Subject: SYBB

Term: Spring 2014

SYBB 411A: Survey of Bioinformatics: Technologies in Bioinformatics (100/9873)

MW 12:30-01:45 PM Mar 31-Apr 25

Patel, V; Yohannes, E

The SYBB survey series is composed of the following course sequence: (A) Technologies in Bioinformatics, (B) Data Integration in Bioinformatics, (C) Translational Bioinformatics, and (D) Programming for Bioinformatics. Each standalone section of this course series introduces students to an aspect of a bioinformatics project - from (A) data collection, to (B) data integration, to (C) research applications, with a fourth module (D) introducing basic programming skills. Students have the option of enrolling in all four courses or choosing the individual modules most relevant to their background and goals. A. Technologies in Bioinformatics: This is a 4-week course that introduces students to the high-throughput technologies used to collect data for bioinformatics projects in the fields of proteomics, metabolomics, and genomics. In particular, we will be focusing on mass spectrometry, sequencing, and (micro)arrays. Students enrolled in 411A will be expected to write an essay and give an oral presentation at the end of the course. Recommended preparation: BIOL 214, 215, or 250.

SYBB 411D: Survey of Bioinformatics: Programming for Bioinformatics (100/9872)

MW 12:30-01:45 PM Feb 24-Mar 28

Bebek, G; Patel, V

The SYBB survey series is composed of the following course sequence: (A) Technologies in Bioinformatics, (B) Data Integration in Bioinformatics, (C) Translational Bioinformatics, and (D) Programming for Bioinformatics. Each standalone section of this course series introduces students to an aspect of a bioinformatics project - from (A) data collection, to (B) data integration, to (C) research applications, with a fourth module (D) introducing basic programming skills. Students have the option of enrolling in all four courses or choosing the individual modules most relevant to their background and goals. D. Programming for Bioinformatics: This is a month-long course that will introduce students to bioinformatics software and programming in the R language; this course is designed for those with little or no prior programming experience. Students will gain hands-on experience working with R packages and functions designed for bioinformatics applications. Students will be evaluated by their performance on a take-home project. Recommended preparation: BIOL 214, 215, or 250

SYBB 422: Clinical Informatics at the Bedside and the Bench (Part II) (100/8827)

T 05:30-08:30 PM Jan 13-Apr 28

Patel, V

This course is part of a two semester series that provides student with an overview of the field of clinical informatics. SYBB 422 focuses on the use of informatics in public health, epidemiology, and translational bioinformatics; topics include: pharmacosurveillance, comparative effectiveness research, and personalized medicine. Through lectures and in-depth readings of literature in the field, students will learn to approach problems in clinical medicine through the lens of "informatics", the science of information, with a focus on application over theory. Students are not required to have a background in programming or statistics; however, technical aspects of programming and statistical tools will be discussed throughout the semester.

SYBB 459: Bioinformatics for Systems Biology (100/6848)

MW 01:45-03:00 PM Jan 13-Apr 28

Koyuturk, M

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 (100/6860)

R 12:00-01:00 PM Jan 13-Apr 28

Miyagi, M

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 (100/6861)

F 01:00-04:00 PM Jan 13-Apr 28

Dazard, J; Miyagi, M

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 600: Cloud Computing & Data Science (100/6960)

M 04:00-07:00 PM Jan 13-Apr 28

Zhang, G; Sahoo, S

Offered as EECS 600 and SYBB 600.

SYBB 601: Systems Biology and Bioinformatics Research (100/6954)

Miyagi, M; Schenkel, J

(Credit as arranged.)

SYBB 651: Thesis MS (100/6955)

Miyagi, M; Schenkel, J

(Credit as arranged.)