The Biocomputing Research Lab

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Daniel Asarnow

Contact

  • Email: dasarnow at sfsu dot edu
  • Research Assistant, Department of Computer Science
  • Graduate Student, Department of Chemistry & Biochemistry

Biography

I currently hold a research staff position with the Biocomputing and Media Research Lab at SFSU, and am a candidate for the M.Sc. in Chemistry, Biochemistry concentration (expected 2013). I am the recepient, with Dean's Honors, of the B.Sc. in Biochemistry and Molecular Biology from the University of California, Santa Cruz (2009).

I support open source software in academia and have contributed an access layer for the CATH protein classification system to the BioJava bioinformatics library.

I also have substantial experience in the education sphere, where I have been a teaching assistant for the Department of Computer Science at SFSU (2011), as well as a CalTeach intern (2007), an instructor for Science Advenctures (2006), and an Explainer at the The Exploratorium, Inc. (2003-06).

Research Interests

My work with Professor Rahul Singh lies in the new field of "computational phenomics," which seeks to relate the range of observed behaviors of dynamic biological systems to underlying biochemical interactions.

Our research is highly interdisciplinary in nature, and includes efforts in biological image analysis and computer vision, chemical information systems, structural bioinformatics, and biological time-series analysis.

This work has immediate applications in automated drug discovery, especially for neglected tropical diseases such as schistosomiasis, filariasis and onchoceriasis. The etiological agents of these illnesses are complex macroparasites with highly evolved relationships to their human hosts. We believe that the response of such disesase systems to drug insult are best understood within a framework for computational phenomics which rigorously approaches the deep connection between behavioral phenotypes and therapeutic agents.

Scholarships and Awards

I was awarded the ARCS graduate scholarship in 2010, and received the State University Grant continuously from 2009 to 2012 (when all coursework was completed).

Publications

  • D. Asarnow and Rahul Singh, "Determination of Quantal Dose-Response Characteristics in Phenotypic Assays using Supervised Classification," San Francisco State University Technical Report, 2014. [PDF]
  • L. Rojo-Arreola, T. Long, D. Asarnow, B.M. Suzuki, R. Singh and C.R. Caffrey, "Chemical and genetic validation of the statin drug target for the potential treatment of the helminth disease, schistosomiasis," PLoS ONE, 9(1): e87594, 2014. (Corresponding author C.R. Caffrey). [PDF]
  • D. Asarnow and R. Singh, "Automatic Classification of Protein Structures Using Low-Dimensional Structure Space Mappings," BMC Bioinformatics, 15(Suppl 2):S1, 2014. (Corresponding author R. Singh). [PDF]
  • R. Singh, H. Yang, B. Dalziel, D. Asarnow, W. Murad, D. Foote, M. Gromley, J. Stillman, and S. Fisher, "Towards Human-Computer Synergistic Analysis of Large-Scale Biological Data", BMC Bioinformatics, 14(Suppl 14):S10, 2013. (Corresponding author R. Singh). [PDF]
  • D. Asarnow and R. Singh, "The Impact of Parameters and Structural Diversity in Maps of the Protein Universe," BMC Proceedings, 7 (Suppl 7):S1, 2013. (Corresponding author R. Singh).
  • D. Asarnow and R. Singh, "Segmenting the Etiological Agent of Schistosomiasis for High-Content Screening," IEEE Transactions on Medical Imaging, vol. 32, no. 6, pp. 1007-10018, 2013. (Corresponding author R. Singh). [PDF]
  • D. Asarnow and R. Singh, "Segmentation of Parasites for High-Content Screening using Phase Congruency and Grayscale Morphology", International Symposium on Visual Computing (ISVC), 2012, Lecture Notes in Computer Science, Vol. 7431, pp. 51-60, Springer, 2012. [PDF]
  • H. Lee*, A. Moody-Davis, U. Saha, B. Suzuki, D. Asarnow, S. Chen, M. Arkin, C. Caffrey, and R. Singh*, "Quantification and Clustering of Phenotypic Screening Data Using Time Series Analysis for Chemotherapy of Schistosomiasis", BMC Genomics, 12 (Suppl 1):S4, 2012 (*H. Lee and R. Singh equal contributors. Corresponding author R. Singh). [PDF]
  • R. L. Nguyen, B. W. Lintner, I. L. Pena, P. Tipgunlakant, J. Soman, I. Birukou, J. S. Olson, D. E. Asarnow, D. S. Kliger, R. A. Goldbeck, and R. M. Esquerra, "The Effect of Non-Coordinated Water in the Heme Pocket on the Ligand Binding Dynamics of Heme Proteins," Biophysical Journal, vol. 98, no. 3, Supplement 1, p. 639a–640a, Jan. 2010.
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