Current Courses


BIOINF-525: Foundations of Bioinformatics and Systems Biology

I serve as lead instructor and course director for Foundations of Bioinformatics and Systems Biology (BIOINF525). This course provides an introduction to the principles and practical approaches of bioinformatics as applied to genes and proteins. Offered in the winter term each year BIOINF525 is currently comprised of three one credit modules covering:

  1. Foundations of Bioinformatics;
  2. Statistics in Bioinformatics; and
  3. Systems Biology.

Wondering why you should take this course? See the praise for the 2015 class from official student evaluations and visit the 2016 course website to find out more.


BIOINF-606: Introduction to Biocomputing

I serve as a principal instructor and co-course director for Introduction to Biocomputing (BIOINF606). This hands-on one week course introduces new graduate students to computational tools, techniques and best practices that foster reproducible research in bioinformatics, genome informatics and biostatistics.

Offered at the start of the fall term each year, major concepts and tools covered include the unix system, version control, data management, software compilation, task automation and cluster computing.

See the student feedback for the 2015 class and visit the 2016 course website to find out more.


BIOINF-575: Programming Laboratory in Bioinformatics

BIOINF575 introduces general computer programming, relational databases, and statistical programming as tools to solve problems in bioinformatics data analysis. I currently teach five sessions in this course covering:


International Workshop: Applied Structural Bioinformatics

This one week hands-on workshop for graduate students and faculty introduced cutting edge methods in structural bioinformatics and computational structural biology. The 2015 course was held at the University of Bergen, Norway (Sept/Oct 2015); with a related 2013 course held at Jawaharlal Nehru University (JNU) and the University of Delhi, India (Dec 2013).


BIOINF-527: Introduction to Bioinformatics

I guest lecture for BIOINF527 covering the following topics:


ScreenCast1.1


GIDAS: High School Student Instruction and Outreach

I currently serve as an instructor and mentor for both the annual High School Genes In Disease and Symptoms (GIDAS) club and the Ann Arbor Computational Biology Camp (for 9th-12th grade students). GIDAS club activities run from August through June with the purpose of having high school students both learn and participate in computational biology research. Through GIDAS, I have presented lectures to groups of 25-40 selected high school students from the Ann Arbor, Detroit and Flint areas. These lectures introduced genomics and bioinformatics concepts and were followed with small group based research projects exploring public gene expression data sets. I mentored students in the use of online bioinformatics tools and databases, as well as how to formulate their hypotheses and present their results in poster and oral formats. In the Ann Arbor Computational Biology Camps for high schoolers, I have taught week long summer sessions to over 50 students in UNIX computing and data analysis with the R programing language. An important component of these camps is their intended amplifying effect, with attendees instructed to disseminate what they learn to their school peers via their school’s GIDAS club.


Future Courses

The following new courses are coming soon.

BIOINF-526*: Fundamentals of Biomedical Informatics

This new course (*coming in 2017/18) builds on BIOINF525 and will be composed of six four week one credit modules, namely:

  • Foundations of Bioinformatics
  • Genome and Epigenome Informatics
  • Statistics for Bioinformatics
  • Systems and Network Biology
  • Data Science
  • Clinical Informatics


Coursera MOOC: Introductory Bioinformatics

Coursera is an open online course delivery platform which provides an exciting and unique opportunity to explore new teaching models and provide global access to our knowledge and expertise. I have prepared a completely new curriculum for this MOOC (massive on-line open course) comprised of three 20-25 minute videos per week for 8 weeks covering:

  • Introductory Molecular Bioinformatics (week 1),
  • Structural Bioinformatics (week 2),
  • Genomics (week 3),
  • Epigenomics (week 4),
  • Proteomics (week 5),
  • Metabolomics (week 6) and
  • Systems Biology (week 7).
  • The Future of Bioinformatics and Systems Biology (week 8)

There are also weekly homework assignments and regular quizzes within each video segment. We are currently in the recording phase with a planned release date of Summer 2017.


BIOINF-800: Computational Biophysics & Structure Based Drug Discovery

This graduate-level seminar course will walk students through the major techniques of biomolecular simulation and computer-aided drug design. This will include application of massively parallel molecular dynamics simulations and associated analysis techniques to enable new discoveries within the vast quantity of digital data, such as finding new potential drug leads through virtual screening and small molecule docking. Lectures on course concepts will be closely combined with hands-on tutorials that allow the practical application of computational methods and statistical data analysis in a project-based format. Students will be granted access to the national supercomputers centers as well as local high performance computing cluster resources to run their simulations and analyze the resulting data.
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Previous Courses

Discontinued courses and select individual past lectures.

Below you will find previous course details along with links to select lecture slides, workshop material and software tutorials.


Bio3D: Interactive Tools for Structural Bioinformatics

Invited lecture and hands-on tutorial at the University of Bergen, Norway (Spring 2015).


Structural Bioinformatics (PDF)

Advances in Molecular Dynamics of Biomolecules

Four lectures with integrated lab sessions at JNU (Jawaharlal Nehru University) and University of Delhi, India. (Fall 2013).


RStudio Git and GitHub hands-on lecture

Summer camp for high-school students (miRcore) - 17 Aug 2016.


Special Topics in Biological Physics

Natures Molecular Machines - Spring 2014.


Introduction to Molecular Motors

California State University, San Marcos, USA, 2011


Molecular Motors and Electrostatics

National Biomedical Computation Resource Summer Institute, San Diego Supercomputer Center, USA, 2010.


Electrostatics and Diffusion

National Biomedical Computation Resource Summer Institute, San Diego Supercomputer Center, USA, 2010.


Protein Form and Function in Cytoskeletal Transport Systems

California State University, San Marcos, USA, 2009 University of California, San Diego, USA, 2008


Advanced Methods for Biomolecular Simulation

CCPB training workshop, University of Nottingham, UK, 2007.


Additional postgraduate level guest lectures on The R language, Why do we use UNIX?, working with UNIX, Computational Chemistry, Biomolecular Structure, Chemical Equilibria, and Protein Form and Function.