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Masters/Ph.D. Program

 

AADR group
 Faculty, Staff, Graduate Students in Oral Biology and PathologyFaculty, Graduate Students and DDS students at the AADR/IADR Meeting

Introduction:

Oral Biology and Pathology is part of the School of Dental Medicine within the Health Sciences Center. The Department of Oral Biology and Pathology offers two graduate degrees, which are granted through the Graduate School at Stony Brook University.  The department offers a PhD in Oral Biology and Pathology and an MS in Biomedical Sciences (Track in Oral Biology and Pathology).  These degrees can also be obtained as part of a combined DDS/PhD program or a combined DDS/MS program.  The MS in Biomedical Sciences (Track in Oral Biology and Pathology) may also be obtained as part of a combined degree program leading to an Advanced Certificate in Endodontics/MS, Advanced Certificate in Orthodontics/MS, or an Advanced Certificate in Periodontics/MS. 

The main function of these advanced degree programs is to train educators and researchers to staff dental and medical schools, dental and medical research institutes, dental and medical industrial laboratories, and to provide relevant basic science training for dentists and physicians taking postdoctoral specialty training. In addition, the graduate programs offered in the Oral Biology and Pathology Department are of particular interest to industry-based scientists seeking additional training and advanced degrees.

The course work consists of an in-depth exposure to knowledge, directly and indirectly related to oral biology and its related sciences, and is coupled with appropriate individual research, tutorial and thesis/dissertation programs.

While the department is interested in all aspects of oral biology, active programs of research presently being conducted include the following:

  • development, metabolism, and control of the oral microflora on the teeth and various epithelial surfaces;
  • oral putrefaction, malodor, and gingivitis;
  • interrelationship between systemic and oral diseases;
  • mechanisms of and therapies for dentinal hypersensitivity;
  • ultrastructure and metabolism of healthy and diseased periodontal tissues with an emphasis on remodeling and matrix metalloproteinases;
  • salivary gland function in normal and diseased states/secretory mechanisms, etiology, monitoring of and therapy for oral dryness (xerostomia)
  • biology of epithelial growth and differentiation; epithelial gene therapy; mechanisms of epidermal and oral carcinogenesis;
  • Oral and dental stem cells
  • biology of skin and mucosal grafting; wound repair;
  • acquired and innate immunity; inflammation and fibrosis

Besides a commitment to basic oral and medically related science, the Department is committed to technology transfer and its relation to clinical care. It is a leader in translational research and continues to develop products for the oral and medically related health market. The  Department has brought into the University more than 12 million dollars in royalty income. Clinical trials are carried out to assess the safety and efficacy of various products developed by the Department in conjunction with many U.S. and foreign industrial companies. Research grants are primarily from NY State, the National Institute of Dental and Cranial Research (NIDCR), National Institute of Arthritis, Musculoskeletal and Skin Diseases (NIAMS) and industrial companies.

 
Further details may be obtained from the Graduate Program Director, Dr. Stephen Walker;
e-mail: stephen.walker@stonybrook.edu 

Facilities:

The Department currently occupies 18,000 square feet of space in Dutchess and Westchester Halls comprised of offices, research laboratories, special facilities and rooms with special equipment. These include:

  • extensive tissue culture facilities especially for growth of keratinocytes, fibroblasts and other cell types.
  • The Living Skin Bank, which can produce clinical grade cell therapies is housed in the Department of Oral Biology and Pathology under the scientific direction of Dr. Marcia Simon. 
       
     skin bank
      
  • gene transfer facility to provide high titer retroviral and lentiviral vectors for stem cell transduction in addition too directing the University Stem Cell Gene Transfer and Viral Vector Core (SCGTC)

     

  • isotope counters
  • preparative ultra and analytical centrifuges
  • atomic absorption; amino acid analyzer
  • halimeter and oral malodor diagnostic accessories.
  • gas and high-pressure liquid chromatography systems
  • high-voltage, and polyacrylamide gel electrophoresis systems
  • fluorescence densitometer and microdensitometer ; ultraviolet/visible spectrophotometers
  • fluorescence microscopes and other microscopes of various types
  • automated micro-hardness tester
  • specialized anaerobic bacteriology facility; automated colony counters
  • electronic, mechanical and wood shop facilities

In addition, Stony Brook University Supports a number of Research Core Facilities, which are coordinated under the Office of Scientific Affairs. The goal of these facilities is to provide commonly used technologies to the campus, and thus facilitate the research processes.

The university libraries maintain 1.7 million bound volumes and 3 million publications in microformat, and subscribe to approximately 13,300 periodicals and serial titles. Excellent collections are available in the biology and chemistry libraries. The Health Sciences Library contains more than 250,000 volumes and subscribes to 4,300 periodical and serial titles. Almost all of the dental research journals are included in this collection.


Faculty:

Acting Chair: Lucille London

Distinguished Professors: Lorne M. Golub, Israel Kleinberg

Professors: Steven D. London, Barry R. Rifkin, Marcia Simon, Soosan Ghazizadeh

Associate Professors: Ying Gu, Lucille London, Stephen Walker

Clinical Professor: Barry Cooper

Clinical Associate Professor: Arthur Goren

Research Assistant Professors: Don P. Codipilly, Hsi Ming Lee

Clinical Assistant Professors: Raveena Jagwani, Michael F. Paccione

Research Scientists: Robi Chatterjee, Jay Gary Gao, Zegong Zhang

Adjunct Distinguished Service Professor: Dr. David W. Krause

Adjunct Professors: David Baker, Robert Greenwald, Maria Emanuel Ryan, Mark S. Wolff

Adjunct Associate Professor: Timo Sorsa

Professors Emeriti: Hershall W. Kaufman, Thomas F. McNamara, Leo Sreebny, Lorne B. Taichman

Research Professor Emeritus: Nungavarm Ramamurthy


Admission:

MS Degree

Students with a baccalaureate degree in the biological sciences are eligible to apply for the MS in Biomedical Sciences with a track in Oral Biology.  The MS degree offers the non-dental student with the foundation for a more advanced degree or additional training to individuals such as laboratory technicians, research scientists, or secondary school teachers who may benefit from increased scientific knowledge. The M.S. curriculum is of approximately two years' duration and offers studies focused on basic and translational oral and related sciences.

PhD Degree:

This program is designed to ensure that graduates will develop the skills to initiate independent research in oral biology. The dissertation research comprises a significant part of the student’s course of study, which is at the leading edge of basic and translational biomedical sciences related to craniofacial development, oral health, disease processes and clinical therapies. The main function of this program is to train oral biology educators and researchers to staff dental and medical schools, dental research institutes, dental and medical industrial laboratories, and to provide relevant basic science training for dentists and physicians taking postdoctoral specialty training. In addition, this program has been of particular interest to industrial based scientists seeking additional training and advanced degrees as demonstrated by our alumni.

Combined DDS/PhD Degree:

Revolutionary discoveries and developments in fields such as molecular biology, biotechnology, biomaterials, tissue engineering, and regeneration therapy will radically alter how oral health care providers will diagnose and treat patients. In addition, there is a critical shortage of dental school faculty across the country, a scenario that is getting worse each year. To address these and many other projected changes in the profession, there is a need to develop a significant number of clinically trained scientists and scientifically trained clinicians. The DDS/PhD program seeks to do this by integrating the DDS program with the PhD in Oral Biology and Pathology.

All applicants must fulfill all prerequisite dental school requirements for admittance to the DDS Program and apply through AADSAS.  The AADSAS application deadline is December 1st.

 Applicants are also required to complete the Graduate School Application https://app.applyyourself.com/AYApplicantLogin/fl_ApplicantLogin.asp?id=sunysb-gs.  The University Ph.D. application deadline is January 5th.

The combined Ph.D./DDS Program is approximately seven years in length.

 The DAT may be substituted for the GRE Examination.

 For more specific information, please contact the Program Director:

Dr. Stephen Walker
Stephen.walker@stonybrook.edu  

Combine DDS/MS Degree:

 The DDS/MS program is designed to prepare outstanding clinical scientists thoroughly versed in clinical research capable of addressing significant issues in oral health. The master's degree adds an additional year so that students graduate with both degrees in five years. The DDS/MS degree provides considerable depth to the clinical degree, including a broad understanding of modern biomedical research. Having the M.S. degree strengthens any subsequent application to clinical specialty programs or academic positions.

Applicants interested in the combined DDS/MS Program must first be admitted to the DDS Program at Stony Brook University. Outstanding applicants will be invited to submit a second application after matriculation in the graduate school, submitted at any time during the first two years of study. For the combined DDS/MS, applicants must apply separately to both the DDS program and the MS program.

Combined MS Degree with Advanced Certificate (AC) Programs

The combined MS with an Advanced Certificate in (Endodontics, Orthodontic, or Periodontics) is available to residents in these Advanced Specialty Education Programs. Entry into the combined MS in Biomedical Sciences (Oral Biology and Pathology Track) requires a separate application to the MS program and the AC program.  Although we encourage students to apply to the MS program prior to or during their first year in the AC programs, students already in the AC Programs may apply prior to their final year. 

 Students should confer with the Directors of their Advanced Certificate Program:

Jerome Cymerman, DMD
Division Director of Endodontics
Program Director, Advanced Certificate Program in Endodontics

Richard Faber, DDS, MS
Acting Chair, Department of Orthodontics and Pediatric Dentistry
Program Director, Advanced Certificate Program in Orthodontics

Vincent J. Iacono, DMD
Distinguished Service Professor and Tarrson Family Professor of Periodontology
Chair, Department of Periodontics
Program Director, Advanced Certificate Program in Periodontics, Director of Post-Graduate Studies

For admissions to all of the graduate programs offered in the Oral Biology and Pathology Department, in addition to the minimum Graduate School requirements, the following are required:

  1. A bachelor's degree and grade point average of 3.3 in the sciences and 3.0 overall are required for admission into either the M.S. in Biomedical Sciences or Ph.D. program in Oral Biology and Pathology.
  2. In addition to their transcripts, applicants are required to submit three letters of recommendation and proof of satisfactory performance on the General Aptitude and Advanced parts of the Graduate Record Examination (GRE). Satisfactory performance on the Dental Admission Test (DAT) can substitute for the GRE at the discretion of the graduate program director.
  3. All applicants are screened by the credentials committee of the Department. Interviews and discussions are arranged with faculty members and graduate students where possible.
  4. Formal approval for acceptance into the program is given by the Graduate School.


To obtain applications and for more information, please access the Graduate School Web Site!


Degree Requirements:

 

The Graduate Program in Oral Biology and Pathology follows the guidelines, requirements and milestones set by the Graduate School (http://grad.stonybrook.edu/academics/graduation_information.php). The program also has requirements that are specific to the Oral Biology and Pathology program. The program recognizes that students from different backgrounds enter our program. Therefore, while following specific guidelines, the program also has incorporated a degree of flexibility. 

PhD PROGRAM: DEGREE REQUIREMENTS AND MILESTONES

The PhD degree is on average completed between 5 – 6 years. The requirements for the Ph.D. include both didactic and research courses.  A passing grade is considered a “B” or better. There are five elements

1.  Core Courses:  Each student must complete and pass the Oral Biology and Pathology Systems Courses (HDO 560, HDO 561, and HDO 562).

2.  Seminar:  Every semester each student must participate in and pass the Oral Biology and Pathology Seminar (HDO690). 

3.  Elective Courses:  Each student must pass at least four graduate level basic science course in related disciplines within and/or outside the department. The elective courses are chosen by the student in consultation with their dissertation advisor and Graduate Program Director. These courses should expand the student’s knowledge in fields related to their dissertation research. Course listings in various programs can be found at: http://sb.cc.stonybrook.edu/gradbulletin/current/courses/browse/byname/

4.  Advancement to Candidacy Exam: Students will prepare a written dissertation proposal in consultation with their Advisor.  The proposal will be in the format of a research grant application in accordance with current NIH guidelines with page limitations to not exceed 10 pages.  The written proposal will be shared with a Dissertation Advisory Committee (DAC). A public seminar is presented by the student to members of his or her advisory committee, the department and the University community at large, in which the student defends the proposal. This is followed by a further defense by the student before his or her advisory committee. Upon passing the exam and completion of all required coursework, the Graduate Program Director will submit a request to the Graduate School for the student’s Advancement to Candidacy.

5. Dissertation: A major part of the Ph.D. is research and the development of a dissertation (http://grad.stonybrook.edu/academics/thesis_dissertation_guidelines.php) on the findings. Each student must carry out original research that culminates in a written dissertation that is presented publicly and successfully defended. Areas of research are listed above but others may also be possible.

MS PROGRAMS: DEGREE REQUIREMENTS AND MILESTONES

The MS curriculum is approximately two years' in duration and provides basic and translational oral and related biological science training. The requirements for the MS degree include both didactic and research courses. There are four elements:

1.  Core Courses:  Each student must complete and pass the Oral Biology and Pathology Systems Courses (HDO 560, HDO 561, and HDO 562).

2.  Seminar:  Every semester, each student must participate in and pass the Oral Biology and Pathology Seminar (HDO690). 

3.  Elective Courses:  Each student must pass at least two graduate level basic science courses in related disciplines within and/or outside the department. The elective courses are chosen by the student in consultation with their thesis advisor, Program Advisory Committee, Thesis Committee and/or GPD. These courses should expand the student’s knowledge in fields related to their thesis research. Course listings in various programs can be found at: http://sb.cc.stonybrook.edu/gradbulletin/current/courses/browse/byname/

4.  Thesis Research:  An original research thesis is required for completion of the MS degree. Each student must carry out research (HDO599) culminating in a written thesis, which is defended before the student’s Thesis Committee. For the M.S. degree, the student defends the thesis only to the student’s dissertation committee. If the thesis is recommended for approval, the determination is submitted to the Graduate School for final decisions to award the degree

The Combined Degree Programs: DDS/PhD PROGRAM; DDS/MS; Advanced Certificate/MS: DEGREE REQUIREMENTS AND MILESTONES

The requirements for the PhD/DDS program and the DDS/MS program are similar as those for students in the stand alone PhD program or MS program with the following exceptions: Students who obtain a passing grade in HDO501 will not be required to take HDO560 and students who obtain a passing grade in HDO601 will not be required to take HDO561 and HDO562. Students may also opt to use Med500b (Molecular Foundations of Medicine) as an elective in lieu of MCB656-Cell Biology.

The requirements for the Advanced Certificate/MS are similar as those in the stand alone MS program.  Because students in these programs have a DDS from a US or Canadian institution, they participate in a more advanced oral biology and pathology course consisting of: HDO 531-Normal and reparative tissue development in the oral cavity; HDO 532-Host-parasite interactions; and HDO 533-Regional anatomy, orofacial neuroscience and pain conditions.   In addition, students in these programs are required to participate in multiple seminar courses in which they present the current basic science literature in their field. These students are not required to take the oral biology journal club (HDO690).

Courses:
HDO 500 Biology of the Oral Mineralized Tissues
This course deals with the basic chemistry, crystallography, ultrastructure, and metabolism of the calcium phosphates involved in the formation and physiological and pathological resorption of the various mineralized tissues found in or associated with the oral cavity (enamel, dentin, cementum, bone). Ectopic calculus formation will be examined. Prerequisites: HDO 560, 561, 562, and 563 or their equivalent.  Fall and Spring
Prerequisite:  Admission to Graduate Health Sciences Program
3 credits, Letter graded (A, A-, B+, etc.)

HDO 510 Salivary Metabolism and Secretion

Consideration is given to the normal and abnormal structure and function of the glandular systems found in the oral cavity. The composition, regulation, and functions of the secretions from the major and minor salivary glands will receive particular attention.  Prerequisites:  HDO 560, 561, 562, and 563 or their equivalent.  Fall and Spring
Prerequisite:  Admission to Graduate Health Sciences Program
3 credits, Letter graded (A, A-, B+, etc.)


HDO 520 Oral Microbial Systems
This course explores the oral microbiome as determined using both live culture and molecular “next generation sequencing” methodologies with a focus on changes in the oral microbiome during oral disease. 
Prerequisite: HDO 560, 561, and 562 or their equivalent.  Fall
Prerequisite:  Admission to Graduate Health Sciences Program
3 credits, Letter graded (A, A-, B+, etc.)

HDO 530 Molecular Biology and Pathology of the Periodontium
This course deals with the ultrastructure and biochemical composition of the periodontal tissues, remodeling of the extracellular matrix with an emphasis on the role of metalloproteinases; the microbial interrelations with the organic and inorganic components of the periodontal tissues, the biochemical dynamics of gingival inflammation and wound healing, and the metabolic processes responsible for the composition and flow of gingival crevicular fluid.  Prerequisites: HDO 560, 561 and 563 or their equivalent.  Fall and Spring.  Please note that this may be taken twice for a total of 4 credits.
Prerequisite:  Admission to Graduate Health Sciences Program
2 credits, Letter graded (A, A-, B+, etc.)

HDO 534  Research Design and Biostatistics
This course aims to improve the understanding of basic research methods and statistical concepts and principles and introduce some fundamental statistical tools, in the context of oral health research. The first part of this course covers basic assumptions and concepts of clinical and biomedical research, research methodologies, critical thinking, and evidence-based dentistry. Residents will develop the skills needed to recognize the quality of the scientific evidence and the quality of various publications, the ability to conduct an evidence-based analysis of the literature, and the ability to present an evidence-based presentation on a controversial topic related to dentistry. The components of a research proposal and the basic elements of compliance will be discussed. The second part of the course covers concepts from statistics such as: summarizing, organizing, and presenting different types of sample data; simple probability; discrete and continuous probability distributions such as the Binomial and Normal distributions; the mean and variance of a probability distribution; sampling distributions; hypothesis testing; statistical significance; confidence intervals; non-parametric techniques; ANOVA; correlation and regression; categorical data analysis, tests for proportions, and Chi-Squared tests. Students will apply the techniques learned in class on a given data set, where they will analyze the data and perform statistical testing. The third part of the course students will discuss and evaluate the statistical methods used in relevant papers as well as in proposed student’s projects.
Prerequisite: Enrollment in a graduate program in the School of Dental Medicine. Fall, 1 credit, Letter grades (S/U)

HDO 535 Epithelial Keratinization and Differentiation
Epithelial Keratinization and Differentiation The course examines the growth and differentiation of startified sqamous epithelia. Particular emphasis is placed on molecular events involved in the differentiation program. Consideration is also given to mechanisms involved in oral and cutaneous disorders.
Prerequisites: Permission of instructor required; HBP 531 suggested; students must have had a background in cellular biochemistry molecular biology. Fall and Spring, 2 credits, Letter graded (A, A-, B+, etc.)

 

HDO 540 Laboratory Techniques in Biomedical Research
This course aims to introduce theoretical principles and experimental techniques used for laboratory investigation in biomedical research.  Students will familiarize themselves with the instrumentation and techniques used to investigate different molecular and cell biological problems through a combination of lectures and demonstrations. Various topics will be covered such as tissue culture and isolation and characterization of DNA, RNA and proteins using various techniques. Students will be introduced to recombinant DNA technology including cloning in various non-viral and viral vectors that allow modulation of gene expression. Transgenic mice technology and Cre-lox system and gene editing technologies will be introduced. In addition, the use of mass spectrometry, microarray and DNA deep sequencing to understand biological processes will be discussed.
Prerequisite: Enrollment in the MS or PhD program in Oral Biology and Pathology.  Fall, 2 credits, Letter graded (S/U)

HDO 550 Oral Diagnostics and Therapeutic Technology, Lectures and Laboratory Techniques
Recent advances in the use and development of research technology for the early diagnosis and treatment monitoring of oral and systemic disease. Special attention is paid to the principles of technology transfer including patents and patenting; searching of on-line databases is a key component. The course includes relationships of dry mouth to salivary physiology, diabetes, and drug medications; salivary film measurements, wetting of oral surfaces, viscoelasticity and lubricity; the use of the Periotron and enzyme assays for the diagnosis of gingivitis and periodontal disease; instrumentation used in sensitive teeth measurement and evaluation of treatment effectiveness using oral compositions and iontophoresis; oral candidiasis and denture stomatitis and early detection and causes of dental caries; oral malodor measurements including use of the Halimeter and its use in the formulation of oral compositions. Application to clinical practice and clinical studies is covered.   Prerequisites: HDO 560, 561, 562, and 563 or their equivalent.  Fall and Spring
Prerequisite:  Admission to Graduate Health Sciences Program
3 credits, Letter graded (A, A-, B+, etc.)

HDO 560 Oral Biology and Pathology I
The first of four comprehensive courses on molecular structure, biochemical and physiological function, developmental anatomy and pathology of the various systems that constitute the oral apparatus. Covers the embryological development of the face and oral cavity and the biology and pathology of the oral mineralized tissues. Prerequisites: Undergraduate degree in basic science. Fall and Spring
Prerequisite:  Admission to Graduate Health Sciences Program
3 credits, Letter graded (A, A-, B+, etc.)

HDO 561 Oral Biology and Pathology II
The second of four comprehensive courses on molecular structure, biochemical and physiological function, developmental anatomy and pathology of the various systems that constitute the oral apparatus. Covers the biology and pathology of the periodontal structures and the microbiology of the oral cavity.  Prerequisites: Undergraduate degree in basic science. Fall and Spring
Prerequisite:  Admission to Graduate Health Sciences Program
3 credits, Letter graded (A, A-, B+, etc.)

HDO 562 Oral Biology and Pathology III
This course is the third of four comprehensive courses on molecular structure, biochemical and physiological function, developmental anatomy, and pathology of the various systems that constitute the oral apparatus. The course consists of' the following two units of instruction; (1) the biology and pathology of the salivary glands and their products and (2) the biology and pathology of the periodontal structures, Prerequisites: Undergraduate degree in basic science.
Fall and Spring
Prerequisite:  Admission to Graduate Health Sciences Program
3 credits, Letter graded (A, A-, B+, etc.)


HDO 563 Oral Biology and Pathology IV
This course is the last of four comprehensive courses on molecular structure, biochemical and physiological function, developmental anatomy and pathology of the various systems that constitute the oral apparatus. Covers the biology and pathology of the oral sensory systems and the biology and pathology of oral motor systems. Prerequisites: Undergraduate degree in basic. Fall and Spring
Prerequisite:  Admission to Graduate Health Sciences Program
3 credits, Letter graded (A, A-, B+, etc.)

HDO 590 Research Projects in Oral Biology and Pathology
Individual laboratory projects closely supervised by faculty members to be carried out in their research laboratories.  Prerequisite: Enrollment in a MS or PhD program in Oral Biology and Pathology.  Fall and Spring
Prerequisite:  Admission to Graduate Health Sciences Program
3 credits, Letter graded (A, A-, B+, etc.)


HDO 599 Graduate Research
Original investigations undertaken with supervision of a faculty member.  Prerequisite: Enrollment in a MS or PhD program in Oral Biology and Pathology.  Fall and Spring
Prerequisite:  Admission to Graduate Health Sciences Program
1-12 credits, Letter graded (A, A-, B+, etc.)

HDO 690 Oral Biology and Pathology Seminars
Research seminars by students, staff, and visiting scientists which may include review of current literature and presentation of student research.
Prerequisite: Enrollment in the MS or PhD program in Oral Biology and Pathology.  Fall and Spring, 1 credit, Letter graded (S/U).  May be repeated for credit.

HDO 695 Oral Biology and Pathology Teaching Practicum
Practice instruction in the teaching of oral biology and pathology at the undergraduate level carried out under faculty orientation and supervision.   Prerequisite: Permission of instructor required. Fall and Spring
Prerequisite:  Admission to Graduate Health Sciences Program
1 credits, Letter graded (A, A-, B+, etc.)

HDO 699 Dissertation Research in Oral Biology and Pathology
Dissertation Research, Prerequisite: Advancement to Candidacy Passing, Fall, Spring, and Summer.
Prerequisite:  Admission to Graduate Health Sciences Program
1-9 credits, Letter graded (A, A-, B+, etc.)

HDO 805 Summer Research In Oral Biology and Pathology
Summer Research, Prerequisite: Enrollment in a MS or PhD program in Oral Biology and Pathology.
Prerequisite:  Admission to Graduate Health Sciences Program
0 credits, S/U grading

 

 


Links

American Dental Education Association

American Dental Association

International/American Association of Dental Research

National Institute of Dental and Craniofacial Research (NIDCR)