Genetics, Genomics and Development

2014-15 Tuition

$20,800

Application deadlines

Fall, Dec. 8; no Spring admission

Requirements summary

  • all Graduate School Requirements, including the TOEFL Exam for Non-Native English Applicants
  • three recommendations
  • GRE general test
  • GRE subject test in biology or biochemistry advised

Degrees

  • Ph.D.

Subjects

  • Genetics (Ph.D.)

Major concentrations

  • developmental biology
  • genetics
  • Genomics

The Field of Genetics and Development (see Sections I-VII below) requires graduate students to take one semester of BioMG7810, one semester of BioMG8340, three courses in a breadth requirement, two semesters of BioMG7800, a course on ethical issues in science (e.g. BioMG 7510, Ethical Issues and Professional Responsibilities), and attend and participate in the Wednesday Field Seminars (12:20 pm; BioMG7860). Attendance at Friday Molecular Biology & Genetics Seminars (4:00 pm; BioMG7870) is also required. Additional course requirements, including the graduate minor, are set by the members of the student’s Special Committee. The Graduate School does not impose course credit or grade requirements except that you must complete a minimum of six semesters of satisfactory work in residence. Grades below B- in a student’s major area, however, do not constitute satisfactory performance.

Graduate students are required to pass an oral qualifying examination before the beginning of their fifth semester and must obtain at least two semesters of teaching experience during their program of study.

Course Descriptions:

The Field of Genetics and Development (see Sections I-VII below) requires graduate students to take one semester of BioMG7810, one semester of BioMG7840, three courses in a breadth requirement, two semesters of BioMG7800, a course on ethical issues in science (e.g., BioMG7510, Ethical Issues and Professional Responsibilities), and attend and participate in the Wednesday Field Seminars (12:20 pm; BioMG7860). Attendance at Friday Molecular Biology & Genetics Seminars (4:00 pm; BioMG7870) is also required. Additional course requirements, including the graduate minor, are set by the members of the student’s Special Committee.  Grades below B- in a student’s major area, however, do not constitute satisfactory performance.  Students are strongly encouraged to complete their breadth and minor requirements by the end of their first year.  See sample below.

I. BioMG7810 (2 credits), Problems in Genetics and Development, a problem solving course.  All entering students take this course in the Fall semester of their first year.  It meets every Tuesday once a week; each week’s discussion is led by a different professor.  The problem sets consist of guided critical reviews of instructive and informative research papers, and expose you to a diversity of topics and approaches in genetics and development.  Weekly problem sets and papers are handed out a week in advance; written answers are turned in the following week and discussed with the faculty member in charge of that particular week. 

II. BioMG8340 (2 credits), Quantitative Biology for Molecular Biology and Genetics.  This course meets twice a week for six weeks in the spring semester and focuses on the quantitative tools necessary for analyzing experimental data derived from modern experiments in molecular biology and genetics.  Classes will be both lecture- and discussion-based with problem sets.  Students will be instructed on the use of statistical programs and required to both individually and collaboratively re-evaluate data from the primary literature.  The goal is to provide a foundation for further individual study of more advanced quantitative techniques as needed in individual research programs.  The course is restricted to first year students in the Field of Biochemistry, Molecular and Cell Biology and the Field of Genetics and Development. 

III. BioMG7800 (1 credit, S/U only), Current Topics in Genetics and Development, a seminar course.  Students will be required to take two BioMG7800 courses, with at least one of the BioMG7800’s focusing on material presented by each week’s MB&G seminar speaker (see below). BioMG7800 stresses presentation skills; generally, each student presents one seminar per course based on current research literature in the course topic.  Students will be given formal feedback on their presentation by course instructors.  This course is led by a different faculty member each semester so that the focus varies.  The Graduate Field Assistant can tell you what faculty member will be responsible for a given semester.

Two to three BioMG7800 courses are offered each year, one to two of which are focused on a specific topic, and one is focused on the MB&G seminar series.  For the BioMG7800 focused on the MB&G seminar series, the student’s presentation should be designed to encourage discussion of experiments performed by the speaker and his/her field of interest.

IV. BioMG7510, Ethical Issues and Professional Responsibilities, a discussion course.  All incoming students are required to take this or a comparable course in scientific ethics. BioMG7510 is offered in the Spring semester.  The opportunity to discuss these issues openly will be an important and valuable part of your graduate training.

V. BioMG7860 and BioMG7870.  All post-first year students sign up for one credit of BioMG7860 (in-house seminar series) and one credit of BioMG7870 (invited seminar series) each semester.  First year graduate students only sign up to audit these two courses.

VI. Breadth requirement. Students are to take a minimum of three courses from the list below (categories A-E) with at least one course taken from each of three separate categories.  A course in category A may be exempted with the approval of the DGS if the student has already taken a similar statistics course.  The Field recommends that a student with limited background in a particular category take a course in that grouping that stresses fundamental concepts. Note that classes that a student takes in the new breadth requirement can count towards the minor requirement.

A.    Statistics
BTRY6010 Statistical Methods (F)

B.    Biochemistry, Molecular, and Cellular Biology
BIOMG4370 Cell Proliferation and Senescence (S)
BIOMG6310 Proteins: Structure, Function and Dynamics (F)
BIOMG6330 Biosynthesis of Macromolecules (F)
BIOMG6390 The Nucleus (S)
BIOMG6360 Functional Organization of Eukaryotic Cells (S)
BIOPL4440 Plant Cell Biology (F)
BIOPL4620 Plant Biochemistry (S)

C. Genetics
BIOMG4860 Advanced Eukaryotic Genetics (S)
BIOMG4850 Bacterial Genetics (F)
BIOMG4000 Genomics (F)
BIOMG6080 Epigenetics (F)
PLBR 6060 Advanced Plant Genetics (S)

D. Population Genetics and Evolution
BIOMG4810 Population Genetics (F)
BIOMG4840 Molecular Evolution (S)
BIOMG4870 Human Genomics (F)
BTRY 6830 Quantitative Genomics and Genetics (S)
BIOEE4800 Ecological Genetics (S)

E. Development
BIOMG4400 Stem Cell Biology: Basic Science and Clinical Applications (F and S)
BIOMG4610 Development and Evolution (S) -- offered alternate springs; odd-numbered years
BIOMG4890 Mammalian Embryology (S)
BIOMG6870 Developmental Genetics (S) -- offered alternate springs; even-numbered years)
BIOPL4220 Plant Development (F)

 

VII. Minor Requirement in One Subject Area:  You should discuss with potential committee members the requirements of the program in which you plan to minor since some have quite specific course requirements.  Below are the current requirements for several of the common minors.  In general, completion of the minor requires at least two courses at the 400 level or higher.  You are urged to discuss, as soon as possible, how you will satisfy the minor requirements with both the prospective committee member and if necessary with the DGS for the field under which the minor is administered.

            1) Development (Field of Genetics and Development) - requires two courses in Development (see below) that are beyond BioMG3850.  Note that BioMG3850 should be taken in addition to these two courses if a student lacks the appropriate background.  Participation in a weekly Developmental Biology Journal Club is strongly encouraged (see Journal Clubs).

            2) Genetics (Field of Genetics and Development) - has no formal requirements; individual course requirements may be specified by your committee members (usually 2 or 3 advanced courses at the 400 level or above and BioMG2810, if necessary).

            3) Biochemistry (Field of Biochemistry, Molecular and Cell Biology) - requires 6 or more credits of advanced course work.  Some suggestions for appropriate courses:  BioMG4370, 6310, 6320, 6330, 6360, 6380, 6390, 7380 and Chem6680, 6720, and 6770.  The 6 credits can be put together in any way that satisfies the BMCB faculty member representing the minor.  If the student's lab background in this area is weak, the BMCB faculty committee member may require that the lab course BioMG4400 also be taken.  He/she might also approve a course not offered by BMCB but still relevant, including any of the one-half credit minicourses.

            4) Cell Biology (Field of Biochemistry, Molecular and Cell Biology) - same requirement as for Biochemistry minor (above).

            5) Microbiology (Field of Microbiology) - the requirements for a minor in Microbiology are ultimately up to the discretion of your minor advisor.  Generally, students are expected to complete at least two of the five one-credit modules in Microbiology (BioMI6900).  The Modules in Microbiology include Microbial Structure and Function, Microbial Genetics, Microbial Pathogenesis, Microbial Physiology and Diversity, and Environmental Microbiology.

            6) Plant Molecular Biology (Field of Plant Biology) - completion of three 1-credit sections of BioPL6530 and 6520 (including BioPL6530, Section 01, Concepts and Techniques in Plant Molecular Biology) with a grade of B- or better, as well as satisfactory completion of two other courses to be selected by the minor advisor in either a plant-related area or in genetics, biochemistry, or cell biology.  Satisfactory participation in the Plant Molecular Biology Journal Club for two semesters is also required (BioPL7420, Current Topics in Plant Molecular Biology).

            7) Plant Cell Biology (Field of Plant Biology) - satisfactory completion of Plant Cell Biology (BioPl4440) or Survey of Cell Biology (BioMG4320), and the following three 1-credit sections of BioPl6520: Section 5/Molecular Biology of Plant Organelles, Section 6/Proteomics in Plant Biology; and Section 7/Plant Cell Walls: Structure to Proteome) or alternative courses as approved by the minor advisor.

            8) Evolutionary Biology (Field of Ecology and Evolutionary Biology) - no specific requirements.  Discuss expected background with your prospective minor committee member.

            9) Genomics (Minor Field) - requires BioMG4000, BioMG4010, and two one credit modules in the minor curriculum, or other qualifying courses, as approved by the Special Committee.

            10) Biometry (Field of Biometry) - discuss course work with your prospective minor committee member.

            11) Computational Biology (Field of Computational Biology) - discuss course work with your prospective minor committee member.

            12) Neurobiology and Behavior (Field of Neurobiology and Behavior) - discuss course work with your prospective minor committee member.

A sample schedule in the new system for a Development Minor:

Fall Year 1
1.   BioMG7810/BioMG8340
2.   BioMG4870 Human Genomics (category C)
3.   BioMG6870 Developmental Genetics (category D, also counts for the minor)
4.   Rotation/NSF fellowship submission

Spring Year 1
1.    BioMG6360 Functional Organization of Eukaryotic Cells (category A)
2.    BioMG4830 Advanced Developmental Biology (minor)
3.    BioMG7800 or a course of interest, perhaps in the minor.
4.    Rotations

Fall Year 2
1.    Teaching Fellow
2.    BioMG7800-coupled to the MB&G seminar
3.    Thesis research*

Spring Year 2
1.    Teaching Fellow
2.    Ethics
3.    Thesis research*

Fall Year 3
1.    A-exam.
2.    Thesis research*

Spring Year 3 and beyond: Thesis research*

*As part of their thesis research, students are expected to participate in lab/department journal clubs.

Application:
Only students intending to acquire a Ph.D. degree are admitted. Applicants must submit GRE general test scores and are advised to submit scores on the GRE subject test in biology or biochemistry, cell and molecular biology. Evidence of previous successful research experience will greatly strengthen an application.

Eric Alani -- Concentrations: genetics; Research interests: analysis of DNA mismatch repair and genome stability in yeast
Charles Aquadro -- Concentrations: genetics; Research interests: molecular population genetics and molecular evolution in Drosophila and humans
Daniel Barbash -- Concentrations: genetics; Research interests: evolutionary genetics, developmental genetics, molecular evolution, speciation
Adam Boyko -- Concentrations: genetics; Research interests: Canine genomics; evolutionary and population genetics; adaptation; computational biology; genetic architecture of complex traits and diseases; artificial selection; village dogs
Anthony Bretscher -- Concentrations: genetics; Research interests: microfilament organization and function in vertebrates and yeast
Nicolas Buchon -- Concentrations: developmental biology; genetics; Research interests: Intestinal physiology; stem cells; host microbe relationships
Jonathan Butcher -- Concentrations: developmental biology; Research interests: mechanobiology of embryonic development; regeneration; tissue engineering; developmental redux in aging
Andrew Clark -- Concentrations: genetics; Research interests: population genetics; evolutionary genomics; genetics of complex traits
Paula Cohen -- Concentrations: genetics; Research interests: DNA repair proteins in mammalian meiosis and germ cell development
David Deitcher -- Concentrations: developmental biology; Research interests: molecular mechanisms of neurotransmitter release; molecular neurobiology and neurogenetics
Angela (Searle) Douglas -- Concentrations: genetics; Research interests: Host-microbe interactions; insect nutrition and immunity
Scott Emr -- Concentrations: genetics; Research interests: regulation of cell signaling; membrane trafficking; phosphoinositide kinases; protein kinases; ubiquitin modifications
Thomas Fox -- Concentrations: genetics; Research interests: genes of mitochondria and their regulation by nuclear genes in yeast
Maria Garcia-Garcia -- Concentrations: developmental biology; genetics; Research interests: regulation of cell motility during embryonic development in mice and flies
Michael Goldberg -- Concentrations: developmental biology; genetics; Research interests: Drosophila genetics; genes required for proper chromosome segregation and morphology
Andrew Grimson -- Concentrations: genetics; Research interests: Eukaryotic gene regulation; post-transcriptional gene regulation; small RNAs; microRNAs; UTRs; evolution
Zhenglong Gu -- Concentrations: genetics; Research interests: metabolic networks; Saccharomyces
Maureen Hanson -- Concentrations: genetics; Research interests: plant mitochondrial gene expression; RNA editing; cytoplasmic male sterility
Richard Harrison -- Concentrations: genetics; Research interests: molecular evolution; mechanisms of speciation; genetic basis of evolutionary change
Susan Henry -- Concentrations: genetics; Research interests: genetic regulation; phospholipid biosynthesis in yeast; transcriptional regulation; signal transduction
Jian Hua -- Concentrations: genetics; Research interests: signalling of temperature responses and defense responses, regulation of growth homeostasis, Arabidopsis genetics
Tim Huffaker -- Concentrations: genetics; Research interests: microtubule-based motility in yeast
Alon Keinan -- Concentrations: genetics; Research interests: human population genomics; statistical genetics; molecular evolution; human complex disease risk prediction; evolutionary dynamics
Kenneth Kemphues -- Concentrations: developmental biology; genetics; Research interests: patterning in early development of C. elegans; establishment of polarity
Douglas Knipple (Geneva) -- Concentrations: developmental biology; genetics; Research interests: molecular genetic studies of neuroexcitatory and inhibitory neuronal proteins of insects
Natasza Kurpios -- Concentrations: developmental biology; Research interests: tissue morphogenesis; cell shape and architecture; organ development; gut morphogenesis; mammary gland biology; breast cancer
Brian Lazzaro -- Concentrations: genetics; Research interests: population genetics; molecular evolution; insect immunity
Sylvia Lee -- Concentrations: genetics; Research interests: genetics of aging in C. elegans, insuling signaling in C. elegans
Ruth Ley -- Concentrations: genetics; Research interests: microbiome; microbial population genetics; co-evolution of microbes and host
Sergiy Libert -- Concentrations: Genomics; Research interests: Aging; longevity; sirtuins; behavior; neurodegeneration
David Lin -- Concentrations: developmental biology; Research interests: axon guidance and target formation during the development of the mouse olfactory system, using genetic, in vitro, and genomic approaches
John Lis -- Concentrations: genetics; Genomics; Research interests: gene structure and regulation in Drosophila
Jun (Kelly) Liu -- Concentrations: developmental biology; Research interests: mesodermal cell fate specification in C. elegans; nuclear envelope function during development
Jason Locasale -- Concentrations: genetics; Research interests: Cancer Metabolism, Systems Biology, Epigenetics, Computational Biology, Metabolomics, Cancer Genomic
Jason Mezey -- Concentrations: genetics; Research interests: quantitative genetics/genomics; statistical genetics; computational biology; pathway modeling; molecular evolution
June Nasrallah -- Concentrations: genetics; Research interests: molecular genetics of self-incompatibility in plants
Alexander Nikitin -- Concentrations: developmental biology; genetics; Research interests: Cancer pathogenesis, stem cells, microRNAs, genetically modified mouse models, stem cell pathology
Drew Noden -- Concentrations: developmental biology; Research interests: craniofacial development in vertebrate embryos; mechanisms of cell migration
Colin Parrish -- Concentrations: genetics; Research interests: evolution and host range of parvoviruses
Wojciech (Wojtek) Pawlowski -- Concentrations: genetics; Research interests: mechanisms of meiosis; meiotic recombination
Joseph Peters -- Concentrations: genetics; Research interests: chromosome integrity (transposition, DNA replication, recombination and repair); functional genomics
Jeffrey Pleiss -- Concentrations: genetics; Research interests: genome-wide approaches; microarray; high-throughput sequencing; RNA biology; pre-mRNA processing; splicing
Ling Qi -- Concentrations: genetics; Research interests: adipocytes; metabolic syndrome; obesity; diabetes; stress response
Shu-Bing Qian -- Concentrations: genetics; Research interests: nutrient sensing mechanism; protein homeostasis and adaptive stress response
Robert Reed -- Concentrations: developmental biology; Genomics; Research interests: Evolutionary developmental biology; functional genomics; developmental pattern formation
Eric Richards -- Concentrations: genetics; Research interests: epigenetics; DNA methylation; nuclear organization
Jeffrey Roberts -- Concentrations: genetics; Research interests: regulation of gene expression in phage lambda
Adrienne Roeder -- Concentrations: developmental biology; genetics; Research interests: Role of cell division and growth in plant development and patterning
Michael Scanlon -- Concentrations: developmental biology; genetics; Research interests: Shoot meristem structure and function; leaf development; embryogenesis
John Schimenti -- Concentrations: genetics; Research interests: mouse developmental genetics, meiosis, recombination, mutagenesis, embryonic stem cells
Jeffrey Scott -- Concentrations: genetics; Research interests: the genetics, molecular biology and biochemistry of insecticide resistance; insect cytochrome P450s
Adam Siepel -- Concentrations: genetics; Research interests: bionformatics; comparative genomics; evolutionary genomics
Marcus Smolka -- Concentrations: genetics; Research interests: DNA damage; cell signaling; proteomics
Paul Soloway -- Concentrations: genetics; Genomics; Research interests: functional genomic analysis in mice; epigenetics
David Stern -- Concentrations: developmental biology; genetics; Research interests: regulation of plant organelle gene expression
Nathan Sutter -- Concentrations: genetics; Research interests: complex trait mapping; quantitative genetics of dogs and other domestic mammal
Tudorita Tumbar -- Concentrations: developmental biology; genetics; Research interests: understanding the molecular mechanisms involved in governing stem cell function in mouse tissue
Bik-Kwoon Tye -- Concentrations: genetics; Research interests: genome structure and eukaryote DNA replication in yeast
Robert Weiss -- Concentrations: genetics; Research interests: molecular mechanisms for the maintenance of genomic stability; cellular responses to DNA damage; mouse models of human cancer
Mariana Wolfner -- Concentrations: developmental biology; genetics; Research interests: molecular genetics of reproductive proteins and nuclear envelopes in Drosophila
Haiyuan Yu -- Concentrations: Research interests: integrating information from DNA sequences, gene expression, protein structures and other functional genomics datasets to elucidate gene functions; network topology and its evolution; techniques for making accurate prognoses for various diseases, especially cancer; analyzing genome-wide protein interactome maps; three-dimensional protein structures
Haiyuan Yu -- Concentrations: genetics; Research interests: biomedical systems biology with both high-throughput experimental and integrative computational methodologies, aiming to understand gene functions and their relationships within complex molecular networks and how perturbations to such systems may lead to various human diseases.

Graduate School Professors (emeritus)

Peter Bruns -- Concentrations: Research interests:
Ross MacIntyre -- Concentrations: genetics; Research interests: gene structure and function in Drosophila
Stanley Zahler -- Concentrations: Research interests:

Graduate Education Assessment:  Graduate Field of Genetics and Development

 

Learning outcomes

Measures of outcome

 

Time frame

Source of information

Master a foundational   knowledge of genetics and development

 

Course selection and   grades

1st 2  years

Course transcript

Written and oral component   of A exam

2nd year

A exam thesis proposal

Responses to questions at   annual seminar

2nd year and   beyond

Written evaluation by   thesis committee members at annual meeting

Develop critical thinking   skills

 

Performance in problems   courses

1st year

Course transcript

Performance on A exam

2nd year

Written evaluation by exam   committee members

Yearly committee meeting

2nd year and   beyond

Written evaluation by   thesis committee members at annual meeting

Successfully plan and   execute original research

 

Performance on A exam

2nd year

Written evaluation by exam   committee

Annual progress report

Publications

2nd year and   beyond

Written evaluation by   thesis committee members at annual meeting

Present data national meetings

2nd year and   beyond

Annual Progress reports

Obtain external funding

2nd year and   beyond

Annual Progress reports

Develop written   communication skills

 

Written A exam proposal

2nd year

Written evaluation by exam   committee members

Annual progress report

2nd year and   beyond

Annual Progress reports

Written evaluation by   thesis committee members at annual meeting

Written manuscripts

2nd year until   all publications submitted and in press

Publications

Written thesis

Upon completion of thesis

Written evaluation by exam   committee members

Develop oral communication   skills

Oral component of A exam

2nd year

Written evaluation by exam   committee members

Annual seminar

Annually

Written evaluation by   thesis committee members at annual meeting

Oral component of B exam

At thesis defense

Written evaluation by exam   committee members

Understand and practice   responsible conduct of research

Attend BIOMG 7510 -   Ethical Issues and Professional Responsibilities.

After 1st year

Course transcript

Attend additional   workships for responsible conduct of research as required.

As required

Registration information   from program organizers

Annual Progress reports

Perform PhD research in   compliance with ethical and professional expectations.

For entire graduate   training

Written evaluation by   thesis committee members at annual meeting