Mark Bieda

Scientist

My name is Mark Bieda. I am a computational biologist/bioinformatician. I have a rare combination of 10+ years computational and 10+ years wet-lab experience. I have expertise in Cancer Biology, Genomics/Bioinformatics, and Neuroscience.
AB Harvard
PhD Stanford

About Me

I’m basically interested in doing great science that makes a difference. I try. The focus of my work is computational biology, mostly bioinformatics. I received my AB in Biochemistry from Harvard and my PhD in Neuroscience from Stanford. I have expertise in neuroscience, genomics/bioinformatics, and cancer biology. I’ve published in Nature, Cell, Genome Research, BMC Bioinformatics, and several other journals. I’ve worked on my own projects, collaborated with small groups, and been a part of big consortia (I was part of the ENCODE pilot project for about 3 years).


This is the personal website of Mark C. Bieda, the biomedical scientist. There are other Mark Biedas, at least one who works in fields allied to mine. But I'm the guy publishing in bioinformatics, genomics, and neuroscience.

Mission

In short - I'm interested in doing great science that affects the bigger world. This leads to projects in various areas and I have a particular interest in cancer genomics and neurogenomics.

I like having a mix of collaborative projects. I am happiest when projects have both wet and dry lab components (although I focus on the dry lab side).

I have a rare combination of very extensive computational experience and very extensive wet-lab experience. This has led to range of interesting projects.

See Expertise for a short (and optional longer) description of my various areas of technical expertise.


Neuroscience (including Neurogenomics)

Highlights:

  • PhD in Neuroscience, Stanford University
  • publications in bioinformatics as applied to neurogenomics
  • very extensive wet lab experience
  • several publications in neurogenomics and physiology
  • ~6 years and continuing service on the Research Management Committee of NeuroDevNet (now Kid's Brain Health Network), a CIHR network of excellence

Why neuroscience?

Because the brain is fundamentally mysterious (just think consciousness, among many mysteries) and the brain is an exceptionally interesting complex system. In recent times, I have become very interested in brain disorders, ranging from neurodevelopmental disorders (e.g. autism) to mental disease (e.g. bipolar disease; drug addiction) to degenerative diseases (Alzheimer’s disease in particular).

Click here for Neuroscience and Neurogenomics Publications



Genomics and Bioinformatics

(Small clarification: I use “genomics” as a catch-all term to include all the ‘omics fields – from studies of the transcriptome to the epigenome to the genome to many others).

Highlights:

  • former member of ENCODE pilot project
  • E2F1 (and other E2Fs) localization – overturned expected results
  • ChIP-seq, RNA-seq, general sequence alignment and other expertise
  • focus on genome-scale analysis and results
  • highly cited work in neurogenomics and cancer genomics
  • won international competition for ChIP-chip algorithm development
  • ongoing focus of Bieda lab
  • ongoing service component – work on NeuroDevNet and with CBCF grant panel focuses on genomics/bioinformatics issues

Why genomics and bioinformatics?

“The proper study of mankind is man” – Alexander Pope

Understanding the genome is essential for understanding what it is to be human. This is a huge, complex, difficult to unravel topic. Hence, I’m interested. Genomics impacts all areas of biology (just as genetics does) and bioinformatics is absolutely essential for correct interpretation of (nearly all) genomic datasets. So I became very interested in genomics and bioinformatics.

My work has focused on genome-scale epigenetics and, for the past 10 years, bioinformatics dealing with epigenetic datasets.

Click here for Genomics and Bioinformatics Publications



Cancer Biology

Highlights:

  • critical work on localization of E2F1, a important cell-cycle gene, in cancer
  • wet-lab molecular biology expertise
  • work on liver cancer and glioblastoma
  • work on cancer stem cells
  • expertise in critical genomic technologies that are revolutionizing cancer biology

Why cancer biology?

Cancer is obviously important. But I never thought I would work on cancer. Why? Because there are hard problems, and then there are really, really hard problems. The genomic variability of cancer (even within a single tumor from a patient) led me to believe that cancer was a truly super-complex problem. I despaired on getting a good handle on such a variable phenomenon.
The rise of genomics changed my perspective. Now, we can easily do single cell (!!) genomes and transcriptomes. So suddenly… the complexity of cancer is meeting its match in biological techniques that are being rapidly translated into the clinic.
It’s a super-exciting time to be doing cancer biology. And it will be great for patients, doctors, and the health care system. I’m personally excited. The recently introduced CRISPR technology, combined with large-scale genomic analysis, offers a whole new set of possibilities for cancer biology.

Click here for Cancer Biology Publications

Science is competitive, so these project descriptions focus on general areas instead of specific projects.

Algorithm Development in Bioinformatics

Good data analysis is essential for genomics. We are working on developing significantly better algorithms in this canonical "Big Data" area. We look for areas in which we can make a big impact.

Integrative meta-analysis of ‘omics datasets

There has been a massive expansion in the number, type, and quality of datasets in the ‘omics fields (genomics, epigenomics, transcriptomics… etc). To take advantage of this multifaceted data, we need ways of intelligently combining datasets. We are currently working with area-specific collaborators on large scale analysis.

Reproducible research

There is an enormous amount of publically-available data. Bioinformatics must make it easier for everyone to access and analyze this data. So far, we, as a field, haven’t succeeded in this. Scientific workflow systems are the focus of our work in this area.

Expertise

My primary areas of expertise are neuroscience and genomics/bioinformatics. I’ve personally done a large amount of wet-lab and computational work, as indicated by my publications. I have several current projects in these areas.

My secondary area of expertise is cancer biology. I’ve published several papers in this area/related to this area and I have served on the Canadian Breast Cancer Foundation Prairie-PNWT grant panel for several years.

More detailed, longer version coming soon.

Highlights:

  • currently Co-Director of the Bioinformatics Stream in the BHSC program at the University of Calgary Cumming School of Medicine
  • set educational policy for program/stream
  • developed several new courses
  • teach sequence alignment and variant analysis, ChIP-seq and RNA-seq analysis
  • teach full course on R and Bioconductor programming, including advanced topics
  • guest lectures on various topics in bioinformatics, from obesity to cancer genomics

I am the Co-Director of the Bioinformatics Stream in the BHSC program at the University of Calgary Cumming School of Medicine; I was recently Acting Director for the 2014-2015 academic year. Along with the rest of the directors, I make educational policy decisions. I actively teach bioinformatics and genomics. Courses include advanced courses focusing on detailed analysis of current areas of bioinformatics study (recently, ChIP-seq dataset analysis) and a course dedicated to R and Bioconductor. I also give guest lectures related to these topics, including ones on genomics as applied to obesity and cancer.

All of my courses emphasize a combination of theory with hands-on application. I believe that university education should take advantage of online courses and many other innovations. I'll be writing soon on these topics.

Contact Info

  • I'm always interested in new opportunities, new collaborations, and scientific discussions.
  • email: mark dot bieda dot online at gmail dot com
  • www.markbieda.com