CV

Peter Allen, Ph. D.

Resides in the Greater Seattle Area

Contact: pballen via gmail

Highlights of research activities

My research is focused on DNA nanotechnology, including colloidal self-assembly and designed chemical reaction networks. I have integrated this technology with my knowledge and experience in laser fluorescence detection and microfluidics. I have programmed lab automation and data analysis including image analysis in Mathematica, MATLAB and LabView. My research interests include the expansion of DNA-directed self-assembly to include biocompatible materials with designed, self-assembled sub-structures to influence and engineer tissue growth.

Under Daniel Chiu at the University of Washington in the Department of Chemistry, I studied microfabrication of microfluidic devices for biological analyses. This culminated in the use of capillary electrophoresis for the chemical analysis of the contents of single 100 nm diameter vesicles and single mitochondria. The ability to use sensitive fluorescence detection for precise, small volume analyses remains a strong interest that is being expanded in the Allen lab.

In Andrew Ellington’s lab at the University of Texas, I studied the design and application of DNA reaction networks. This included paper-based assays for the detection of isothermally amplified DNA, theoretical and experimental studies of chemical localization in macro-scale gels by DNA sequence, and the self-assembly of colloidal gels based on DNA “smart glue.” This final project is the foundation for future materials-based research in the Allen lab.

My research at the University of Idaho integrated Aptamers, microparticle synthesis, and chemical sensing using DNA nanotechnology. My students and I seleced aptamers against several disease-relevant proteins, Drosophila melanogaster virus particles, and against light-up dyes.

Research and Professional Experience:

Biotech startup company                                Senior Scientist

6/2020 – current

I work for a biotech company in the Seattle area.

University of Idaho                                           Assistant Professor,                 Chemistry

1/15 – 5/2020

I served as an assistant professor of chemistry in the analytical division at the University of Idaho. My research focussed on DNA aptamers-based biosensors. This includes DNA nanotechnology-based sensors and a generation of hydrogel colloids for surface-immobilized amplification.

 

University of Texas                                          Postdoctoral Fellow,    Chemistry/ICMB

9/09 – 12/14

I was a postdoctoral fellow under Andrew D. Ellington. My research is in self-assembly mediated by DNA nanotechnology and computation. The other side of my research is to apply DNA reactions to the detection of nucleic acid analytes and integrated the result into a paper-fluidic detector for point-of-care diagnosis.

 

University of Washington                                 Research Assistant,     Chemistry

6/01 – 8/09

I wrote my dissertation under Prof. Daniel T. Chiu on the use of microfluidics in analyzing small, biological samples in vitro and in vivo. For the capstone, I analyzed single, 100 nm synthetic vesicles (1 attoliter volume) and single mitochondria with capillary electrophoresis and laser induced fluorescence. I led six projects to completed publications and mentored two undergraduate students.

University of Washington                                 Teaching Assistant,     Chemistry

4/08 – 6/08

Taught introductory organic chemistry laboratory under Prof. Michael Gelb. I was responsible for laboratory safety, instruction on experimental protocol, and grading. My philosophy of teaching is to seek first to understand, then to be understood. Many confusions can be cleared if the instructor takes the time to understand them.

 

Education

INSTITUTION AND LOCATION DEGREE YEAR FIELD OF STUDY
University of Washington, Seattle B.S. 2003 Chemistry, with Honors
University of Washington, Seattle B.S. 2003 Biochemistry, with Honors
University of Washington, Seattle M.S. 2008 Chemistry
University of Washington, Seattle Ph. D. 2008 Chemistry

Awards:

National Merit Scholar (1999)

Harold Scholar (1999)

Washington Promise Scholar (1999)

Dolphin Scholar (1999)

NSF/REU Fellow (2001)

Pfizer Undergraduate Research Fellow (2002)

Mindlin fellowship for Creativity in the Sciences (2003)

 Member, Phi Beta Kappa (2003)

U. of Washington Nanotech early bird fellowship (2003)

Finalist, Hertz Graduate Fellowship (2003)

NSF Nanotechnology “Early Bird” fellowship (2003)

NSF Graduate Research Fellowship (2004-2007)

Finalist, Life Sciences Research Foundation

NIH National Research Service Award Fellow (2010-2012)

 

46 Peer-Reviewed Publications in Chronological Order:

  1. P.B. Allen, I. Rodriguez, C.L. Kuyper, R.M. Lorenz, P. Spicar-Mihalic, D.T. Chiu (2003) “Selective electroless and electrolytic deposition of metal for applications in microfluidics: Fabrication of a microthermocouple” Anal. Chem. 75, 1578.
  2. M. Lorenz, C.L. Kuyper, P.B. Allen, L.P. Lee, D.T. Chiu (2004) “Direct laser writing on electrolessly deposited thin metal films for applications in micro and nanofluidics” Langmuir 20, 1833.
  3. P.B. Allen, B.R. Doepker, D.T. Chiu (2007) “Fourier Transform Capillary Electrophoresis with Laminar-Flow Gated Pressure Injection” Anal. Chem.79, 6807.
  4. E. Sgro, P.B. Allen, D.T. Chiu (2007) “Thermoelectric Manipulation of Aqueous Droplets in Microfluidic Devices” Anal. Chem. 79, 4845.
  5. P.B. Allen, D.T. Chiu (2008) “Alzheimer’s disease protein Abeta(1-42) does not disrupt isolated synaptic vesicles” Biochim Biophys Acta. – Mol. Basis Dis. 1782, 326.
  6. P.B. Allen, A.E. Sgro, D.L. Chao, B.E. Doepker, J.S. Edgar, K. Shen, D.T. Chiu (2008) “Single-synapse ablation and long-term imaging in live C. elegans” J. Neurosci. Meth. 173, 20.
  7. P.B. Allen, D.T. Chiu (2008) “Calcium-Assisted Glass-to-Glass Bonding for Fabrication of Glass Microfluidic Devices” Anal. Chem. 80, 7153.
  8. A. Dendramis, P.B. Allen, P.J. Reid, D.T. Chiu (2008) “Spectrally tunable uncaging of biological stimuli from nanocapsules” Chem. Commun. 2008, 4795.
  9. P.B. Allen, B.E. Doepker, and D.T. Chiu (2009) “Laboratory Exercise: Microfluidics and Diffusion,” Chem. Educator, 14, 61.
  10. P.B. Allen, B.E. Doepker, and D.T. Chiu, (2009) “High-Throughput Capillary-Electrophoresis Analysis of the Contents of a Single Mitochondria,” Anal. Chem. 81, 3784.
  11. P.B. Allen, G. Milne, B.D. Doepker, and D.T. Chiu. (2010) “Pressure-driven laminar flow switching for rapid exchange of solution environment around surface adhered biological particles,” Lab Chip 10, 727.
  12. P.B. Allen and A.D. Ellington, (2011) “Sequential injection analysis for optimization of molecular biology reactions,” Anal. Chem. 83, 2194.
  13. B. Zeigler, P.B. Allen, and D.T. Chiu, (2011) “Probing rotational viscosity in synaptic vesicles,” Biophys. J. 100, 2846.
  14. E. Sgro, A.L. Nowak, N.A. Austin, K.L. Custer, P.B. Allen, D.T. Chiu, and S. M Bajjalieh (2011) “A high-throughput method for generating uniform microislands for autaptic neuronal cultures,” J. Neurosci. Meth. 198, 230.
  15. Wan, M.A.I. Mahmood, N. Li, P.B. Allen, Y.T. Kim, R. Bachoo, A.D. Ellington and S.M. Iqbal (2011) “Nanotextured substrates with immobilized aptamers for cancer cell isolation and cytology,” Cancer, DOI: 10.1002/cncr.26349
  16. P.B. Allen, S.A. Arshad, B. Li, X. Chen, A.D. Ellington. “DNA circuits as amplifiers for the detection of nucleic acids on a paperfluidic platform” Lab Chip. 2012. 12, 2951.
  17. P.B. Allen, X. Chen, Z.B. Simpson, and A.D. Ellington “Modeling Scalable Pattern Generation in DNA Reaction Networks.” Conf. Proc. ALIFE 13. (2012) p 441-448
  18. Wan, D. Tamuly, P.B. Allen, Y-T. Kim, R. Bachoo, A.D. Ellington, S. Iqbal. “Proliferation and migration of tumor cells in tapered channels.” Biomed Microdevices. 2013 Aug;15(4):635–43.
  19. Tang, R. Deschner, P. Allen, Y. Cho, P. Sermas, A. Maurer, A.D. Ellington, C.G. Willson. “Analysis of DNA-Guided Self-Assembly of Microspheres Using Imaging Flow Cytometry” J. Am. Chem. Soc. 2012. DOI: 10.1021/ja3066896
  20. Wan, Y. Liu,  P.B. Allen,  W. Asghar,  M.A.I. Mahmood,  J. Tan,  H, Duhon,  Y. Kim,  A.D. Ellington and S.M. Iqbal “Capture, Isolation and Release of Cancer Cells with Aptamer-functionalized Glass Beads.” Lab Chip (2012). 12, 4693-4701.
  21. Ilyas, A.; Asghar, W.; Allen, P. B.; Duhon, H.; Ellington, A. D.; Iqbal, S. M. Electrical Detection of Cancer Biomarker Using Aptamers with Nanogap Break-Junctions. Nanotechnology 2012, 23 (27), 275502 DOI: 10.1088/0957-4484/23/27/275502.
  22. P.B. Allen, X. Chen, A.D. Ellington. “Spatial Control of DNA Reaction Networks by DNA Sequence.” Molecules (2012) 17(12):13390–13402
  23. P.B. Allen, X. Chen, Z.B. Simpson, A.D. Ellington. “Modeling Scalable Pattern Generation in DNA Reaction Networks.” Natural computing (2013) doi:10.1007/s11047-013-9392-7
  24. Deschner, T. Hao, P.B. Allen, C. Hall, R. Hlis, A.D. Ellington, C.G. Willson. “Polyfunctional Microscale Particles for Programmed Self Assembly.” Chemistry of Materials (2014) 26 (3), pp 1457–1462.
  25. P. Melancon, M. Zhou, R. Zhang, C. Xiong, P.B. Allen, Q. Huang, M. Wallace, J.N. Myers, R.J. Stafford, D. Liang, A.D. Ellington, C. Li. “Selective Uptake and Imaging of Aptamer- and Antibody-Conjugated Hollow Nanospheres Targeted to Epidermal Growth Factor Receptors Overexpressed in Head and Neck Cancer.” ACS Nano (2014) 8 (5), pp 4530–4538.
  26. Deschner, R.; Tang, H.; Allen, P.; Hall, C.; Hlis, R.; Ellington, A.; Willson, C. G. Progress Report on the Generation of Polyfunctional Microscale Particles for Programmed Self-Assembly. Mater. 2014, 26 (3), 1457–1462 DOI: 10.1021/cm403637v.
  27. P.B. Allen, Z. Khaing, C.E. Schmidt, A.D. Ellington. “3D printing with nucleic acid adhesives.” ACS Biomaterials Science and Engineering (2015) 1, 19-26.
  28. Mahmood, M. A. I.; Hasan, M. R.; Khan, U. J. M.; Allen, P. B.; Kim, Y.-T.; Ellington, A. D.; Iqbal, S. M. One-Step Tumor Detection from Dynamic Morphology Tracking on Aptamer-Grafted Surfaces. Technology (Singap World Sci) 2015, 3 (4), 194–200 DOI: 10.1142/S2339547815500089.
  29. Damase, T. R.; Stephens, D.; Spencer, A.; Allen, P. B. Open Source and DIY Hardware for DNA Nanotechnology Labs. Journal of Biological Methods 2015, 2 (3), 24 DOI: 10.14440/jbm.2015.72.
  30. Jung, C.; Allen, P. B.; Ellington, A. D. A Stochastic DNA Walker That Traverses a Microparticle Surface. Nat Nanotechnol 2016, 11 (2), 157–163 DOI: 10.1038/nnano.2015.246.
  31. S. M. Chirieleison, P. B. Allen, Z. B. Simpson, A. D. Ellington, and X. Chen, “Pattern transformation with DNA circuits,” Nat Chem, vol. 5, no. 12, pp. 1000–1005, Dec. 2013, doi: 10.1038/nchem.1764.
  32. P. B. Allen, Z. Khaing, C. E. Schmidt, and A. D. Ellington, “3D Printing with Nucleic Acid Adhesives,” ACS Biomater Sci Eng, vol. 1, no. 1, pp. 19–26, Jan. 2015, doi: 10.1021/ab500026f.
  33. T. R. Damase, D. Stephens, A. Spencer, and P. B. Allen, “Open source and DIY hardware for DNA nanotechnology labs,” Journal of Biological Methods, vol. 2, no. 3, p. 24, Aug. 2015, doi: 10.14440/jbm.2015.72.
  34. M. Islam et al., “Nanotextured polymer substrates show enhanced cancer cell isolation and cell culture,” Nanotechnology, vol. 26, no. 22, p. 225101, Jun. 2015, doi: 10.1088/0957-4484/26/22/225101.
  35. T. R. Damase, A. D. Ellington, and P. B. Allen, “Purification of single-stranded DNA by co-polymerization with acrylamide and electrophoresis,” BioTechniques, vol. 62, no. 6, Jun. 2017, doi: 10.2144/000114557.
  36. T. R. Damase, A. Spencer, B. Samuel, and P. B. Allen, “Biomimetic Molecular Signaling using DNA Walkers on Microparticles,” Sci Rep, vol. 7, no. 1, p. 4081, Jun. 2017, doi: 10.1038/s41598-017-04316-1.
  37. C. Jung, P. B. Allen, and A. D. Ellington, “A Simple, Cleated DNA Walker That Hangs on to Surfaces,” ACS Nano, Jul. 2017, doi: 10.1021/acsnano.7b02693.
  38. T. R. Damase, T. A. Miura, C. E. Parent, and P. B. Allen, “Application of the Open qPCR instrument for the in vitro selection of DNA aptamers against Epidermal Growth Factor Receptor and Drosophila C virus,” ACS Comb. Sci., Jan. 2018, doi: 10.1021/acscombsci.7b00138.
  39. M. M. Islam, A. Loewen, and P. B. Allen, “Simple, low-cost fabrication of acrylic based droplet microfluidics and its use to generate DNA-coated particles,” Scientific Reports, vol. 8, no. 1, p. 8763, Jun. 2018, doi: 10.1038/s41598-018-27037-5.
    T. R. Damase and P. B. Allen, “Designed and Evolved Nucleic Acid Nanotechnology: Contrast and Complementarity,” Bioconjugate Chem., vol. 30, no. 1, pp. 2–12, Jan. 2019, doi: 10.1021/acs.bioconjchem.8b00810.
  40. T. R. Damase and P. B. Allen, “Idiosyncrasies of thermofluorimetric aptamer binding assays,” BioTechniques, Feb. 2019, doi: 10.2144/btn-2018-0128.
    M. Moshari, D. Koirala, and P. B. Allen, “Facile Fabrication of DNA Biosensors Based on Oxidized Carbon Black and Graphite Oxide,” Proceedings, vol. 41, no. 1, Art. no. 1, 2019, doi: 10.3390/ecsoc-23-06612.
  41. N. Yensen and P. B. Allen, “Open Source All-Iron Battery for Renewable Energy Storage,” HardwareX, p. e00072, Jul. 2019, doi: 10.1016/j.ohx.2019.e00072.
    N. K. Agrawal et al., “Oligonucleotide-functionalized hydrogels for sustained release of small molecule (aptamer) therapeutics,” Acta Biomater, vol. 102, pp. 315–325, Jan. 2020, doi: 10.1016/j.actbio.2019.11.037.
  42. T. R. Damase, M. M. Islam, M. Shipley, and P. B. Allen, “Thioflavin T as a noncovalent reporter for a label-free, non-enzymatic, catalytic DNA amplifier,” Methods Appl Fluoresc, vol. 8, no. 4, p. 045001, Jul. 2020, doi: 10.1088/2050-6120/aba357.
  43. L. R. Fredericks, M. D. Lee, C. R. Roslund, A. M. Crabtree, P. B. Allen, and P. A. Rowley, “The design and implementation of restraint devices for the injection of pathogenic microorganisms into Galleria mellonella,” PLoS One, vol. 15, no. 7, p. e0230767, 2020, doi: 10.1371/journal.pone.0230767.
  44. M. M. Islam, V. M. Ghielmetti, and P. B. Allen, “Graphene oxide assisted light-up aptamer selection against Thioflavin T for label-free detection of microRNA,” Scientific Reports, vol. 11, no. 1, Art. no. 1, Feb. 2021, doi: 10.1038/s41598-021-83640-z.
  45. D. Koirala, N. Yensen, and P. B. Allen, “Open source all-iron battery 2.0,” HardwareX, vol. 9, p. e00171, Apr. 2021, doi: 10.1016/j.ohx.2020.e00171.
  46. M. Moshari, D. Koirala, and P. B. Allen, “Electrochemical biosensors based on divinyl sulfone conjugation of DNA to graphene oxide electrodes,” J Solid State Electrochem, vol. 25, no. 5, pp. 1667–1678, May 2021, doi: 10.1007/s10008-021-04930-0.

 

Invited and Contributed Talks:

Frontiers in Single-Molecule Biophysical Chemistry and Imaging symposium at the ACS national meeting, September 2006.

Wixforth lab, University of Augsburg, Germany. August, 2008.

Technological Advances in RNA Therapy Institute for Research in Immunology and Cancer, University of Montreal, July 2011.

Materials Research Society Directed Self-Assembly of Materials Workshop

Nashville, Tennessee, September, 2011

3D printing of DNA-assembled microspheres into objects. DNA19. September 2013.