Robert M. Hubley

Software Engineer
Computational Biology
Institute for Systems Biology
1441 North 34th Street
Seattle, WA 98103-8904

Voice: (206) 732-1292
FAX: (206) 732-1260
EMAIL: rhubley@systemsbiology.org

Work Bio

I currently work in the Computational Biology group at the Institute for Systems Biology. Under the direction of Dr. Arian Smit my focus has been the improvement of computational methods for annotating interpersed repeats in genomic sequences. I have also pursued using repetitive elements as means of calculating DNA substitution rates in varous species. Under the direction of Dr. Reudi Aebersold I have worked on improving tandem mass spectrometry analsysis software and methods for large scale data management. For additional information on my background see my resume.

Publications

Jiang Z., Hubley R, Smit A.F.A, and Eichler E.
DupMasker: A tool for annotating primate segmental duplications
Genome Research May 23, 2008, 10.1101/gr.078477.108 Abstract

K. Han, M. Konkel, J. Xing, H. Wang, J. Lee, T. Meyer, C. Huang, E. Sandifer, K. Hebert,
E. W. Barnes, R. Hubley, W. Miller, A. Smit, B. Ullmer, and M. Batzer
Mobile DNA in Old World Monkeys: A Glimpse Through the Rhesus Macaque Genome
Science 13 April 2007 316: 238-240 [DOI: 10.1126/science.1139462] (in Reports) PDF

Pedrioli P., Eng J., Hubley R., Brian P., Nilsson E., and Aebersold R.
A Standard Open Representation of Mass Spectrometry Data and its
Application in a Proteomics Research Environment,
Nature Biotechnology 2004 Abstract

Robert M Hubley, Eckart Zitzler and Jared C Roach
Evolutionary Algorithms for the Selection of Single Nucleotide Polymorphisms,
BMC Bioinformatics 2003 PDF

Hubley R., Zitzler E., Siegel A.F., Roach J.
Multiobjective Genetic Marker Selection,
Parallel Problem Solving from Nature 2002 PDF

Paul T Spellman et al. 2002.
Design and implementation of microarray gene expression markup language (MAGE-ML).
Genome Biology 2002 3: research 0046.1-research 0046.9 PDF

Kolker E., Tjaden B.C., Hubley R., Trifonov E.N., Siegel A.F.
Spectral analysis of distributions: finding periodic components in
eukaryotic enzyme length data.
OMICS J. Integr. Biol. 6, 123-130 (2002) PDF

Smit A.F.A., Hubley R.M.
"A few more common, ancient interspersed repeats in the human genome."
Repbase Reports 1:(4) p. 22 (2001) Repbase

International Human Genome Sequencing Consortium.
Initial sequencing and analysis of the human genome
Nature 409, 860-921 (2001) The Human Genome Project
Summary | Full text | PDF | Supplementary

Recently Submitted

Personal Bio

My fiance and I built two wooden strip kayaks ( Redfish King design ) which we use quite often on trips in the Northwest.

In addition to kayaking you can find me working on one project or another. Recently I designed the control and communications system for a real time ocean water remote monitoring system ( http://orca.ocean.washington.edu/index.html ).

I wrote this MD5 reference implementation in VB and Java quite awhile ago now but for some reason it remains very popular: freevbcode

I contributed code to the ECJ Project ( A Java-based Evolutionary Computation Research System ) which implements the multiobjective optimization Strength Pareto Evolutionary Algorithm ( SPEA2 - Ekart Zitzler et al. ) under the ECJ framework.

We built a Hot Tub Boat which was featured on Make Magazine's blog.

Also I have started a photoblog ( like everyone else in the world ). If you are interested you can find it here.