Student Co-Authored Publications

Journal Articles

1. Alessandra Luchini, David H. Geho, Barney Bishop, Duy Tran, Cassandra Xia, Robert L. Dufour, Clinton D. Jones, Virginia Espina, Alexis Patanarut, Weidong Zhou, Mark M. Ross, Alessandra Tessitore,, Emanuel F. Petricoin III, and Lance A. Liotta. Smart hydrogel particles: biomarker harvesting: one-step affinity purification, size exclusion, and protection against degradation. Nano Lett. 2008 Jan;8(1):350-61.

2. Virginia Espina, Kirsten H. Edmiston, Michael Heiby, Mariaelena Pierobon, Manuela Sciro, Barbara Merritt, Stacey Banks, Jianghong Deng, Amy J. VanMeter, David H. Geho, Lucia Pastore, Joel Sennesh, Emanuel F. Petricoin III, and Lance A. Liotta. A Portrait of Tissue Phosphoprotein Stability in the Real-world Clinical Tissue Procurement Process. Mol Cell Proteomics. 2008 Oct:7(10): 1998-2018.

3. Caterina Longo, Alexis Patanarut, Tony George, Barney Bishop, Weidong Zhou, Mark M Ross, Virginia Espina, Giovanni Pellacani, Emanuel Petricoin, Lance Liotta, Alessandra Luchini. Core-Shell Hydrogel Particles Harvest, Concentrate and Preserve Labile Low Abundance Biomarkers, PLoS1. 2009 Mar:4(3):1-14.

4. Patanarut A, Luchini A, Botterell PJ, Mohan A, Longo C, Vorster P, Petricoin EF, Liotta LA, Bishop B. Synthesis and characterization of hydrogel particles containing Cibacron Blue F3G-A. Colloids Surf A Physicochem Eng Asp. 2010 Jun;362(1-3):8-19.

5. Dixon, E., Schweibenz, T., Hight, A., Kang, B., Dailey, A., Kim, S., Chen, M, Kim, Y., Neale, S., Groth, A., Ike, T., Khan, S., Schweibenz, B., Lieu, D., Stone, D., Orellana, T., and Couch, R.D. Bacteria-Induced Static Batch Fungal Fermentation of the Diterpenoid Cyathin A3, a Small Molecule Inducer of Nerve Growth Factor. J. Ind. Microbiol. and Biotech. August 2010.

6. Temple Douglas, Davide Tamburro, Claudia Fredolini, Benjamin Espina, Benjamin S. Lepene, Leopold Ilag, Virginia Espina, Emanuel F. Petricoin III, Lance A. Liotta, Alessandra Luchini. The use of hydrogel microparticles to sequester and concentrate bacterial antigens in a urine test for Lyme disease. Biomaterials (2010).

7. Manes NP, Dong L, Zhou W, Du X, Reghu N, Kool AC, Choi D, Bailey CL, Petricoin EF 3rd, Liotta LA, Popov SG. Discovery of mouse spleen signaling responses to anthrax using label-free quantitative phosphoproteomics via mass spectrometry. Mol. Cell Proteomics 2011 Mar;10(3):M110.000927.

8. Dixon E, Clubb C, Pittman S, Ammann L, Rasheed Z, Kazmi N, Keshavarzian A, Gillevet P, Rangwala H, Couch RD. Solid-Phase Microextraction and the Human Fecal VOC Metabolome. PLOS1 (2011) Apr: 6(4):e18471.

9. Tamburro D, Fredolini C, Espina V, Douglas TA, Ranganathan A, Ilag L, Zhou W, Russo P, Espina BH, Muto G, Petricoin EF, Liotta LA, Luchini A. Multifunctional Core-Shell Nanoparticles: Discovery of Previously Invisible Biomarkers [Internet]. Journal of the American Chemical Society 2011 Nov.

10. Iyer SC, Wang D, Iyer EPR, Trunnell SA, Meduri R, Shinwari R, Sulkowski MJ, Cox DN. The RhoGEF Trio Functions in Sculpting Class Specific Dendrite Morphogenesis in Drosophila Sensory Neurons. PLoS ONE 2012 Mar;7(3):e33634.

11. Kehn-Hall K, Narayanan A, Lundberg L, Sampey G, Pinkham C, Guendel I, Van Duyne R, Senina S, Schultz KL, Stavale E, Aman MJ, Bailey C, Kashanchi F. Modulation of GSK-3β Activity in Venezuelan Equine Encephalitis Virus Infection. PLoS ONE 2012;7(4):e34761.

12. Austin D, Baer A, Lundberg L, Shafagati N, Schoonmaker A, Narayanan A, Popova T, Panthier JJ, Kashanchi F, Bailey C, Kehn-Hall K. p53 Activation following Rift Valley Fever Virus Infection Contributes to Cell Death and Viral Production. PLoS ONE 2012;7(5):e36327.

13. Chiechi A, Mueller C, Boehm KM, Romano A, Benassi MS, Picci P, Liotta LA, Espina V. Improved Data Normalization Methods for Reverse Phase Protein Microarray Analysis of Complex Biological Samples. BioTechniques 2012 Sep;0(0):1-7.

14. Bhandarkar AR, Banerjee R, Seshaiyer P. On the Stability of Lung Parenchymal Lesions with Applications to Early Pneumothorax Diagnosis. Comput. Math. Methods Med. [Internet]. 2013 May 14

15. Federici G, Gao X, Slawek J, Arodz T, Shitaye A, Wulfkuhle JD, et al. Systems analysis of the NCI-60 cancer cell lines by alignment of protein pathway activation modules with “-OMIC” data fields and therapeutic response signatures. Mol Cancer Res MCR. 2013 Jun;11(6):676–85.

16. Shafagati N, Narayanan N, Baer A, Fite K, Pinkham C, Bailey C, Kashanchi F, Lepene B, Kehn-Hall K. 2013. The Use of NanoTrap Particles as a Sample Enrichment Method to Enhance the Detection of Rift Valley Fever Virus. PLoS Neglected Tropical Diseases. Jul 4;7(7):e2296.

17. Blair MG, Nguyen NN-Q, Albani SH, L’Etoile MM, Andrawis MM, Owen LM, et al. Developmental changes in structural and functional properties of hippocampal AMPARs parallels the emergence of deliberative spatial navigation in juvenile rats. J Neurosci Off J Soc Neurosci. 2013 Jul 24;33(30):12218–28.

18. Iyer EPR, Iyer SC, Sullivan L, Wang D, Meduri R, Graybeal LL, et al. Functional Genomic Analyses of Two Morphologically Distinct Classes of Drosophila Sensory Neurons: Post-Mitotic Roles of Transcription Factors in Dendritic Patterning. PLoS ONE. 2013 Aug 15;8(8):e72434.

19. Sikdar S, Rangwala H, Eastlake E, Hunt I, Nelson A, Devanathan J, et al. Novel Method for Predicting Dexterous Individual Finger Movements by Imaging Muscle Activity Using a Wearable Ultrasonic System. IEEE Trans Neural Syst Rehabil Eng Publ IEEE Eng Med Biol Soc. 2013 Aug 28;

20. Owen JA, Barreto E, Cressman JR. Controlling Seizure-Like Events by Perturbing Ion Concentration Dynamics with Periodic Stimulation. PLoS ONE. 2013 Sep 16;8(9):e73820.

21. Nordman, J., Philips, W., Kodama, N., Clark, S., Del Negro, C., Kabbani, N. Axon targeting and function of the alpha 7 nicotinic receptor in developing hippocampal neurons via Gprin1. J Neurochem. 2014 May;129(4):649-62.

22. Masso, M., Chuang, G., Hao, K., Jain, S., and Vaisman, I.I. (2014). Structure-based predictors of resistance to the HIV-1 integrase inhibitor Elvitegravir. Antiviral Res. 106, 5–12.

23. Madsen C, Hooper I, Lundberg L, Shafagati N, Johnson A, Senina S, de la Fuente C, Hoover LI, Fredricksen BL, Dinman J, Jacobs JL, Kehn-Hall K. Small molecule inhibitors of Ago2 decrease Venezuelan equine encephalitis virus replication. Antiviral Res. 2014 Oct 18;112C:26-37.

24. Haymond A, Johny C, Dowdy T, Schweibenz B, Villarroel K, Young R, Mantooth CJ, Patel T, Bases J, Jose GS, Jackson ER, Dowd CS, and Couch RD. Kinetic Characterization and Allosteric Inhibition of the Yersinia pestis 1-Deoxy-D-Xylulose 5-Phosphate Reductoisomerase (MEP Synthase). PLoS One. 2014 Aug 29;9(8):e106243.

25. Mehta, R., Neupane, A., Wang, L., Goodman, Z., Baranova, A., and Younossi, Z.M. (2014). Expression of NALPs in adipose and the fibrotic progression of non-alcoholic fatty liver disease in obese subjects. BMC Gastroenterol. 14, 208.

26. N. Shafagati, L. Lundberg, A. Baer, A. Patanarut, K. Fite, B. Lepene, and K. Kehn-Hall, “The use of nanotrap particles in the enhanced detection of rift valley Fever virus nucleoprotein,” PloS One, vol. 10, no. 5, p. e0128215, 2015.

27. Amaya, M., Keck, F., Lindquist, M., Voss, K., Scavone, L., Kehn-Hall, K., Roberts, B., Bailey, C., Schmaljohn, C., and Narayanan, A. (2015). The ubiquitin proteasome system plays a role in venezuelan equine encephalitis virus infection. PloS One 10, e0124792.

28. Reddy, S., and Seshaiyer, P. (2015). Stability analysis of a model of atherosclerotic plaque growth. Comput. Math. Methods Med. 2015, 164035.

29. Albani, S.H., Andrawis, M.M., Abella, R.J.H., Fulghum, J.T., Vafamand, N., and Dumas, T.C. (2015). Behavior in the elevated plus maze is differentially affected by testing conditions in rats under and over three weeks of age. Front. Behav. Neurosci. 9, 31.

30. A. Benedict, N. Bansal, S. Senina, I. Hooper, L. Lundberg, C. de la Fuente, A. Narayanan, B. Gutting, and K. Kehn-Hall, “Repurposing FDA-approved drugs as therapeutics to treat Rift Valley fever virus infection,” Virology, vol. 6, p. 676, 2015.

31. Kajal Gupta, Sameer Singh and Monique Van Hoek. Short, Synthetic Cationic Peptides Have Antibacterial Activity against Mycobacterium smegmatis by Forming Pores in Membrane and Synergizing with Antibiotics, Antibiotics 2015, 4(3), 358-378; doi:10.3390/antibiotics4030358

32. Michael Piccione and Sven Fuhrmann. Creating a 3D Campus Scene Using Esri CityEngine. ArcUser, Winter 2016.

33. Shafagati, Nazly, Katherine Fite, Alexis Patanarut, Alan Baer, Chelsea Pinkham, Soyeon An, Benjamin Foote, Benjamin Lepene, and Kylene Kehn-Hall. 2016. “Enhanced Detection of Respiratory Pathogens with Nanotrap Particles.” Virulence, May, 0.

34. Kaur, B., Moses, S., Luthra, M., Ikonomidou, V.N., 2016. "Remote heartbeat signal detection from visible spectrum recordings based on blind deconvolution", Proc. SPIE 9871, Sensing and Analysis Technologies for Biomedical and Cognitive Applications, pp. 987103-987103–9.

35. Kaur, B., Moses, S., Luthra, M., Ikonomidou, V.N., 2016. "Robustness of remote stress detection from visible spectrum recordings", Proc. SPIE 9871, Sensing and Analysis Technologies for Biomedical and Cognitive Applications, pp. 987104-987104–9.

36. Pinkham, C., An, S., Lundberg, L., Bansal, N., Benedict, A., Narayanan, A., Kehn-Hall, K., 2016. The role of signal transducer and activator of transcription 3 in Rift Valley fever virus infection. Virology 496, 175–185.

37. Keck, F., Brooks-Faulconer, T., Lark, T., Ravishankar, P., Bailey, C., Salvador-Morales, C., and Narayanan, A. (2017). Altered mitochondrial dynamics as a consequence of Venezuelan Equine Encephalitis Virus infection. Virulence 0.

38. Glass, E. M., Garzon, J. L., Lawler, S., Paquier, E., & Ferreira, C. M. (2017). Potential of marshes to attenuate storm surge water level in the Chesapeake Bay. Limnology and Oceanography,63(2), 951-967. doi:10.1002/lno.10682

39. Condensation-incompetent Ketosynthase inhibits trans-Acyltransferase activity”
Authors: Reham Al-Dhelaan, Paul S. Russo, Sean E. Padden, Anthony Amaya, Debbie W. Dong, Young-Ok You
Journal: ACS Chemical Biology-accepted


Projects Presented at Scientific Conferences

1. Amy J. VanMeter, Isela Gallagher, Valerie S. Calvert, Jianghong Deng, Michele Signore, Julia D. Wulfkuhle, Vineela Ayyagari, Christopher W. Walker, Mariaelena Pierobon, Virginia Espina, Emanuel F. Petricoin III, and Lance A. Liotta. Protein signal pathway mapping: Screening potential drug targets for Multiple Myeloma. The American Association of Cancer Research Conference, San Diego CA, April 2008.

2. Alessandra Tessitore, Mark Ross, Weidong Zhou, Virginia Espina, Nishant Trivedi, Lance A. Liotta, and Emanuel F. Petricoin III. Isolation and Identification of Candidate Peptidomic Biomarker Proteins for Prostate Cancer Detection. HUPO Conference, Bethesda, MD, March 2008.

3. Julia D. Wulfkuhle, Rosa Gallagher, Aybike Birerdinc, Michael Estep, Jianghong Deng, Ami Patel, Barbara Merritt, Lucia Pastore, Anna Baranova, Emanuel F. Petricoin III, Lance A. Liotta and Kirsten Edmiston. Proteomic and Genomic Analysis of DCIS and the Tumor Microenvironment: Implications for Early Programming of the Invasive Phenotype. The American Association of Cancer Research Conference, San Diego CA, April 2008.

4. Silvestri, A. Colombatti, V.S. Calvert, J. Deng, A. Schoonmaker, E. Mammano, C. Belluco, F. De Marchi, D. Nitti, L.A. Liotta, E.F. Petricoin and M. Pierobon. "Pathway Profiling of Laser Capture Microdissected Primary Colorectal Cancer: Development of Prognostic Fingerprint Based on Functional Signal Transduction Biomarker." Joint Metastasis Research Society-AACR Special Conference on Metastasis, August 3-7 2008, Vancouver, Canada.

5. Nathan P. Manes, Li Dong, Weidong Zhou, Nikitha Reghu, Arjan C. Kool, Charles Bailey, Emanuel F. Petricoin III, Lance A. Liotta, Serguei G. Popov. Discovery of Anthrax Biomarkers Using Label-Free Quantitative Phosphoproteomics and LC-LTQ-Orbitrap-MS(/MS). 57th American Society for Mass Spectrometry Conference, June 4, 2009, Philadelphia, PA.

6. Virginia Espina, Claudius Mueller, Alex Reeder, Annalise Schoonmaker, Stacey Banks, Lucia Pastore, Kirsten Edmiston, Emanuel F. Petricoin, III, and Lance A. Liotta. Stabilization Chemistry for Universal Application to Protein, RNA, DNA and Morphology Preservation. 10th Principal Investigators Meeting for the IMAT (Innovative Molecular Analysis Technologies) Program, Oct. 7-9, 2009, Bethesda, MD.

7. Paul D. Cooper, Christine J. Franzel, John F. Cooper. Thermochemical Constraints of the Old Faithful Model for Radiation-Driven Cryovolcanism on Enceladus. The American Astronomical Society Division of Planetary Science (DPS) Conference, Oct 3-8, 2010, Pasadena,CA.

8. Smith VF, Bishop BM, Papanastasiou EA, Jehangir M, Choi H, van Hoek ML. Significance of Stereochemistry in Short Antimicrobial Peptides. Biophysical Journal 2011 Feb;100(3, Supplement 1):495a.

9. Eswar Prasad R. Iyer, Srividya Chandramouli Iyer, Ramakrishna Meduri, Dennis Wang, and Daniel N. Cox. Functional genomic analyses reveal complex transcriptional regulatory networks mediating dendritic architecture. Virginia Academy of Science Annual Meeting, May 2011.
Richmond, VA.
* Abstract Received J. Shelton Horsley Research Award    

10. Alex Chen and Jason Kinser. Multi-Domain Data Modeling for Biometrics. Applied Imagery Pattern Recognition Annual Workshop, October 11-13, 2011, Washington D.C.

11. Joseph Renaud and Padmanabhan Seshaiyer. Mathematical Modeling of the Fluid-Structure Interactions in Cerebral Saccular Aneurysms by Implicit Finite Difference Methods. Shenandoah Undergraduate Mathematics and Statistics Conference at James Madison University, September 29, 2012.
* Awarded best poster in Applied Mathematics

12. Alexandra Zeller and Padmanabhan Seshaiyer. Mathematical Modeling of the Symbiotic Relationship between Rhizobium Bacteria and Legumes. Shenandoah Undergraduate Mathematics and Statistics Conference at James Madison University, September 29, 2012.

13. Baldelli E., Moran J.C., Masalu N., Hassan S., Rambau P., Jackson K., Ludovini V., Pistola L., Tofanetti F.R., Siggillino A., Petricoin E.F., Pierobon M., Crino’ L. Protein Network Mapping of Retinoblastomas for the Identification of Therapeutic Targets. American Society of Clinical Oncology (ASCO), Chicago, Illinois, June 2014.

14. Eric Wang, William Xu, Suhas Sastry, Songsong Liu, and Kai Zeng. "Hardware Module-based Message Authentication in Intra-Vehicle Networks". ACM/IEEE ICCPS 17, April 2017.

15. Renee Li, Andreas Züfle, Liang Zhao, and Georgios Lamprianidis. Modeling and Prediction of People's Needs (Vision Paper). In Proceedings of the 1st ACM SIGSPATIAL Workshop on Analytics for Local Events and News (LENS'17). ACM, New York, NY, USA, Article 3, 4 pages.

16. Jinhyung D. Park, Erik Seglem, Eric Lin, and Andreas Züfle. Protecting User Privacy: Obfuscating Discriminative Spatio-Temporal Footprints. In Proceedings of the 1st ACM SIGSPATIAL Workshop on Recommendations for Location-based Services and Social Networks(LocalRec'17), ACM, New York, NY, USA, Article 2, 4 pages.

17. Chaudhry S, Mathieu C, Bedi D, O’Kelley, Chitnis P, Hoemann CD. Ultrasound-based assessment of tissue resurfacing in a rabbit model of bone marrow stimulation to repair a chronic articular cartilage defect, Orthopedic Research Society, March 2019.

18. S. Mehrpour, T. D. LaToza and R. K. Kindi, "Active Documentation: Helping Developers Follow Design Decisions," 2019 IEEE Symposium on Visual Languages and Human-Centric Computing (VL/HCC), Memphis, TN, USA, 2019, pp. 87-96.

19. K. Chugh, A. Y. Solis and T. D. LaToza, "Editable AI: Mixed Human-AI Authoring of Code Patterns," 2019 IEEE Symposium on Visual Languages and Human-Centric Computing (VL/HCC), Memphis, TN, USA, 2019, pp. 35-43. This won the Best Paper Award Honorable Mention award at VL/HCC.

Book Chapter

1. VanMeter A, Camerini S, Polci ML, Tessitore A, Trivedi N, Heiby M, Kamal Y, Hansen J, Espina V, Petricoin III E, Liotta LA, Zhou W. Low Molecular Weight Protein Fractionation for Biomarker Discovery. Molecular Profiling, Methods and Protocols. Methods in Molecular Biology, Vol 823. Humana Press, 2012.


1. Temple Douglas, Lance A. Liotta, Claudia Fredolini, Davide Tamburro, Alessandra Luchini. Improved Lyme Disease Diagnostic Testing Using Hydrogel Bait Containing Nanoparticles, Filed Nov 2009.

2. Scott Martin, Peter Chick, Daniel Te, Brandon Parker. Networked Activity Monitoring via Electronic Tools in an Online Group Learning Course and Regrouping Students during the Course Based on the Monitored Activity. Filed September 2016.