Robert M. Hubley
Software Engineer
Computational Biology
Institute for Systems Biology
401 Terry Avenue North
Seattle, WA 98109-5234
Voice: (206) 732-1292
FAX: (206) 732-1260
EMAIL: rhubley@systemsbiology.org
W o r k B i o
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 various species. As part of the ISB/Luxembourg initiative I worked on one of the first teams to analyze the complete genomic sequences of a family of four. Our team is now studying several genetic diseases through the lense of family genomics. Under the direction of Dr. Reudi Aebersold I have worked on improving
tandem mass spectrometry analysis software and methods for large scale
data management. For additional information on my background see my resume.
P u b l i c a t i o n s
Jared C. Roach, Gustavo Glusman, Robert Hubley, Stephen Z. Montsaroff, Alisha K. Holloway, Denise E. Mauldin, Deepak Srivastava, Vidu Garg, Katherine S. Pollard, David J. Galas, Leroy Hood, Arian F.A. Smit
Chromosomal Haplotypes by Genetic Phasing of Human Families
American Journal of Human Genetics, September 2011 [doi:10.1016/j.ajhg.2011.07.023] Abstract
Devin P. Locke et al.
Comparative and demographic analysis of orang-utan genomes
Nature 2011; 469:529-533 [doi:10.1038/nature09687] Full
Heidi J. T. Pagan, Jeremy D. Smith, Robert M. Hubley and David A. Ray
PiggyBac-ing on a primate genome: Novel elements, recent activity and horizontal transfer
Genome Biology and Evolution, May 2010, [doi:10.1093/gbe/evq021] Abstract
Jared C. Roach, Gustavo Glusman, Arian F. A. Smit, Chad D. Huff, Robert Hubley, Paul T. Shannon, Lee Rowen, Krishna P. Pant, Nathan Goodman, Michael Bamshad, Jay Shendure, Radoje Drmanac, Lynn B. Jorde, Leroy Hood, David J. Galas
Analysis of Genetic Inheritance in a Family Quartet by Whole-Genome Sequencing
Science March 10, 2010, [DOI: 10.1126/science.1186802] Abstract
Wesley C. Warren, et al
The genome of a songbird
Nature Jan 6, 2010, 464, 757-762 (1 April 2010) Abstract
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
R e c e n t l y S u b m i t t e d
M e e t i n g s / C o u r s e s
FASEB Summer Research Conferences - Mobile Elements in Mammalian Genomes, 2011
FASEB Summer Research Conferences - Mobile Elements in Mammalian Genomes, 2009
Woods Hole Oceanograhic Institute - Genetic Regulatory Networks Course, 2008
International Congress on Transposable Elements, 2008
FASEB Summer Research Conferences - Mobile Elements in Mammalian Genomes, 2007
The Wellcome Trust Genome Center - Genome Informatics, 2006
Arctic Region Supercomputer Center - Faculty Camp, 2002
The Wellcome Trust Genome Center - Microarray and Gene Expression Database Jamboree, 2001
J o u r n a l s
Reviewer for Oxford Journals - Bioinformatics, 2006 - present
P e r s o n a l B i o
My wife and I built two wooden strip kayaks ( Redfish King design ) which we use quite often on trips in the Northwest.
My interest in embedded controllers ( BitsyX, TattleTale, AVR, and Arduino etc ) has led to some fun consulting projects including:
- I designed the control and communications computer
for a remote, real time, ocean water monitoring system ( http://orca.ocean.washington.edu/index.html ).
- "WaterLogged" - An underwater data logger using Atmel's XMega chip for oceanographic instruments.
- And most importantly Arduino controllers for LED cove and stair lighting.
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.
