GGSC 615: Aquatic Models
CRN: 62569
Min CR: 3
Schedule Type: Lecture 
Instructor: Ryan M Centini (P)

Description

This course will cover the basic anatomy, biology, life history, husbandry, and research applications for a variety of aquatic organisms used as animal models of human disease in biomedical research. Species discussed will include zebrafish, Medaka, Xiphorous, Onchorynchus, Xenopus, and Axolotls.

GGSC 620: Bioinformatics
CRN: 66464
Min CR: 3
Schedule Type: Lecture Online 
Instructor: David Crossman, Chen Huang (P)

Description

Introduction to computational tools and bioinformatics databases used in the fields of genetics and genomic sciences. This course will cover a wide variety of different bioinformatics applications, which will be taught through use of available on-line bioinformatics resources. Topics covered include large-scale genomic databases, sequence analysis systems, protein sequence analysis, structural bioinformatics, protein folding, and homology modeling.

GGSC 690: Bioinformatics Model Systems Gen Disorders
CRN: 61715
Min CR: 3
Schedule Type: Lecture  
Instructor: Bobby L Jones (P)

Description

Invertebrate and non-human vertebrate species are commonly used in scientific research work to provide significant insights into human genetic processes and disease. This course focuses on the different methods and strategies by which researchers use these systems for genetic and genomic analyses of human biology and relevant disorders. Model organisms covered include, but are not limited to nematodes (C. elegans), fruit flies (Drosophila sp.), zebrafish (Danio rerio), and mice (Mus musculus).

INFO 601: Introduction to Bioinformatics
CRN: 62026
Min CR: 3
Schedule Type: Lecture Online 
Instructor: Zechen Chong (P)

Description

Introduction to bioinformatics and computational biology, with emphasis on concepts and application of informatics tools to molecular biology. It covers biological sequence analysis, gene prediction, genome annotation, gene expression analysis, protein structure prediction, evolutionary biology and comparative genomics, bioinformatics databases, cloud computing, basic R-based data analysis, simple programming skills using Perl, Linux/Unix environment and command lines, visual analytics, and social/legal aspects of open science. It will have a class research project component.

INFO 662: Biomed Appl Nat Lang Processing
CRN: 62037
Min CR: 3
Schedule Type: Lecture Online 
Instructor: John D Osborne (P)

Description

Students will be introduced to Natural Language Processing (NLP) including core linguistic tasks such as tokenization, lemmatization/stemming, POS tagging, parsing and chunking. Applications will focus on Deep Learning methods using pytorch with a focus in information extraction including Named Entity Recognition, semantic role labeling, word sense disambiguation, normalization, summarization, question answering and text classification. Applications and data will have a biomedical focus, but no biology or medical background is required.

INFO 673: Clinical Informatics JC
CRN: 62070
Min CR: 0
Max CR: 1
Schedule Type: Lecture 
Instructor: James J Cimino (P)

Description

Students will learn how to read, present, and critique primary research publications in clinical informatics. Journal club participants will present high-impact recent journal publications selected by course instructors and learn how to read the paper, write critiques, and organize analysis insights into review papers. Students must show evidence of prior preparation prior to journal clubs and write critiques to show comprehension of the topics throughout the semester. 

INFO 691: Bioinformatics Seminar I
CRN: 64963
Min CR: 1
Schedule Type: Lecture Seminar
Instructor: Amy Wang (P)

Prerequisites 

Graduate level INFO 601, minimum grade of C 

Description

For master’s student only. Students will learn how to prepare, present, and critique research presentations in bioinformatics by attending seminar presentations made by presenters. Seminars are presented by graduate students, faculty, visitors, or online speakers. Students must show evidence of prior preparation, active participation, and documented comprehension of the topics.

INFO 693: Bioinformatics Journal Club
CRN: 64960
Min CR: 2
Schedule Type: Lecture
Instructor: Jake Y Chen (P)

Description

Students will learn how to read, present, and critique primary research publications in bioinformatics. Journal club participants will present high-impact recent journal publications selected by course instructors and learn how to read the paper, write critiques, and organize analysis insights into review papers. Students must show evidence of prior preparation prior to journal clubs and write critiques to show comprehension of the topics throughout the semester.

INFO 696: Intro to Biomed Info Research
CRN: 66344
Min CR: 3
Schedule Type: Lecture Online
Instructor: Amy Wang (P)

Description

Biomedical informatics is the art and science of collecting, representing and analyzing patient and biomedical information and translating insights from the information into better health and new medical discoveries. The spectrum of informatics applications ranges from molecules (bioinformatics) to individuals and populations (clinical and public health informatics). We will examine the scientific field and research methods that form the foundation for biomedical informatics research. The course will include didactics, readings, hands-on tool explorations, and a summative work product. This foundational course is intended for informatics majors and students in allied fields (e.g., health, biological, or computer sciences) who are interested in exploring the field of informatics.

INFO 701: Introduction to Bioinformatics
CRN: 62025
Min CR: 3
Schedule Type: Lecture 
Instructor: Zechen Chong (P)

Description

Introduction to bioinformatics and computational biology, with emphasis on concepts and application of informatics tools to molecular biology. It covers biological sequence analysis, gene prediction, genome annotation, gene expression analysis, protein structure prediction, evolutionary biology and comparative genomics, bioinformatics databases, cloud computing, basic R-based data analysis, simple programming skills using Perl, Linux/Unix environment and command lines, visual analytics, and social/legal aspects of open science. It will have a class research project component.

INFO 762: Biomed Appl Nat Lang Processing
CRN: 62056
Min CR: 3
Schedule Type: Lecture 
Instructor: John D Osborne (P)

Description

Students will be introduced to Natural Language Processing (NLP) including core linguistic tasks such as tokenization, lemmatization/stemming, POS tagging, parsing and chunking. Applications will focus on Deep Learning methods using pytorch with a focus in information extraction including Named Entity Recognition, semantic role labeling, word sense disambiguation, normalization, summarization, question answering and text classification. Applications and data will have a biomedical focus, but no biology or medical background is required.

INFO 773: Clinical Informatics JC
CRN: 63802
Min CR: 1
Schedule Type: Lecture 
Instructor: James J Cimino (P)

Description

Students will learn how to read, present, and critique research publications in clinical informatics. Journal Club participants will present high-impact recent journal publications selected by course instructors and learn how to read the paper, write critiques, and organize analysis insights into review papers. Students must show evidence of prior preparation prior to journal clubs and write critiques to show comprehension of the topics throughout the semester.

INFO 791: Bioinformatics Seminar I
CRN: 64964
Min CR: 1
Schedule Type: Lecture 
Instructor: Amy Wang (P)

Prerequisites

Graduate level INFO 701, minimum grade of C

Description

For doctoral student only. Students will learn how to prepare, present, and critique research presentations in bioinformatics by attending seminar presentations made by presenters. Seminars are presented by graduate students, faculty, visitors, or online speakers. Students must show evidence of prior preparation, active participation, and documented comprehension of the topics.

INFO 793: Bioinformatics Journal Club
CRN: 64943
Min CR: 2
Schedule Type: Lecture
Instructor: Jake Y Chen (P)

Description

Students will learn how to read, present, and critique primary research publications in bioinformatics. Journal club participants will present high-impact recent journal publications selected by course instructors and learn how to read the paper, write critiques, and organize analysis insights into review papers. Students must show evidence of prior preparation prior to journal clubs and write critiques to show comprehension of the topics throughout the semester.

INFO 796: Intro to Biomed Info Research
CRN: 64942
Min CR: 3
Schedule Type: Lecture Online
Instructor: Amy Wang (P)

Description

Biomedical informatics is the art and science of collecting, representing and analyzing patient and biomedical information and translating insights from the information into better health and new medical discoveries. The spectrum of informatics applications ranges from molecules (bioinformatics) to individuals and populations (clinical and public health informatics). We will examine the scientific field and research methods that form the foundation for biomedical informatics research. The course will include didactics, readings, hands-on tool explorations, and a summative work product. This foundational course is intended for informatics majors and students in allied fields (e.g., health, biological, or computer sciences) who are interested in exploring the field of informatics