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Selected Publications

Please click on a research topic/cluster name below for select publications by HSRI faculty. Links to journal articles may require a subscription (accessible from on-campus IP addresses)



Basic & Behavioral Neuroscience selected publications


Jiang Y, Pitmon E, Berry J, Wolf FW, McKenzie Z, and Lebestky TJ. A Genetic Screen To Assess Dopamine Receptor (DopR1) Dependent Sleep Regulation in Drosophila. G3: Genes, Genomes, Genetics (Bethesda). 2016 Dec 7;6(12):4217-4226. doi: 10.1534/g3.116.032136.



Biomolecular Research selected publications


Gay L, Miller MR, Ventura PB, Devasthali V, Vue Z, Thompson HL, Temple S, Zong H, , Cleary Michael D., Stankunas K, Doe CQ.  Mouse TU tagging: a chemical/genetic intersectional method for purifying cell type-specific nascent RNA. Genes and Development. 2013. Jan. 1; 27: 98-115.


Touma JJ, Weckerle FF, Cleary MD.  Drosophila Polycomb complexes restrict neuroblast competence to generate motorneurons.  Development.  2012 Feb; 139(4): 657-666.


"Morphology transition in lipid vesicles due to in-plane order and topological defects" L.S. Hirst, A. Ossowski, M. Fraser, J. Geng, J.V. Selinger and R.L.B. Selinger, in press, Proc. natl. Acad. Sci. (2013)


 “A Potent Strategy to Inhibit HIV by binding both gp120 and gp41”  Ioannis Kagiampakis, Arbi Gharibi, Marie K. Mankowski, Beth A. Snyder, Roger G. Ptak, Kristabelle Alatas, and Patricia J. LiWang Antimicrobial Agents and Chemotherapy 55, 264-275 (2011).


"Highly Potent Chimeric Inhibitors Targeting Two Steps of HIV Cell Entry" Bo Zhao, Marie K. Mankowski, Beth A. Snyder, Roger G. Ptak, and Patricia J. LiWang J. Biol. Chem 286, 28370-28381 (2011).


“The role of individual carbohydrate-binding sites in the function of the potent anti-HIV lectin Griffithsin” Jie Xue, Yongguang Gao, Bart Hoorelbeke, Ioannis Kagiampakis, Bo Zhao, Borries Demeler, Jan Balzarini, and Patricia J. LiWang  Molecular Pharmaceutics 4, 2613-2625 (2012).


“Cationic Intermediates in Friedel-Crafts Acylation: Structural Information from Theory and Experiment”, H. Zhu, M. P. MeyerChem. Comm. 201147, DOI: 10.1039/c0cc02286a.




Biosimulation & Modeling selected publications

Li Q, King SJ, Xu J. Native kinesin-1 does not bind preferentially to GTP-tubulin-rich microtubules in vitroCytoskeleton (Hoboken). 2017 Jul 12. doi: 10.1002/cm.21386. [Epub ahead of print] 


Michael W. Gramlich, Leslie Conway, Winnie H. Liang, Joelle A. Labastide, Stephen J. King, Jing Xu, and Jennifer L. Ross, "Single Molecule Investigation of Kinesin-1 Motility Using Engineered Microtubule Defects" orts. 2017; 7: 44290.  Published online 2017 Mar 13. doi:  10.1038/srep44290


P.J. Becich, B.P. Stark, H.S. Bhat and D.H. Ardell, "CMCpy: Genetic Code-Message Coevolution Models in Python," Evolutionary Bioinformatics 9:111-125 (2013)


P. Holloway, K.M. Swenson, D.H. Ardell, and N. El-Mabrouk, "Evolution of Genome Organization by Duplication and Loss: An Alignment Approach," RECOMB 7262/2012:94-112 (2012)


J. Hsin, A. Gopinathan and K.C. Huang, " Nucleotide-dependent conformations of FtsZ dimers and force generation observed through molecular dynamics simulations," Proc. Natl. Acad. Sci. USA, 109 (24):9432 (2012)


C. M. Isborn, A. W. Goetz, M. A. Clark, R. C. Walker, and T. J. Martinez, "Electronic Absorption Spectra from MM and ab initio QM/MM Molecular Dynamics: Environmental Effects on the Absorption Spectrum of Photoactive Yellow Protein," Journal of Chemical Theory and Computation, 8, 5092-5106 (2012)


C. Fang, F. V. Filipp, J. W. Smith, "Unusual binding of ursodeoxycholic acid to ileal bile acid binding protein: role in activation of FXRα," J Lipid Res. Apr;53(4):664-73. doi: 10.1194/jlr.M021733. PubMed PMID 22223860 (2012)


F. V. Filipp, B. Ratnikov, J. De Ingeniis, J. W. Smith, A. L. Osterman, D. A. Scott, "Glutamine-fueled mitochondrial metabolism is decoupled from glycolysis in melanoma," Pigment Cell Melanoma Res. Nov;25(6):732-9. doi:10.1111/pcmr.12000. PubMed PMID 22846158 (2012)



K. Leiderman and A.L. Fogelson, “The influence of intraclot transport on the development of platelet thrombi under flow,” Bulletin of Mathematical Biology, Oct., 1-29 (2012)


K. Leiderman and A. L. Fogelson,"Grow with the flow: a spatial–temporal model of platelet deposition and blood coagulation under flow," Mathematical Medicine and Biology, 28, 47-84 (2011)


J. Yamada, J. L. Phillips, S. Patel, G. Goldfien, A. Calestagne-Morelli, H. Huang, R. Reza, J. Acheson, V. V. Krishnan, S. Newsam, A. Gopinathan, E. Y. Lau, M. E. Colvin, V. N. Uversky and M. F. Rexach,"A Bimodal Distribution of Two Distinct Categories of Intrinsically Disordered Structures with Separate Functions in FG Nucleoporins," Molecular & Cellular Proteomics, 9, 2205-2224 (2010)


A. Derdowski, S. S. Sindi, C. L. Klaips, S. DiSalvo and T. R. Serio,"A Size Threshold Limits Prion Transmission and Establishes Phenotypic Diversity," Science, 330, 680-683 (2010)


S. S. Sindi and T. R. Serio,"Prion dynamics and the quest for the genetic determinant in protein-only inheritance," Current Opinion in Microbiology, 12, 623-630 (2009)




Cancer Research selected publications

Edwards L, Gupta R, Filipp FV. "Hypermutation of DPYD Deregulates Pyrimidine Metabolism and Promotes Malignant Progression". Molecular Cancer Research. 2016 Feb;14(2):196-206.  doi: 10.1158/1541-7786.MCR-15-0403. Epub 2015 Nov 25.


Wilson S, Qi J, Filipp FV. Refinement of the androgen response element based on ChIP-Seq in androgen-insensitive and androgen-responsive prostate cancer cell lines. Scientific Reports. 2016 Sep 14;6:32611. doi: 10.1038/srep32611.


Tiffen J, Wilson S, Gallagher SJ, Hersey P, Filipp FV. Somatic Copy Number Amplification and Hyperactivating Somatic Mutations of EZH2 Correlate With DNA Methylation and Drive Epigenetic Silencing of Genes Involved in Tumor Suppression and Immune Responses in Melanoma. Neoplasia. 2016 Feb;18(2):121-32. doi: 10.1016/j.neo.2016.01.003 


Song, A. V. & Halpern-Felsher, B. L. (in press). Predictive Relationship between Adolescent Oral and Vaginal Sex: Results from a Prospective, Longitudinal Study. Archives of Pediatrics and Adolescent Medicine.


Morrell, H. E. R., Song, A. V., & Halpern-Felsher, B. L. (in press). Changes in smoking-related perceptions of risk and benefits over time. Health Psychology.


Song, A. V. & Ling, P. M. (in press). Social smoking and cessation: Do emerging adult social smokers intend to quit? American Journal of Public Health.




Decision Making selected publications



Song, A. V. & Halpern-Felsher, B. L. (in press). Predictive Relationship between Adolescent Oral and Vaginal Sex: Results from a Prospective, Longitudinal Study. Archives of Pediatrics and Adolescent Medicine.


Morrell, H. E. R., Song, A. V., & Halpern-Felsher, B. L. (in press). Changes in smoking-related perceptions of risk and benefits over time. Health Psychology.


Song, A. V. & Ling, P. M. (in press). Social smoking and cessation: Do emerging adult social smokers intend to quit? American Journal of Public Health.


A. Derdowski, S. S. Sindi, C. L. Klaips, S. DiSalvo and T. R. Serio,"A Size Threshold Limits Prion Transmission and Establishes Phenotypic Diversity," Science, 330, 680-683 (2010)


S. S. Sindi and T. R. Serio,"Prion dynamics and the quest for the genetic determinant in protein-only inheritance," Current Opinion in Microbiology, 12, 623-630 (2009)




Environment & Health selected publications

Ricardo Cisneros, Paul Brown, Linda Cameron, Erin Gaab, Mariaelena Gonzalez, Steven Ramondt, David Veloz, Anna Song, and Don Schweizer. Understanding Public Views about Air Quality and Air Pollution Sources in the San Joaquin Valley, California.  Journal of Environmental and Public Health Volume 2017 (2017) Article ID 4535142, 7 pages. Published 2 April 2017.


Paul BrownLinda CameronRicardo Cisneros, Rachel Cox, Erin GaabMariaelena Gonzalez, Steven Ramondt, and Anna Song.  Latino and Non-Latino Perceptins of the Air Qualty in California's San Joaquin Valley. . 2016 Dec; 13(12): 1242.

Chen, Y. and Whalley, A. (2012) "Green Infrastructure: The Effects of Urban Rail Transit on Air Quality." American Economic Journal: Economic Policy, 4(1): 58-97.


C.-C. Tsao, J. E. Campbell, M. Mena-Carrasco, S. N. Spak, G. R. Carmichael, and Y. Chen, (2012) “Biofuels that Cause Land-Use Change May Have Much Larger Non-GHG Air Quality Emissions than Fossil Fuels,”Environmental Science & Technology, 46(19):10835-41. doi: 10.10.1021/es30185x.


Dawson, M.N. (2012) Parallel phylogeographic structure in ecologically similar sympatric sister taxa.Molecular Ecology 21:987-1004.


Forman, H.J., Critical Methods in Free Radical Biology & Medicine, Free Radical Biology and Medicine, Volume 47, Supplement 2, 2009, Page S207, ISSN 0891-5849, 10.1016/j.freeradbiomed.2009.09.013. 


E. Hanna, P. Huybrechts, J. Cappelen, K. Steffen, R. C. Bales, E. Burgess, J. R. McConnell, J. P. Steffensen, M. Van den Broeke, L. Wake, G. Bigg, M. Griffiths, D. Savas, Greenland Ice Sheet surface mass balance 1870 to 2010 based on Twentieth Century Reanalysis, and links with global climate forcing, JGR Atmospheres,D24121, doi:10.1029/2011JD016387, 2011



Health Disparities selected publications


Almeida, Paul D. and Roxana Delgado. 2008. “Gendered Networks and Health Care Privatization.” Advances in Medical Sociology 10: 273-299.


Mallios, R. R., Ojcius, D. M. & Ardell, D. H. An iterative strategy combining biophysical criteria and duration hidden Markov models for structural predictions of Chlamydia trachomatis sigma66 promoters. BMC Bioinformatics 10, 271 (2009).


Coutinho-Silva R, Ojcius DM. Role of extracellular nucleotides in the immune response against intracellular bacteria and protozoan parasites. Microbes Infect. 2012 May 23. [Epub ahead of print] PubMed PMID: 22634346. 


Shimada K, Crother TR, Karlin J, Dagvadorj J, Chiba N, Chen S, Ramanujan VK, Wolf AJ, Vergnes L, Ojcius DM, Rentsendorj A, Vargas M, Guerrero C, Wang Y, Fitzgerald KA, Underhill DM, Town T, Arditi M. Oxidized mitochondrial DNA activates the NLRP3 inflammasome during apoptosis. Immunity. 2012 Mar 23;36(3):401-14. Epub 2012 Feb 16. PubMed PMID: 22342844; PubMed Central PMCID: PMC3312986. 


Somboonna N, Wan R, Ojcius DM, Pettengill MA, Joseph SJ, Chang A, Hsu R, Read TD, Dean D. Hypervirulent Chlamydia trachomatis clinical strain is a recombinant between lymphogranuloma venereum (L(2)) and D lineages. MBio. 2011 May 3;2(3):e00045-11. doi: 10.1128/mBio.00045-11. Print 2011. PubMed PMID: 21540364; PubMed Central PMCID: PMC3088116.


Abdul-Sater AA, Saïd-Sadier N, Lam VM, Singh B, Pettengill MA, Soares F, Tattoli I, Lipinski S, Girardin SE, Rosenstiel P, Ojcius DM. Enhancement of reactive oxygen species production and chlamydial infection by the mitochondrial Nod-like family member NLRX1. J Biol Chem. 2010 Dec 31;285(53):41637-45. Epub 2010 Oct 19. PubMed PMID: 20959452; PubMed Central PMCID: PMC3009891.


Abdul-Sater AA, Saïd-Sadier N, Padilla EV, Ojcius DM. Chlamydial infection of monocytes stimulates IL-1beta secretion through activation of the NLRP3 inflammasome. Microbes Infect. 2010 Aug;12(8-9):652-61. Epub 2010 Apr 29. PubMed PMID: 20434582.


Pettengill MA, Lam VW, Ojcius DM. The danger signal adenosine induces persistence of chlamydial infection through stimulation of 2b receptors. PLoS One. 2009 Dec 14;4(12):e8299. PubMed PMID: 20011598; PubMed Central PMCID: PMC2788228.


Yilmaz O, Sater AA, Yao L, Koutouzis T, Pettengill M, Ojcius DM. ATP-dependent activation of an inflammasome in primary gingival epithelial cells infected by Porphyromonas gingivalis. Cell Microbiol. 2010 Feb;12(2):188-98. Epub 2009 Oct 6. PubMed PMID: 19811501; PubMed Central PMCID: PMC2807919


Abdul-Sater AA, Koo E, Häcker G, Ojcius DM. Inflammasome-dependent caspase-1 activation in cervical epithelial cells stimulates growth of the intracellular pathogen Chlamydia trachomatis. J Biol Chem. 2009 Sep 25;284(39):26789-96. Epub 2009 Jul 31. PubMed PMID: 19648107; PubMed Central PMCID: PMC2785367.


Depaoli, S. (2012). The ability for posterior predictive checking to identify model mis-specification in Bayesian growth mixture modeling. Structural Equation Modeling, 19, 534{560.



Neurodevelopmental outcomes in infants with birth asphyxia in developing countries. Journal of Pediatrics. Carlo, W.D., Goudar S.S., Pasha, O., Chomba, E., McClure, E.M., Biasini, F.J.,  Wallander, J.L., Thorsten, V., Chakraborty, H., Wright, L.L., & the BRAIN-HIT Committee and the NICHD Global Network for Women's and Children's Health Research. (in press). 


Racial/ethnic disparities in health-related quality of life and health in children are largely mediated by family contextual differences. Academic Pediatrics. Wallander, J.L., Fradkin, C., Chien, A.T., Mrug, S., Banspach, S.W., Davies, S., Elliott, M.N., Franzini, L., & Schuster, M.A. (in press).


Quality of life among Asian American children. Journal of Asian American Psychology. Fradkin, C., Wallander, J.L.,  Yamakawa, Y.,  Schwebel, D.C., Chien, A.,  Le, Y.-C.,  Li, D.,  Elliott, M, & Schuster, M. (in press). 


Racial and Ethnic Health Disparities among Fifth-Graders in Three Cities. New England Journal of Medicine 23 August 2012 n engl j med 367;8. Mark A. Schuster, M.D., Ph.D., Marc N. Elliott, Ph.D., David E. Kanouse, Ph.D., Jan L. Wallander, Ph.D., Susan R. Tortolero, Ph.D., Jessica A. Ratner, B.A., David J. Klein, M.S., Paula M. Cuccaro, Ph.D., Susan L. Davies, Ph.D., and Stephen W. Banspach, Ph.D.


Valdez Z, Ramírez AS, Estrada E, Grassi K, Nathan S.  Community Perspectives on Access to and Availability of Healthy Food in Rural Low-Resource, Latino CommunitiesPreventing Chronic Disease. 2016 Dec 15;13:E170. doi: 10.5888/pcd13.160250.


Ramirez ASDiaz Rios LK,  Valdez Z, Estrada E,  Ruiz A. Bringing Produce to the People: Implementing a Social Marketing Food Access Intervention in Rural Food Deserts. Journal of Nutrition Education and Behavior. 2017 Feb; 49(2):166-174.e1. doi: 10.1016/j.jneb.2016.10.017. Epub 2016 Dec 9. 


Ramírez AS, Willis G, Rutten LF.  Understanding Spanish-Language Response in a National Health Communications Survey: Implications for Health Communication ResearchJournal of Health Communication. 2017 May;22(5):442-450. doi: 10.1080/10810730.2017.1304470. Epub 2017 Apr 17.


Ramírez AS, Estrada E, Ruiz A. Mapping the Health Information Landscape in a Rural, Culturally Diverse Region: Implications for Interventions to Reduce Information Inequality.  Journal of Primary Prevention 2017 Aug; 38(4):345-362. doi:10.1007/s10935-017-0466-7. 




Immunity & Infectious Diseases selected publications

Beaudin AForsberg EC.  To B1a or not to B1a: do hematopoietic stem cells contribute to tissue-resident immune cells?  2016 Dec 15;128(24):2765-2769. Epub 2016 Oct 31.


Beaudin A, Boyer S, Perez-Cunningham, Hernandez G, Derderian S, Jujjavarapu C, Aaserude E, MacKenzie T, Forsberg E. A Transient Developmental Hematopoietic Stem Cell Gives Rise to Innate-Like B and T cells. Cell Stem Cell.2016 Dec 1;19(6):768-783. doi: 10.1016/j.stem.2016.08.013. Epub 2016 Sep 22.


Choi, J. Oxidative stress, endogenous antioxidants, alcohol, and hepatitis C: pathogenic interactions and therapeutic implications. Free Radical Biology & Medicine52(7):1135-1150, 2012.


Seronello, S.; Montanez, J.; Presleigh, K.; Barlow, M.; Park, S.B.; and Choi, J. Ethanol and reactive species increase basal sequence heterogeneity of hepatitis C virus RNA and produce variants with reduced susceptibility to antivirals. PLoS One 6(11):327436, 2011.


McLelland B, Gravano D, Castillo J, Montoy S and Manilay JO. (2011). Enhanced Isolation of Adult Thymic Epithelial Cell Subsets for Multiparameter Flow Cytometry and Gene Expression Analysis. Journal of Immunological Methods, Epub 2011 Feb 23. PMID: 21354161


Cain, C. J., Rueda, R., McLelland, B. T., Collette, N. M., Loots, G. G., Manilay, J. O. (2012) Absence of Sclerostin Adversely Affects B Cell Development. Journal of Bone and Mineral Research, 2012 Jul;27(7):1451-61. doi: 10.1002/jbmr.1608. PMID: 22434688 


H. Kim, N. Bai, A.K. Bhunia, G.B. King, E.D. Hirleman, and E.W. Bae, "Development of an Integrated Optical Analyzer for Characterization of Growth Dynamics of Bacterial Colonies," Journal of Biophotonics



General Biomedical Sciences selected publications

Flores NM, Oviedo NJ, and Sage J. Essential role for the planarian intestinal GATA transcription factor in stem cells and regeneration. Developmental Biology. 2016 Oct 1;418(1):179-88. doi: 10.1016/j.ydbio.2016.08.015. Epub 2016 Aug 16.


Zhang W, Zhu D, Lun M, Li C. Multiple pinhole collimator based X-ray luminescence computed tomography. Biomedical Optical Express. 2016 Jun 3;7(7):2506-23. doi: 10.1364/BOE.7.002506. eCollection 2016.


Peiris TH, Ramirez D, Barghouth PG, Ofoha U, Davidian D, Weckerle F, Oviedo NJ.  Regional signals in the planarian body guide stem cell fate in the presence of genomic instability 2016 May 15;143(10):1697-709. doi: 10.1242/dev.131318. Epub 2016 Mar 24.

Peiris TH, García-Ojeda ME, and Oviedo NJ. Alternative flow cytometry strategies to analyze stem cells and cell death in planarians. Regeneration (Oxf). 2016 Mar 16;3(2):123-35. doi: 10.1002/reg2.53. eCollection 2016


Loots, G. G., and I. Ovcharenko, “ECRBase: Database of Evolutionary Conserved Regions, Promoters, and Transcription Factor Binding Sites in Vertebrate Genomes,” Bioinformatics 22(23):1-3 (2006).


Hatano R, Luna JI, Mercurio K, Glaser D, Leppert V, McCloskey KE.  Endothelial Cells Derived from Embryonic Stem Cells Respond to Cues from Topographical Surface Patterns Microvascular Research (submitted July, 2012)


Blancas AA, Wong L, Glaser DE, McCloskey KE.  Specialized Tip/Stalk- and Phalanx-like Endothelial Cells from Embryonic Stem Cells. Stem Cells and Development (submitted  July 6, 2012)


Glaser, DE Burns A, Hatano R, Medrzycki M, Fan Y,  McCloskey KE,  Specialized Mouse Embryonic Stem Cells for Studying Vascular Development. Stem Cells and Development (submitted  July 3, 2012).


Vázquez-Medina, JP, DE Crocker, HJ Forman, RM Ortiz. 2010. Prolonged fasting does not increase oxidative damage or inflammation in a naturally adapted mammal, the northern elephant seal. J Experimental Biology, In Press


General Behavioral Medicine selected publications

Meyer OL, Liu XL, Tancredi D, Ramirez AS, Schulz R, Hinton L. Acculturalion level and caregiver outcomes from a randomized iinterventinon trial to enhance caregivers' health: evidence from REACH II.  Aging and Mental Health. 2017 Apr 24:1-8. doi: 10.1080/13607863.2017.1317330. [Epub ahead of print]


Cameron LD, Durazo A, Ramírez AS, Corona R, Ultreras M, Piva S.  Cultural and Linguistic Adaptation of a Healthy Diet Text Message Intervention for Hispanic Adults Living in the United States. Preventing Chronic Disease. 2016 Dec 15;13:E170. doi: 10.5888/pcd13.160250.

Cameron L, Marteau T, Brown P, Klein W, Sherman K. Communication Strategies for Enhancing Understanding of the Behavioral Implications of Genetic and Biomarker Tests for Disease Risk: The Role of Coherence. Journal of Behavioral Medicine (in press).