草莓社区

Center for Biomedical Informatics members (highlighted) have engaged in the following funded projects:

1. NIH R01 (1R01DK146430-01), 02/04/2026-01/31/2031, Critical Crystal-Bacteria and Host Interactions Contributing to Kidney Stone Formation. Andrew Lawrence Schwaderer (Indiana University, contact PI), Alan Wolfe (Loyola, MPI), Qunfeng Dong (Loyola, MPI), Xiang Gao (Loyola, co-I)
2. NIH R25 (2R25DK122954-06), 03/15/2026-01/31/2031, Undergraduate Research Experience in Transdisciplinary Benign Urologic Disease, Catherine E. Putonti (Loyola, PI), Alan Wolfe (Loyola, co-I), Thythy Pham (Loyola, co-I), Qunfeng Dong (Loyola, co-I) 
3. NIH R01 (R01AG082135), 04/15/2023-12/31/2027, Sex-specific regulation of microRNAs in Alzheimer Disease. Toni R. Pak (Loyola, PI), Qunfeng Dong (Loyola, co-I)
4. NIH R21 (R21AI163638), 04/25/2022 – 03/31/2024, A Microbial Model for the Formation of Calcium Oxalate and Calcium Phosphate Stones, Multiple Principal Investigators: Andrew L. Schwaderer (Indiana University School of Medicine, contact PI), Alan J. Wolfe (Loyola, co-PI), Qunfeng Dong (Loyola, co-PI); co-Investigator, Xiang Gao (Loyola, co-I).
5. NIH R25 (2020-2025) Undergraduate Research Experience in Transdisciplinary Benign Urologic Disease. Catherine Putonti (multi-PI), Alan Wolfe (multi-PI), and Qunfeng Dong (multi-PI). Elizabeth R. Mueller (co-I). 
6. Loyola Research Funding Committee (RFC), Role of Bladder Microbiome in Response to Intravesical BCG Therapy for Bladder Cancer  (Jan 1st, 2019 – Dec 31, 2019). PI, Dr. Gopal Gupta; Co-Investigators: Drs. Alan Wolfe, and Qunfeng Dong
7. NIH R01 (1R01AI134727-01A1), The Role of the Skin Microbiome in Cutaneous Ulcers in Children in the Tropics (07/13/2018 – 06/30/2021). PI (Dr. Stanley Spinola, Indiana University Medical School), Co-Investigators: Drs. David E Nelson (Indiana), Yunlong Liu (Indiana), Barry P Katz (Indiana), Julia Williams (Indiana), Katherine R Fortney (Indiana), and Qunfeng Dong (Loyola)
8. NIH T54, Summer Research Experience for Medical Students in Inflammation and Infectious Disease (07/20/2017-06/30/2022). PI: Edward Campbell, Co-PI: Elizabeth Muller. Faculty mentors: Francis Alonzo, Susan Baker, Larissa Bresler, Cynthia Brincat, Mashkoor Choudhry, Mark Cichon, Nina Clark, Andrew Dingwall, Qunfeng Dong, Adam Driks, Jawed Fareed, Colleen Fitzgerald, Makio Iwashima, Katherine Knight, Jennifer Layden, Phong Le, Caroline Le Poole, Herbert Mathews, Katherine Radek, Susan Uprichard, Karen Visick, and Alan Wolfe.
9. 草莓社区 Cardiovascular Research Institute grant (AU103331), 2016-2017, Developing novel bioinformatics software for gene expression network analysis, PI, Dr. Qunfeng Dong
10. Loyola Research Funding Committee (RFC), Kidney Stone Urinary Microbiota in the Context of Metabolic Syndrome. (Jan 1st, 2017 – Dec 31, 2017). PI, Dr. Kristin Baldea, Co-Investigators: Drs. Ahmer Farooq, Larisa Bresler, Thomas Turk, Alan Wolfe, Xiang Gao, and Qunfeng Dong
11. United States – Israel Binational Science Foundation #2012063, Relationships between rodents and bacterial diversities, (2013 – 2017). Investigators: Drs. Hawlena Hadas, Ben Gurion University, Beer Sheva, Israel; Clay Keith, Fuqua Clay, Indiana University, Qunfeng Dong, Loyola. 
12. Maternal obesity and immune developmental programming, role of the microbiome (NIH R21 HD088948-01, 08/01/2016 - 07/31/2019). Multi–PIs: Drs. Ellen Kraig and Cun Li (UTHSCSA) and Dr. Qunfeng Dong (Loyola). Co-investigator: Dr. Xiang Gao (Loyola).
13. The female urinary microbiome and urinary incontinence (NIH R01 DK104718, 12/01/2015-11/30/2020), PI - Drs. Linda Brubaker & Alan Wolfe, 草莓社区 Stritch School of Medicine. Co-investigators: Drs. Cynthia Brincat, Qunfeng Dong, Colleen Fitzgerald, Stephanie Kliethermes, Elizabeth Mueller, Paul Schreckenberger, Michael Zilliox.
14. The role of urethral microbiome in idiopathic urethritis in men (NIH R01 5R01AI116706, 12/01/2015-11/30/2020). PI: Drs. David Nelson and Byron Batteiger, Indiana University School of Medicine. Co-investigators: Drs. Janet Arno (Indiana Univ.), Barry Katz (Indiana Univ.), Qunfeng Dong(Loyola).
15. The Female Urinary Microbiome: Adjacent Microbiomes and Clinical Associations (NIH P20 DK108268, 12/01/2015-11/30/2017). PI: Dr. Alan Wolfe, 草莓社区 Stritch School of Medicine. Co-investigators: Drs. Linda Brubaker, Qunfeng Dong, Stephanie Kliethermes, Elizabeth Mueller, Michael Zilliox.
16. Variability of Male Urinary Microbiota in the Context of Benign Prostatic Hyperplasia and Response to Surgical Treatment (LUMC Intramual Grant 2015-2017). PI: Dr. Ahmer V. Farooq, 草莓社区. Co-PI: Drs. Jeffery Branch, Larissa Bresler, Qunfeng Dong, Alan J. Wolfe.
17.  (NIH U01, 2013-2018). PI: Drs. Homer Twigg III (Indiana University School of Medicine) and George Weinstock (The Jackson Laboratory). Co-investigators: Drs. Kenneth Knox (University of Arizona), David Nelson (Indiana Univ.), Barry Katz (Indiana Univ.), Qunfeng Dong (Loyola).
18. (NSF 03/01/2013-02/28/2019). PI: Dr. Erik Vollbrecht, Iowa State University. Co-investigators: Drs. Sarah Hake (UC Berkeley, USDA), Dave Jackson (Cold Spring Harbor Laboratory), (Carnegie Institution for Science, Stanford University), Torbert Rocheford (Purdue University), Andrea Eveland (Donald Danforth Plant Science Center), Qunfeng Dong (Loyola).
19. (American Diabetes Association, 2013-2016). PI: Dr. Nicolas Musi, University of Texas Health Science Center in San Antonio. Co-investigator: Qunfeng Dong (Loyola).
20. Diversity and dynamic stability of the ocular surface microbiome (NIH R01 2012-2017). PI: Drs. Valery Shestopalov (University of Miami School of Medicine) and Russell Van Gelder (University of Washington). Co-investigators: Drs. David Nelson (Indiana Univ.), Qunfeng Dong (Loyola).
21. (NIH U01, 2009-2015). PI: Dr. Homer Twigg III (Indiana University School of Medicine) and Dr. George Weinstock (The Jackson Laboratory). Co-investigators: Drs. Kristina Crothers (Yale University), Kenneth Knox (University of Arizona), Richard Gregory (Indiana Univ.), David Nelson (Indiana Univ.), Barry Katz (Indiana Univ.), Yuzhen Ye (Indiana Univ.), Qunfeng Dong (Loyola).
22. (NIH UH2/UH3 2009-2013)鈥�. PI: Dr. J. Dennis Fortenberry (Indiana Univ.). Co-investigators: Drs. David Nelson, George Weinstock, Erica Sodergren, Barbara Van Der Pol, Sarah Wiehe, Mary Ott, Barry Katz, Qunfeng Dong.
23. (NIH 2009-2011).  PI: Dr. Jeoffrey Fox (Indiana University).  Co-investigators: Drs. Yves Brun, Peter Cherbas, Qunfeng Dong, J. Dennis Fortenberry, Roger Innes, David Nelson, Marlon Pierce, Craig Stewart, Homer Twigg.

Center for Biomedical Informatics members (highlighted) have published the following: 

1. Baeuerle, E., Semwal, M. K., Nie, J., Zhang, N., Liang, H., Ganapathy, V., Sathavarodom, N., Fernandez, R., Wang, C. P., Espinoza, S., Dong, Q., Yang, Z., Kostic, A., & Musi, N. (2026). Effect of Sevelamer versus Bifidobacterium longum on Insulin Sensitivity in Subjects with Obesity. Obsity accepted for publication
2. Brothwell, J. A., Toh, E., Xing, Y., Dong, Q., Xu, L. H., Giacani, L., Beiras, C. G., Mitjà, O., Gao, X., & Spinola, S. M. (2026). The etiology of exudative cutaneous ulcers in a yaws-endemic community prior to receipt of antimicrobials is similar to that found in communities after mass treatment with azithromycin. mSphere, 11(3), e0091925. https://doi.org/10.1128/msphere.00919-25
3. Hurst, J. H., Xing, Y., Dong, Q., Hoberman, A., Gao, X., & Shaikh, N. (2025). Age and antibiotic use influence longitudinal dynamics of the upper respiratory microbiome in children with recurrent acute otitis media. mSphere, 10(12), e0046825.  
4. Yap, JQ., Nikouee, A., Kim, M., Cao, Q., Rademacher, DJ., Lau, JE., Arora, A., Zou, LY., Sun, Y., Szweda, L., Sadek, H., Elliot, S., Roos, B., Glassberg, MK., Ji, HL., Gao, X., Dong, Q., Zang, QS. (2025) Myocardial pyruvate dehydrogenase kinase 4 drives sex-specific cardiac responses to endotoxemia. JCI Insight. 2025 Jul 8;10(13):e191649. doi: 10.1172/jci.insight.191649. PMID: 40626362; PMCID: PMC12288905
5. Xing, Y., Bormes, G., Bai, J., Liu, F., Dong, Q., & Gao, X. Identification of secretion-related genes as potential non-invasive biomarkers for assessing NASH fibrosis severity. Journal of Biomedical Research and Practice. 2024 Vol 3 Article ID: 100016
6. Ashley C.N., Broni E., Wood C.M., Okuneye T., Ojukwu M-P.T., , Dong Q, Gallagher C., Miller III W.A. (2024). Identifying potential monkeypox virus inhibitors: an in silico study targeting the A42R protein. Front. Cell. Infect. Microbiol., 04 March 2024 Sec. Molecular Viral Pathogenesis
   Volume 14 - 2024 | 
7. Claudia Vilo C, Galetovic A, Dong Q, Go虂mez-Silva B (2023).  Austin J Proteomics Bioinform. & Genomics. 2023; 8(1): 1034.
8. Toh E, Xing Y, Gao X, Jordan SJ, Batteiger TA, Batteiger BE, Van Der Pol B, Muzny CA, Gebregziabher N, Williams JA, Fortenberry LJ, Fortenberry JD, Dong Q*, Nelson DE. . Cell Rep Med. 2023 Mar 21;4(3):100981. doi: 10.1016/j.xcrm.2023.100981. PMID: 36948151; PMCID: PMC10040456. *co-corresponding author
9. Griesenauer B, Xing Y, Fortney KR, Gao X, González-Beiras C, Nelson DE, Ren J, Mitjà O, Dong Q*, Spinola SM. . PLoS Negl Trop Dis. 2022 Dec 19;16(12):e0011009. doi: 10.1371/journal.pntd.0011009. PMID: 36534698; PMCID: PMC9810193. *co-corresponding author
10. Claudia Vilo, Qunfeng Dong, Alexandra Galetovic, Benito Gómez-Silva (2022)  Microorganisms July 27; 10(8):1517. doi: 10.3390/microorganisms10081517.
11. Linda Brubaker, Jean-Philippe Gourdine, Nazema Siddiqui, Amanda Holland, Thomas Halverson, Roberto Limeira, David Pride, Lenore Ackerman, Catherine Forster, Kristin Jacobs, Krystal Thomas-White, Catherine Putonti, Qunfeng Dong, Michael Weinstein, Emily Lukacz, Lisa Karstens, and Alan Wolfe (2021) . mSystems. 2021 Aug 31;6(4):e0137120. doi: 10.1128/mSystems.01371-20. Epub 2021 Jul 20. PMID: 34282932; PMCID: PMC8409733.
12. Toh E, Gao X, Williams JA, Batteiger T, Coss LA, Gebregziabher N, LaPradd M, Ren J, Geisler WM, Dong Q, Xing Y, Ermel AC, Nelson DE, Jordan S (2021) . Sex Transm Dis. 2022 Jan 1;49(1):67-75. doi: 10.1097/OLQ.0000000000001509. PMID: 34618416; PMCID: PMC8665015.
13. Linda Brubaker, Catherine Putonti, Qunfeng Dong, Alan Wolfe (2021) . Mamm Genome. 2021 Aug;32(4):232-238. doi: 10.1007/s00335-021-09862-8. Epub 2021 Mar 2. PMID: 33651197. 
14. Chen C.X.*, Carpenter, J.S., Gao, X.*, Toh, E., Dong, Q, Nelson, D.E., Mitchell, C., Fortenberry, J. D. (2021). . Nursing Research. (*co-corresponding authors), Vol. 70, No. 4, July/August 2021. doi:10.1097/NNR.0000000000000510
15. Kelly R. Reveles, Eric H. Young, Amina R.A.L. Zeidan, Qunfeng Dong (2021) , Editor(s): Nicolas Musi, Peter J. Hornsby, In Handbooks of Aging, Handbook of the Biology of Aging (Ninth Edition), Academic Press, 2021, Pages 367-389, ISBN 9780128159620, .
16. Brad Griesenauer, Camila González-Beiras, Kate Fortney, Huaiying Lin, Xiang Gao, Charmie Godornes, David Nelson, Barry Katz, Sheila A. Lukehart, Oriol Mitja, Qunfeng Dong, and Stanley Spinola (2020) . mBio. , Jan 2021, 12 (1) e03162-20; DOI: 10.1128/mBio.03162-20
17. Xiang Gao and Qunfeng Dong (2020)  Journal of the American Medical Informatics Association Open Access, 10 Nov 2020, ooaa062, doi:10.1093/jamiaopen/ooaa062 
18. Qunfeng Dong and Xiang Gao (2020)   Journal of the American Medical Informatics Association Open Access. 23 October 2020, ooaa049, doi:10.1093/jamiaopen/ooaa049
19. Xiang Gao and Qunfeng Dong (2020)  Journal of the American Medical Informatics Association, 28 Sept 2020, ocaa246, doi:10.1093/jamia/ocaa246 [Featured as Editor's Choice]
20. Jin J. Zhou , Jing Zhai ; Hua Zhou , Yin Chen , Stefano Guerra , Ian Robey , George M. Weinstock , Erica Weinstock , Qunfeng Dong , Kenneth S Knox , and Homer L Twigg III (2020) . American Journal of Respiratory and Critical Care Medicine (the Blue Journal), August 12, 2020 doi:10.1164/rccm.202004-1086LE
21. Yue Xing, Xiao Li, Xiang Gao and Qunfeng Dong (2020)  Front. Genetics., 17 July 2020 doi: 10.3389/fgene.2020.00783
22. Yue Xing, Xiao Li, Xiang Gao and Qunfeng Dong (2020)  Front. Microbiol., 25 June 2020. doi:10.3389/fmicb.2020.01502.
23. Xiang Gao and Qunfeng Dong (2020)  Journal of the American Medical Informatics Association Open Access, 13 Apirl 2020, ooaa025, doi:10.1093/jamiaopen/ooaa025
24. Travis Price, Huaiying Lin, Xiang Gao, Krystal Thomas-White, Evann Hilt, Elizabeth Muelier, Alan Wolfe*, Qunfeng Dong*, and Linda Brubaker* (2020) , American Journal of Obstetrics and Gynecology, 2020;S0002-9378(20)30512-3. doi:10.1016/j.ajog.2020.04.033 *co-corresponding author
25. Travis Price, Birte Wolff, Thomas Halverson, Roberto Limeira, Linda Brubaker, Qunfeng Dong, Elizabeth Mueller, and Alan Wolfe (2020) , mBio, Apr 2020, 11 (2) e00475-20; DOI: 10.1128/mBio.00475-20
26. Benito Gómez-Silva, Claudia Vilo-Muñoz, Alexandra Galetovi膰, Qunfeng Dong, Hugo G. Castelán-Sánchez, Yordanis Pérez-Llano, María del Rayo Sánchez-Carbente, Sonia Dávila-Ramos, Nohemí Gabriela Cortes-López, Liliana Martínez-Ávila, Alan D.W. Dobson, Ramón Alberto Batista-García (2019)  Microorganisms 7(12), 619. doi:10.3390/microorganisms7120619.
27. Shin A*#, Gao X#, Bohm M, Lin H, Gupta A, Nelson DE, Toh E, Teagarden S, Siwiec R, Dong Q*, Wo JM (2019) . Clinical and Translational Gastroenterology in Vol. 10, No. 8, August 2019. (*co-first, #co-corresponding authors) *co-corresponding author
28. Lin H, Rong R, Gao X, Revanna K, Zhao M, Bajic P, Jin D, Hu C, and Dong Q (2019)  23 August 2019 Journal of the American Medical Informatics Association Open Access 2(3) 353-359. PMID: 31984368.
    
29. Dornbier R, Bajic P, Van Kuiken M, Jardaneh A, Lin H,Gao X, Knudsen B, Dong Q*, Wolfe A* and Schwaderer A* (2019) . Urolithiasis June 4 2019. *co-corresponding author
30. Leduc I, Fortney K, Janowicz D, Zwickl B, Ellinger S, Katz B, Lin H, Dong Q, and Spinola S (2019) American Society for Microbiology. Infection and immunity, 87(7), e00112-19.
31. Shannon MB, Limeira R, Johansen D, Gao X, Lin H, Dong Q*, Wolfe AJ*, Mueller ER* (2019) . International Urogynecology Journal, 30(8), 1261-1267.  *co-corresponding author
32. Fok CS, Gao X, Lin H, Thomas-White KJ, Mueller ER, Wolfe AJ*, Dong Q*, Brubaker L* (2018) . Int Urogynecol J. 2018 Sep 28 . *co-corresponding author 
33. Thomas-White KJ, Gao X, Lin H, Fok CS, Mueller ER, Dong Q*, Brubaker L*, Wolfe AJ*. (2018)   Int Urogynecol J. 2018 Aug 16.  *co-corresponding author
34. Carla G. Leon, Ruben Moraga, Cristian Valenzuela, Concetta Gugliandolo, Angelina Lo Giudice, Maria Papale, Claudia Vilo, Qunfeng Dong, Carlos T. Smith, Ramon Rossello-Mora, Jorge Yañez, Victor L. Campos (2018)  (Atacama Desert, Chile). PLoS ONE 13(5): e0195080.
35. Galan-Davila AK, Ryu J, Dong K, Xiao Y, Dai Z, Zhang D, Li Z, Dick AM, Liu KD, Kamat A, Lu M, Dong Q, Liu F, Dong LQ. (2018)  . J Biol Chem. 2018 Feb 26. pii: jbc.RA118.002162. doi: 10.1074/jbc.RA118.002162.
    
36. Xiang Gao, Huaiying Lin, Qunfeng Dong (2017); , mSphere, Volume: 2, Issue: 6.
37. Irit Messika, Mario Garrido, Hadar Kedem, Victor China, Yoni Gavish,Qunfeng Dong, Clay Fuqua, Keith Clay, and Hadas Hawlena (2017) . Oecologia (2017): 1-13.
38. Xiang Gao, Huaiying Lin, Kashi Revanna, Qunfeng Dong, (2017) . BMC Bioinformatics 2017 May 10;18(1):247.
39. Plichta J, Gao X, Lin H, Dong Q, Toh E, Nelson D, Grice E, Radek, K. (2017) . Shock: Injury, Inflammation, and Sepsis: Laboratory and Clinical Approaches. surgery, 138(2), 127-32.
40. Plichta J, Holmes C, Nienhouse V, Puszynski M, Gao X, Dong Q, Lin H, Sinacore J, Zilliox M, Toh E, Nelson D, Gamelli R, Radek K. . Critical care medicine 45, no. 6 (2017): e543-e551.
41. Kubal, Shekhar, Richard Mangus, Lin Huaiying, Gao Xiang, Qunfeng Dong, Evelyn Toh, Natalia Rush et al.  Transplantation 101, no. 6S2 (2017): S40-S41.
42. Rylance J, Kankwatira A ,Nelson D, Toh E, Day R, Lin H, Gao X, Dong Q, Sodergren E, Weinstock G, Heyderman R, Twigg H, Gordon Y (2016) . BMC microbiology, 16(1), 182.
43. Twigg H, Knox K, Zhou J, Crothers K, Nelson D, Toh E, Day R, Lin H, Gao X, Dong Q, Mi D, Katz B, Sodergren R, Weinstock G (2016) . American Journal of Respiratory and Critical Care Medicine 10.1164/rccm.201509-1875OC 2016.
44. Dong Q (2015) . Next Generat Sequenc & Applic 2: 121. doi:10.4172/jngsa.1000121
45. Van Rensburg J, Lin H, Gao X, Toh E, Fortney K, Ellinger S, Zwickl B, Janowicz D, Katz B, Nelson D, Dong Q, Spinola S (2015) . mBio 6(5):e01315-15. doi:10.1128/mBio.01315-15.
46. Vilo C, Galetovic A, Araya JE, Gómez-Silva B, Dong Q (2015) . Genome Announc. 3(4):e00955-15. doi:10.1128/genomeA.00955-15.
47. Cohen C, Toh E, Munro D, Dong Q, Hawlena H (2015) . ISME J. 2015 Jan 9. doi: 10.1038/ismej.2014.255.
48. Nienhouse V, Gao X, Dong Q, Nelson DE, Toh E, McKinley K, Schreckenberger P, Shibata N, Fok SC, Mueller ER, Brubaker L, Wolfe AJ, Radek KA (2014) . 9(12): e114185. doi: 10.1371/journal.pone.0114185.
49. Gavish Y, Kedem H, Messika I, Cohen C, Toh E, Munro D, Dong Q, Fuqua C, Clay K, Hawlena H (2014) . 9(10): e109677. doi: 10.1371/journal.pone.0109677.
50. Vilo C, Benedik M, Ilori M, Dong Q (2014) . Genome Announc. 2:(4)e00664-14. doi:10.1128/genomeA.00664-14.
51. Vilo C, Benedik M, Ilori M, Dong Q (2014) . Genome Announc. 2(3):e00474-14. doi:10.1128/genomeA.00474-14.
52. Jones AM, Xuan Y, Xu M, Wang RS, Ho CH, Lalonde S, You CH, Sardi MI, Parsa SA, Smith-Valle E, Su T, Frazer KA, Pilot G, Pratelli R, Grossmann G, Acharya BR, Hu HC, Engineer C, Villiers F, Ju C, Takeda K, Su Z, Dong Q, Assmann SM, Chen J, Kwak JM, Schroeder J, Albert R, Rhee SY, Frommer WB (2014) . Science, 344(6185), 711-716.
53. Kedem H, Gavish Y, Messika I, Cohen C, Toh E, Munro D, Dong Q, Fuqua C, Clay K, Hawlena H (2014) . PLoS ONE 9(10): e109677. doi:10.1371/journal.pone.0109677.
54. Twigg HL, Nelson DE, Day RB, Gregory RL, Dong Q, Rong R, Knox K, Crothers K, Sodergren E, Weinstock G (2014) AST Journal, Ann Am Thorac Soc. 2014 Jan;11 Suppl 1:S72-3. doi: 10.1513/AnnalsATS.201306-162MG.0061959.
55. Zhou M, Rong R, Munro D, Zhu C, Gao X, Zhang Q, Dong Q (2013) . PLoS One 8(4): e61516. doi:10.1371/journal.pone.0061516.
56. Kuehn J, Gorden P, Munro D, Rong R, Dong Q, Plummer P, Wang C, Phillips J (2013) .PLoS One 8(4): e61959. doi:10.1371/journal.pone.0061959.
57. Vilo C, Benedik M, Kunz D, Dong Q (2012) . Journal of Bacteriology 194(23):6618-9.
58. Revanna K, Munro D, Gao A, Chiu C, Pathak A, Dong Q (2012) . BMC Bioinformatics 13:190. doi:10.1186/1471-2105-13-190.
59. Vilo C, Dong Q (2012) . Metagenomics. doi:10.4303/mg/235551.
60. Hawlena H, Rynkiewicz E, Toh E, Alfred A, Durden LA, Hastriter MW, Nelson DE, Rong R, Munro D, Dong Q, Fuqua C, Clay K (2012) . The ISME Journal 28 June 2012; doi: 10.1038/ismej.2012.71.
61. Nelson DE, Dong Q, Van Der Pol B, Fan B, Toh E, Katz BP, Mi D, Rong R, Weinstock GM, Sodergren E, Fortenberry JD (2012) . PLoS ONE 7(5): e36298. doi:10.1371/journal.pone.0036298.
62. Meckfessel MH, Blancaflor EB, Plunkett M, Dong Q, Dickstein R (2012) . Plant Physiol, 2012 May;159(1):299-310.
63. Wolfe A, Toh E, Shibata N, Rong R, Kenton K, Fitzgerald MP, Mueller ER, Schreckenberger P, Dong Q, Nelson D, Brubaker L (2012) . J Clin Microbiol. 50(4):1376-1383.
64. Hughes A, Ruan Y, Ekanayake S, Bae S-H, Dong Q, Rho M, Qiu J, Fox G (2012) . BMC Bioinformatics 2012, 13(Suppl 2):S9 doi:10.1186/1471-2105-13-S2-S9.
65. Revanna K, Chiu CC, Bierschank E, Dong Q (2011) . BMC Bioinformatics 12(1):316. Ranked as “highly accessed” paper by the journal.
66. Dong Q, Nelson DE, Toh E, Diao L, Gao X, Fortenberry J, Van Der Pol B (2011) . PLOS ONE 6(5): e19709. doi:10.1371/journal.pone.0019709.
67. Dong Q, Brulc JM, Iovieno A, Bates B, Garoutte A, Miller D, Revanna K, Gao X, Antonopoulos DA, Slepak VZ, Shestopalov VI (2011) . Investigative Ophthalmology and Visual Science. 52(8):5408-13.
68. Nelson DE, Van Der Pol B, Dong Q, Revanna K, Fan B, Easwaran S, Sodergren E, Weinstock GM, Diao L, Fortenberry JD (2010) . PLOS ONE 5(11): e14116. doi:10.1371/journal.pone.0014116.
69. Colbourne JK, Pfrender ME, Gilbert D, Thomas WK, Tucker A, Oakley TH, Tokishita S, Aerts A, Arnold GJ, Basu MK, Bauer DJ, Caceres CE, Carmel L, Casola C, Choi J, Detter JC, Dong Q, Dusheyko S, Eads BD, Frohlich T, Geiler-Samerotte KA, Gerlach D, Hatcher P, Jogdeo S, Krijgsveld J, Kriventseva EV, Kultz D, Laforsch C, Lindquist E, Lopez J, Manak JR, Muller J, Pangilinan J, Patwardhan RP, Pitluck S, Pritham EJ, Rechtsteiner A, Rho M, Rogozin IB, Sakarya O, Salamov A, Schaack S, Shapiro H, Shiga Y, Skalitzky C, Smith Z, Souvorov A, Sung W, Tang Z, Tsuchiya D, Tu H, Vos H, Wang M, Wolf YI, Yamagata H, Yamada T, Ye Y, Shaw JR, Andrews J, Crease TJ, Tang H, Lucas SM, Robertson HM, Bork P, Koonin EV, Zdobnov EM, Grigoriev IV, Lynch M, Boore JL (2011) . Science vol. 331 pp. 555-561. DOI:10.1126/science.1197761.
70. Podicheti R, Dong Q (2011) . Current Protocols in Bioinformatics 2011 Mar;Chapter 9:Unit 9.14. Baxevan A, Petsko G, Stein L, Stormo G (ed.), John Wiley & Sons, Inc. NJ, U.S.A.
71. Fortenberry D, Nelson DE, Dong Q (2010) . Nature Precedings.
72. Podicheti R, Revanna K, Dong Q (2010) WebGBrowse 2.0 - A web server supporting multiple versions of the Generic Genome Browser for customizable genome annotation display. F. Columbus (ed.), Web Servers: Types, Software and Applications, Nova Science Publishers, Inc. Hauppauge, NY, U.S.A.
73. Hemmerich C, Buchlein A, Podicheti R, Revanna K, Dong Q (2010) . Bioinformatics 26: 1122-1124.
74. Podicheti R, Dong Q (2010) . Cold Spring Harbor Protocols (invited submission) 2010(3):pdb.prot5392. doi:10.1101.
75. Podicheti R, Gollapudi R, Dong Q (2009) . Bioinformatics 25(12):1550-1.
76. Revanna K, Krishnakumar V, Dong Q (2009) . Bioinformatics 25(7):956-7.
77. Tang Z, Choi JH, Hemmerich C, Sarangi A, Colbourne JK, Dong Q (2009) . BMC Genomics, 10:174.
78. Durden C, Dong Q (2009) . Bioinformation, 3(7), 296-298.
79. Pallickara S, Pierce M, Dong Q, Kong C (2009) . 8th International Conference on Parallel Processing and Applied Mathematics, Wroclaw, Poland.
80. Gollapudi R, Revanna K, Hemmerich C, Schaack S, Dong Q (2008) . BMC Genomics 9, 414.
81. Lushbough CM, Duvick J, Dong Q, Jennewein D, Reynoldson J, Brendel V (2008) . In H.R. Arabnia, M.Q. Yang, and J.Y. Yang (eds.), Proceedings of the International Conference on Bioinformatics & Computational Biology (BIOCOMP'08).
82. Dong Q, Wilkerson MD, Brendel V (2007) . BMC Bioinformatics 8, 151.
83. Schlueter SD, Wilkerson MD, Dong Q, Brendel V (2006) . Genome Biol. 7, R111.
84. Dong Q, Lawrence CJ, Schlueter SD, Wilkerson MD, Kurtz S, Lushbough C, Brendel V (2005) . Plant Physiol. 139, 610-618.
85. Dong Q, Brendel V (2005) . In J.M. Walker (ed.),The Proteomics Protocols Handbook, Humana Press, U.S.A, pp. 555-570.
86. Dong Q, Kroiss L, Oakley FD, Wang B, Brendel V (2005) . In Molecular Evolution: Producing the Biochemical Data, E.A. Zimmer and E.H. Roalson (eds.), Methods Enzymol, 395, 400-418.
87. Dong Q, Schlueter SD, Brendel V (2004) . Nucl. Acids Res. 32, D354-D359.
88. Fernandes JF, Dong Q*, Schneider B, Morrow DJ, Nan GL, Brendel V, Walbot V (2004) . Genome Biol. 5, R82. (*Co-first author.)
89. Lawrence CJ, Dong Q, Polacco ML, Seigfried TE, Brendel V (2004) . Nucl. Acids Res. 32, D393-D397.
90. Dong Q, Roy L, Freeling M, Walbot V, Brendel V (2003) . Nucl. Acids Res. 31, 244-247.
91. Schlueter SD, Dong Q, Brendel V (2003) . Nucl. Acids Res. 31, 3597-3600.
92. Dong Q, Wu Z (2003) . J. Global Optimization 26, 321-333.
93. Dong Q, Wu Z (2002) . J. Global Optimization 22, 365-375.