Courses

SYBB 310: Healthcare Data Analytics in R. 3 Units

As part of the Data Science Minor, SYBB 310 is designed to introduce students to the basic tools used in data science, focusing on elementary statistics and building up to regression models. In this course, we will provide hands-on training in statistical programming through the use of the open-source statistical computing language, R. Over the semester, students will gain a practical understanding of the essential statistics needed for data science, and students will apply these principles using R to analyze a large dataset of 10,000 patients. de-identifed electronic medical records. No background in statistics or programming is expected for this course.

SYBB 311/411 Survey of Bioinformatics. 4 Units

This course is offered as four separate 1-month long units (1 credit each): (1) Technologies in Bioinformatics, (2) Data Integration in Bioinformatics, (3) Translational Bioinformatics, and (4) Programming for Bioinformatics. These courses are designed to take a student through the entire workflow of a bioinformatics research project - from data collection, to data integration, to research applications. Graduate students can select specific units based on their needs. Overall course grade will be an average of the unit grades. Course Unit Descriptions:

  1. 311/411A: Technologies in Bioinformatics: This course introduces students to the high-throughput technologies used to collect data for applications in genomics, proteomics, and metabolomics (e.g. mass spectrometry; gene sequencing; yeast-two-hybrid; microarrays).
  2. 311/411B: Data Integration in Bioinformatics: This course introduces students to the conceptual models used to integrate and interpret data collected by high-throughput technologies. These models range from knowledge organization structures (e.g. biomedical ontologies) to models of interaction (e.g. gene coexpression networks or protein interaction networks), as well as statistical concepts for dealing with such data.
  3. 311/411C: Translational Bioinformatics: This course introduces students to the clinical and real-world applications of bioinformatics, e.g. pharmacogenomics, GWAS of particular diseases, personalized medicine, systems medicine, microbiome analysis, etc. This course shows students how bioinformatic technologies and methods of data integration can be combined for various applications in biomedical research.
  4. 311/411D: Programming for Bioinformatics: This course will serve as a basic introduction to 1-2 programming languages, focusing on the applications, tools, and packages specifically related to bioinformatics. R, Python, Java, C++, and/or Perl may be taught as the instructor sees fit.
  5. SYBB 311/411 Course Page

SYBB 388. Undergraduate Systems Biology Research. 3 Units

This course is designed for undergraduates students in the College of Arts and Sciences and the School of Engineering who wish to have research experience in proteomics, bioinformatics, or related areas under the sponsorship of faculty members affiliated with the Center for Proteomics and Bioinformatics or the Systems Biology and Bioinformatics program. The student is required to work a minimum of 10 hours per week in the lab for the standard unit of 3 credits per semester. Areas of research include cellular proteomics, structural proteomics, genomics, interaction proteomics, computational/statistical biology, bioinformatics tool development and clinical research informatics. A written report must be approved by the sponsor and submitted to the director of the Center for Proteomics and Bioinformatics before credit is granted. A public presentation is required. Offered as BIOL 388 and SYBB 388.

SYBB 388S. Undergraduate Systems Biology Research. 3 Units

This course is designed for undergraduates students in the College of Arts and Sciences and the School of Engineering who wish to have research experience in proteomics, bioinformatics, or related areas under the sponsorship of faculty members affiliated with the Center for Proteomics and Bioinformatics or the Systems Biology and Bioinformatics program. The student is required to work a minimum of 10 hours per week in the lab for the standard unit of 3 credits per semester. Areas of research include cellular proteomics, structural proteomics, genomics, interaction proteomics, computational/statistical biology, bioinformatics tool development and clinical research informatics. A written report must be approved by the sponsor and submitted to the director of the Center for Proteomics and Bioinformatics before credit is granted. A public presentation is required. Offered as BIOL 388S and SYBB 388S.

SYBB 321/421. Clincal Informatics at the Bedside and the Bench Part I. 3 Units

This two semester series provides students with an overview of the field of clinical informatics, focusing on the content areas outlined by the American Medical Informatics Association; the first semester will emphasize the use of informatics in clinical settings (i.e. "the bedside"), and the second semester will emphasize the use of informatics in public health, epidemiology, and translational bioinformatics (i.e. "the bench"). Through lectures, readings, and projects, students will learn to approach problems in clinical medicine through the lens of .informatics,. the science of information, with a focus on applications over theory. As clinical informatics revolves around the development and use of electronic medical records (EMRs), students will be familiarized with EMRs through a hands-on lab simulating clinical workflows.

SYBB 459. Bioinformatics for Systems Biology. 3 Units.

Description of omic data (biological sequences, gene expression, protein-protein interactions, protein-DNA interactions, protein expression, metabolomics, biological ontologies), regulatory network inference, topology of regulatory networks, computational inference of protein-protein interactions, protein interaction databases, topology of protein interaction networks, module and protein complex discovery, network alignment and mining, computational models for network evolution, network-based functional inference, metabolic pathway databases, topology of metabolic pathways, flux models for analysis of metabolic networks, network integration, inference of domain-domain interactions, signaling pathway inference from protein interaction networks, network models and algorithms for disease gene identification, identification of dysregulated subnetworks network-based disease classification. Offered as EECS 459 and SYBB 459.

SYBB 501. Biomedical Informatics and Systems Biology Journal Club. 0 Units.

The purpose of this journal club is to provide an opportunity for students to critically discuss a wide variety of informatics and systems biology topics and to present their works in progress. A wide range of informatics and systems theory approaches to conducting biomedical research will be accomplished through the guided selection of articles to be discussed during the club. Potential articles will be chosen from scientific journals including: Nature, Science, BMC Bioinformatics, BMC Systems Biology, the Journal of Bioinformatics and Computational Biology, and the Journal for Biomedical Informatics. During journal presentations, trainees will be expected to lead a discussion of the article that leads to the critical evaluation of the merit of the article and its implication for biomedical informatics and systems biology. The Journal Club will also provide a forum for trainees to present proposed, on-going, and completed research. Trainees will attend and participate in the Journal Club throughout their tenure in the program. The Journal Club will meet twice a month and each trainee will be required to present one journal article and one research in progress presentation yearly. The Journal Club will also include sessions where issues related to the responsible conduct of research are reviewed and extended.

SYBB 555. Current Proteomics. 3 Units.

This course is designed for graduate students across the university who wish to acquire a better understanding of fundamental concepts of proteomics and hands-on experience with techniques used in current proteomics. Lectures will cover protein/peptide separation techniques, protein mass spectrometry, bioinformatics tools, and biological applications which include quantitative proteomics, protein modification proteomics, interaction proteomics, structural genomics and structural proteomics. Laboratory portion will involve practice on the separation of proteins by two-dimensional gel electrophoresis, molecular weight measurement of proteins by mass spectrometry, peptide structural characterization by tandem mass spectrometry and protein identification using computational tools. The instructors' research topics will also be discussed. Recommended preparation: CBIO 453 and CBIO 455. Offered as PHRM 555 and SYBB 555.

SYBB 601. Systems Biology and Bioinformatics Research. 1 - 18 Unit.

(Credit as arranged.)

SYBB 651. Thesis MS. 1 - 18 Unit.

(Credit as arranged.)

SYBB 701. Dissertation PhD. 1 - 18 Unit.

(Credit as arranged.) Prereq: Predoctoral research consent or advanced to Ph.D. candidacy milestone.