Subject: SYBB

Term: Spring 2018

SYBB 312R: Basic Statistics for Engineering and Science Using R Programming (101/7138)

TR 02:30-03:45 PM Jan 16-Apr 30

Mondal, A

For advanced undergraduate students in engineering, physical sciences, life sciences. Comprehensive introduction to probability models and statistical methods of analyzing data with the object of formulating statistical models and choosing appropriate methods for inference from experimental and observational data and for testing the model's validity. Balanced approach with equal emphasis on probability, fundamental concepts of statistics, point and interval estimation, hypothesis testing, analysis of variance, design of experiments, and regression modeling. Note: Credit given for only one (1) of STAT 312, STAT 312R, STAT 313, STAT 333, STAT 433 or SYBB 312R. Offered as STAT 312R and SYBB 312R.

SYBB 312R: Basic Statistics for Engineering and Science Using R Programming (102/10284)

TR 01:00-02:15 PM Jan 16-Apr 30

Brynjarsdottir, J

For advanced undergraduate students in engineering, physical sciences, life sciences. Comprehensive introduction to probability models and statistical methods of analyzing data with the object of formulating statistical models and choosing appropriate methods for inference from experimental and observational data and for testing the model's validity. Balanced approach with equal emphasis on probability, fundamental concepts of statistics, point and interval estimation, hypothesis testing, analysis of variance, design of experiments, and regression modeling. Note: Credit given for only one (1) of STAT 312, STAT 312R, STAT 313, STAT 333, STAT 433 or SYBB 312R. Offered as STAT 312R and SYBB 312R.

SYBB 319: Applied Probability and Stochastic Processes for Biology (101/10140)

MW 02:15-03:30 PM Jan 16-Apr 30

Thomas, P

Applications of probability and stochastic processes to biological systems. Mathematical topics will include: introduction to discrete and continuous probability spaces (including numerical generation of pseudo random samples from specified probability distributions), Markov processes in discrete and continuous time with discrete and continuous sample spaces, point processes including homogeneous and inhomogeneous Poisson processes and Markov chains on graphs, and diffusion processes including Brownian motion and the Ornstein-Uhlenbeck process. Biological topics will be determined by the interests of the students and the instructor. Likely topics include: stochastic ion channels, molecular motors and stochastic ratchets, actin and tubulin polymerization, random walk models for neural spike trains, bacterial chemotaxis, signaling and genetic regulatory networks, and stochastic predator-prey dynamics. The emphasis will be on practical simulation and analysis of stochastic phenomena in biological systems. Numerical methods will be developed using a combination of MATLAB, the R statistical package, MCell, and/or URDME, at the discretion of the instructor. Student projects will comprise a major part of the course. Offered as BIOL 319, EECS 319, MATH 319, SYBB 319, BIOL 419, EBME 419, MATH 419, PHOL 419, and SYBB 419.

SYBB 387: Undergraduate Research in Systems Biology (100/10391)

Bebek, G

This course provides students research experience in data science, proteomics, bioinformatics, and clinical informatics under the guidance of faculty affiliated with the Systems Biology and Bioinformatics program. Areas of research include production of big data at bench (cellular proteomics, structural proteomics, genomics, and interaction proteomics) and analysis of big data such as 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.

SYBB 387: Undergraduate Research in Systems Biology (101/10630)

LaFramboise, T

This course provides students research experience in data science, proteomics, bioinformatics, and clinical informatics under the guidance of faculty affiliated with the Systems Biology and Bioinformatics program. Areas of research include production of big data at bench (cellular proteomics, structural proteomics, genomics, and interaction proteomics) and analysis of big data such as 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.

SYBB 388: Undergraduate Research (300/6723)

Chance, M

Permit must be issued by the Biology Office.

SYBB 388: Undergraduate Research (301/6724)

Lodowski, D

Permit must be issued by the Biology Office.

SYBB 388: Undergraduate Research (303/6725)

Yang, S

Permit must be issued by the Biology Office.

SYBB 388S: Undergraduate Research - SAGES Capstone (300/6726)

Chance, M

Permit must be issued by the Biology Office.

SYBB 388S: Undergraduate Research - SAGES Capstone (301/6727)

Lodowski, D

Permit must be issued by the Biology Office.

SYBB 388S: Undergraduate Research - SAGES Capstone (303/6728)

Yang, S

Permit must be issued by the Biology Office.

SYBB 412: Survey of Bioinformatics: Programming for Bioinformatics (100/7178)

TR 02:30-03:45 PM Jan 16-Apr 30

Bebek, G

SYBB 412 is a 3 credit-course that will introduce students to bioinformatics analysis and programming in the R language. This course is designed for those with little or no prior programming experience. However, advanced programmers can still learn bioinformatics pipelines and software packages to conduct research. Students will gain hands-on experience working with bioinformatics software, R packages and functions designed for bioinformatics applications. Programming for Bioinformatics course mainly focuses on R (rproject.org), and introduces students to basic programming in R, what packages are available, and teaches an introductory hands-on experience working with R by walking through the students in analyzing large -omics datasets. At the end of the class, the students are assessed with a small-scale project, where they analyze a publicly available dataset and produce a short report.

SYBB 419: Applied Probability and Stochastic Processes for Biology (101/10141)

MW 02:15-03:30 PM Jan 16-Apr 30

Thomas, P

Applications of probability and stochastic processes to biological systems. Mathematical topics will include: introduction to discrete and continuous probability spaces (including numerical generation of pseudo random samples from specified probability distributions), Markov processes in discrete and continuous time with discrete and continuous sample spaces, point processes including homogeneous and inhomogeneous Poisson processes and Markov chains on graphs, and diffusion processes including Brownian motion and the Ornstein-Uhlenbeck process. Biological topics will be determined by the interests of the students and the instructor. Likely topics include: stochastic ion channels, molecular motors and stochastic ratchets, actin and tubulin polymerization, random walk models for neural spike trains, bacterial chemotaxis, signaling and genetic regulatory networks, and stochastic predator-prey dynamics. The emphasis will be on practical simulation and analysis of stochastic phenomena in biological systems. Numerical methods will be developed using a combination of MATLAB, the R statistical package, MCell, and/or URDME, at the discretion of the instructor. Student projects will comprise a major part of the course. Offered as BIOL 319, EECS 319, MATH 319, SYBB 319, BIOL 419, EBME 419, MATH 419, PHOL 419, and SYBB 419.

SYBB 472: BioDesign (100/7086)

T 06:00-08:30 PM Jan 16-Apr 30

Drummond, C

Need a permit, please contact Prof. Colin Drummond at colin.drummond@case.edu Cross-listed with IIME 472 and EBME 472

SYBB 501: Biomedical Informatics and Systems Biology Journal Club (100/6607)

R 12:00-01:00 PM Jan 16-Apr 30

Lodowski, D

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 and Bioinformatics (100/6608)

F 01:00-04:00 PM Jan 16-Apr 30

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 related bioinformatics as well as hands-on experience with techniques used in current proteomics. Lectures will cover protein/peptide separation techniques, protein mass spectrometry, and biological applications which include quantitative proteomics, protein modification proteomics, interaction proteomics, structural genomics and structural proteomics. Also, it will cover experimental design, basic statistical concept and issues related to high-dimensional data from high-throughput technologies. 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. It will also include bioinformatics tools for protein identification and protein-protein interaction networks. The instructors' research topics will also be discussed. Recommended preparation: CBIO 453, CBIO 455, and PQHS 431. Offered as PHRM 555 and SYBB 555.

SYBB 601: Systems Biology and Bioinformatics Research (100/6649)

Miyagi, M

(Credit as arranged.)

SYBB 601: Systems Biology and Bioinformatics Research (101/10085)

Lodowski, D

(Credit as arranged.)

SYBB 651: Thesis M.S. (100/6650)

Miyagi, M

(Credit as arranged.)

SYBB 651: Thesis M.S. (101/6780)

Bebek, G

(Credit as arranged.)

SYBB 651: Thesis M.S. (102/10087)

Lodowski, D

(Credit as arranged.)

SYBB 651: Thesis M.S. (103/10881)

Varadan, V

(Credit as arranged.)

SYBB 701: Dissertation Ph.D. (101/6764)

Barnholtz-Sloan, J

(Credit as arranged.)

SYBB 701: Dissertation Ph.D. (102/6765)

Lodowski, D

(Credit as arranged.)

SYBB 701: Dissertation Ph.D. (103/6766)

Chance, M

(Credit as arranged.)

SYBB 701: Dissertation Ph.D. (104/7168)

Barnholtz-Sloan, J

(Credit as arranged.)