Student and Alumni Bibliography
David J. Auerbach
David J. Auerbach, Yin Lina, Huiyi Miaoa, Raffaello Cimbroa, Michelle J. DiFiorea, Monica E. Gianolinia, Lucinda Furcib, Priscilla Biswasb, Anthony S. Faucia, and Paolo Lussoa: “Identification of the platelet-derived chemokine CXCL4/PF-4 as a broad-spectrum HIV-1 inhibitor” PNAS. View Online.
He is also an Associate Dean at RPCI and has a strong interest in designing innovative and interdisciplinary graduate level training programs, both at the PhD and MS level. For example, he established a program entitled CanSys, through the European Union-United States Atlantis Program, which fuses RPCI with two EU universities (The University of Luxembourg and the Free University, Amsterdam). The CanSys program develops quantitative modeling skills in MS students through taught courses and research undertaken at each of the three member institutes. He is also leading the development of graduate curricula at RPCI.
Click here for Dr. Campbell’s Podcast.
Click here for Dr. Campbell’s Blog.
Click here for a list of Dr. Campbell’s publications.
Christina S. Chang
Following her graduation from JHU with Master’s of Science in Biotechnology, concentration in Biodefense, she joined as a visiting scientist fellow at the Federal Bureau of Investigation Laboratory working on counter-terrorism forensic science research.
Suthanthiran M, Schwartz JE, Ding R, Abecassis M, Dadhania D, Samstein B, Knechtle SJ, Friedewald J, Becker YT, Sharma VK, Williams NM, Chang CS, Hoang C, Muthukumar T, August P, Keslar KS, Fairchild RL, Hricik DE, Heeger PS, Han L, Liu J, Riggs M, Ikle DN, Bridges ND, Shaked A: “Urinary-cell mRNA profile and acute cellular rejection in kidney allografts.” The New England Journal of Medicine 369(1) published in 2013. View online.
Yang H, Cheng EY, Sharma VK, Lagman M, Chang C, Song P, Ding R, Muthukumar T, Suthanthiran M: “Dendritic cells with TGF-β1 and IL-2 differentiate naive CD4+ T cells into alloantigen-specific and allograft protective Foxp3+ regulatory T cells.” Transplantation 93(6) published in 2012. View online.
Cheng EY, Sharma VK, Chang C, Ding R, Allison AC, Leeser DB, Suthanthiran M, Yang H: “Diannexin decreases inflammatory cell infiltration into the islet graft, reduces β-cell apoptosis, and improves early graft function.” Transplantation 90(7) published in 2010. View online.
Dadhania D, Snopkowski C, Ding R, Muthukumar T, Chang C, Aull M, Lee J, Sharma VK, Kapur S, Suthanthiran M: “Epidemiology of BK virus in renal allograft recipients: independent risk factors for BK virus replication.” Transplantation 86(4) published in 2008. View online.
Shin-ya Takemura, Arjun Bharioke, Zhiyuan Lu, Aljoscha Nern, Shiv Vitaladevuni, Patricia K. Rivlin, William T. Katz, Donald J. Olbris, Stephen M. Plaza, Philip Winston, Ting Zhao, Jane Anne Horne, Richard D. Fetter, Satoko Takemura, Katerina Blazek, Lei-Ann Chang, Omotara Ogundeyi, Mathew A. Saunders, Victor Shapiro, Christopher Sigmund, Gerald M. Rubin, Louis K. Scheffer, Ian A. Meinertzhagen & Dmitri B. Chklovskii: “A visual motion detection circuit suggested by Drosophila connectomics” Nature 500 published August 2013. View Online.
Kathryn Cole and Merry Lee Bain: “Post-market device surveillance in the US: the MedWatcher platform.” SCRIP Regulatory Affairs published in 2013. Click to download (PDF).
Zuoxiang Xiao, Qun Jiang, Jami Willette-Brown, Sichuan Xi, Feng Zhu, Sandra Burkett, Timothy Back, Na-Young Song, Mahesh Datla, Zhonghe Sun, Romina Goldszmid, Fanching Lin, Travis Cohoon, Kristen Pike, Xiaolin Wu, David S. Schrump, Kwok-Kin Wong, Howard A. Young, Giorgio Trinchieri, Robert H. Wiltrout and Yinling Hu: “The Pivotal Role of IKKa in the Development of Spontaneous Lung Squamous Cell Carcinomas,” Cell Press, April 2013. View Online.
Professor Dennis has practiced immigration law and researches in immigration law and patent law. She also serves as a Deputy Editor for the American Bar Association’s Section of International Law – International Law News, and as Editor-in-chief for the International Journal of Liability and Scientific Enquiry.
Professor Dennis holds a J.D. from Temple University, a B.A. from Rutgers University, a M.S. in Biotechnology from The Johns Hopkins University, and a M.A.Ed. in Higher Education from Trident University. She is admitted to the Pennsylvania bar, the U.S. Court of Appeals for the Second Circuit, and the U.S. Patent and Trademark Office.
Dennis, Johanna K.P. “What’s mine is mine and what’s yours is mine too: Converging U.S. intellectual property exhaustion doctrines.” Computer Law & Security Review 30:1 published in 2014. View online.
Dennis, Johanna K.P. “Owning Methods of Conducting Business in Cyberspace” Cyberspace Law Ed. Hannibal Travis. Routledge, 2013. View online.
Sean is currently in his fifth year of doctoral research in the area of HIV-host protein interactions. His doctoral thesis has focused on the assembly of a viral E3 ubiquitin ligase complex including HIV-1 accessory protein, viral infectivity factor (Vif) and host factors that are required for Vif function and HIV survival. His work has further characterized how all of these proteins come together using in vitro and in vivo cell based assays. Sean has co-authored eleven peer-reviewed publications and was a recipient of the Ruth L. Kirschtein National Research Service Award Pre-doctoral Fellowship.
In addition to his doctoral research, Sean was an analyst intern with the Johns Hopkins Office of Technology Transfer until November 2013. In this capacity, he reviewed new technologies from multiple fields, including the life and physical sciences as well as medical devices and software applications. Furthermore, he performed prior art, patentability, as well as market analyses in order to generate a technical report and marketing summary for each invention.
Sean will defend his dissertation February 10, 2014 and pursue a career in life sciences research and/or consulting at a biotechnology/pharmaceutical company, a government research agency, or a private firm.
Click here for a list of Sean’s publications.
Waleed Haso, Damiel W. Lee, Nirali N. Shah, Maryalice Stetler-Stevenson, Constance M. Yuan, Ira H. Pastan, Dimiter S. Dimitrov, Richard A. Morgan, David J. FitzGerald, David M. Barrett, Alan S. Wayne, Crystal L. Mackall, and Rimas J. Orentas: “Anti-CD22-chimeric antigen receptors targeting B cell precursor acute lymphoblastic leukemia.” Blood Journal, published December 2012. View Online.
Click here for a list of Ross’ publications.
Jim F. Huggett, Carole A. Foy, Vladimir Benes, Kerry Emslie, Jeremy A. Garson, Ross Haynes, Jan Hellemans, Mikael Kubista, Reinhold D. Mueller, Tania Nolan, Michael W. Pfaffl, Gregory L. Shipley, Jo Vandesompele, Carl T. Wittwer, and Stephen A. Bustin: “The Digital MIQE Guidelines: Minimum Information for Publication of Quantitative Digital PCR Experiments” Clinical Chemistry 59:6 published in 2013. Click to download (PDF).
Seth worked in Emergency Medicine for three years as a Lead Research Associate on a grant funded by AHRQ to reduce the amount of ionizing radiation patients with renal colic receive from CT scans. During his time in Emergency Medicine Seth also became a Filemaker developer. Using these skills he created databases from scratch that house all patient-related study data for the department of Emergency Medicine’s federally funded research, which totals more than 8 million dollars in grants per year. The databases he created are accessible via iPad’s and allow for live electronic data capture in the Emergency Room.
Because of Seth’s success in Emergency Medicine, he has consulted for other departments in the Yale School of Medicine, including the departments of Otolaryngology Surgery and Endocrine Surgery; helping their study teams determine what type of data, services and databases will best suit their needs.
Outside Yale University, Seth is the database manager for a collaborative project between Kiaser Permanente Santa Clara Medical Center in California and Wellington Regional Hospital in New Zealand. He also is a Usability and Functionality Consultant and is currently helping a small tech start-up, SherlockMD, in Los Angeles, CA get their first website and iOS app launched. Lastly, he helps Health Bridges International, a non-profit organization dedicated to improving people’s health in developing countries through sustainable methods, with the analysis of data they have collected in Peru to examine the effectiveness of their programs.
Seth currently works for the Yale Center for Clinical Investigation as an OnCore Research Coordinator. Seth started the JHU Biotechnology program in the fall of 2013 and plans to concentrate his studies in bioinformatics. After graduating he hopes to use his degree to help bridge the gap between the clinical research world and the IT world. Seth is particularly interested in translational bioinformatics and using big data from the electronic medical record to perform disease phenotyping.
Moore, C., Daniels, B., Singh, D., Luty, S., Molinaro, A., & Gross, C. (2013). “Prevalence and Clinical Importance of Alternative Causes of Symptoms Using a Renal Colic Computed Tomography Protocol in Patients With Flank or Back Pain and Absence of Pyuria.” Academic Emergency Medicine, 20(5), 470-478. Click to download (PDF).
Herbst, M.K., Rosenberg, G., Daniels, B., Gross, C.P., Singh, D., Molinaro, A., Luty, S., Moore, C.L. (2014) “Effect of Provider Experience on Clinician-Performed Ultrasonography for Hydronephrosis in Patients With Suspected Renal Colic.” Annals of Emergency Medicine View Online.
Christopher L Moore, Scott Bomann, Brock Daniels, Seth Luty, Annette Molinaro, Dinesh Singh, Cary P Gross: “Derivation and validation of a clinical prediction rule for uncomplicated ureteral stone—the STONE score: retrospective and prospective observational cohort studies” BMJ published in 2014. Click to download (PDF).
Nipun A. Mistry
Christopher J. Donnelly, Ping-Wu Zhang, Jacqueline T. Pham, Aaron R. Heusler, Nipun A. Mistry, Svetlana Vidensky, Elizabeth L. Daley, Erin M. Poth, Benjamin Hoover, Daniel M. Fines, Nicholas Maragakis, Pentti J. Tienari, Leonard Petrucelli, Bryan J. Traynor, Jiou Wang, Frank Rigo, C. Frank Bennett, Seth Blackshaw, Rita Sattler, and Jeffrey D. Rothstein, “RNA Toxicity from the ALS/FTD C9ORF72 Expansion Is Mitigated by Antisense Intervention,” Neuron 80, published October 2013. Click to download (PDF).
Peter K. Todd and Henry L. Paulson, “C9orf72-Associated FTD/ALS: When Less Is More,” Neuron 80, published October 2013. Click to download (PDF).
Jarrett D. Morrow
Jarrett D. Morrow and Brandon W. Higgs: CallSim: Evaluation of Base Calls Using Sequencing Simulation, ISRN Bioinformatics, published 2012. View Online.
Dr. Atara Noiade
Atara Noiade, “The Impact of FDA Enforcement of DSHEA on the Practice of Traditional Asian Herbal Medicine,” Update magazine, published December 2012. Click to download (PDF).
Atara Noiade, “Drug Reimportation: Is It the Solution to the High Cost of Prescription Drugs in the US?” Regulatory Focus magazine, published April 2013. Click to download (PDF).
During his post-doctoral work, Houtan was supervised under Dr. Coetzee who is well known for his expertise in molecular biology, specifically works with ChIP-Chip and epigenetics in the area of prostate cancer. Recently his involvement with Genome-wide association studies (GWAS) to characterize risk loci in prostate cancer has received a lot of attention around the world. In the ‘post-GWAS’ era, the aim is to understand the functional consequences underlying cancer risk loci. In doing so, novel biological insights may be revealed leading to clinical benefits, including the development of reliable biomarkers, effective screening and disease prevention strategies. GWAS have identified more than 50 genetic risk loci for prostate cancer, however exactly how they affect risk is unknown. In this project, Houtan determined such mechanisms, revealing novel genes and preventive risk strategies. This work was the first comprehensive look at the 50+ risk loci for prostate cancer and provided a vital link to further study the biology of the proposed regions with emphasis on androgen receptor signaling. Houtan’s experience in Dr. Laird and Dr. Coetzee’s lab has enriched his skills and allowed him the opportunity to learn new areas of science.
Currently, Houtan is an assistant professor at the University of Sao Paulo at the Ribeirao Preto Medical School in the department of genetics. Houtan’s goal as an assistant professor is to develop the bioinformatics courses and program and study the area of genomics and epigenomics in human cancer.
Michela Biancolella, Barbara K Fortini, Stephanie Tring, Sarah J. Plummer, Gustavo A. Mendoza-Fandino, Jaana Hartiala, Michael J. Hitchler, Chunli Yan, Fredrick R. Schumacher, David V. Conti, Christopher K. Edlund, Houtan Noushmehr, Simon G. Coetzee, Robert S. Bresalier, Dennis J. Ahnen, Elizabeth L. Barry, Benjamin P.
Burman, Judd C. Rice, Gerhard A. Coetzee, Graham Casey: “Identification and Characterization of Functional Risk Variants for Colorectal Cancer Mapping to Chromosome 11q23.1″ Oxford University Press published in 2013. View Online.
Cameron W. Brennan, Roel G.W. Verhaak, Aaron McKenna, Benito Campos, Houtan Noushmehr, et al.: “The Somatic Genomic Landscape of Glioblastoma” Cell 155 published October 2013. View online.
The Cancer Genome Atlas Research Network, John N Weinstein, Eric A Collisson, Gordon B Mills, Kenna R Mills Shaw, Brad A Ozenberger, Kyle Ellrott, Ilya Shmulevich, Chris Sander & Joshua M Stuart: “The Cancer Genome Atlas Pan-Cancer analysis project” Nature Genetics 45:10 published October 2013. View online.
Suhn Kyong Rhie, Simon G. Coetzee, Houtan Noushmehr, Chunli Yan, Jae Mun Kim, Christopher A. Haiman, Gerhard A. Coetzee: “Comprehensive Functional Annotation of Seventy-One Breast Cancer Risk Loci” PLoS ONE 8:5 published May 2013. View online.
Paul D P Pharoah, et al: “GWAS meta-analysis and replication identifies three new susceptibility loci for ovarian cancer” Nature Genetics 45:4 published April 2013. View online.
Jennifer Permuth-Wey, Kate Lawrenson, Howard C. Shen, et al: “Identification and molecular characterization of a new ovarian cancer susceptibility locus at 17q21.31″ Nature Communications 4:1627 published March 2013. View online.
Jennifer S. Dickey, Yanira Gonzalez, Baikuntha Aryal, Steven Mog, Asako J. Nakamura, Christophe E. Redon, Ulrich Baxa, Elliot Rosen, Gang Cheng, Jacek Zielonka, Palak Parekh, Karen P. Mason, Joy Joseph, Balaraman Kalyanaraman, William Bonner, Eugene Herman, Emily Shacter, V. Ashutosh Rao: “Mito-Tempol and Dexrazoxane Exhibit Cardioprotective and Chemotherapeutic Effects through Specific Protein Oxidation and Autophagy in a Syngeneic Breast Tumor Preclinical Model.” PLoS ONE 8(8) published in 2013. View online.
Priyanka works in a Crystallography lab and is part of a team that is actively involved in seeking active state Neurotensin structure as close as it can get to native human protein form. Priyanka is also involved in a Career Development committee of NIH, as a part of which she organized bi-monthly panels on current Science based career fields which are developing today. Avid reader and rock climber, Priyanka hopes to continue her pursuit of Science more from a Management point of view in the future.
Jim F. White, Nicholas Noinaj, Yoko Shibata, James Love, Brian Kloss, Feng Xu, Jelena Gvozdenovic-Jeremic, Priyanka Shah, Joseph Shiloach, Christopher G. Tate & Reinhard Grisshammer: “Structure of the agonist-bound neurotensin receptor” Nature 490 published in 2012. Click to download (PDF).
Maria Ximena Sosa
Maria Ximena Sosa,I. K. Ashok Sivakumar,Samantha Maragh, Vamsi Veeramachaneni, Ramesh Hariharan, Minothi Parulekar, Karin M. Fredrikson, Timothy T. Harkins, Jeffrey Lin, Andrew B. Feldman, Pramila Tata, Georg B. Ehret, Aravinda Chakravarti: “Next-Generation Sequencing of Human Mitochondrial Reference Genomes Uncovers High Heteroplasmy Frequency” PLoS Comput Biol 8(10) published October 2012. View Online.
Srirangan Sampath, Shambu Bhat, Simone Gupta, Ashley O’Connor, Maria Ximena Sosa, Andrew B. West, Dan E. Arking, Aravinda Chakravarti: “Defining the Contribution of CNTNAP2 to Autism Susceptibility” PLoS ONE 8(10) published October 2013. View Online.
Andrew W. Tanner
Carabetta, V. J., A. W. Tanner, T.M. Greco, M. Defrancesco, I.M. Cristea, and D. Dubnau (2013). “A complex of YlbF, YmcA and YaaT regulates sporulation, competence and biofilm formation by accelerating the phosphorylation of Spo0A.” Molecular microbiology 88(2): 283-300. View Online.
Ryan C. Thompson, Iosif Vardinogiannis and Thomas D. Gilmore: “Identification of an NF-κB p50/p65-responsive site in the human MIR155HG promoter” BMC Molecular Biology 14:24 published in 2013. Click to download (PDF).
Ryan C. Thompson, Iosif Vardinogiannis and Thomas D. Gilmore: “The Sensitivity of Diffuse Large B-Cell Lymphoma Cell Lines to Histone Deacetylase Inhibitor-Induced Apoptosis Is Modulated by BCL-2 Family Protein Activity” PLOS ONE 8:5 published May 2013. Click to download (PDF).
Alex Zhavoronkov, Ph.D.
Alex Zhavoronkov, Nawazish Mirza, Irog Artuhov, Edouard Debonneuil. “Evaluating the impact of recent advances in biomedical sciences and the possible mortality decreases on the future of health care and Social Security in the United States” Pensions 2012 Dec 14. 17, 241 – 251. doi: 10.1057/pm.2012.28. View Online.
Anastasia A. Zabolotneva, Alex Zhavoronkov, Andrew V. Garazha, Sergey A. Roumiantsev and Anton A. Buzdin. “Characteristic patterns of microRNA expression in human bladder cancer”
Gene. doi: 10.3389/fgene.2012.00310. View Online.
Moskalev A, Plyusnina E, Shaposhnikov M, Shilova L, Kazachenok A, Zhavoronkov A. ”The role of D-GADD45 in oxidative, thermal and genotoxic stress resistance” Cell Cycle. 2012 Oct 24;11(22). View Online.
Zhavoronkov A, Smit-McBride Z, Guinan KJ, Litovchenko M, Moskalev A. “Potential therapeutic approaches for modulating expression and accumulation of defective lamin A in laminopathies and age-related diseases.” J Mol Med (Berl). 2012 Oct 23. View Online.
Nepomnyashchaya YN, Artemov AV, Roumiantsev SA, Roumyantsev AG, Zhavoronkov A. “Non-invasive prenatal diagnostics of aneuploidy using next-generation DNA sequencing technologies, and clinical considerations.” Clin Chem Lab Med. 2012 Sep 29;0(0):1-14. doi: 10.1515/cclm-2012-0281.
Moskalev AA, Smit-McBride Z, Shaposhnikov MV, Plyusnina EN, Zhavoronkov A, Budovsky A, Tacutu R, Fraifeld VE. “Gadd45 proteins: relevance to aging, longevity and age-related pathologies” Ageing Res Rev. 2012 Jan;11(1):51-66. doi: 10.1016/j.arr.2011.09.003
Zhavoronkov A, Cantor CR. “Methods for structuring scientific knowledge from many areas related to aging research” PLoS One. 2011;6(7):e22597. doi: 10.1371/journal.pone.0022597. View Online.
Bobrov P, Frolov A, Cantor C, Fedulova I, Bakhnyan M, Zhavoronkov A. ”Brain-computer interface based on generation of visual images” PLoS One. 2011;6(6):e20674. doi: 10.1371/journal.pone.0020674. View Online.
V. A. Tverdislov,, L. V. Yakovenko,, A. A. Zhavoronkov. “Chirality as a problem of biochemical physics” Russian Journal of General Chemistry, November 2007, Volume 77, Issue 11, pp 1994-2005. View here (PDF).
Dating AI: A Guide to Falling In Love with Artificial Intelligence
Alex Zhavoronkoff, Ph.D.
Re/Search Publications, San Francisco, 2012, ISBN: 978-1889307350
The Ageless Generation: How Advances in Biomedicine Will Transform the Global Economy
Alex Zhavoronkov, Ph.D.
Palgrave Macmillan, New York, 2013, ISBN: 978-0230342200
Jamie Austin (Faculty Member)
Austin, Jamie. Fundamentals of Canadian Regulatory Affairs, Fourth Edition. Published in 2013. View online.
Eric Langer (Faculty Member)
He lectures extensively on pricing and channel management topics, and teaches at Johns Hopkins University and American University: Biotechnology Marketing, Marketing Management, Services Marketing, Advertising Strategy, and Bioscience Communication. He has developed numerous courses, classes and seminar programs, including Marketing in a Regulated Environment, Marketing Technical Products, and TechniManagement.™ In 1989 he co-founded BioPlan Associates, Inc. a biotechnology and life sciences marketing company that provides information, market research, pricing, and market analysis to biotechnology and healthcare organizations. He has launched and managed marketing programs for product lines ranging from $500k to $500 million. His company works with both large and small clients at commercial biotechs, non-profit organizations, and governments in assessing and evaluating markets, and marketing strategies and tactics.
Click here for a list of Eric’s publications.
Joshua Orvis (Faculty Member)
Click here for a list of Joshua’s publications.
Click here to read Joshua’s Reddit AMA Session.
Mathumathi Rajavel (Faculty Member)
She is teaching for AAP Program since 2001 (core and elective courses) both online and onsite. She is currently an Assistant Professor at Morgan State University and her research involves manipulating bacteriophages to combat infections caused by multi-drug resistant bacterial pathogens.
Fouts DE, Klumpp J, Bishop-Lilly KA, Rajavel M, Willner KM, Butani A, Henry M, Biswas B, Li M, Albert MJ, Loessner MJ, Calendar R,
Sozhamannan S. (2013). Whole genome sequencing and comparative genomic analyses of two Vibrio cholerae O139 Bengal-specific Podoviruses to other N4-like phages reveal extensive genetic diversity. Virol J. 28; 10: 165. View online.