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GENETICS & EPIGENETICS

Research in G&E labs is broadly focused on the fundamental genetic, epigenetic, and genomic mechanisms that control cell growth and differentiation, and that cause cancer and other human diseases.

PROGRAM REQUIREMENTS

Genetics & Epigenetics (G&E) PhD and Masters students are required to fulfill GSBS and Program-specific course requirements as listed below, in addition to the GSBS PhD degree and MS degree requirements. Requirements for students doing a secondary area of concentration in G&E are also listed. PhD students must pass the G&E candidacy exam to advance to candidacy. In addition, all students affiliated with G&E are expected to attend the annual G&E Retreat and present the findings of their research project. Students are also highly encouraged to participate in program activities throughout the year to enhance their education and support the development of their professional network. 

G&E Course Requirements

PhD Students

In addition to the general GSBS course requirements, the G&E Program requires the following courses:

  • GS04 1253 Principles of Genetics and Epigenetics
  • GS04 1811 G&E Scientific Writing (or equivalent) *
  • GS04 1821 G&E Oral Scientific Presentations
  • One or more elective course(s) or course modules (at least 3 credits)

Any GSBS course(s) can be chosen for the elective. Students should work with the G&E program director, their research mentor and/or Advisory Committee to use this elective to customize their studies to support their educational objectives.

* Students may take the GSBS Scientific Writing course or most Program-specific scientific writing courses to fulfill this requirement.

MD/PhD Students

The same as for PhD student listed above with one (1) exception: MD/PhD students are not required to take the three (3) elective course credits required for PhD students.

PhD Students with a Secondary Area of Concentration in G&E:

  • GS04 1253 Principles of Genetics and Epigenetics

In addition, they are expected to attend the annual G&E Program retreat and actively participate in some other G&E activities each year

MS Students

  • GS04 1253 Principles of Genetics and Epigenetics

Not required but suggested:

  • G&E Oral Scientific Presentations (GS04 1821) or equivalent
  • G&E Scientific Writing (GS04 1811) or equivalent

Suggested Elective Course Taught By G&E Faculty
Pragmatic Bioinformatics for Bench Scientists (1 credit)
Advanced Topics in Epigenetics (1 credit)
Practical Bioinformatics (1 credit)
Advanced Topics in DNA Repair (1 credit)
Introduction to Bioinformatics (3 credits)
Critical Thinking in Science (1 credit)
Developmental Biology (3 credits)
Principles of Stem Cell Biology (2 credits)

Course Descriptions

  • Advanced Topics in DNA Repair
    Course Detail

    GS04 1241 (1 credits)
    Fall

    Cole, Francesca. One semester hour. Fall, annually. Grading System: Pass/Fail. Prerequisite: GS21 1017: Foundations of Biomedical Research (Core Course). Audit permitted. 

    This 5-week course, which will start from November 5 to December 14, 2018, is designed for students to explore the hypotheses, logic, principles, and approaches that best exemplify the field of DNA repair.  Each week, there will be a one-hour open format discussion of a DNA repair topic led by a faculty member and a two-hour journal club discussion of recent papers that highlight the weekly topic moderated by at least two faculty members. The discussion will occur on Mondays from 9 to 10 a.m. and the journal club will occur on Fridays from 9 to 11 a.m. The course will take place at The University of Texas MD Anderson Cancer Center, Smithville Campus and be video conferenced to the main campus (Houston), with the exception of one week when the campus and video conference sites will be reversed. There will be no specified presenters or pre-prepared slides for the journal club. The course will cover: Nucleotide Excision Repair and Human Disease, DNA Repair in the Context of Chromatin, Meiosis and Homologous Recombination, Antibody Generation as a Model for DNA Repair, and Targeting DNA Repair for Cancer Therapy. Instructors will be faculty in the Epigenetics and Molecular Carcinogenesis Department.

  • Advanced Topics in Epigenetics
    Course Detail

    GS04 1231 (1 credits)
    Fall

    Bedford, Mark and Chen, Taiping. One semester hour. Fall, annually. Grading System: Pass/Fail. Prerequisite: GS21 1017: Foundations of Biomedical Research (Core Course). Audit permitted. 

    The purpose of this course is to facilitate student learning, at an early stage of their research careers, regarding the development of basic approaches and techniques in epigenetics, as well as highlighting major discoveries that will cover current and advanced topics in epigenetics.  This 5-week course, which will start from August 27 to September 28, 2018,  covers 5 weekly publication-based discussions and data analysis sessions that will take place in two 1.5-hour weekly sessions, Mondays from 9-10:30 a.m. and Fridays from 9-10:30 a.m. at The University of Texas MD Anderson Cancer Center, Smithville Campus. Each class will consist of a 90-minute discussion of a primary epigenetic paper from the literature, with the student leading the discussion, moderated by course co-organizers. There will be no pre-prepared slides or specified presenters. Instructors will be faculty from the Department of Epigenetics & Molecular Carcinogenesis.

  • Critical Thinking in Science
    Course Detail

    GS21 1061 (1 credits)
    Summer Session

    Mattox, William. One semester hour. Summer, annually. Grading System: Pass or Fail. Prerequisite: General knowledge of biology or biomedicine.

    In this course students will develop skills for critically and professionally evaluating the significance, logic and presentation of scientific studies. Class sessions will emphasize student discussion and debate of topics including experimental design, the logical interpretation of results, scientific fraud, controversial results, dogma, and effective critique. Through class exercises students will gain understanding of the peer review process and will develop skills required to write critiques of manuscripts and research proposals.

  • Developmental Biology
    Course Detail

    GS04 1073 (3 credits)
    Fall

    Behringer, Richard; Eisenhoffer, George. Three semester hours. Fall, annually. Grading System: Letter Grade. Prerequisite: consent of instructor

    Developmental Biology is one of the fundamental modern biological disciplines. This course provides an in-depth examination of the basic cellular, molecular, and genetic mechanisms by which a fertilized egg transforms into an organism with fully differentiated and functioning tissues and organs. Topics covered will include cell-to-cell communication, embryo patterning, tissue morphogenesis, cell differentiation, progenitor cells, advantages and disadvantages of classical and genetic model organisms for analyzing development, postembryonic development and regeneration, and the profound implications of developmental biology for medicine. The course is divided into hands-on lab modules, utilizing primary model organisms to examine the basic principles of developmental biology and will discuss current debates and recent findings that have yet to be simplified for textbook presentation.

  • G&E Oral Scientific Presentations
    Course Detail

    GS04 1821 (1 credits)
    Spring

    Chen, Jichao; Hofmann, Marie-Claude. One semester hour. Spring, annually. Grading System: Pass or Fail. Prerequisites:  GSBS Core Course and student must be at least in their second year to take this course. Audit permitted.

    The class is designed for second year students who have chosen their thesis lab and are preparing for their candidacy exam.  The students will use their thesis project as a template to develop a 20-minute scientific presentation.  All aspects of the presentation will be covered including title and introduction slides, organizing your data into a story, model slides and conclusions and answering questions.  In addition to the 20-minute presentation students will also give two 90-second elevator talks one to a scientific group and one to a non-scientists group.  Students will also present a 10 minute chalk talk based on the research plan that is based on the data from their 20-minute talk. This course is designed to prepare the student for the oral defense portion of their candidacy exam and to prepare the student to present their work in both short and long format platform presentations.

  • G&E Scientific Writing
    Course Detail

    GS04 1811 (1 credits)
    Fall

    Prakash, Siddharth; Parker-Thornburg, Jan; McDonnell, Timothy. One semester hour. Fall, annually. Grading System: Pass or Fail. Prerequisites: Consent of instructor and student must be at least in their second year to take this course.

    This course is designed for second year students who have already chosen their thesis lab. Students will be taught how to write scientific papers. The goal of the class will be for each student to write a review of the literature of their field of research for submission and publication.

    >> This course fulfills the GSBS Scientific Writing requirement. <<

  • Introduction to Bioinformatics
    Course Detail

    GS01 1143 (3 credits)
    Spring and Fall

    Chen, Ken and Navin, Nicholas. Three-credit hour. Fall and Spring annually. Grading System: Letter Grade.

    This course is intended to be an introduction to concepts and methods in bioinformatics with a focus on analyzing data merging from high throughput experimental pipelines such as next-gen sequencing. Students will be exposed to algorithms and software tools involved in various aspects of data processing and biological interpretation. Though some prior programming experience is highly recommended, it is not a requirement.

  • Practical Bioinformatics
    Course Detail

    GS04 1251 (1 credits)
    Fall

    Liu, Bin; Wood, Richard; Shen, Jianjun. One semester hour. Fall, annually. Grading System: Pass/Fail. Prerequisite: GS21 1017: Foundations of Biomedical Research (Core Course). Audit permitted.

    The purpose of this course is to facilitate student learning, at an early stage of their research careers, regarding the basis and implementation of bioinformatics techniques that are especially applicable to research in modern molecular biology.  This 5-week course, which will start from October  9 to November 5, 2020, will provide introductory tools in bioinformatics in six areas. This course will cover 5 weekly publication-based discussions and data analysis sessions that will take place in a three-hour weekly session, Fridays from 9:00 am - 12:00 noon that will taught online via Zoom. Each lecture period will start with a one-hour discussion of a primary bioinformatics paper from the literature, with student-led discussion, moderated by course co-organizers. The class will then work on computers to analyze some of the data and understand how figures were generated. Instructors will be faculty from the Department of Epigenetics & Molecular Carcinogenesis.

  • Pragmatic Bioinformatics for Bench Scientists
    Course Detail

    GS04 1781 (1 credits)
    Summer Session

    Chen, Jichao. One semester hour. Summer, annually. Grading System: Letter Grade. Prerequisite: None.

    Bioinformatics is becoming essential in the genomic era. Witnessing both the power and the complexity of bioinformatics, bench scientists, despite providing most of the biological insights, often feel left out as simply data generators, and frustrated when collaborating with data analyzers. This course, taught by bench scientists who have published on specific bioinformatics topics, aims to empower bench scientists with valid statistical and computational methods to be able to explore data and communicate with computational scientists. It is pragmatic because it covers as-needed theoretical background and teaches usable, instead of efficient, programming in the format of a dry-lab protocol that generates publication-quality figures. It consists of 6 modules covering principles, RNA, DNA, protein, images, and freeware. Each module takes 4 hours of class time, which consists of one 30-minute background and three 1-hour sessions with significant hands-on time. Grades are based on homework.

  • Principles of Genetics and Epigenetics
    Course Detail

    GS04 1253 (3 credits)
    Spring

    Fornage, Myriam; Krahe, Ralf; Santos, Margarita . Three-semester hour. Spring annually. Grading System: Letter Grade. Prerequisite: GS21 1017/18: Foundations of Biomedical Research. Audit permitted. 

    The Principles of Genetics and Epigenetics class is designed for students who have a major interest in the aspects of epigenetics, experimental and human genetics.  Students are required to have completed the core course. This class will provide in-depth instruction on four areas: 1) Experimental genetics, 2) Human genetics, 3) Epigenetics, 4) Functional bioinformatics.  The class will be held three times a week for one hour and students are expected to actively participate in the course by initiating discussions, asking questions, and providing constructive comments.  Students will be evaluated by attendance, participation, and performance on a mid-term and final examination.  This course is designed to prepare the student to generate novel hypothesis-driven projects in the areas of genetics and epigenetics.

  • Principles of Stem Cell Biology
    Course Detail

    GS04 1072 (2 credits)
    Spring

    Davis, Brian and Yoshimoto, Momoko. Two semester hours. Spring,  annually. Prerequisite: consent of instructor

    Stem cells, be they embryonic or somatic, play crucial roles in the development and functional maintenance of individual organ systems and complete organisms. As has already been well demonstrated for the blood-forming system through bone marrow transplantation, stem cells can be utilized clinically for treatment of genetic or acquired diseases. The next couple of decades will undoubtedly provide many more successful clinical applications of stem cells in regenerative medicine. Stem cells may also play critical roles themselves in the initiation and maintenance of certain diseases, such as cancer. This course will provide a present-day understanding of the precise definition, molecular characterization, and biological function of stem cells. Our focus will primarily be on fundamental issues regarding stem cells, as well as on their wide range of potential future applications. Completion of this course will adequately prepare students to both identify and understand fundamental issues in current stem cell research, as well as to contribute themselves to advancing this field through research.

  • Stem Cells in Biomedicine
    Course Detail

    GS04 1081 (1 credits)
    Fall

    Geng, Yong-Jian. One semester hour. Fall, annually. Grading System: Letter Grade. Prerequisite: Consent of instructor.

    A stem cell is a cell from the embryo, fetus, or in any adult organs, that has the ability to reproduce itself for long periods of time, and at a given signal, give rise to many specialized cell types in the body. Apart from embryonic stem cells, adult stem cells maintain this capability throughout the life of an organism. In recent years, scientific advances have suggested that stem cells could be of great potential use in the treatment of a variety of diseases.

    The objective of this graduate school course is to provide the students with information about stem cell origin, their role in early development, their isolation and therapeutic promises for the future. This course will also offer students a great opportunity to take part of recent and ground breaking advances in stem cell biology. All in all, the material presented is intended to evoke more interest in the field of stem cell biology, both for the student, the layman, as well as for the bench scientist.  Ultimately, the long term goal is to encourage future research in finding alternative therapeutic modalities in stem cell-related diseases, such as cancer, Parkinson’s, diabetes, atherosclerosis, congenital diseases, and Alzheimer’s disease. This course is taught by a group of high profile scientists with a broad expertise in stem cell biology, biochemistry, clinical applications, and ethics.


G&E CANDIDACY EXAM

Genetics and Epigenetics (G&E) Program students are required to take an on-topic candidacy exam in which the research proposal is based on the student's current or planned dissertation research. Click here for the timing of the exam and deadlines which are set by the GSBS.  

The G&E on-topic candidacy exam will evaluate 1) the student's ability to formulate a hypothesis, design experiments to test the hypothesis, and interpret potential outcomes; and 2) the student's breadth of knowledge in the biomedical sciences, focusing on fundamental knowledge required to understand modern biomedical research.  As noted above, the exam will be on the student's current or planned thesis research.  The G&E on-topic exam follows the GSBS on-topic exam format except for the following features:

  • Guidance

The student can seek help from anybody, on any topic, to prepare for the exam.  

  • Written Proposal

The written component of the exam will follow the NIH pre-doctoral fellowship format (same as the GSBS format). It must be submitted at least two weeks before the oral examination. Preliminary studies generated by the student are not required but can be part of the written proposal. The written proposal should include:

  • A brief statement regarding the importance of the work;
  • A specific, testable, mechanistic, and well-reasoned hypothesis;
  • One or two specific aims that directly test the hypothesis with feasible, interpretable experiments.  Sub-aims are allowed. The topic can be based on the mentor's grant application but plagiarism is not acceptable.

The written proposal will be evaluated by the Examining Committee and a written critique by each member will be provided to the candidate by the chair of the committee after the exam. The critique will follow a modified NIH format.

  • Oral Examination

At the beginning of the oral exam, the student will present an oral overview of the proposal (up to 10 minutes) without computer support. The student may have a hard copy of their proposal with them during the oral exam. Questioning will begin immediately after the overview presentation.  During the oral examination, the student should:

  • Be aware of the relevant literature;
  • Demonstrate an understanding of the goals of the research;
  • Propose mechanistic testable experiments;
  • Understand the potential outcomes of the experiments and how they would be interpreted;
  • Present alternative approaches if the primary approaches do not work;
  • Explain the potential scientific and/or health impact of the proposed research

The emphasis of the exam is on logic, experimental design, abandoning hypotheses in the light of new data, and interpreting unexpected outcomes.

  • Examining Committee Composition

The Examining Committee composition will mostly follow GSBS rulesThe committee will include a minimum of two G&E faculty members, and up to three members of the student's Advisory Committee. Following GSBS rules, the student's advisor may not serve on the committee. The student will select the chair of their exam committee from a pre-approved list of G&E faculty members. For the 2021-2022 academic year, the approved faculty are Dr. Mark Bedford and Dr. Michael Galko. In case neither of them are available, Dr. Jichao Chen or Dr. Francesca Cole will serve as the exam committee chair.

  • Breadth of Knowledge

The exam will also explore the student's breadth of knowledge. Each committee member will ask at least one question from broad topics in biomedical research. At least five different topics must be addressed. Each question will explore the limits of the student's knowledge in that particular area. The chair will ensure that each committee member asks at least one breadth question and that at least five different topics are covered. The topics include but are not limited to:

  • Genetics/Genomics
  • Gene expression
  • Epigenetics
  • RNA
  • Proteins
  • Cell biology
  • Cell cycle
  • Genome integrity
  • Signaling pathways
  • Developmental biology
  • Human disease

G&E ACADEMIC POLICIES

G&E Advisory Committee Composition 

The composition of the Advisory Committee will mostly follow GSBS rules. G&E advisory committees will include a minimum of two G&E faculty members. Students with a second area of research concentration in G&E will include a minimum of one G&E faculty member on their advisory committee.