Genetics, Genomics, and Bioinformatics

Subject abbreviation: GEN College of Natural and Agricultural Sciences

Thomas Girke, Ph.D., Director Program Office, 1140 Batchelor Hall

• (800) 735-0717 or (951) 827-7378

ggb.ucr.edu

Professors

Peter W. Atkinson, Ph.D. (Entomology) Julia N. Bailey-Serres, Ph.D. (Botany and

Plant Sciences) Katherine A. Borkovich, Ph.D. (Microbiology

and Plant Pathology) James Borneman, Ph.D. (Microbiology and

Plant Pathology) Chia-en Angelina Chang, Ph.D. (Chemistry) Meng Chen, Ph.D. (Botany and Plant

Sciences) Xuemei Chen, Ph.D. (Botany and Plant

Sciences) Xinping Cui, Ph.D. (Statistics) Sean Cutler, Ph.D. (Botany and

Plant Sciences) Anupama Dahanukar, Ph.D. (Molecular, Cell

and Systems Biology) Shou-Wei Ding, Ph.D. (Microbiology and Plant

Pathology) Thomas Eulgem, Ph.D. (Botany and Plant

Sciences) Brian A. Federici, Ph.D. (Entomology) Theodore Garland, Ph.D. (Evolution, Ecology

and Organismal Biology) Thomas Girke, Ph.D. (Botany and Plant

Sciences) Adam Godzik, Ph.D. (Biomedical Sciences) Venugopala R. Gonehal, Ph.D.

(Botany and Plant Sciences) John M. Heraty, Ph.D. (Entomology) Tao Jiang, Ph.D. (Computer Science and

Engineering) Hailing Jin, Ph.D. (Microbiology and Plant

Pathology) Howard S. Judelson, Ph.D. (Microbiology and

Plant Pathology) Isgouhi Kaloshian, Ph.D. (Nematology) Marcus Kaul, Ph.D. (Biomedical Sciences) Paul B. Larsen, Ph.D. (Biochemistry) Karine G. Le Roch, Ph.D. (Molecular, Cell and

Systems Biology) Bai-Lian “Larry” Li, Ph.D. (Botany and Plant

Sciences) Xuan Liu, Ph.D. (Biochemistry) Stefano Lonardi, Ph.D. (Computer Science

and Engineering) Morris F. Maduro, Ph.D. (Molecular, Cell and

Systems Biology) Ernest Martinez, Ph.D. (Biochemistry) Manuela Martins-Green, Ph.D. (Molecular, Cell

and Systems Biology) Dmitri A. Maslov, Ph.D. (Molecular, Cell and

Systems Biology) David Nelson, Ph.D. (Botany and Plant

Sciences) Leonard P. Nunney, Ph.D. (Evolution, Ecology

and Organismal Biology) Alexander S. Raikhel, Ph.D. (Entomology) Anandasankar Ray, Ph.D. (Molecular, Cell and

Systems Biology) David Reznick, Ph.D. (Evolution, Ecology and

Organismal Biology) Mikeal L. Roose, Ph.D. (Botany and Plant

Sciences) Caroline Roper, Ph.D. (Microbiology and

Plant Pathology) Joel Sachs, Ph.D., (Evolution, Ecology and

Organismal Biology) Frances M. Sladek, Ph.D. (Molecular, Cell and

Systems Biology) Stephen R. Spindler, Ph.D. (Biochemistry) Patricia S. Springer, Ph.D. (Botany and Plant

Sciences) Jason E. Stajich, Ph.D. (Microbiology and

Plant Pathology) Linda L. Walling, Ph.D. (Botany and Plant

Sciences) Susan R. Wessler, Ph.D., Distinguished

Professor of Genetics (Botany and Plant Sciences) Shizhong Xu, Ph.D. (Botany and Plant

Sciences) Raphael Zldovetski, Ph.D. (Molecular, Cell and

Systems Biology) Associate Professors

Emma Aronson, Ph.D. (Microbiology and

Plant Pathology) Jeffrey B. Bachant, Ph.D. (Molecular, Cell and

Systems Biology) Gregor Blaha, Ph.D. (Biochemistry) Paul DeLey, Ph.D. (Nematology) Adler Dillman, Ph.D. (Nematology) Wefeng Gu, Ph.D. (Molecular, Cell and

Systems Biology) Rong Hai, Ph.D. (Microbiology and Plant

Pathology) Ansel Hsiao, Ph.D. (Microbiology and Plant

Pathology) Arthur Jia, Ph.D. (Botany and Plant Sciences) Ted Karginov, Ph.D. (Molecular, Cell and

Systems Biology) Amy Litt, Ph.D. (Botany and Plant Sciences) Wenxiu Ma, Ph.D. (Statistics) Patricia Manosalva, Ph.D. (Microbiology and

Plant Pathology) Meera G. Nair, Ph.D. (Biomedical Sciences) James Ng, Ph.D. (Microbiology and Plant

Pathology) Constance I. Nugent, Ph.D. (Molecular, Cell

and Systems Biology) Sean O’Leary, Ph.D. (Biochemistry) Martín M. Riccomagno, Ph.D. (Molecular, Cell

and Systems Biology) Naoki Yamanaka, Ph.D. (Entomology) Sika Zheng, Ph.D. (Biomedical Sciences)

Assistant Professors

Alan Brelsford, Ph.D. (Evolution, Ecology and

Organismal Biology) Sihem Cheloufi, Ph.D. (Biochemistry) Qi Chen, Ph.D. (Biomedical Sciences) Patrick Hunt Degnan, Ph.D. (Microbiology

and Plant Pathology) Sydney Glassman, Ph.D. (Microbiology and

Plant Pathology) Simon C. “Niels” Groen, Ph.D. (Nematology) Erica Heinrich, Ph.D. (Biomedical Sciences) Daniel Koenig, Ph.D. (Botany and Plant

Sciences) Wei Vivian Li, Ph.D. (Statistics) Yanran Li, Ph.D. (Chemical and Environmental

Engineering) Yujie Men, Ph.D. (Department of Chemical

and Environmental Engineering) Jernej Murn, Ph.D. (Biochemistry) Dawn H. Nagel, Ph.D. (Botany and Plant

Sciences) Maria Ninova, Ph.D. (Biochemistry) Jaimie Van Norman, Ph.D. (Botany and Plant

Sciences)

The Genetics, Genomics, and Bioinformatics Graduate Program (GGB) administers a program leading to the Ph.D. in Genetics, Genomics, and Bioinformatics. GGB is an interdepartmental program that includes faculty from the departments of Biochemistry, Botany and Plant Sciences, Computer Science and Engineering, Entomology, Environmental Sciences, Molecular, Cell, and Systems Biology, Nematology, Plant Pathology and Microbiology, and Statistics, as well as the Division of Biomedical Sciences.

The program is structured to allow maximum flexibility in the design of an individual student course program and research goals. A primary objective is to allow students to develop a capability in research as rapidly as possible, consistent with the student’s initial preparation.

Students are expected to meet all general requirements of the Graduate Division as printed in the Graduate Studies section of this catalog.

Admission Submission of GRE scores (verbal, quantitative and analytical) is mandatory for admission. Applicants with any B.A. or B.S. degree and an adequate background in the biological and/ or computational sciences will be considered. The specific entry requirements include courses in genetics, biology, chemistry, calculus, computer science, and statistics. Please refer to the Program Guidelines for details. GGB evaluates applications on a continual basis from October to May, however, it normally considers applications for teaching and research assistantships at the same time as fellowships; therefore, students are strongly encouraged to complete their applications for admission and support as early as possible. Normally, fellowships are awarded in January, for students entering the following fall quarter.

The program offers the Ph.D. degree in Genetics, Genomics, and Bioinformatics.

Course Work The course curriculum consists of three core classes and one or more elective classes. The core curriculum is composed of one genetics, one genomics and one bioinformatics course, while one or more elective classes can be chosen from an area of a student’s specialization.

Core Classes (breadth requirements) Students will take one course from each of the following three areas (A-C).

(A) Molecular Genetics

GEN 203 – Advanced Genetic Analysis of Model Organisms or MCBL 221 – Microbial Genetics or BPSC/BCH 231 – Plant Genome

Students may choose other alternatives after approval by their guidance committee and graduate advisor.

(B) Genomics

GEN 241 (former GEN 240A) – Advances in Genomics (C) Bioinformatics

GEN 242 (former GEN 240B) – Data Analysis in Genome Biology GDIV 403 – Research and Scholarship Ethics; must be taken within one year of advancement to candidacy

Elective Classes (areas of specialization) Students must take one or more classes from the following areas. Students can also choose elective courses other than the ones listed below after approval by their guidance committee and graduate advisor.

Genetics

• CMDB 201 – Molecular Biology

• GEN 206 – Gene Silencing

• CMDB/GEN/BCH 209 – Ribonucleic Acid

(RNA) Biology

• BPSC/BIOL 148 – Quantitative Genetics

• BPSC/BCH 231 – Plant Genome

• BIOL/MCBL 221 – Microbial Genetics

• EEOB 214 – Evolutionary Genetics

• ENTX 204 – Genome Maintenance and

Stability

• EEOB 216 – Theory of Evolution

Computational Biology and Statistics

• BPSC 234 – Statistical Genomics

• CS 141 – Intermediate Data Structures and

Algorithms

• CS 100 – Software Construction

CS 234 – Computational Methods for Biomolecular Data

• CS 238 – Algorithmic Techniques in

Computational Biology

• GEN 220 – Computational Analysis of High

Throughput Biological Data

• STAT 110 – Biostatistical Methods in Life

Sciences

• STAT 155 – Probability and Statistics for

Science and Engineering

• STAT 201A/B/C – Theory of Probability and

Statistics (replaces 160A/B)

• STAT 201A/B/C – Elements of Probability

and Statistical Theory

• STAT 160B – Elements of Probability and

Statistical Theory

• STAT 161 – Introduction to Probability

Models

Seminars The GEN 261 seminar (Seminar in Genetics, Genomics, and Bioinformatics) must be taken every quarter.

Supplemental Courses Students may wish to take additional courses to supplement their graduate training. These courses will be tailored to the specific student’s needs and decided upon in consultation with their major professors.

Classes that emphasize genetics, genomics, bioinformatics and other related areas are given in the List of Potential Courses in the GGB Graduate Student Handbook. Students should consider some training in the ethics of use of genetically modified organisms, impact of patents on application of bioinformatics/genomics data, and/or use of databases with bioinformatics/genomics information in a clinical setting.

Additional Units taken to maintain 12-unit course load Graduate students will register for 12 units per quarter to maintain full-time status. These units will include any lecture and seminar courses taken for the quarter. Typically students will also register for Directed Research (GEN 297) prior to advancement to candidacy or Research for Dissertation (GEN 299) after passing the Qualifying Exam.

The Ph.D. is a research degree, and, accordingly, the goal of the program is to train students in the theoretical and experimental foundations of modern genetics. Students are strongly encouraged to participate in lab rotations, select a major professor and begin research work early in their training (during the first year of residence).

Written and Oral Qualifying Examinations Students are advanced to candidacy following successful completion of a written preliminary examination and an oral qualifying examination.

Dissertation and Final Oral Examination Successful completion of a final oral dissertation defense is also required.

Foreign Language Requirement None

Teaching Requirement Each student must have at least two quarters of teaching experience. This requirement may be satisfied by serving as a teaching assistant in a genetics-related course.

Professional Development Training Ph.D. graduate students fulfill their professional training requirement through enrollment in GEN 261 and GDIV 403.

Normative Time to Degree 15 quarters

The multidisciplinary interdepartmental graduate program in Genetics, Genomics, and Bioinformatics offers instruction and research training leading to the M.S. degree in Genetics, Genomics, and Bioinformatics. A Thesis (Plan

• I) or Comprehensive Exam (Plan II) M.S. degree

in Genetics, Genomics, and Bioinformatics is available under special circumstances, when the work leading to the Ph.D. degree cannot be completed. Whether either of these options is appropriate will be decided by the student’s Guidance Committee either at the end of the first year or the time of the oral qualifying examination. Reference the Minimum Degree Requirements for the Master’s degree (for Plan I and Plan II) in the Graduate Studies section of the General requirements.