Timeline of your degree. This is a typical plan; there will be lots of variation across the different CMB tracks. Please see track specific requirement information below.
* Typically tracks require 1-2 additional course requirements. These courses can be taken anytime in the second or third year.
Choosing a research adviser and a thesis research project are some of the most significant decisions you will make in graduate school. First year lab rotations provide students the opportunity to explore different research interests and lab management styles prior to the selection of a Ph.D. supervisor. Students will have the opportunity to complete three rotations within the first academic year. You may do first year research rotations with any faculty member on the Cell and Molecular Biology, Biochemistry or Microbiology Graduate Studies Committees.
Complete three research rotations during the first year.
Students join the laboratory of a Ph.D. mentor after 3 rotations (typically by May 10). From that point forward, the emphasis of the student's training is on laboratory research rather than formal course work.
Individual programs of study are tailored to the student's interests, but each student must complete the 4 core courses and any track-specific course requirements. Students must register for nine hours each semester, with credits available from graded courses and/or research hours, and maintain a cumulative grade point average (GPA) of 3.0 or higher (in order to maintain satisfactory academic progress at The University of Texas at Austin). Beyond these basic rules, coursework choices are subject to approval by the supervising professor and the graduate adviser.
MOL 395J. Genes, Genomes, and Gene Expression Detailed consideration of prokaryotic and eukaryotic mechanisms of DNA replication and transcription; post-transcriptional processing of transcription products; mechanism and regulation of the translation of messenger RNAs.
MOL 395G. Structure and Function of Proteins and Membranes Detailed consideration of the structure and function of proteins, with discussion of enzyme mechanisms and kinetics, the biochemistry of energy production, and the metabolism of lipids and nucleotides. A one-year undergraduate sequence in biochemistry is required.
MOL 395F. Genetics, Genomics and Epigenetics Basic principles of Mendelian and molecular genetics, and an exploration of the genetic toolbox using examples of analytic methods and modern manipulations; focus on the genetic analysis of model organisms; use of genetic tools in dissecting complex biological pathways, developmental processes and regulatory systems. An introductory course in genetics is strongly recommended.
MOL 395H. Cellular Systems: From Biology to Disease and Back Again Detailed consideration of mechanisms of growth control, cell regulation, mitosis, cell signaling, protein targeting, and the integration of these processes in various cellular processes.
Specific requirements and course options may be found under the Tracks tab.
In preparation for the qualifying exam, 2nd Year students are required to take BIO391 Grant Writing & Presentation Skills. BIO391 is a writing-intensive course for 2nd year Ph.D. student in the fall semester that involves writing of an NIH-style grant proposal on their own research, presentation of the proposal to the class, and practice in identifying specific aims in research areas outside their primary area. The class is taken by students in the Microbiology, Biochemistry, and Cell and Molecular Biology Programs.
In the fall semester of the first year, all CMB students take the core courses Genes, Genomes, and Gene Expression (MOL 395J) and Structure and Function of Proteins and Membranes (MOL 395G). In the spring semester of the first year, individual tracks may allow students to substitute track-specific courses for Cellular Systems, (MOL 395H) or Genetics, Genomics and Epigenetics, (MOL 395F), or both. Please note that the approved track core course lists are constantly changing and students should consult with both the 1st year Graduate Adviser and the student's potential Track Representative if they wish to substitute a track-specific course for one of the spring core courses. Tracks may also have requirements for the elective courses taken by students in the track.
In the fall of the second year, all CMB students are required to take Grant Writing and Presentation Skills (BIO391). Additionally, tracks may require that one or more elective courses be taken in the second or third year and completed no later than the fourth year. Students must consult their PI, Track Representative and the CMB website (icmb.utexas.edu/cmb) about the requirements for their specific track. These courses are listed on the CMB website under "Program Requirements", and should be selected in consultation with the student's PI and Track Representative. Journal club courses are NOT suitable as electives, although note that some tracks may have additional journal club or seminar course requirements.
The specific requirements for each track are listed below.
While computational analysis is now widely used in the vast majority of cellular and molecular biology, students in the Bioinformatics and Computational Biology Track will have an increased emphasis on the computational aspect. What constitutes significant computation is dependent on the lab and project, with an allowance for a significant amount of diversity in scope. And while all of the computational projects must address a topic in cellular and molecular biology, the definition of computation is broad. Programming languages can vary from Java, C++, and Python, to R, SQL, and matlab. And while the balance between pure programming vs. data analysis can vary, the thesis projects should have a significant amount of both, e.g. 80:20; 50:50; 20:80. Projects can have an emphasis on the development of a new algorithm (e.g. protein folding), data processing with Python for statistical analysis, use of sophisticated database management systems for big data applications to name just a few.
All BCB students should take one class from the list below. In addition, these track-specific courses may be substituted for the default spring 1st year course (MOL 395H Cell Biology or MOL 395F Genetics) -- this is effective for the 2019-20 cohort. Students who opt to substitute one of the below courses for a spring core course are still required to take one additional BCB elective that may be chosen from the pre-approved list below, or in consultation with their PI and Graduate Adviser or Track Representative.
Demonstrate competence in computer programming. It is expected that all BCB Track students can program in at least one language (e.g. Python or other scripting languages, Java, SQL, R, Matlab, etc.). No one language is specified since the language of choice varies across different research applications. This competency can be demonstrated through coursework or through practical experience. Contact the Track Representative and the student's PI with any questions or to request for a variance.
Demonstrate competence in the fundamentals of Biostatistics and/or Data Science (e.g. sequence analysis). It is expected that BCB Track students can interpret and perform basic statistical analyses and/or rigorous data analysis and communicate effectively with a statistician and/or domain scientist for more sophisticated analyses. This competency can be demonstrated through coursework or through practical experience.
The CDB Track is for graduate students interested in the mechanisms controlling fundamental eukaryotic cell processes and development. Within these broad and interrelated disciplines the individual laboratories affiliated with the CDB track focus on understanding the molecular and cellular basis of cell division, growth, differentiation, and movement; spatial patterning and morphogenesis of developing embryos; and the evolution of developmental mechanisms. CDB researchers utilize both plant and animal model organisms along with state-of-the-art methods in molecular biology, biochemistry, proteomics, genetics, and genomics. There is also a strong emphasis on microscopy, especially time-lapse microscopy of cellular and subcellular processes in live cells and embryos. The primary goal of the CDB track faculty is to support and mentor the next generation of outstanding cell and developmental biologists.
Students that join the CDB track must successfully complete the following three CMB core courses: Genes, Genomes and Gene Expression (MOL395J); Structure and Function of Proteins and Membranes (MOL395G); and Grant Writing and Presentation Skills (BIO391). In addition, CDB track students must take two of the following three courses: Genetics, Genomics and Epigenetics (MOL395F); and Cell Biology (MOL 395H), or Developmental Biology (BIO383K, Stein – taught every other year: Fall 2019, Fall 2021). It is possible that in future years, Plant Growth and Development may be offered and can substitute the Developmental Biology course. In addition, students who choose the CDB track will take one graduate-level elective, selected in consultation with the student's faculty advisor and the CDB track representative. This elective can be the third of the three choices listed above or one of the courses on the pre-approved list shown below or another appropriate course offering. Courses that have not been pre-approved require the approval of the CDB track representative. Electives should be completed by the end of the third year.
Plant Growth and Development (BIO388E, Huq) – not scheduled to be taught in the next several years.
Beginning their 3rd year of graduate training, students must enroll and actively participate in the presentation and discussion of the current scientific literature in neuroscience. A list of appropriate journal clubs is available from the track representative. As faculty, we strongly recommend (and students PIs may require) that students serve as a teaching assistant in a graduate or undergraduate course in neuroscience, neurobiology, or neuropharmacology at least once in their graduate career.
The Plant Molecular Biology faculty address fundamental biological questions important to plant development, physiology and evolution at molecular, cellular and organismal levels. Plants not only provide us with food, fiber and shelter but have also provided the experimental systems for major advances in science such as the discovery of hereditary laws (Gregor Mendel's work in garden peas), the discovery of transposable elements (Barbara McClintock's work in maize) and the discovery of RNA interference (co-suppresion in petunia). Arabidopsis thaliana, a fast growing flowering plant with a completely sequenced genome, has become a major model organism for studies in genetics, development, cell biology and evolutionary biology.
Faculty with research interests in plant molecular biology represents a broad range on several frontiers of plant molecular biology. These include cell fate determination, cellulose biosynthesis and fiber development, signal transduction, gene regulation by light and environmental cues, RNA splicing, translational regulation, function of duplicate genes and genomes, comparative genomics, plant pathogen interactions, molecular systematics, and phenotypic evolution.
Students interested in plant molecular biology are encouraged to explore the exciting research in the laboratories listed below.
The Qualifying Exam, often called the "qual" or "prelim", is a major milestone in the Ph.D. program. The purpose of the Qualifying Examination is to evaluate a graduate student's aptitude to perform original and independent research, and to write a doctoral dissertation. The examination provides a means for a faculty committee to assess the student's mastery of concepts and methodological approaches by evaluating the student's (1) general knowledge and fundamental understanding of cellular and molecular biology, (2) ability to design, articulate, explain and defend the proposed aims and research approach of their dissertation research, and (3) to critically evaluate and develop a set of experimentally testable hypotheses for a selected topic in cellular and molecular biology that is not their research specialty. The ultimate goal of the Qualifying Examination is to ensure that the student has achieved a sufficiently high level of knowledge and skills necessary for successful completion of a Ph.D. dissertation.
All graduate students in their second year who have passed the appropriate number of required courses will take the Qualifying Exam to advance to candidacy. If a student has not passed all the core courses with a grade of B or above, or, if they are an international student and are not yet "certified for employment with student contact," the Qualifying Exam will be delayed to within 3 months of completing these requirements. The exam must be taken before the end of the student's fourth long semester. The Qualifying Exam is normally taken in the spring semester of a student's second year. (Students who have not taken the Qualifying Exam by the end of their second year must write an explanatory letter of appeal to the GSC Chair and will be assigned a probationary status until further notice).
At the beginning of the spring semester (usually in January), exam-eligible graduate students will submit to the CMB Graduate Coordinator (i) a one-paragraph summary (100-200 words) of their intended research proposal (abstract), and (ii) a list of four CMB GSC faculty members, in consultation with their faculty adviser, who might be appropriate to serve on their examination committee. The GSC will use this information to form the student's Qualifying Exam Committee.
The student will be notified of the composition of their Qualifying Exam Committee within 30 days after submission of their abstract. Upon learning the members of their exam committee, the student is responsible for scheduling their Qualifying Examination, which involves polling the committee members and their PI for their availability for a 2.5-hour timeslot. Upon finding a time when all members can attend, the student must reserve a room for the exam and notify the CMB Graduate Coordinator and their exam committee members of the date, time and location of the exam. If the student's PI cannot attend the exam, they will be required to provide the committee chair with a short statement on the student's progress. The deadline for the written portion of the exam are relative to each student's exam date (detailed below in article 5); all students are responsible for meeting their relative deadlines. The Graduate Coordinator will provide the committee chair with the student's file, containing the Qualifying Exam results form and their transcript, which will need to be brought to the exam.
The Qualifying Exam consists of written and oral components. The written component is submitted prior to the Qualifying Exam and will form a large basis of the oral exam.
The Written Proposal, based on a topic of choice but usually aligned to the student's dissertation research, must be submitted to the CMB Graduate Coordinator and distributed to faculty members of the examination committee no less than 14 days before the Qualifying Exam. The Written Proposal should be modeled on and follow the format of a NIH F31 pre-doctoral fellowship application. As a guide, the general format of the Written Proposal is listed below but students should download the F31 application guide to obtain additional information about the contents and formatting of these applications.
The proposal will consist of the following sections. (Note that the margins on all sides cannot be less than ½", and the allowable fonts no smaller than Times 12, or Georgia or Arial 11. All information presented in figures and tables must be legible and easily readable by all committee members.
(b) The oral component of the Qualifying Exam should be scheduled to last 2.5 hours. Students are not allowed to bring refreshments for their exam committee to the Qualifying Exam. At the beginning of the meeting, the student will be excused and the exam committee will briefly discuss the materials that were submitted by the student, and the specific exam format and questioning procedures. Additionally, the committee will discuss the student's academic standing and progress, and the student's faculty adviser should be asked for input about these issues. If the faculty adviser cannot attend the exam, he/she will be asked to submit written comments to the committee chair, which should be shared with the committee at this time. The student will re-enter, and the exam will begin with the on-topic proposal followed by the off-topic proposal. At the completion of both proposals, the student will again exit and the committee will discuss the outcome of the exam; the committee should ask the PI again for input. Students will receive outcomes for each of the written and oral portions of the exam. The first portion of the exam will focus on the topics and projects covered in the Written Proposal (approximately one hour, but the time will vary), and the second portion will focus on the topics and projects covered in the selected research paper and the Off-topic Specific Aims Page. The Qualifying Exam Committee, whose aim is to realize the purpose and goals of the Qualifying Exam, will decide the times devoted to each proposal and the specific format of the oral exam.
The student should prepare a 15-minute presentation, with a maximum of 15 slides, for the written component. The brief presentation will introduce the background material, and the proposed research goals and projects. The presentation should include an introduction that states the broad research question(s), an overview of the present state of knowledge, and the background work leading to the proposed projects, questions and hypotheses. This should be followed by a description of each of the specific aims, the experimental approach and anticipated results. Students may practice their on-topic presentation in front of any audience they choose.
During and after the presentation, the examiners will question the student in order to assess the student's depth of knowledge in the topic areas and understanding of the experimental approaches. The committee will ask general questions as well as questions pertaining to the specific topic area. Students may be asked to draw or explain concepts using the whiteboard. One purpose of the exam is to probe a student's breadth and depth of knowledge, so the committee may spend more time on areas where it is not clear whether the student has extensive knowledge, and correspondingly less time on areas where the student demonstrates expertise.
Composition of the Qualifying Examination Committee: The Qualifying Exam Committee will be comprised of three faculty members. Ideally, two of these faculty will be members of the "Committee of 15" (a select group of CMB GSC faculty, also referred to as "Q15") and one faculty member (not a member of the Committee of 15) will be selected from the list of four submitted by the student and who has expertise in the general area covered in the student's Written Proposal. One of the Q15 committee members will be assigned the role of Chair. If it is not possible to have two members of the Q15 on a committee, the committee will consist of one Q15 member, one faculty from the student's list of four if possible, and one additional faculty member with appropriate expertise appointed by the GSC chair (who may or may not be on the student's list of four). In this case the Q15 committee member will be the chair. Each of the committee members will submit a published paper to the Graduate Coordinator, which will form the basis of the student's OSAP. The student's faculty adviser is encouraged to attend the Qualifying Exam but is not obliged to do so. If the faculty adviser cannot attend the exam, he/she will be asked to submit written comments to the committee chair, which will be shared with the committee at the exam. If in attendance, the faculty adviser is expected to be a silent observer and may speak only by permission of members of the exam committee.
Qualifying Exam Outcomes and Consequences: At the conclusion of the examination (usually when committee members have no further questions), the student will again be asked to leave the room. The PI will be asked for any additional input and then he/she will also be asked to leave the room. The committee will then deliberate the outcome of the examination. The entire committee as a group will then call the student back into the room to convey its decision. The student's advisor, if still present, may come back into the room along with the student. A student may pass the Qualifying Exam unconditionally, or may fail one or more portions of the exam. Additionally, the committee may vote to conditionally pass the student but ask for revisions of the written proposal or for the student to take additional coursework. (Serving as a TA for a course in an area that the student was deemed deficient cannot be a requirement for a conditional pass.) Possible outcomes are (1) Pass; (2) Conditional Pass (with conditions specified by the exam committee); (3) Re-examination of one or more parts of the Qualifying Exam at a later date; (4) Termination of work toward the Ph.D.
A student given the option to repeat the Qualifying Exam must do so by within three to four months of the original exam, except in exceptional circumstances requiring exemption by the CMB GSC Chair. At least one member of the student's original Qualifying Exam Committee must agree to serve on the subsequent exam committee. All three members may re-serve. The PI may request to the CMB GSC Chair that one or two members of the committee be replaced. A student who fails to pass the relevant portions of the examination a second time must leave the graduate program by the end of the following long semester.
A student who is not offered the option of re-examination must terminate work towards a Ph.D. and may not re-register in the CMB Program.
After you submit your application, it is routed to your PI, then to the Graduate Advisor, the GSC Chair, and finally to the Graduate Dean. Once you are admitted to candidacy, you no longer register for "research problems" but instead must be registered for "dissertation hours" every long semester. Your first semester of candidacy, you will enroll in dissertation hours with course numbers that end with an "R" (MOL 399R, MOL 699R, and MOL 999R). All subsequent semesters you must enroll in dissertation hours with a course number ending with a "W" (MOL 399W, MOL 699W, or MOL 999W).
You will select your dissertation committee in consultation with your supervising professor. The committee is typically comprised of five faculty members, including the student's PI. The PI chairs the committee, and at least one member must be from outside the CMB GSC or the student's primary academic unit or department (e.g., Pharmacy, Biomedical Engineering, Molecular Biosciences etc.). If specific expertise is needed for a project (e.g. Engineering), one committee member may be a tenured track faculty member at another institution (non-UT faculty must have permission of the Graduate Advisor and Graduate School).
Students may retain their Qualifying Exam Committee members as their Dissertation Committee, but this is not a requirement. Students should consult with their PI and Graduate Advisor to form a suitable permanent Dissertation Committee. Students should explicitly confirm with proposed committee members that they agree to serve on the Dissertation Committee. Any changes in committee membership should be made prior to application for candidacy. Once students are admitted to candidacy, they must meet with their Dissertation Committee yearly until the final defense. These Annual Committee Meetings are documented and made official by a form provided by the Graduate Coordinator.
It is sometimes necessary to change the membership of the Dissertation Committee prior to completion of the dissertation. The Graduate Adviser and the Graduate Dean must approve the "Petition for A Change to the Doctoral Committee" form found on the Graduate School website here. Changes for the sole purpose of constituting a more compliant committee will not be approved. Changes in the committee must be completed well in advance of the dissertation defense.
If a student elects to have a scholar from off-campus serve on the Dissertation Committee, they must be appropriately credentialed to serve on a Dissertation Committee. The Graduate Adviser and Graduate Dean will approve an addition of such a committee member only under exceptional circumstances, and only if the expertise he/she offers cannot be provided by a faculty member on campus. Students should consult with the Graduate Adviser for approval prior to contacting faculty members outside of UT Austin.
Once a student has passed their Qualifying Exam and has been admitted to candidacy, their first committee meeting should be held within six months. They are required to hold a meeting with their Dissertation Committee annually thereafter to review their progress. Following this meeting, the committee will prepare a written summary of recommendations that emerged from the meeting, the chair of the committee will indicate approval by endorsing the summary, and the final document will be submitted to the Graduate Coordinator and will become a part of the student's file.
If a student has not completed the dissertation within three years of admission to candidacy, the results of the annual review will be presented with recommendations to the GSC Executive Committee. The Executive Committee will decide what actions are required.
Although the supervising professor provides day-to-day guidance, all members of the committee are expected to be available for consultation and students should feel free to ask for advice from them or any faculty member.
All contact with undergraduates, staff and faculty involves a high degree of responsibility, diplomacy and courtesy.
Your reputation in the department is partially established by your teaching performance.
The Graduate Office reserves the right to refuse any graduate student an assignment as a teaching assistant.
All graduate students are required to attend the TA Training Workshop before they will be eligible to TA. This seminar is offered twice a year in August and January. It is designed to help you become an effective teaching assistant during your graduate career and to prepare you for teaching and presentations later in your careers.