Research Output 1963 2019

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Conference contribution
2018

Characterizing protein-DNA binding event subtypes in CHIP-exo data

Yamada, N., Lai, W., Farrell, N., Pugh, B. F. & Mahony, S. A., Jan 1 2018, Research in Computational Molecular Biology - 22nd Annual International Conference, RECOMB 2018, Proceedings. Springer Verlag, p. 291-292 2 p. (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); vol. 10812 LNBI).

Research output: Chapter in Book/Report/Conference proceedingConference contribution

DNA-binding Protein
DNA
Proteins
2017

Smartphone chloridometer for point-of-care applications

Zhang, C., Kim, J. P., Creer, M., Yang, J. & Liu, Z., Jan 1 2017, Ultrafast Nonlinear Imaging and Spectroscopy V. Liu, Z., Shi, K., Khoo, I. C. & Psaltis, D. (eds.). SPIE, 103800I. (Proceedings of SPIE - The International Society for Optical Engineering; vol. 10380).

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Smartphones
sweat
Chlorides
Diagnostics
chlorides
2016
4 Citations (Scopus)

Fidelity of Nucleotide Incorporation by the RNA-Dependent RNA Polymerase from Poliovirus

Cameron, C. E., Moustafa, I. & Arnold, J. J., Jan 1 2016, DNA Replication Across Taxa, 2016. Kaguni, L. S. & Oliveira, M. T. (eds.). Academic Press, p. 293-323 31 p. (Enzymes; vol. 39).

Research output: Chapter in Book/Report/Conference proceedingConference contribution

RNA Replicase
Poliovirus
Nucleotides
Viruses
Antiviral Agents
2015
8 Citations (Scopus)

Preliminary evaluation of a research experience for undergraduates (REU) program: A methodology for examining student Outcomes

Follmer, D. J., Zappe, S. E., Gomez, E. W. & Kumar, M., 2015, 122nd ASEE Annual Conference and Exposition: Making Value for Society. American Society for Engineering Education

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Students
Personnel rating
Chemical engineering
Refining
2014
1 Citation (Scopus)

An integrated model of multiple-condition ChIP-Seq data reveals predeterminants of Cdx2 binding

Mahony, S., Edwards, M. D., Mazzoni, E. O., Sherwood, R. I., Kakumanu, A., Morrison, C. A., Wichterle, H. & Gifford, D. K., Jan 1 2014, Research in Computational Molecular Biology - 18th Annual International Conference, RECOMB 2014, Proceedings. Springer Verlag, p. 175-176 2 p. (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); vol. 8394 LNBI).

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Integrated Model
Chip

High-throughput single molecule detection using nanophotonic/microfluidic hybrid chip

Zhao, Y., Chen, D., Benkovic, S. & Huang, T. J., Jan 1 2014, 18th International Conference on Miniaturized Systems for Chemistry and Life Sciences, MicroTAS 2014. Chemical and Biological Microsystems Society, p. 1811-1813 3 p.

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Nanophotonics
Microfluidics
Throughput
Proteins
Molecules

Microfluidic cell co-culture using standing surface acoustic wave (SSAW)

Li, S., Guo, F., Chen, Y., Ding, X., Li, P., Cameron, C. E. & Huang, T. J., Jan 1 2014, 18th International Conference on Miniaturized Systems for Chemistry and Life Sciences, MicroTAS 2014. Chemical and Biological Microsystems Society, p. 533-535 3 p. (18th International Conference on Miniaturized Systems for Chemistry and Life Sciences, MicroTAS 2014).

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Microfluidics
Surface waves
Acoustic waves
Biocompatibility
Acoustics
2013

CARS holography

Edwards, P. S., Shi, K., Hu, J., Xu, Q., Wang, Y., Psaltis, D. & Liu, Z., Dec 1 2013, 2013 IEEE Photonics Conference, IPC 2013. p. 372-373 2 p. 6656592

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Holography
holography
Imaging techniques
imaging techniques
Labels

Detecting interacting mutation clusters in HIV-1 drug resistance

Zhang, Y., May 27 2013, BIOINFORMATICS 2013 - Proceedings of the International Conference on Bioinformatics Models, Methods and Algorithms. p. 34-43 10 p. (BIOINFORMATICS 2013 - Proceedings of the International Conference on Bioinformatics Models, Methods and Algorithms).

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Drug Resistance
HIV-1
Mutation
Proteins
Drug therapy

Tunable standing surface acoustic wave (SSAW)-based multichannel droplet sorter

Li, S., Ding, X., Guo, F., Chen, Y., Cameron, C. E. & Huang, T. J., Jan 1 2013, 17th International Conference on Miniaturized Systems for Chemistry and Life Sciences, MicroTAS 2013. Chemical and Biological Microsystems Society, p. 311-313 3 p. (17th International Conference on Miniaturized Systems for Chemistry and Life Sciences, MicroTAS 2013; vol. 1).

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Surface waves
Acoustic waves
Oils
Acoustics
Water
2012
1 Citation (Scopus)

Using student Ambassadors to relay themes from Changing the Conversation in Engineering First Year Seminars

Zappe, S. E., Marshall, M., Gomez, E. D., Gomez, E. W. & Lueking, A., 2012, 119th ASEE Annual Conference and Exposition. American Society for Engineering Education

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Technical presentations
Students
Health
Chemical engineering
Curricula
2011

Coherent anti-Stokes Raman scattering (CARS) holographic biological imaging

Edwards, P. S., Shi, K., Hu, J., Xu, Q., Wang, Y., Psaltis, D. & Liu, Z., Dec 1 2011, CLEO: Science and Innovations, CLEO_SI 2011.

Research output: Chapter in Book/Report/Conference proceedingConference contribution

holography
Raman scattering
selectivity
Raman spectra
Imaging techniques

Coherent anti-Stokes Raman scattering (CARS) holographic biological imaging

Edwards, P. S., Shi, K., Hu, J., Xu, Q., Wang, Y., Psaltis, D. & Liu, Z., Sep 1 2011, 2011 Conference on Lasers and Electro-Optics: Laser Science to Photonic Applications, CLEO 2011. 5950424. (2011 Conference on Lasers and Electro-Optics: Laser Science to Photonic Applications, CLEO 2011).

Research output: Chapter in Book/Report/Conference proceedingConference contribution

holography
Raman scattering
selectivity
Raman spectra
Imaging techniques
2010
9 Citations (Scopus)

Optimization methods for selecting founder individuals for captive breeding or reintroduction of endangered species

Miller, W., Wright, S. J., Zhang, Y., Schuster, S. C. & Hayes, V. M., 2010, Pacific Symposium on Biocomputing 2010, PSB 2010. p. 43-53 11 p.

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Endangered Species
Combinatorial optimization
Linear programming
Breeding
Animals
2009
9 Citations (Scopus)

Simultaneous history reconstruction for complex gene clusters in multiple species

Zhang, Y., Song, G., Hsu, C. H. & Miller, W., Dec 1 2009, Pacific Symposium on Biocomputing 2009, PSB 2009. p. 162-173 12 p. (Pacific Symposium on Biocomputing 2009, PSB 2009).

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Multigene Family
Genes
History
Pongo
Chromosomes, Human, Pair 19
2 Citations (Scopus)

Whole-genome analysis of gene conversion events

Hsu, C. H., Zhang, Y., Hardison, R. C. & Miller, W., Dec 1 2009, Comparative Genomics - International Workshop, RECOMB-CG 2009, Proceedings. p. 181-192 12 p. (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); vol. 5817 LNBI).

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Genome
Genes
Gene
Interval
Genomics
2008
12 Citations (Scopus)

Reconstructing the evolutionary history of complex human gene clusters

Zhang, Y., Song, G., Vinař, T., Green, E. D., Siepel, A. & Miller, W., Jul 21 2008, Research in Computational Molecular Biology - 12th Annual International Conference, RECOMB 2008, Proceedings. p. 29-49 21 p. (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); vol. 4955 LNBI).

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Genes
Gene
Computational Analysis
Duplication
Sequencing
2007

Gene prediction in metagenomic libraries using the self organising map and high performance computing techniques

McCoy, N., Mahony, S. A. & Golden, A., Aug 3 2007, Distributed, High-Performance and Grid Computing in Computational Biology International Workshop, GCCB 2006, Proceedings. p. 99-109 11 p. (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); vol. 4360 LNBI).

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Self organizing maps
Self-organizing Map
High Performance
Genes
Gene
2005

Sombrero: Integrating self-organizing neural networks in the search for dna binding motifs

Mahony, S. A., Benos, P. V., Smith, T. J. & Golden, A., 2005, WSOM 2005 - 5th Workshop on Self-Organizing Maps. p. 677-685 9 p.

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Transcription factors
DNA sequences
DNA
Neural networks
Processing
2003

A new approach to gene prediction using the self-organizing map

Mahony, S. A., Smith, T. J., McInerney, J. O. & Golden, A., Jan 1 2003, Proceedings of the 2003 IEEE Bioinformatics Conference, CSB 2003. Institute of Electrical and Electronics Engineers Inc., p. 444-445 2 p. 1227365. (Proceedings of the 2003 IEEE Bioinformatics Conference, CSB 2003).

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Self organizing maps
Genes
Proteins
1985
48 Citations (Scopus)

EFFECTS OF METHYL AND FLUORINE SUBSTITUTION ON THE METABOLIC ACTIVATION AND TUMORIGENICITY OF POLYCYCLIC AROMATIC HYDROCARBONS.

Hecht, S. S., Amin, S., Melikian, A. A., LaVoie, E. J. & Hoffmann, D., Dec 1 1985, ACS Symposium Series. Harvey, R. G. (ed.). ACS, p. 85-105 21 p. (ACS Symposium Series).

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Fluorine
Polycyclic Aromatic Hydrocarbons
Substitution reactions
Chemical activation
Epoxy Compounds