Shareef M. Dabdoub

Personal Data

Present Position

Education

Previous Positions

Peer-Reviewed Publications

1. Longo, P.L., Dabdoub, S.M., Kumar, P.S., Artese, H.P.C., Dib, S.A., Romito, G.A., Mayer, M.P.A. Glycemic Status Affects the Subgingival Microbiome of Diabetic Patients Journal of Clinical Periodontology (2018): In Press. Co-first author. doi:10.1111/jcpe.12908
2. Kumar, P.S., Dabdoub, S.M., Hegde, R., Ranganathan, N., Mariotti, A. Site-level risk predictors of peri-implantitis: A retrospective analysis Journal of Clinical Periodontology 45, no. 5 (2018): 597-604. doi:10.1111/jcpe.12892
3. Mason, M.R., Chambers, S., Dabdoub, S.M., Thikkurissy, S., Kumar, P.S. Characterizing oral microbial communities across dentition states and colonization niches Microbiome 6, no. 1 (2018): 67-77. doi:10.1186/s40168-018-0443-2
4. Ganesan, S.M., Joshi, V., Fellows, M.L., Dabdoub, S.M., Nagaraja, H.N., O'Donnell, B., Deshpande, R.N. and Kumar, P.S. A tale of two risks: smoking, diabetes and the subgingival microbiome. The ISME journal 11 (2017): 2075–2089. doi:10.1038/ismej.2017.73
5. Queiroz, L.A., Casarin, R.CV, Dabdoub, S.M., Tatakis, D.N., Sallum, E.A. and Kumar, P.S. Furcation Therapy With Enamel Matrix Derivative: Effects on the Subgingival Microbiome. Journal of Periodontology 88, no. 7 (2017): 617-625. doi:10.1902/jop.2017.160542
6. Dabdoub, S.M., Ganesan, S.M. and Kumar, P.S. Comparative metagenomics reveals taxonomically idiosyncratic yet functionally congruent communities in periodontitis. Scientific Reports 6 (2016). doi:10.1038/srep38993
7. Dabdoub, S.M., Fellows, M.L., Paropkari, A.D., Mason, M.R., Huja, S.S., Tsigarida, A.A. and Kumar, P.S. PhyloToAST: Bioinformatics tools for species-level analysis and visualization of complex microbial datasets. Scientific Reports 6 (2016). doi:10.1038/srep29123
8. Dabdoub, S.M., Rumpf, R.W., Shindhelm, A.D., and Ray W.C. MoFlow: Visualizing conformational changes in molecules as molecular flow improves understanding. 5th Symposium on Biological Data Visualization (BioVis) (2015). doi:10.1186/1753-6561-9-S6-S5
9. Tsigarida, A.A., Dabdoub, S.M., Nagaraja, H.N., and P.S. Kumar. The Influence of Smoking on the Peri-Implant Microbiome. Journal of Dental Research 94, no. 9 (2015): 1202-1217. Co-first author. doi: 10.1177/0022034515590581
10. Mason, M.R., Preshaw, P.M., Nagaraja, H.N., Dabdoub, S.M., Rahman, A., and Kumar, P.S. The subgingival microbiome of clinically healthy current and never smokers. The ISME journal 9 (2014): 268-272. doi:10.1038/ismej.2014.114
11. Dabdoub, S.M., Tsigarida, A.A., and Kumar, P.S. Patient-specific Analysis of Periodontal and Peri-implant Microbiomes. Journal of Dental Research 92, no. 12 suppl (2013):168S-175S. doi:10.1177/0022034513504950.
12. Justice, S.S., Li, B., Downey, J.S., Dabdoub, S.M., Brockson, M.E., Probst, G.D., et al. Aberrant Community Architecture and Attenuated Persistence of Uropathogenic Escherichia coli in the Absence of Individual IHF Subunits. PLoS ONE 7, no. 10 (2012):e48349. doi:10.4103/0970-1591.98455.
13. Dabdoub, S.M., VanderBrink, B.A., Justice, S.S., and Ray, W.C. Quantitating pathogenic biofilm architecture in biopsied tissue. Proceedings of IEEE/ACM VisWeek, Workshop on Visual Analytics in Healthcare (Oct. 2011):49-52, Providence RI. (acceptance ~50%)
14. Dabdoub, S.M., Ray, W.C., and Justice, S.S. FIND: A new software tool and development platform for enhanced multicolor flow analysis. BMC Bioinformatics 12, no. 1 (2011): 145. doi:10.1186/1471-2105-12-145.
15. Dabdoub, S.M., Justice, S.S., and Ray, W.C. A dynamically masked gaussian can efficiently approximate a distance calculation for image segmentation. In Software Tools and Algorithms for Biological Systems, pp. 425-432. Springer New York, 2011. (acceptance ~15%). doi:10.1007/978-1-4419-7046-6_42.
16. Dabdoub, S.M., Mohan, A., and Ray, W.C. Visualizing molecular uncertainty: a path to the path, Proceedings of ACM SIGGRAPH 2008 posters, pp 128, (2008). (acceptance ~17%). doi:10.1145/1400885.1401022.

Invited and Editor-Reviewed Publications

1. Dennis J. Horvath Jr., Shareef M. Dabdoub, Birong Li, Brian A. VanderBrink, and Sheryl S. Justice. New Paradigms of Urinary Tract Infections: Implications for patient management. Indian Journal of Urology 28, no. 2 (2012): 154-158. doi: 10.4103/0970-1591.98455

Invited Presentations

1. Invited speaker, Identifying Site-specific Predictors and Biomarkers of Peri-implantitis Using Dual Transcriptomics. IADR/AADR/CADR General Session & Exhibition, San Francisco, California, March 2017.
2. Invited speaker, Computational Analysis of Disease-Associated Functional Shifts in the Periodontal Microbiome. The 13th Biennial Congress of the Anaerobe Society of the Americas, Nashville, Tennessee, July 2016.
3. Invited speaker, Computational analysis of disease-associated functional shifts in the periodontal microbiome. Genome Informatics, Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, October 2015.
4. Invited speaker, PhyloToAST: Bioinformatics tools for species-level analysis and visualization of complex microbial communities. Bioinformatics Open Source Software Conference, Dublin, Ireland, July 2015.
5. Invited speaker, MoFlow: Visualizing Conformational Changes as Molecular Flow Improves Understanding. 5th Symposium on Biological Data Visualization @ ISMB/ECCB, Dublin, Ireland, July 2015.
6. Invited speaker, FIND: A new software tool and development platform for enhanced multicolor flow analysis. FlowCAP II Summit 2011, U.S. NIH Campus (NIAID), Bethesda, Maryland, September 2011.
7. Invited speaker, FIND: A new software tool and development platform for enhanced multicolor flow analysis. Ohio Branch American Society for Microbiology, Spring Meeting 2011, Akron, Ohio, April 2011.
8. Invited poster, Aesthetics and Understanding in Molecular Motion. Shareef M. Dabdoub, Sheryl S. Justice, and William C. Ray, The 21st Annual IEEE Visualization Conference, Salt Lake City, Utah, October 2010.
9. Invited speaker, Alternate methods for visualization and analysis of Flow Cytometry data. The Research Institute at Nationwide Children's Hospital, Annual Research Forum, Columbus, Ohio, May 2009.
10. Invited speaker, Exploiting biological coherency in classification and segmentation. Ohio Branch American Society for Microbiology, Spring Meeting 2009, Granville, Ohio, April 2009.

Contributed Visualizations, Exhibits and Art in Science

1. Nationwide Children's Hospital, Musical Motion, Research Building Lobby Art, RBIII. Large-format print. 2012.
2. Australian Bioinformatics Network, Editorial invitation, Folding Beauty, 2013, Science Art Gallery http://australianbioinformatics.net

Honors and Awards

Released Software

Name: PhyloToAST (Phylogenetic Tools for Analysis of Species-level Taxa) Software sites: http://phylotoast.org/ Purpose: The PhyloToAST project is a collection of python code and scripts that modify the QIIME pipeline by adding/changing several steps including: support for cluster-computing, multiple primer support (eliminate primer bias), enhanced support for species-specific analysis, and additional visualization tools that can be used with other pipelines and software providing standard formats such as BIOM tables and CSV. Operating Systems: Platform Independent Programming Language: Python License MIT

Name: FIND (Flow Investigation using N-Dimensions) Software site: http://justicelab.org/find Purpose: To provide users of Flow Cytometry analysis software a means to enhance their analysis of multicolor data sets by providing access to automated population discovery algorithms and novel visualizations through a platform, modeled after the NIH-sponsored ImageJ, leveraging a sophisticated plugin system that allows authors of such algorithms to distribute their software to users without advanced technical skills or programming experience. Operating Systems: Platform Independent Programming Language: Python License GPLv3

Name: ProkaryMetrics Software site: http://justicelab.org/pkm Purpose: To provide users with the tools to analyze microbial biofilms through the 3D reconstruction of fluorescent microscopy image data and the manual annotation of bacteria. ProkaryMetrics allows full 3D interaction with such data sets and provides users with visual and quantitative analysis tools to gather quantitative measurements on individuals as well as the biofilm as a whole. Operating Systems: Platform Independent Programming Language: Python License: GPLv3

Dissertation Topic

One characteristic of modern science is that scientists are able to gather massive amount of information, often from highly heterogenous sources. Such large and varying data sets require computational processing and visualization in order to reliably extract understanding from them. My dissertation involved three projects with the same goal of designing computational approaches to usefully analyzing and visualizing scientific data.

The first project centered around uropathogenic E. coli (UPEC), the major causative agent of urinary tract infections, a disease that is associated with over $4 billion in costs annually in the United States. UPEC form intracellular biofilms within the bladder, but little is known about these structures. Using a mouse model, we captured fluorescent micrograph z-stacks of infected bladder epithelial cells and I created custom software to reconstruct and analyze the image data in 3D. Using this software, I was able to record the positions of the individual bacteria in the biofilm image data. Recording this data and deriving a number of quantitative measures describing the biofilms, I established significant differences in architecture between the wild type bacteria and a particular mutant. This work is intended to be generalizable to different biofilm forming species, and should increase the level of quantitative investigation possible in biofilm studies.

The focus of the second project was the increasingly high-dimensional data produced in Flow Cytometry (FC) experiments. FC allows antibody-marked cells to be identified by emitted light detection, and while standard technology is capable of producing 18-dimensional data, the gold standard for analysis is segmentation by manual placement of geometric shapes. Many machine learning algorithms have been developed in the last 20 years to replace manual processes, but the vast majority of users have no practical means to access these solutions. In order to solve this problem of communication, I developed a software platform providing basic functionality expected by users, as well as a powerful plugin system for developers. Using this software, developers have a ready-made distribution method and users have easy access to new methods for data analysis and visualization of their data.

For the final project, I created a new method for visualizing molecural structural motion such as occurs during protein conformational change. Current methods for visualizing this sort of data generally involves either overlaid/side-by-side display of snapshots of the structure over time or animation of the data. Unfortunately in many cases, especially those with more complex motion, these visualizations tend to be more confusing than helpful. Taking inspiration from visual representations of fluid dynamics data, the new method, called Moflow, displays the paths of atoms as they travel through space over time. Along with other visual cues to indicate time, structure, and motion, Moflow bridges static display with animation while remaining suitable for print or animation and displaying the motion data in a way not possible with current methods.

Teaching

Instructor: The Ohio State University, DENT 8993: Introduction to Bioinformatics. Summer 2014.

Instructor: The Ohio State University, DENT 8993: Introduction to Bioinformatics. Summer 2013.

Teaching Assistant: The Ohio State University, Biophysics 702: Advanced Experimental Methods. Dr. William Ray Instructor, Autumn 2010.

Lab Instructor: The Ohio State University, Biology 114: Form, Function, Diversity and Ecology. Dr. Thomas Hetherington Instructor, Spring 2006.

Memberships

Employment Experience

Selected Abstracts

1. Shareef M. Dabdoub, William C. Ray, and Sheryl S. Justice. Quantitative analysis and comparison of intracellular biofilms in E. coli induced cystitis. 18th Annual Midwest Microbial Pathogenesis Conference, University of Michigan (Ann Arbor), October 2010.
2. Sheryl Justice, Birong Li, Jennifer Downey, Shareef Dabdoub, Elizabeth Brockson, Duane Probst, Steven Goodman. Homodimers of IHF retain function during the pathogenesis of uropathogenic Escherichia coli. 18th Annual Midwest Microbial Pathogenesis Conference, University of Michigan (Ann Arbor), October 2010.
3. Shareef M. Dabdoub, William C. Ray, and Sheryl S. Justice. Quantitative analysis and comparison of intracellular biofilms in E. coli induced cystitis. Center for Microbial Interface Biology Research Retreat, Columbus, OH, September 2011.
4. Blake R. Szelestey, Shareef M. Dabdoub, Sheryl S. Justice, and Kevin M. Mason. Heme Availability Influences Biofilm Development And Architecture By Nontypeable Haemophilus Influenzae. Center for Microbial Interface Biology Research Retreat, Columbus, OH, September 2011.
5. Shareef M. Dabdoub, William C. Ray, and Sheryl S. Justice. FIND: A new software tool and development platform for enhanced multicolor flow analysis. 10th Annual OSUMC Research Day, Columbus, OH, April 7, 2011.
6. Shareef M. Dabdoub and Sheryl S. Justice. Let computers do the math: Automatic population discovery in Flow Cytometry analysis, 17th Annual Midwest Microbial Pathogenesis Conference, Washington University (St. Louis), September 2010.
7. Shareef M. Dabdoub and William C. Ray. Flow-Visualization for Studying Molecular Motions, 5th Annual Ohio Collaborative Conference on Bioinformatics, The Ohio State University, Columbus, OH. June 2010.
8. Shareef M. Dabdoub, Sheryl S. Justice, and William C. Ray. Counting Bacteria: Fluorescent image segmentation in colony member enumeration, 16th Annual Midwest Microbial Pathogenesis Conference, Purdue University. October 2009.
9. Shareef M. Dabdoub and Sheryl S. Justice. FIND: Flow Investigation using N-Dimensions, Imaging and Flow Cytometry Research Day, The Ohio State University, Columbus, OH. September 2009.
10. Shareef M. Dabdoub, Sheryl S. Justice, and William C. Ray. Exploiting Biological Coherency in Classification and Segmentation, 7th Annual OSUMC Research Day, The Ohio State University, Columbus, OH, April 10, 2008.
11. Shareef M. Dabdoub, Sheryl S. Justice, and William C. Ray. Exploiting Biological Coherency in Classification and Segmentation, 15th Annual Midwest Microbial Pathogenesis Conference, Chicago, IL. September 2007.
12. Shareef M. Dabdoub, Sheryl S. Justice, and William C. Ray. Exploiting Biological Coherency in Classification and Segmentation, 2nd Annual Ohio Collaborative Conference on Bioinformatics, Miami, OH. July 2007.
13. Birong Lee, Dennis J. Horvath Jr., Shareef M. Dabdoub, Santiago Partida-Sanchez, William C. Ray, and Sheryl S. Justice. Filamentation by Escherichia coli Subverts Innate Immune Defenses During Urinary Tract Infection, Center for Microbial Interface Biology Research Retreat, The Ohio State University, Columbus, OH. June 2007.