I have come to believe that Bioinformatics education is severely lacking across the world. Most course work is inadequate, practitioners insufficiently well trained, propagating misconceptions and fallacies. Substantial resources are spent on ineffectual training, needless travel, expensive workshops, "bioinformatics for dummies" type of training. Unsurprisingly, with little effect.

After waiting a decade for a solution, I understood that it is not going to happen unless I take the matters into my own hands. This is the genesis of the Biostar Handbooks, initially a single book, now a series of volumes totaling over 1000 pages, focusing solely on the practical aspects of bioinformatics data analysis. We took inspiration from the poem that says:

Beyond a high school education
I'll be teaching a whole nation
that yearns
to learn

The Biostar Handbooks

The Biostar Handbooks introduce readers to bioinformatics, the scientific discipline at the intersection of biology, computer science, and statistical data analytics dedicated to the digital processing of genomic information.

• The Biostar Handbook - An introduction to Bioinformatics as a scientific field.
• The Art of Bioinformatics Scripting - Learn advanced Unix and Bash scripting skills.
• RNA-Seq by Example - Master RNA-Seq data analysis.
• Corona Virus Genome Analysis - Advanced topics devoted to the study of the Coronavirus.

The Biostar Handbook

The Art of Bioinformatics Scripting

RNA-Seq by Example

Coronavirus Genome Analysis

The Biostar Handbooks deliver simple, concise, and relevant information for those looking to understand the field of bioinformatics as a data science. It is a comprehensive, practical handbook that covers all major application areas of bioinformatics.

Get notified

A few times a year we send out emails summarizing the changes made to the book

Teaching

I teach the BMMB 852: Applied Bioinformatics course in resident instruction in the Fall and online during the Spring semester. Typically the course fills up very quickly once registration opens so please plan accordingly.

Research and Publications

I have worked and published in three distinct scientific fields: bioinformatics, computer science and statistical physics. Lately I have been working mostly in collaborations via the Bioinformatics Consulting Center. In this capacity I advise and meet with students from a wide range of departments.

• List of publications »
• Google Scholar Profile »
• Biostars Profile »

Biostars: Bioinformatics Questions and Answers

Ten years ago I have created the Biostars: Question and Answer website that runs on an open source software and aims to support and sustain scientific communities. Today it serves millions users per year and it has become the most visited bioinformatics information resource in the world.

• See the code at Biostar Central »

Over past five years Biostar powered sites met the information needs of over ten million users and served over fifty million page views.

Software Development

I have extensive software engineering experience having served as primary or lead developer on numerous web based software pacakges. While I have certification as a Java and XML developer currently I only program in Python (and occasionally C) see also Python vs Perl:

• GitHub account »
• Software projects at Penn State »

Writing code is one of my passions. Even this website is generated with a custom software that I have written see: pyblue.

Bioinformatics Consulting Center at Penn State

I serve as the director of the Bioinformatics Consulting Center (BCC) at Penn State. Our center offers bioinformatics data analysis services that cover multiple application domains of high throughput sequencing. Services range from routine data manipulation steps to developing novel, domain specific methodologies. Our center is also in charge of distributing and managing the sequencing data produced by the Penn State Genomics Core Sequencing Facilities.

Visit the Bioinformatics Consulting Center for more details.