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

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.

Hubley, R., Finn, R. D., Clements, J., Eddy, S. R., Jones, T. A., Bao, W., ... & Wheeler, T. J. (2016). The Dfam database of repetitive DNA families. Nucleic acids research, 44(D1), D81-D89. Full

Rosenbloom, K. R., Armstrong, J., Barber, G. P., Casper, J., Clawson, H., Diekhans, M., ... & Harte, R. A. (2015). The UCSC genome browser database: 2015 update. Nucleic acids research, 43(D1), D670-D681. Full

Hoen DR, Hickey G, Bourque G, Casacuberta J, Cordaux R, Feschotte C, Fiston-Lavier AS, Hua-Van A, Hubley R, Kapusta A, Lerat E. A call for benchmarking transposable element annotation methods. Mobile DNA. 2015 Aug 4;6(1):13. Full

Green, R. E., Braun, E. L., Armstrong, J., Earl, D., Nguyen, N., Hickey, G., ... & Kern, C. (2014). Three crocodilian genomes reveal ancestral patterns of evolution among archosaurs. Science, 346(6215), 1254449.

Carbone, L., Harris, R. A., Gnerre, S., Veeramah, K. R., Lorente-Galdos, B., Huddleston, J., ... & Anaclerio, F. (2014). Gibbon genome and the fast karyotype evolution of small apes. Nature, 513(7517), 195-201.

Hu, H., Roach, J. C., Coon, H., Guthery, S. L., Voelkerding, K. V., Margraf, R. L., ... & Wang, S. (2014). A unified test of linkage analysis and rare-variant association for analysis of pedigree sequence data. Nature biotechnology, 32(7), 663-669.

Li H, Glusman G, Hu H, Caballero J, Hubley R, Witherspoon D, Guthery SL, Mauldin DE, Jorde LB, Hood L, Roach JC. Relationship estimation from whole-genome sequence data. PLoS Genet. 2014 Jan 30;10(1):e1004144. Full

Wheeler TJ, Clements J, Eddy SR, Hubley R, Jones TA, Jurka J, Smit AF, Finn RD.
Dfam: a database of repetitive DNA based on profile hidden Markov models.
Nucleic Acids Res., 2013 Jan;41(Database issue):D70-82. doi: 10.1093/nar/gks1265. Epub 2012 Nov 30. PMCID: PMC3531169 Full

Jerilyn A Walker, Miriam K Konkel, Brygg Ullmer, Christopher P Monceaux, Oliver A Ryder, Robert Hubley, Arian FA Smit, Mark A Batzer
Orangutan Alu quiescence reveals possible source element: support for ancient backseat drivers
Mobile DNA, 2012; 3:8 doi:10.1186/1759-8753-3-8 Full

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

M e e t i n g s / C o u r s e s

FASEB Summer Research Conferences - Mobile Elements in Mammalian Genomes, 2015

TE Annotation Workshop - 2014

FASEB Summer Research Conferences - Mobile Elements in Mammalian Genomes, 2013

Fujihara Seminar - A New Horizon of Retroposon Research - 2012

Genomic Impact of Eukaryotic Transposable Elements - ASILOMAR, 2012

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

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.