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Loyola University Chicago graduate student Taylor Miller-Ensminger works on experiments in the Bioinformatics Lab

Stritch - Center for Biomedical Informatics

Center for Biomedical Informatics

The Center for Biomedical Informatics collaborates with biomedical scientists to develop computational solutions for their research projects. Our style is to become an integral part of each project, actively engaging in experimental design, data analysis, publication authorship, and grant writing. Contact us if you would like to collaborate on any biomedical informatics projects. 

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Projects

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

  1. 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)
  2. 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).
  3. 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). 
  4. 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
  5. 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)
  6. 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.
  7. Loyola University Chicago Cardiovascular Research Institute grant (AU103331), 2016-2017, Developing novel bioinformatics software for gene expression network analysis, PI, Dr. Qunfeng Dong
  8. 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
  9. 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. 
  10. 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).
  11. The female urinary microbiome and urinary incontinence (NIH R01 DK104718, 12/01/2015-11/30/2020), PI - Drs. Linda Brubaker & Alan Wolfe, Loyola University Chicago Stritch School of Medicine. Co-investigators: Drs. Cynthia Brincat, Qunfeng Dong, Colleen Fitzgerald, Stephanie Kliethermes, Elizabeth Mueller, Paul Schreckenberger, Michael Zilliox.
  12. 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).
  13. The Female Urinary Microbiome: Adjacent Microbiomes and Clinical Associations (NIH P20 DK108268, 12/01/2015-11/30/2017). PI: Dr. Alan Wolfe, Loyola University Chicago Stritch School of Medicine. Co-investigators: Drs. Linda Brubaker, Qunfeng Dong, Stephanie Kliethermes, Elizabeth Mueller, Michael Zilliox.
  14. 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, Loyola University Chicago. Co-PI: Drs. Jeffery Branch, Larissa Bresler, Qunfeng Dong, Alan J. Wolfe.
  15. Genomic Prediction of Chronic Pulmonary Inflammation in HIV Infection (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).
  16. Natural variation and drought responses in developing maize inflorescences (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), José R. Dinneny (Carnegie Institution for Science, Stanford University), Torbert Rocheford (Purdue University), Andrea Eveland (Donald Danforth Plant Science Center), Qunfeng Dong (Loyola).
  17. Mechanism of microbiome-induced insulin resistance in humans (American Diabetes Association, 2013-2016). PI: Dr. Nicolas Musi, University of Texas Health Science Center in San Antonio. Co-investigator: Qunfeng Dong (Loyola).
  18. 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).
  19. Lung microbiome and pulmonary inflammation/immunity in HIV infection (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).
  20. The urethral microbiome in adolescent males (NIH UH2/UH3 2009-2013)​. 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.
  21. Investigation of Cloud Computing to Support Data-Parallel Health Research (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.

 

Publications

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

  1. Claudia Vilo C, Galetovic A, Dong Q, Gómez-Silva B (2023). A Metagenomics Insight in the Cyanosphere of Edible Andean Macrocolonies (Llayta). Austin J Proteomics Bioinform. & Genomics. 2023; 8(1): 1034.
  2. 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. Sexual behavior shapes male genitourinary microbiome composition. Cell Rep Med. 2023 Mar 21;4(3):100981. doi: 10.1016/j.xcrm.2023.100981. PMID: 36948151; PMCID: PMC10040456. *co-corresponding author
  3. Griesenauer B, Xing Y, Fortney KR, Gao X, González-Beiras C, Nelson DE, Ren J, Mitjà O, Dong Q*, Spinola SM. Two Streptococcus pyogenes emm types and several anaerobic bacterial species are associated with idiopathic cutaneous ulcers in children after community-based mass treatment with azithromycin. PLoS Negl Trop Dis. 2022 Dec 19;16(12):e0011009. doi: 10.1371/journal.pntd.0011009. PMID: 36534698; PMCID: PMC9810193. *co-corresponding author
  4. Claudia Vilo, Qunfeng Dong, Alexandra Galetovic, Benito Gómez-Silva (2022) Metagenome-assembled genome of Cyanocohniella sp. LLY from the cyanosphere of Llayta, an edible Andean cyanobacterial microcolony. Microorganisms July 27; 10(8):1517. doi: 10.3390/microorganisms10081517.
  5. 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) Forming Consensus to Advance Urobiome Research. mSystems. 2021 Aug 31;6(4):e0137120. doi: 10.1128/mSystems.01371-20. Epub 2021 Jul 20. PMID: 34282932; PMCID: PMC8409733.
  6. 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) Evaluation of clinical, Gram stain, and microbiological cure outcomes in men receiving azithromycin for acute nongonococcal urethritis: discordant cures are associated with Mycoplasma genitalium infectionSex Transm Dis. 2022 Jan 1;49(1):67-75. doi: 10.1097/OLQ.0000000000001509. PMID: 34618416; PMCID: PMC8665015.
  7. Linda Brubaker, Catherine Putonti, Qunfeng Dong, Alan Wolfe (2021) The Human Urobiome. Mamm Genome. 2021 Aug;32(4):232-238. doi: 10.1007/s00335-021-09862-8. Epub 2021 Mar 2. PMID: 33651197. 
  8. Chen C.X.*, Carpenter, J.S., Gao, X.*, Toh, E., Dong, Q, Nelson, D.E., Mitchell, C., Fortenberry, J. D. (2021). Associations between dysmenorrhea symptom-based phenotypes and vaginal microbiome: A Pilot StudyNursing Research. (*co-corresponding authors), Vol. 70, No. 4, July/August 2021. doi:10.1097/NNR.0000000000000510
  9. Kelly R. Reveles, Eric H. Young, Amina R.A.L. Zeidan, Qunfeng Dong (2021) Chapter 17 - Microbiome changes in aging, 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, https://doi.org/10.1016/B978-0-12-815962-0.00017-2.
  10. 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) Streptococcus pyogenes is Associated with Idiopathic Cutaneous Ulcers in Children on a Yaws-Endemic Island. mBio. , Jan 2021, 12 (1) e03162-20; DOI: 10.1128/mBio.03162-20
  11. Xiang Gao and Qunfeng Dong (2020) A Primer on Bayesian Analysis for Prevalence Estimation in COVID-19 Research. Journal of the American Medical Informatics Association Open Access, 10 Nov 2020, ooaa062, doi:10.1093/jamiaopen/ooaa062 
  12. Qunfeng Dong and Xiang Gao (2020) Bayesian Estimation of the Seroprevalence of Antibodies to SARS-CoV-2.  Journal of the American Medical Informatics Association Open Access. 23 October 2020, ooaa049, doi:10.1093/jamiaopen/ooaa049
  13. Xiang Gao and Qunfeng Dong (2020) A Bayesian Framework for Estimating the Risk Ratio of Hospitalization for People with Comorbidity Infected by the SARS-CoV-2 Virus. Journal of the American Medical Informatics Association, 28 Sept 2020, ocaa246, doi:10.1093/jamia/ocaa246 [Featured as Editor's Choice]
  14. 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) Supraglottic Lung Microbiome Taxa Are Associated with Pulmonary Abnormalities in an HIV Longitudinal CohortAmerican Journal of Respiratory and Critical Care Medicine (the Blue Journal), August 12, 2020 doi:10.1164/rccm.202004-1086LE
  15. Yue Xing, Xiao Li, Xiang Gao and Qunfeng Dong (2020) Natural polymorphisms are present in the furin cleavage site of the SARS-CoV-2 spike glycoprotein. Front. Genetics., 17 July 2020 doi: 10.3389/fgene.2020.00783
  16. Yue Xing, Xiao Li, Xiang Gao and Qunfeng Dong (2020) MicroGMT: A Mutation Tracker for SARS-CoV-2 and Other Microbial Genome Sequences. Front. Microbiol., 25 June 2020. doi:10.3389/fmicb.2020.01502.
  17. Xiang Gao and Qunfeng Dong (2020) A Logistic Model for Age-Specific COVID-19 Case-Fatality Rates.  Journal of the American Medical Informatics Association Open Access, 13 Apirl 2020, ooaa025, doi:10.1093/jamiaopen/ooaa025
  18. Travis Price, Huaiying Lin, Xiang Gao, Krystal Thomas-White, Evann Hilt, Elizabeth Muelier, Alan Wolfe*, Qunfeng Dong*, and Linda Brubaker* (2020) Bladder Bacterial Diversity Differs In Continent and Incontinent Women: A Cross-Sectional Study, American Journal of Obstetrics and Gynecology, 2020;S0002-9378(20)30512-3. doi:10.1016/j.ajog.2020.04.033 *co-corresponding author
  19. Travis Price, Birte Wolff, Thomas Halverson, Roberto Limeira, Linda Brubaker, Qunfeng Dong, Elizabeth Mueller, and Alan Wolfe (2020) Temporal Dynamics of the Adult Female Lower Urinary Tract Microbiota, mBio, Apr 2020, 11 (2) e00475-20; DOI: 10.1128/mBio.00475-20
  20. Benito Gómez-Silva, Claudia Vilo-Muñoz, Alexandra Galetović, 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) Metagenomics of Atacama lithobiontic extremophile life unveils highlights on fungal communities, biogeochemical cycles and carbohydrate-active enzymes. Microorganisms 7(12), 619. doi:10.3390/microorganisms7120619.
  21. Shin A*#, Gao X#, Bohm M, Lin HGupta A, Nelson DE, Toh E, Teagarden S, Siwiec R, Dong Q*, Wo JM (2019) Characterization of proximal small intestinal microbiota in patients with suspected small intestinal bacteria overgrowth: A cross-sectional studyClinical and Translational Gastroenterology in Vol. 10, No. 8, August 2019. (*co-first, #co-corresponding authors) *co-corresponding author
  22. Lin H, Rong R, Gao X, Revanna K, Zhao M, Bajic P, Jin D, Hu C, and Dong Q (2019) Disease Correlation Network: A Computational Package for Identifying Temporal Correlations between Disease States from Large-Scale Longitudinal Medical Records 23 August 2019 Journal of the American Medical Informatics Association Open Access 2(3) 353-359. PMID: 31984368.
  23. Dornbier R, Bajic P, Van Kuiken M, Jardaneh A, Lin H,Gao X, Knudsen B, Dong Q*, Wolfe A* and Schwaderer A* (2019) The microbiome of calcium-based urinary stones. Urolithiasis June 4 2019. *co-corresponding author
  24. Leduc I, Fortney K, Janowicz D, Zwickl B, Ellinger S, Katz B, Lin H, Dong Q, and Spinola S (2019) A class I Haemophilus ducreyi strain containing a class II hgbA allele is partially attenuated in humans: implications for HgbA vaccine efficacy trials. American Society for Microbiology. Infection and immunity87(7), e00112-19.
  25. Shannon MB, Limeira R, Johansen D, Gao X, Lin H, Dong Q*, Wolfe AJ*, Mueller ER* (2019) Bladder Urinary Oxygen Tension Is Correlated With Urinary Microbiota CompositionInternational Urogynecology Journal, 30(8), 1261-1267. https://doi.org/10.1007/s00192-019-03931-y *co-corresponding author
  26. Fok CS, Gao X, Lin H, Thomas-White KJ, Mueller ER, Wolfe AJ*, Dong Q*, Brubaker L* (2018) Urinary Symptoms are Associated With Certain Urinary Microbes in Urogynecologic Surgical PatientsInt Urogynecol J. 2018 Sep 28 https://doi.org10.1007/s00192-018-3732-1*co-corresponding author 
  27. Thomas-White KJ, Gao X, Lin H, Fok CS, Mueller ER, Dong Q*, Brubaker L*, Wolfe AJ*. (2018)  Urinary Microbes and Post-Operative Urinary Tract Infection Risk In Urogynecologic Surgical Patients Int Urogynecol J. 2018 Aug 16. https://doi.org/10.1007/s00192-018-3767-3 *co-corresponding author
  28. 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) Effect of the natural arsenic gradient on the diversity and arsenic resistance of bacterial communities of the sediments of Camarones River (Atacama Desert, Chile). PLoS ONE 13(5): e0195080.
  29. 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)  Alternative splicing variant of the scaffold protein APPL1 suppresses hepatic adiponectin signaling and function. J Biol Chem. 2018 Feb 26. pii: jbc.RA118.002162. doi: 10.1074/jbc.RA118.002162.
  30. Xiang Gao, Huaiying Lin, Qunfeng Dong (2017); A Dirichlet-Multinomial Bayes Classifier for Disease Diagnosis with Microbial Compositions, mSphere, Volume: 2, Issue: 6.
  31. Irit Messika, Mario Garrido, Hadar Kedem, Victor China, Yoni Gavish,Qunfeng Dong, Clay Fuqua, Keith Clay, and Hadas Hawlena (2017) From endosymbionts to host communities: factors determining the reproductive success of arthropod vectors. Oecologia (2017): 1-13.
  32. Xiang Gao, Huaiying Lin, Kashi Revanna, Qunfeng Dong, (2017) A Bayesian Taxonomic Classification Method for 16S rRNA Gene Sequences with Improved Species-level Accuracy. BMC Bioinformatics 2017 May 10;18(1):247.
  33. Plichta J, Gao X, Lin H, Dong Q, Toh E, Nelson D, Grice E, Radek, K. (2017) Cutaneous Burn Injury Promotes Shifts in the Bacterial Microbiome in Autologous Donor Skin: Implications for Skin Grafting Outcomes. Shock: Injury, Inflammation, and Sepsis: Laboratory and Clinical Approaches. surgery, 138(2), 127-32.
  34. 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. Cutaneous burn injury modulates urinary antimicrobial peptide responses and the urinary microbiome. Critical care medicine 45, no. 6 (2017): e543-e551.
  35. Kubal, Shekhar, Richard Mangus, Lin Huaiying, Gao Xiang, Qunfeng Dong, Evelyn Toh, Natalia Rush et al. Impact of Intestinal Motility, Mucosal Inflammation and Fecal Microflora on Transplant Intestine Function. Transplantation 101, no. 6S2 (2017): S40-S41.
  36. 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) Household air pollution and the lung microbiome of healthy adults in Malawi: a cross-sectional study. BMC microbiology, 16(1), 182.
  37. 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) Effect of advanced HIV infection on the respiratory microbiome. American Journal of Respiratory and Critical Care Medicine 10.1164/rccm.201509-1875OC 2016.
  38. Dong Q (2015) Mobilizing Undergraduate Students to Develop Practical Bioinformatics Databases and Analysis Tools for Biologists. Next Generat Sequenc & Applic 2: 121. doi:10.4172/jngsa.1000121
  39. 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) The human skin microbiome associates with the outcome of and is influenced by bacterial infection. mBio 6(5):e01315-15. doi:10.1128/mBio.01315-15.
  40. Vilo C, Galetovic A, Araya JE, Gómez-Silva B, Dong Q (2015) Draft genome sequence of a Bacillus bacterium from the Atacama Desert wetlands metagenome. Genome Announc. 3(4):e00955-15. doi:10.1128/genomeA.00955-15.
  41. Cohen C, Toh E, Munro D, Dong Q, Hawlena H (2015) Similarities and seasonal variations in bacterial communities from the blood of rodents and from their flea vectors. ISME J. 2015 Jan 9. doi: 10.1038/ismej.2014.255.
  42. 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) Interplay between Bladder Microbiota and Urinary Antimicrobial Peptides: Mechanisms for Human Urinary Tract Risk Symptom Severity. PLoS ONE 9(12): e114185. doi: 10.1371/journal.pone.0114185.
  43. Gavish Y, Kedem H, Messika I, Cohen C, Toh E, Munro D, Dong Q, Fuqua C, Clay K, Hawlena H (2014) Association of Host and Microbial Species Diversity across Spatial Scales in Desert Rodent Communities. PLoS ONE 9(10): e109677. doi: 10.1371/journal.pone.0109677.
  44. Vilo C, Benedik M, Ilori M, Dong Q (2014) Draft genome sequence of Cupriavidus sp. strain SK-3, a 4-chlorobiphenyl and 4-clorobenzoic acid degrading bacterium. Genome Announc. 2:(4)e00664-14. doi:10.1128/genomeA.00664-14.
  45. Vilo C, Benedik M, Ilori M, Dong Q (2014) Draft genome sequence of Cupriavidus sp. strain SK-4, a di-ortho-substituted biphenyl-utilizing bacterium isolated from polychlorinated biphenyl-contaminated sludge. Genome Announc. 2(3):e00474-14. doi:10.1128/genomeA.00474-14.
  46. 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) Border control—a membrane-linked interactome of Arabidopsis. Science, 344(6185), 711-716.
  47. Kedem H, Gavish Y, Messika I, Cohen C, Toh E, Munro D, Dong Q, Fuqua C, Clay K, Hawlena H (2014) Association of host and microbial species diversity across spatial scales in desert rodent communities. PLoS ONE 9(10): e109677. doi:10.1371/journal.pone.0109677.
  48. Twigg HL, Nelson DE, Day RB, Gregory RL, Dong Q, Rong R, Knox K, Crothers K, Sodergren E, Weinstock G (2014) Comparison of whole and acellular bronchoalveolar lavage to oral wash microbiomes: should acellular bronchoalveolar lavage be the standard? AST Journal, Ann Am Thorac Soc. 2014 Jan;11 Suppl 1:S72-3. doi: 10.1513/AnnalsATS.201306-162MG.0061959.
  49. Zhou M, Rong R, Munro D, Zhu C, Gao X, Zhang Q, Dong Q (2013) Investigation of the effect of type 2 diabetes on subgingival plaque microbiota by high-throughput 16S rDNA pyrosequencing. PLoS One 8(4): e61516. doi:10.1371/journal.pone.0061516.
  50. Kuehn J, Gorden P, Munro D, Rong R, Dong Q, Plummer P, Wang C, Phillips J (2013) Bacterial community profiling of milk samples as a means to understand culture-negative bovine clinical mastitis.PLoS One 8(4): e61959. doi:10.1371/journal.pone.0061959.
  51. Vilo C, Benedik M, Kunz D, Dong Q (2012) Draft genome sequence of the cyanide-utilizing bacterium Pseudomonas fluorescens strain NCIMB 11764. Journal of Bacteriology 194(23):6618-9.
  52. Revanna K, Munro D, Gao A, Chiu C, Pathak A, Dong Q (2012) A web-based multi-genome synteny viewer for customized data. BMC Bioinformatics 13:190. doi:10.1186/1471-2105-13-190.
  53. Vilo C, Dong Q (2012) Evaluation of the RDP Classifier accuracy using 16S rRNA gene variable regions. Metagenomics. doi:10.4303/mg/235551.
  54. 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 arthropod, but not the vertebrate host or its environment, dictates bacterial community composition of fleas and ticks. The ISME Journal 28 June 2012; doi: 10.1038/ismej.2012.71.
  55. 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) Bacterial communities of the coronal sulcus and distal urethra of adolescent males. PLoS ONE 7(5): e36298. doi:10.1371/journal.pone.0036298.
  56. Meckfessel MH, Blancaflor EB, Plunkett M, Dong Q, Dickstein R (2012) Multiple domains in MtENOD8 protein including the signal peptide target it to the symbiosome. Plant Physiol, 2012 May;159(1):299-310.
  57. Wolfe A, Toh E, Shibata N, Rong R, Kenton K, Fitzgerald MP, Mueller ER, Schreckenberger P, Dong Q, Nelson D, Brubaker L (2012) Evidence of uncultivated bacteria in the adult female bladder. J Clin Microbiol. 50(4):1376-1383.
  58. Hughes A, Ruan Y, Ekanayake S, Bae S-H, Dong Q, Rho M, Qiu J, Fox G (2012) Interpolative multidimensional scaling techniques for the identification of clusters in very large sequence sets. BMC Bioinformatics 2012, 13(Suppl 2):S9 doi:10.1186/1471-2105-13-S2-S9.
  59. Revanna K, Chiu CC, Bierschank E, Dong Q (2011) GSV: A web-based genome synteny viewer for customized data. BMC Bioinformatics 12(1):316. Ranked as “highly accessed” paper by the journal.
  60. Dong Q, Nelson DE, Toh E, Diao L, Gao X, Fortenberry J, Van Der Pol B (2011) The microbial communities in male first catch urine are highly similar to those in paired urethral swab specimens. PLOS ONE 6(5): e19709. doi:10.1371/journal.pone.0019709.
  61. Dong Q, Brulc JM, Iovieno A, Bates B, Garoutte A, Miller D, Revanna K, Gao X, Antonopoulos DA, Slepak VZ, Shestopalov VI (2011) Diversity of bacteria at healthy human conjunctiva. Investigative Ophthalmology and Visual Science. 52(8):5408-13.
  62. Nelson DE, Van Der Pol B, Dong Q, Revanna K, Fan B, Easwaran S, Sodergren E, Weinstock GM, Diao L, Fortenberry JD (2010) Characteristic male urine microbiomes associate with asymptomatic sexually transmitted infection. PLOS ONE 5(11): e14116. doi:10.1371/journal.pone.0014116.
  63. 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) The ecoresponsive genome of Daphnia pulex. Science vol. 331 pp. 555-561. DOI:10.1126/science.1197761.
  64. Podicheti R, Dong Q (2011) Administering GBrowse sites with WebGBrowse. 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.
  65. Fortenberry D, Nelson DE, Dong Q (2010) The urethral microbiome of adolescent males. Nature Precedings.
  66. 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.
  67. Hemmerich C, Buchlein A, Podicheti R, Revanna K, Dong Q (2010) An Ergatis-based prokaryotic genome annotation web server. Bioinformatics 26: 1122-1124.
  68. Podicheti R, Dong Q (2010) Using WebGBrowse to visualize genome annotation on GBrowse. Cold Spring Harbor Protocols (invited submission) 2010(3):pdb.prot5392. doi:10.1101.
  69. Podicheti R, Gollapudi R, Dong Q (2009) WebGBrowse - a web server for customized GBrowse. Bioinformatics 25(12):1550-1.
  70. Revanna K, Krishnakumar V, Dong Q (2009) A web-based software system for dynamic gene cluster comparison across multiple genomes. Bioinformatics 25(7):956-7.
  71. Tang Z, Choi JH, Hemmerich C, Sarangi A, Colbourne JK, Dong Q (2009) ESTPiper--a web-based analysis pipeline for expressed sequence tags. BMC Genomics, 10:174.
  72. Durden C, Dong Q (2009) RICHEST - a web server for richness estimation in biological data. Bioinformation, 3(7), 296-298.
  73. Pallickara S, Pierce M, Dong Q, Kong C (2009) Enabling large scale scientific computations for expressed sequence tag sequencing over grid and cloud computing clusters. 8th International Conference on Parallel Processing and Applied Mathematics, Wroclaw, Poland.
  74. Gollapudi R, Revanna K, Hemmerich C, Schaack S, Dong Q (2008) BOV--A web-based BLAST output visualization tool. BMC Genomics 9, 414.
  75. Lushbough CM, Duvick J, Dong Q, Jennewein D, Reynoldson J, Brendel V (2008) TableMaker: an ad hoc query tool for relational databases. In H.R. Arabnia, M.Q. Yang, and J.Y. Yang (eds.), Proceedings of the International Conference on Bioinformatics & Computational Biology (BIOCOMP'08).
  76. Dong Q, Wilkerson MD, Brendel V (2007) Tracembler--software for in-silico chromosome walking in unassembled genomes. BMC Bioinformatics 8, 151.
  77. Schlueter SD, Wilkerson MD, Dong Q, Brendel V (2006) xGDB: open-source computational infrastructure for the integrated evaluation and analysis of genome features. Genome Biol. 7, R111.
  78. Dong Q, Lawrence CJ, Schlueter SD, Wilkerson MD, Kurtz S, Lushbough C, Brendel V (2005) Comparative plant genomics resources at PlantGDB. Plant Physiol. 139, 610-618.
  79. Dong Q, Brendel V (2005) Computational identification of related proteins: BLAST, PSI-BLAST, and other tools. In J.M. Walker (ed.),The Proteomics Protocols Handbook, Humana Press, U.S.A, pp. 555-570.
  80. Dong Q, Kroiss L, Oakley FD, Wang B, Brendel V (2005) Comparative EST analyses in plant systems. In Molecular Evolution: Producing the Biochemical Data, E.A. Zimmer and E.H. Roalson (eds.), Methods Enzymol, 395, 400-418.
  81. Dong Q, Schlueter SD, Brendel V (2004) PlantGDB, plant genome database and analysis tools. Nucl. Acids Res. 32, D354-D359.
  82. Fernandes JF, Dong Q*, Schneider B, Morrow DJ, Nan GL, Brendel V, Walbot V (2004) Genome-wide mutagenesis of Zea mays L. using RescueMu transposons. Genome Biol. 5, R82. (*Co-first author.)
  83. Lawrence CJ, Dong Q, Polacco ML, Seigfried TE, Brendel V (2004) MaizeGDB, the community database for maize genetics and genomics. Nucl. Acids Res. 32, D393-D397.
  84. Dong Q, Roy L, Freeling M, Walbot V, Brendel V (2003) ZmDB, an integrated database for maize genome research. Nucl. Acids Res. 31, 244-247.
  85. Schlueter SD, Dong Q, Brendel V (2003) GeneSeqer@PlantGDB: gene structure prediction in plant genomes. Nucl. Acids Res. 31, 3597-3600.
  86. Dong Q, Wu Z (2003) A geometric build-up algorithm for solving the molecular distance geometry problem with sparse distance data. J. Global Optimization 26, 321-333.
  87. Dong Q, Wu Z (2002) A linear-time algorithm for solving the molecular distance geometry problem with exact inter-atomic distances. J. Global Optimization 22, 365-375.

CONTACT INFORMATION

Qunfeng Dong, PhD
Director, Center for Biomedical Informatics
Professor, Department of Medicine
Stritch School of Medicine, Loyola University Chicago
2160 S. First Avenue Maywood, Illinois 60153
Office: Center for Translational Research & Education 459
Email: qdong@luc.edu  |  Tel: 708-327-9004