral latency. J Biol Chem, 285:33358-70.

Megraw M, Sethupathy P, Gumireddy K, Jensen ST, Huang Q, Hatzigeorgiou AG. (2009). Isoform specific gene auto-regulation via miRNAs: a case study on miR-128b and ARPP-21. Theoretical Chemistry Accounts, Advance Online Publication, DOI:10.1007/s00214-009-0647-4.   [Link to Preprint]

Megraw M, Pereira F, Jensen ST, Ohler U, Hatzigeorgiou AG. (2009). A transcription factor affinity based code for mammalian transcription initiation. Genome Research, 19:644-56.   [Link to Supplementary Material]

Alexiou P, Vergoulis T, Gleditzsch M, Prekas G, Dalamagas T, Megraw M, Grosse I, Sellis T, Hatzigeorgiou AG (2009). miRGen 2.0: a database of microRNA genomic information and regulation. Nucleic Acids Research, 38:D137-D141.

Kawahara Y, Megraw M, Kreider E, Iizasa H, Valente L, Hatzigeorgiou AG, Nishikura K (2008). Frequency and fate of microRNA editing in human brain. Nucleic Acids Research, 36:5270-80.

Zhang L, Volinia S, Bonome T, Calin GA, Greshock J, Yang N, Liu CG, Giannakakis A, Alexiou P, Hasegawa K, Johnstone CN, Megraw MS, Adams S, Lassus H, Huang J, Kaur S, Liang S, Sethupathy P, Leminen A, Simossis VA, Sandaltzopoulos R, Naomoto Y, Katsaros D, Gimotty PA, DeMichele A, Huang Q, B├╝tzow R, Rustgi AK, Weber BL, Birrer MJ, Hatzigeorgiou AG, Croce CM, Coukos G (2008). Genomic and epigenetic alterations deregulate microRNA expression in human epithelial ovarian cancer. PNAS, 105:7004-9.

Megraw M, Sethupathy P, Corda B, Hatzigeorgiou AG (2007). miRGen: A database for the study of animal microRNA genomic organization and function. Nucleic Acids Research, 35:D149-D155.   [Link to miRGen]

Sethupathy P, Megraw M, Hatzigeorgiou AG (2006). A guide through current computational approaches for the identification of mammalian microRNA targets. Nature Methods, 3:881-6.   [Link to TargetCombo website]

Megraw M, Baev V, Rusinov V, Jensen ST, Kalantidis K, Hatzigeorgiou AG (2006). MicroRNA promoter element discovery in Arabidopsis. RNA, 12:1612-9.   [Link to Supplementary Material]

Zhang L, Huang J, Yang N, Greshock J, Megraw MS, Giannakakis A, Liang S, Naylor TL, Barchetti A, Ward MR, Yao G, Medina A, O'brien-Jenkins A, Katsaros D, Hatzigeorgiou A, Gimotty PA, Weber BL, Coukos G (2006). microRNAs exhibit high frequency genomic alterations in human cancer. PNAS, 103:9136-41.

Szafranski K, Megraw M, Reczko M, Hatzigeorgiou AG (2006). Support Vector Machines for Predicting microRNA Hairpins. Proceedings of the 2006 International Conference on Bioinformatics and Computational Biology, 270-276.

Book Chapters

Hatzigeorgiou AG, Megraw M (2010). MicroRNA Promoter Analysis. In Methods in Molecular Biology: Plant MicroRNAs, ed. Blake Meyers and Pamela Green, Humana Press.   [Link to Supplementary Material]

Sethupathy P, Megraw M, Hatzigeorgiou AG (2006). Computational approaches to elucidate microRNA biology. In microRNAs: From Basic Science to Disease Biology, ed. Krishnarao Appasani, Cambridge University Press.

Hatzigeorgiou AG, Megraw M (2006). Computational Analysis of Human DNA Sequences: An Application of Artificial Neural Networks. In Global Optimization, Scientific and Engineering Case Studies, ed. Janos Pinter, Springer.

Sethupathy P, Megraw M, Barrasa MI, Hatzigeorgiou AG (2005). Computational Identification of Regulatory Factors Involved in MicroRNA Transcription. Lecture Notes in Computer Science, 3746:457-468.

Hatzigeorgiou AG, Megraw M (2005). Analysis of DNA Sequences: Hunting for Genes. In Information Processing & Living Systems, ed. Vladimir Bajic and Tan Tin Wee, World Scientific Publishing.

Outside Interests/Hobbies

Hiking, skiing, tennis, juggling.