SBCNY Computer Programming in Systems Biology and Bioinformatics

SBCNY Fellow Spotlights
Jayanth Krishnan Roy Song, currently enrolled in the PhD program at Icahn School of Medicine at Mount Sinai, is the first author of a study published in the journal PNAS, titled "ERK Regulation of Phosphodiesterase 4 Enhances Dopamine-stimulated AMPA Receptor Membrane Insertion".
[PubMed]
Jayanth Krishnan Jayanth Krishnan, currently enrolled in the Accelerated Physician-Scientist Program (BS/MD) at Rensselaer Polytechnic Institute and Albany Medical College, is a recipient of a 2011 Davidson Scholarship. Jay, who conducted research under the mentorship of SBCNY Investigator Avi Ma'ayan, was the winner in the Engineering category at the Westchester Science and Engineering Fair (WESEF). His project was selected as one of the top eight overall projects which earned him a trip to the Intel International Science and Engineering Fair (ISEF).
[Project] [Davidson Fellow Bio] [Putnam Examiner Article]
Johnson Ho Johnson Ho, City College of New York, Biomedical Engineering major, received the 2011 Barry M. Goldwater Scholarship and was selected as the 2011-2012 Valedictorian of the Grove School of Engineering. Johnson was a summer 2009 SBCNY Fellow who worked under the mentorship of Kevin Costa (MSSM, Department of Medicine) on a project titled: Post-Infarction Left Ventricular Remodeling and the Law of Laplace.
[Project] [CCNY News]
Jayanth Krishnan Sara Wildstein from Queens College (Class of 2010), was one of the recipients of the 2010 Jonas E. Salk Scholarship. She is currently a medical student at the Albert Einstein College of Medicine. Under the mentorship of SBCNY Investigator Eric Sobie during the summer of 2009, Sara's project was titled: Computational modeling of 'leaky' ryanodine receptors and triggered arrhythmias in heart cells.
[Project] [2010 Salk Scholars]
Sumer Undergraduate Program

Computer Programming in Systems Biology and Bioinformatics

BSR6803.05 Pharmacology and Systems Biology of Disease and Therapeutics CMC
(customized mini-course)

Course Director: Avi Ma'ayan PhD
E-mail: avi.maayan@mssm.edu

The course meets at 12-34 IMI from 4:00-5:30PM every Tuesday for 10 weeks

Course Description:
This mini course covers computer programming methodologies applied to processing data and analysis of data in the broad fields of Bioinformatics and Systems Biology. Topics covered would include an overview of data structures and algorithms, Python scripting for processing text files, computational platforms such as R and MATLAB as well as web technologies using JavaScript, HTML, XML, PHP, SQL, MySql, and CGI. Students will be required to complete small programming assignments throughout the course

Course Schedule Spring 2012


Date
Topic
Assignment
2/21 Mutual Information and Decision Trees Decision Tree Classifier
2/28 MATLAB Programming M-file assignment
3/6 Data Structures Linked list program
3/13 Python Programming Interactive web-page
3/20 Database Systems Creating a database
3/27 Web Programming Interactive web-page
4/3 GSEA GSEA in R
4/10 PCA PCA in R
4/17 PubMed E-utils, AERS, GeneRIF, OMIM Final project
4/24 Final Project Q & A
Last Updated: 07/15/2015 17:05:52