Faculty Guide

Title

Associate Professor of Computer Science

Computer Science
Volen National Center for Complex Systems

Expertise

Computer Science

Awards and Honors

Theodore and Hane Norman Junior Faculty Research Leave (2008)

Courses Taught

COSI	29a	Discrete Structures
COSI	101a	Fundamentals of Artificial Intelligence
COSI	123a	Statistical Machine Learning
COSI	178a	Computational Molecular Biology

Scholarship

Bei Y. and Hong P.. "Significance Analysis by Minimizing False Discovery Rate." The IEEE International Conference on Bioinformatics and Biomedicine., Philadelphila, PA, USA. October 2012.

Sun X., Hong P., Kulkarni M., Kwon Y., and Perrimon N.. "An Advanced Method for Identifying Protein-Protein Interaction by Analyzing TAP/MS Data." The IEEE International Conference on Bioinformatics and Biomedicine, Philadelphila, PA USA. October 2012.

Anick, P., Hong, P., Xue, N. & Yang, Y.. "Coreference resolution for electronic medical records." the 2011 i2b2/VA/Cincinnati Workshop on Challenges in Natural Language Processing for Clinical Data, Washington, DC.. Oct 22, 2011.

Friedman AA., Tucker G., Singh R., Yan D., Vinayagam A., Hu Y., Binari R., Hong P., Sun X., Porto M., Pacifico S., Murali T., Finley Jr. R. L., Asara J. M., Berger B., Perrimon N.. "Proteomic and Functional Genomic Landscape of Receptor Tyrosine Kinase and Ras to Extracellular Signal–Regulated Kinase Signaling." Science Signaling 4. 196 (2011): p. rs10.

Schulte J., Sepp K. J., Wu C., Hong P., Littleton J. T.. "High-Content Chemical and RNAi Screens for Suppressors of Neurotoxicity in a Huntington's Disease Model." PLoS One 6. 8 (2011): e23841..

Shang Y., Haynes P., Pírez N., Harrington K. I., Guo F., Pollack J., Hong P., Griffith L. C., and Rosbash M.. "Imaging analysis of clock neurons: light buffers the wake-promoting effect of dopamine." Nature Neuroscience 14. (2011): 889–895.

Warner J. L., Anick P., Hong P., and Xue N.. "Natural Language Processing and the Oncologic History: Is There a Match?." Journal of Oncology Practice 7. 4 (2011): e15-e19.

Asara, J., Kulkarni, M., Friedman, A., Yang, X., Hong, P., Engelman, J., and Perrimon, N.. ""Interact-ome" of Components in the Insulin Signaling Pathway in Drosophila and Compared to Human Cancer Cells." US HUPO Proteomics -- from Bench to Clinic, Denver, Colorado, USA. March 7 - 10, 2010.

Li L., Karabacak1 N.M., Cobb J.S., Wang Q., Hong P., Agar1 J.N.. "Memory-efficient calculation of the isotopic mass states of a molecule." Rapid Communications in Mass Spectrometry 24. 18 (2010): 2689-2696.

Lin C., Hong P., Bakal C., and Perrimon N.. "Novel Morphological Phenotypes Discovery in High-Content Screens Using Underused Features.." International Conference on Bioinformatics and Computational Biology, Honolulu, Hawaii, USA. March 24-26, 2010.

Peter Anick, Pengyu Hong, Nianwen Xue, David Anick. "I2B2 2010 Challenge: Machine Learning for Information Extraction from Patient Records." Fourth i2b2/VA Shared-Task and Workshop Challenges in Natural Language Processing for Clinical Data, Washington, DC. November 2010.

Schoemans R., Aigrot M.S., Wu C., Marée R., Hong P., Belachew S., Josse C., Lubetzki C. and Bours V.. "Oligodendrocyte development and myelinogenesis are not impaired by high concentrations of phenylalanine or its metabolites." Journal of Inherited Metabolism Disease (2010).

Schulte J., Sepp K., Jorquera R., Wu C., Song Y., Hong P., and Littleton J.T.. "DMob4/Phocein regulates synapse formation, axonal transport, and microtubule organization." Journal of Neuroscience (2010).

Wu C., Schulte J., Sepp K.J., Littleton J.T., and Hong P.. "Automatic Robust Neurite Detection and Morphological Analysis of Optical Microscopy Neuron Cell Culture Images in High-Content Screening." Neuroinformatics (2010).

Karabacak N.M., Li L., Tiwari A., Hayward L.J., Hong P., Easterling M.L., and Agar A.N.. "Sensitive and specific identification of wild-type and variant proteins from 8 to 669 kDa using top-down mass spectrometry." Molecular & Cellular Proteomics 8. 4 (2009): 846-856.

Sun X. and Hong P.. "Automatic Inference of Multicellular Regulatory Networks Using Informative Priors." International Journal of Computational Biology and Drug Design 2. 2 (2009): 115-133.

Karabacak NM, Li L, Tiwari A, Hayward LJ, Hong P, Easterling ML, and Agar AN. "Sensitive and specific identification of wild-type and variant proteins from 8 to 669 kDa using top-down mass spectrometry." Molecular & Cellular Proteomics (2008).

Li L, Kresh JA, Karabacak NM, Cobb JS, Agar JN, and Hong P. "A Hierarchical Algorithm for Calculating the Isotopic Fine Structures of Molecules." Journal of the American Society for Mass Spectrometry 19. 12 (2008): 1867-1874.

Li L., Kresh J.A., Karabacak N.M., Cobb J.S., Agar J.N., and Hong P.. "A Hierarchical Algorithm for Calculating the Isotopic Fine Structures of Molecules." Journal of the American Society for Mass Spectrometry 19. 12 (2008): 1867-1874.

Lin C, Mak W, Hong P, Sepp K, Perrimon N.. "Intelligent Interfaces for Mining Large-Scale RNAi-HCS Image Databases." IEEE International Symposium on Bioinformatics and Bioengineering, Boston, MA, USA. October 14-17, 2007.

Sepp K.J., Hong P., Lizarraga S.B., Liu J.S., Mejia L.A., Walsh C.A., and Perrimon N.. "Identification of neural outgrowth genes using genome-wide RNAi.." PLoS Genet. 4. 7 (2008).

Zhou R., Hotta I., Denli A.M., Hong P., Perrimon N., and Hannon G.J.. "Comparative Analysis of Argonaute-Dependent Small RNA Pathways in Drosophila." Molecular Cell 32. 4 (2008): 592-599.

Hong, Pengyu. "Interactive Analysis of High-Content Cellular Images via Relevant Feedback.." Workshop on Multiscale Biological Imaging, Data Mining and Informatics, Santa Barbara, CA, USA.. Sep 7-8.

Sun, Xiaoyun and Hong, Pengyu. "Computational modeling of Caenorhabditis elegans vulval induction.." Bioinformatics 12. 23 (2007): i499-507.

Kulkarni, M. M., Booker, M., Silver, S. J., Friedman, A., Hong, P., Perrimon, N., Mathey-Prevot, B.. "Evidence of off-target effects associated with long dsRNAs in Drosophila melanogaster cell-based assays." Nature Methods 3. 10 (2006): 833-838.