Subject: SYBB
Term: Fall 2019
SYBB 311A: Survey of Bioinformatics: Technologies in Bioinformatics (110/7356)
TR 02:30-03:45 PM Aug 26-Sep 27
Bebek, G
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 (120/7357)
T 02:30-03:45 PM Sep 30-Dec 06
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 (130/7358)
R 02:30-03:45 PM Sep 30-Dec 06
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 312R: Basic Statistics for Engineering and Science Using R Programming (102/7662)
TR 11:30-12:45 PM Aug 26-Dec 06
Huang, Q
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 or SYBB 312R.
Offered as STAT 312R and SYBB 312R.
SYBB 387: Undergraduate Research in Systems Biology (100/7362)
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 (101/7363)
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 (102/7364)
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 (103/7365)
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 (300/7327)
Chance, M
Guided laboratory research under the sponsorship of a biology faculty member. May be carried out within the biology department or in associated departments. Appropriate forms must be secured in the biology department office. A written report must be approved by the biology sponsor and submitted to the chairman of the biology department before credit is granted. Only 3 credit-hours may count towards the biology majors or minor.
Offered as BIOL 388 and SYBB 388.
SYBB 388: Undergraduate Research (301/7328)
Lodowski, D
Guided laboratory research under the sponsorship of a biology faculty member. May be carried out within the biology department or in associated departments. Appropriate forms must be secured in the biology department office. A written report must be approved by the biology sponsor and submitted to the chairman of the biology department before credit is granted. Only 3 credit-hours may count towards the biology majors or minor.
Offered as BIOL 388 and SYBB 388.
SYBB 388: Undergraduate Research (302/7329)
Yang, S
Guided laboratory research under the sponsorship of a biology faculty member. May be carried out within the biology department or in associated departments. Appropriate forms must be secured in the biology department office. A written report must be approved by the biology sponsor and submitted to the chairman of the biology department before credit is granted. Only 3 credit-hours may count towards the biology majors or minor.
Offered as BIOL 388 and SYBB 388.
SYBB 388S: Undergraduate Research - SAGES Capstone (300/7330)
Chance, M
Guided laboratory research under the sponsorship of a biology faculty member. May be carried out within the biology department or in associated departments. May be taken only one semester during the student's academic career. Appropriate forms must be secured in the biology department office. A written report must be approved by the biology sponsor and submitted to the chairman of the biology department before credit is granted. A public presentation is required.
Offered as BIOL 388S and SYBB 388S.
SYBB 388S: Undergraduate Research - SAGES Capstone (301/7331)
Lodowski, D
Guided laboratory research under the sponsorship of a biology faculty member. May be carried out within the biology department or in associated departments. May be taken only one semester during the student's academic career. Appropriate forms must be secured in the biology department office. A written report must be approved by the biology sponsor and submitted to the chairman of the biology department before credit is granted. A public presentation is required.
Offered as BIOL 388S and SYBB 388S.
SYBB 388S: Undergraduate Research - SAGES Capstone (302/7332)
Yang, S
Guided laboratory research under the sponsorship of a biology faculty member. May be carried out within the biology department or in associated departments. May be taken only one semester during the student's academic career. Appropriate forms must be secured in the biology department office. A written report must be approved by the biology sponsor and submitted to the chairman of the biology department before credit is granted. A public presentation is required.
Offered as BIOL 388S and SYBB 388S.
SYBB 411A: Survey of Bioinformatics: Technologies in Bioinformatics (110/7349)
TR 02:30-03:45 PM Aug 26-Sep 27
Bebek, G
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 (120/7350)
T 02:30-03:45 PM Sep 30-Dec 06
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 (130/7351)
R 02:30-03:45 PM Sep 30-Dec 06
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 421: Fundamentals of Clinical Information Systems (100/7440)
T 06:00-09:00 PM Aug 26-Dec 06
Drummond, C
Cross-listed with IIME 473 and EBME 473
SYBB 501: Biomedical Informatics and Systems Biology Journal Club (100/7190)
W 11:30-12:30 PM Aug 26-Dec 06
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 (100/7401)
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 (100/7237)
Lodowski, D
(Credit as arranged.)
SYBB 651: Thesis M.S. (102/7410)
Bebek, G
(Credit as arranged.)
SYBB 651: Thesis M.S. (103/7509)
Yang, S
(Credit as arranged.)
SYBB 651: Thesis M.S. (104/7624)
Varadan, V
(Credit as arranged.)
SYBB 651: Thesis M.S. (105/7679)
LaFramboise, T
(Credit as arranged.)
SYBB 651: Thesis M.S. (106/7680)
Lodowski, D
(Credit as arranged.)
SYBB 701: Dissertation Ph.D. (100/7324)
Lodowski, D
(Credit as arranged.)
SYBB 701: Dissertation Ph.D. (101/7325)
Chance, M
(Credit as arranged.)
SYBB 701: Dissertation Ph.D. (102/7326)
Bebek, G
(Credit as arranged.)
SYBB 701: Dissertation Ph.D. (105/7603)
Barnholtz-Sloan, J
(Credit as arranged.)
SYBB 701: Dissertation Ph.D. (104/7734)
Tilton, J
(Credit as arranged.)
SYBB 701: Dissertation Ph.D. (106/7857)
Bush, W
(Credit as arranged.)
SYBB 701: Dissertation Ph.D. (107/7858)
Williams, S
(Credit as arranged.)