Subject: SYBB

Term: Fall 2015

SYBB 311A: Survey of Bioinformatics: Technologies in Bioinformatics (110/7049)

TR 10:00-11:15 AM Aug 25-Sep 22

Bebek, G; Miyagi, M

SYBB 311A/411A is a 5-week course that introduces students to the high-throughput technologies used to collect data for bioinformatics research in the fields of genomics, proteomics, and metabolomics. In particular, we will focus on mass spectrometer-based proteomics, DNA and RNA sequencing, genotyping, protein microarrays, and mass spectrometry-based metabolomics. This is a lecture-based course that relies heavily on out-of-class readings. Graduate students will be expected to write a report and give an oral presentation at the end of the course. SYBB 311A/411A is part of the SYBB survey series which is composed of the following course sequence: (1) Technologies in Bioinformatics, (2) Data Integration in Bioinformatics, (3) Translational Bioinformatics, and (4) Programming for Bioinformatics. Each standalone section of this course series introduces students to an aspect of a bioinformatics project - from data collection (SYBB 311A/411A), to data integration (SYBB 311B/411B), to research applications (SYBB 311C/411C), with a fourth module (SYBB 311D/411D) introducing basic programming skills. Graduate students have the option of enrolling in all four courses or choosing the individual modules most relevant to their background and goals with the exception of SYBB 411D, which must be taken with SYBB 411A. Offered as SYBB 311A, BIOL 311A and SYBB 411A.

SYBB 311B: Survey of Bioinformatics: Data Integration in Bioinformatics (120/7050)

TR 10:00-11:15 AM Sep 24-Oct 27

Bebek, G

SYBB 311B/411B is a five week course that surveys the conceptual models and tools used to analyze and interpret data collected by high-throughput technologies, providing an entry points for students new to the field of bioinformatics. The knowledge structures that we will cover include: biomedical ontologies, signaling pathways, and interaction networks. We will also cover tools for genome exploration and analysis. The SYBB survey series is composed of the following course sequence: (1) Technologies in Bioinformatics, (2) Data Integration in Bioinformatics, (3) Translational Bioinformatics, and (4) Programming for Bioinformatics. Each standalone section of this course series introduces students to an aspect of a bioinformatics project - from data collection (SYBB 311A/411A), to data integration (SYBB 311B/411B), to research applications (SYBB 311C/411C), with a fourth module (SYBB 311D/411D) introducing basic programming. Graduate students have the option of enrolling in all four courses or choosing the individual modules most relevant to their background and goals with the exception of SYBB 411D, which must be taken with SYBB 411A. Offered as SYBB 311B, BIOL 311B, and SYBB 411B.

SYBB 311C: Survey of Bioinformatics: Translational Bioinformatics (130/7051)

R 12:00-01:15 PM Sep 17-Dec 10

Bebek, G

SYBB 311C/411C is a longitudinal course that introduces students to the latest applications of bioinformatics, with a focus on translational research. Topics include: `omic drug discovery, pharmacogenomics, microbiome analysis, and genomic medicine. The focus of this course is on illustrating how bioinformatic technologies can be paired with data integration tools for various applications in medicine. The course is organized as a weekly journal club, with instructors leading the discussion of recent literature in the field of bioinformatics. Students will be expected to complete readings beforehand; students will also work in teams to write weekly reports reviewing journal articles in the field. The SYBB survey series is composed of the following course sequence: (1) Technologies in Bioinformatics, (2) Data Integration in Bioinformatics, (3) Translational Bioinformatics, and (4) Programming for Bioinformatics. Each standalone section of this course series introduces students to an aspect of a bioinformatics project - from data collection (SYBB 311A/411A), to data integration (SYBB 311B/411B), to research applications (SYBB 311C/411C), with a fourth module (SYBB 311D/411D) introducing basic programming. Graduate students have the option of enrolling in all four courses or choosing the individual modules most relevant to their background and goals with the exception of SYBB 411D, which must be taken with SYBB 411A. Offered as SYBB 311C, BIOL 311C and SYBB 411C.

SYBB 311D: Survey of Bioinformatics: Programming for Bioinformatics (140/7052)

TR 10:00-11:15 AM Oct 29-Dec 03

Bebek, G

SYBB 311D/411D is a 1 credit, 5-week 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. Programming for Bioinformatics short course focuses on a platform, in this case R-project (rproject.org), and introduces students to basic programming in R, what packages are available for their use, and teaches an introductory hands-on experience working with R by walking through the students in analyzing a large-omics dataset. 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. The SYBB survey series is composed of the following course sequence: (1) Technologies in Bioinformatics, (2) Data Integration in Bioinformatics, (3) Translational Bioinformatics, and (4) Programming for Bioinformatics. Each standalone section of this course series introduces students to an aspect of a bioinformatics project - from data collection (SYBB 311/411A), to data integration (SYBB 311/411B), to research applications (SYBB 311/411C), with a fourth module (SYBB 311/411D) introducing basic programming. Graduate students have the option of enrolling in all four courses or choosing the individual modules most relevant to their background and goals with the exception of SYBB411D, which must be taken with SYBB411A. Offered as SYBB 311D, BIOL 311D and SYBB 411D.

SYBB 387: Undergraduate Research in Systems Biology (100/7058)

Lodowski, D

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 (101/7059)

Chance, M

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 (102/7060)

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 (103/7061)

Yang, S

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 (300/7005)

Chance, M

Permit must be issued by the Biology Office.

SYBB 388: Undergraduate Research (301/7006)

Lodowski, D

Permit must be issued by the Biology Office.

SYBB 388: Undergraduate Research (302/7008)

Yang, S

Permit must be issued by the Biology Office.

SYBB 388S: Undergraduate Research - SAGES Capstone (300/7009)

Chance, M

Permit must be issued by the Biology Office.

SYBB 388S: Undergraduate Research - SAGES Capstone (301/7010)

Lodowski, D

Permit must be issued by the Biology Office.

SYBB 388S: Undergraduate Research - SAGES Capstone (302/7012)

Yang, S

Permit must be issued by the Biology Office.

SYBB 411A: Survey of Bioinformatics: Technologies in Bioinformatics (110/7038)

TR 10:00-11:15 AM Aug 25-Sep 22

Bebek, G; Miyagi, M

SYBB 311A/411A is a 5-week course that introduces students to the high-throughput technologies used to collect data for bioinformatics research in the fields of genomics, proteomics, and metabolomics. In particular, we will focus on mass spectrometer-based proteomics, DNA and RNA sequencing, genotyping, protein microarrays, and mass spectrometry-based metabolomics. This is a lecture-based course that relies heavily on out-of-class readings. Graduate students will be expected to write a report and give an oral presentation at the end of the course. SYBB 311A/411A is part of the SYBB survey series which is composed of the following course sequence: (1) Technologies in Bioinformatics, (2) Data Integration in Bioinformatics, (3) Translational Bioinformatics, and (4) Programming for Bioinformatics. Each standalone section of this course series introduces students to an aspect of a bioinformatics project - from data collection (SYBB 311A/411A), to data integration (SYBB 311B/411B), to research applications (SYBB 311C/411C), with a fourth module (SYBB 311D/411D) introducing basic programming skills. Graduate students have the option of enrolling in all four courses or choosing the individual modules most relevant to their background and goals with the exception of SYBB 411D, which must be taken with SYBB 411A. Offered as SYBB 311A, BIOL 311A and SYBB 411A.

SYBB 411B: Survey of Bioinformatics: Data Integration in Bioinformatics (120/7039)

TR 10:00-11:15 AM Sep 24-Oct 27

Bebek, G

SYBB 311B/411B is a five week course that surveys the conceptual models and tools used to analyze and interpret data collected by high-throughput technologies, providing an entry points for students new to the field of bioinformatics. The knowledge structures that we will cover include: biomedical ontologies, signaling pathways, and interaction networks. We will also cover tools for genome exploration and analysis. The SYBB survey series is composed of the following course sequence: (1) Technologies in Bioinformatics, (2) Data Integration in Bioinformatics, (3) Translational Bioinformatics, and (4) Programming for Bioinformatics. Each standalone section of this course series introduces students to an aspect of a bioinformatics project - from data collection (SYBB 311A/411A), to data integration (SYBB 311B/411B), to research applications (SYBB 311C/411C), with a fourth module (SYBB 311D/411D) introducing basic programming. Graduate students have the option of enrolling in all four courses or choosing the individual modules most relevant to their background and goals with the exception of SYBB 411D, which must be taken with SYBB 411A. Offered as SYBB 311B, BIOL 311B, and SYBB 411B.

SYBB 411C: Survey of Bioinformatics: Translational Bioinformatics (130/7040)

R 12:00-01:15 PM Sep 17-Dec 10

Bebek, G

SYBB 311C/411C is a longitudinal course that introduces students to the latest applications of bioinformatics, with a focus on translational research. Topics include: `omic drug discovery, pharmacogenomics, microbiome analysis, and genomic medicine. The focus of this course is on illustrating how bioinformatic technologies can be paired with data integration tools for various applications in medicine. The course is organized as a weekly journal club, with instructors leading the discussion of recent literature in the field of bioinformatics. Students will be expected to complete readings beforehand; students will also work in teams to write weekly reports reviewing journal articles in the field. The SYBB survey series is composed of the following course sequence: (1) Technologies in Bioinformatics, (2) Data Integration in Bioinformatics, (3) Translational Bioinformatics, and (4) Programming for Bioinformatics. Each standalone section of this course series introduces students to an aspect of a bioinformatics project - from data collection (SYBB 311A/411A), to data integration (SYBB 311B/411B), to research applications (SYBB 311C/411C), with a fourth module (SYBB 311D/411D) introducing basic programming. Graduate students have the option of enrolling in all four courses or choosing the individual modules most relevant to their background and goals with the exception of SYBB 411D, which must be taken with SYBB 411A. Offered as SYBB 311C, BIOL 311C and SYBB 411C.

SYBB 411D: Survey of Bioinformatics: Programming for Bioinformatics (140/7041)

TR 10:00-11:15 AM Oct 29-Dec 03

Bebek, G

SYBB 311D/411D is a 1 credit, 5-week 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. Programming for Bioinformatics short course focuses on a platform, in this case R-project (rproject.org), and introduces students to basic programming in R, what packages are available for their use, and teaches an introductory hands-on experience working with R by walking through the students in analyzing a large-omics dataset. 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. The SYBB survey series is composed of the following course sequence: (1) Technologies in Bioinformatics, (2) Data Integration in Bioinformatics, (3) Translational Bioinformatics, and (4) Programming for Bioinformatics. Each standalone section of this course series introduces students to an aspect of a bioinformatics project - from data collection (SYBB 311/411A), to data integration (SYBB 311/411B), to research applications (SYBB 311/411C), with a fourth module (SYBB 311/411D) introducing basic programming. Graduate students have the option of enrolling in all four courses or choosing the individual modules most relevant to their background and goals with the exception of SYBB411D, which must be taken with SYBB411A. Offered as SYBB 311D, BIOL 311D and SYBB 411D.

SYBB 421: Fundamentals of Clinical Information Systems (100/11282)

T 06:00-09:00 PM Aug 24-Dec 04

Drummond, C

Technology has played a significant role in the evolution of medical science and treatment. While we often think about progress in terms of the practical application of, say, imaging to the diagnosis and monitoring of disease, technology is increasingly expected to improve the organization and delivery of healthcare services, too. Information technology plays a key role in the transformation of administrative support systems (finance and administration), clinical information systems (information to support patient care), and decision support systems (managerial decision-making). This introductory graduate course provides the student with the opportunity to gain insight and situational experience with clinical information systems (CIS). Often considered synonymous with electronic medical records, the "art" of CIS more fundamentally examines the effective use of data and information technology to assist in the migration away from paper-based systems and improve organizational performance. In this course we examine clinical information systems in the context of (A) operational and strategic information needs, (B) information technology and analytic tools for workflow design, and (C) subsequent implementation of clinical information systems in patient care. Legal and ethical issues are explored. The student learns the process of "plan, design, implement" through hands-on applications to select CIS problems, while at the same time gaining insights and understanding of the impacts placed on patients and health care providers. Offered as EBME 473, IIME 473 and SYBB 421.

SYBB 501: Biomedical Informatics and Systems Biology Journal Club (100/6821)

R 12:00-01:00 PM Aug 24-Dec 04

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 535: Independent Study in Biomedical Informatics (100/7106)

Bebek, G

For students pursuing MS or PhD degrees in SYBB, this course provides the opportunity for in-depth exposure to a subfield of systems biology and/or biomedical informatics. Degree-seeking students can enroll in this course prior to beginning 601 or 701 research. In conjunction with their proposed research advisor, enrolled students will undertake a self-directed study of a subfield of systems biology and/or biomedical informatics pertinent to their research area. The selected readings may also represent topics not covered by the student's coursework. The student's performance will be evaluated in an end-of-semester presentation or report at their advisor's discretion.

SYBB 601: Systems Biology and Bioinformatics Research (100/6877)

Lodowski, D

(Credit as arranged.)

SYBB 651: Thesis MS (100/6907)

Miyagi, M

(Credit as arranged.)

SYBB 651: Thesis MS (102/7116)

Bebek, G

(Credit as arranged.)

SYBB 701: Dissertation PhD (100/7002)

Barnholtz-Sloan, J; Lodowski, D; Miyagi, M; Tilton, J

(Credit as arranged.)

SYBB 701: Dissertation PhD (101/7003)

Chance, M

(Credit as arranged.)

SYBB 701: Dissertation PhD (102/7004)

Lodowski, D

(Credit as arranged.)