Genetics, Genomics, and Bioinformatics

Subject abbreviation: GEN College of Natural and Agricultural Sciences

Zhenyu (Arthur) Jia, Ph.D, Director Program Office, 1140 Batchelor Hall

• (800) 735-0717 or (951) 827-0171

genetics.ucr.edu

Professors Emma Aronson, Ph.D. (Microbiology and Plant Pathology) 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) Xinping Cui, Ph.D. (Statistics) Sean Cutler, Ph.D. (Botany and Plant Sciences) Anupama Dahanukar, Ph.D. (Molecular, Cell and Systems Biology) Adler Dillman, Ph.D. (Nematology) Shou-Wei Ding, Ph.D. (Microbiology and Plant Pathology) Thomas Eulgem, Ph.D. (Botany and Plant Sciences) 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) Zhenyu (Arthur) Jia, Ph.D. (Botany and Plant Sciences) 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) Meera G. Nair, Ph.D. (Biomedical Science) David Nelson, Ph.D. (Botany and Plant Sciences) Anandasankar Ray, Ph.D. (Molecular, Cell and Systems Biology) David Reznick, Ph.D. (Evolution, Ecology and Organismal Biology) 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) 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) Yinsheng Wang, Ph.D. (Chemistry) Shizhong Xu, Ph.D. (Botany and Plant Sciences) Sika Zheng, Ph.D. (Biomedical Sciences) Changcheng Zhou, Ph.D. (Biomedical Sciences)

Associate Professors Jeffrey B. Bachant, Ph.D. (Molecular, Cell and Systems Biology) Ilana Bennett, Ph.D. (Psychology) Gregor Blaha, Ph.D. (Biochemistry) Alan Brelsford, Ph.D. (Evolution, Ecology and Organismal Biology) Polly Campbell, Ph.D. (Evolution, Ecology and Organismal Biology) Sihem Chelourfi, Ph.D. (Biochemistry) Qi Chen, Ph.D. (Biomedical Sciences) Sydney Glassman, Ph.D. (microbiology and Plant Pathology) Weifeng Gu, Ph.D. (Molecular, Cell and Systems Biology) Rong Hai, Ph.D. (Microbiology and Plant Pathology) Ansel Hsiao, Ph.D. (Microbiology and Plant Pathology) Robert Jinkerson, Ph.D. (Chemical and Environmental Engineering) Ted Karginov, Ph.D. (Molecular, Cell and Systems Biology) Wei Vivian Li, Ph.D. (Statistics) Amy Litt, Ph.D. (Botany and Plant Sciences) Wenxiu Ma, Ph.D. (Statistics) Patricia Manosalva, Ph.D. (Microbiology and Plant Pathology) Yujie Men, Ph.D. (Chemical and Environmental Engineering) Jernej Murn, Ph.D. (Biochemistry) Dawn H. Nagel, Ph.D. (Botany and Plant 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) Linlin Zhao, Ph.D. (Chemistry) Assistant Professors Sonali Chaturvedi, Ph.D. (Microbiology and Plant Pathology) Patrick H. Degnan, Ph.D. (Microbiology and Plant Pathology) Simon C. “Niels” Groen, Ph.D. (Nematology) Erica Heinrich, Ph.D. (Biomedical Sciences) Bao-Lam Huynh Ph.D. (Nematology) Sunil Kenchanmane Raju Ph.D. (Botany and Plant Sciences) Daniel Koenig, Ph.D. (Botany and Plant Sciences) Xiaoqian Liu, Ph.D. (Statistics) Maria Ninova, Ph.D. (Biochemistry) Kieran M. Samuk, Ph.D. (Evolution, Ecology and Organismal Biology) Mingxun Wang, Ph.D. (Computer Science and Engineering) Joy Xiang, Ph.D. (Biomedical Sciences) Tingting Xiang, Ph.D. (Bioengineering) Huimin Zhang, Ph.D. (Molecular, Cell and Systems Biology)

The Genetics, Genomics, and Bioinformat- ics 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 Microbiol- ogy, 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 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 cho- sen 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 com- mittee 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 stu- dent’s needs and decided upon in consulta- tion 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 stu- dents 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, according- ly, the goal of the program is to train students in the theoretical and experimental founda- tions of modern genetics. Students are strong- ly 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.

The Oral Qualifying Exam is expected to be taken in-person with the student and all exam committee members physically present in the same room. Remote exceptions (attendance via video call) can be granted for up to two committee members by the GGB Graduate Advisor. However, at a minimum the student and the chair of the committee are expected to attend in-person. Any exceptions for remote attendance need to be well justified and are not a standard option.

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

The Final Defense is expected to be taken in-person with the student and all dissertation committee members physically present in the same location. Remote exceptions (attendance via video call) can be granted for up to two committee members by the GGB Graduate Advisor. Any exceptions for remote attendance need to be well justified and are not a standard option. Defenses are expected to be held in a video enabled room to support remote attendance for a larger audience as well as the committee members that have been approved to attend remotely.

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 profession- al 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.