Publications of Jared Roach

Jared C. Roach

Publications

This page may not be as up to date as my group's page: ISB Family Genomics Group

Glusman, G., Caballero, J., Mauldin, D., Hood, L., and Roach J. C. KAVIAR: an accessible system for testing SNV novelty. Bioinformatics September 28, 2011. PMID: 21965822; PMC3208392 pdf

Roach, J. C., Glusman, G., Hubley, R., Montsaroff, S. Z., Holloway, A. K., Mauldin, D. E., Srivastava, D., Garg, V., Pollard, K. S., Galas, D. J., Hood, L., and Smit, A. F. A. 2011. Chromosomal Haplotypes by Genetic Phasing of Human Families. AJHG 89(3):382-97. PMID: 21855840 pdf

Maziarz M, Janer M, Roach JC, Hagopian W, Palmer JP, Deutsch K, Sanjeevi CB, Kockum I, Breslow N, Lernmark A. 2010. The association between the PTPN22 1858C>T variant and type 1 diabetes depends on HLA risk and GAD65 autoantibodies. Genes & Immunity 11(5):406-15. PMCID: PMC3045194 pdf

Roach, J. C.,* Glusman, G.,* Smit, A. F. A.,* Huff, C. D.,* Hubley, R., Shannon, P. T., Rowen, L., Pant, K. P., Goodman, N., Bamshad, M., Shendure, J., Drmanac, R., Jorde, L. B., Hood, L., and Galas, D. J. 2010. Analysis of genetic inheritance in a family quartet by whole genome sequencing. Science 328(5978):636-9. *Equal contributions. PMCID: PMC3037280 pdf

Roach, J. C. Systems biology of human immunity and disease. 2009. In Meyers, Robert (Ed.) Encyclopedia of Complexity and Systems Science. Springer New York. pdf

Fulton, D. L., Sundararajan, S., Badis, G., Hughes, T. R., Sladek, R.,* and Roach, J. C.,* and Wasserman, W. W.* 2009. TFCat: The curated catalog of mouse and human transcription factors. Genome Biology 10:R29. *Equal contributions. PMCID: PMC2691000 pdf

Hershberg, R., Lipatov, M., Small, P. M., Sheffer, H., Niemann, S., Homolka, S., Roach, J. C., Kremer, K., Petrov, D. A., Feldman, M. W., and Gagneux, S. High functional diversity in Mycobacterium tuberculosis driven by genetic drift and human demography. 2008. PLoS Biology 6(12):e311. Chosen for "Editor's Choice" in Science 322:1758.

Ramsey, S. A., Klemm, S. L., Zak, D. E., Kennedy, K. A., Thorsson, V., Li, B., Gilchrist, M., Gold, E. S., Johnson, C. D., Litvak, V., Navarro, G., Roach, J. C., Rosenberger, C. M., Rust, A. G., Yudkovsky, N., Aderem, A., and Shmulevich, I. 2008. Uncovering a macrophage transcriptional program by integrating evidence from motif scanning and expression dynamics. PLoS Computational Biology 4(3):e1000021.

Gilchrist, M., Thorsson, V., Li, B., Rust, A. G., Korb, M., Roach, J. C., Kennedy, K., Hai, T., Bolouri, H., and Aderem, A. 2008. Systems biology approaches identify ATF3 as a negative regulator of Toll-like receptor 4. Nature 451(7181):1022. pdf (see also original pdf)

Korb, M., Rust, A.G., Thorsson, V., Battail, C., Li, B., Hwang, D., Kennedy, K., Roach, J. C., Rosenberger, C.M., Gilchrist, M., Zak, D., Johnson, C., Marzolf, B., Aderem, A., Shmulevich, I., and Bolouri, H. 2008. The Innate Immune Database (IIDB). BMC Immunology 9:7.

Roach, J. C., Smith, K. D., Strobe, K. L., Nissen, S. M., Haudenschild, C. D., Zhou, D., Vasicek, T. J., Held, G. A., Stolovitzky, G. A., Hood, L., and Aderem, A. 2007. Transcription factor expression in lipopolysaccharide-activated peripheral blood derived mononuclear cells. PNAS 104(41):16245-50.

Jared C. Roach, Kerry Deutsch, Sarah Li, Andrew F. Siegel, Lynn M. Bekris, Derek C. Einhaus, Colleen M. Sheridan, Gustavo Glusman, Leroy Hood, Ake Lernmark, and Marta Janer on behalf of the Swedish Childhood Diabetes Study Group and the Diabetes Incidence in Sweden Study Group. 2006. Genetic mapping at 3-kilobase resolution reveals inositol 1,4,5-triphosphate receptor 3 as a risk factor for type 1 diabetes in Sweden. American Journal of Human Genetics 79(4):614-627. Published online 8/30/2006. pdf

Gustavo Glusman, Shizhen Qin, M. Raafat El-Gewely, Andrew F. Siegel, Jared C. Roach, Leroy Hood, and Arian F. A. Smit. 2006. A third approach to gene prediction suggests thousands of additional human transcribed regions. PLoS Computational Biology 2(3):e18.

Dimitar B. Iliev, Jared C. Roach, Simon Mackenzie, Josep V. Planas, and Frederick W. Goetz. 2005. Endotoxin recognition: In fish or not in fish? FEBS Letters 579(29):6519-28. pdf

Maureen K. Purcell, Kelly D. Smith, Leroy Hood, James R. Winton, and Jared C. Roach. 2005. Conservation of toll-like receptor signaling pathways in teleost fish. Comparative Biochemistry and Physiology; Part D 1(1):77-88. pdf

Asa J. Oudes, Jared C. Roach, Laura S. Walashek, Lillian J. Eichner, Lawrence D. True, Robert L. Vessella, Alvin Y. Liu. 2005. Application of Affymetrix array and Massively Parallel Signature Sequencing for identification of genes involved in prostate cancer progression. BMC Cancer 5:86.

Jared C. Roach, Gustavo Glusman, Lee Rowen, Amardeep Kaur, Maureen K. Purcell, Kelly D. Smith, Leroy Hood, and Alan Aderem. 2005. The evolution of vertebrate toll-like receptors. Proc Natl Acad Sci U S A 102(27):9577-82. pdf

G. A. Stolovitzky, A. Kundaje, G. A. Held, K. H. Duggar, C. D. Haudenschild, D. Zhou, T. J. Vasicek, K. D. Smith, A. Aderem, and J. C. Roach. 2005. Statistical analysis of MPSS measurements: Application to the study of LPS-activated macrophage gene expression. Proc Natl Acad Sci U S A 102(5):1402-7. pdf

Goo YA, Roach J, Glusman G, Baliga NS, Deutsch K, Pan M, Kennedy S, DasSarma S, Ng WV, Hood L. 2004. Low-pass sequencing for microbial comparative genomics. BMC Genomics 5(1):3.

Hubley, R.M., Zitzler, E., and Roach, J. C. 2003. Evolutionary algorithms for the selection of single nucleotide polymorphisms. BMC Bioinformatics 4(1):30. Software available at Sourceforge repository for MAGMA

Hubley, R., Zitzler, E., Siegel, A. F., and Roach, J. 2002. Multiobjective Genetic Marker Selection. Advances in Nature-Inspired Computation: The PPSN VII Workshops 7:32-33. pdf

Aparicio, S., Chapman, J., Stupka, E., Putnam, N., Chia, JM., Dehal, P., Christoffels, A., Rash, S., Hoon, S., Smit, A., Gelpke, M. D., Roach, J., Oh, T., Ho, I. Y., Wong, M., Detter, C., Verhoef, F., Predki, P., Tay, A., Lucas, S., Richardson, P., Smith, S. F., Clark, M. S., Edwards, Y. J., Doggett, N., Zharkikh, A., Tavtigian, S. V., Pruss, D., Barnstead, M., Evans, C., Baden, H., Powell, J., Glusman, G., Rowen, L., Hood, L., Tan, Y. H., Elgar, G., Hawkins, T., Venkatesh, B., Rokhsar, D., and Brenner, S. 2002. Whole-genome shotgun assembly and analysis of the genome of Fugu rubripes. Science 297(5585):1301-10. pdf

Lane, R. P., Roach, J. C., Lee, I. Y., Cutforth, T., Smit, A. F., Axel, R., Trask, B. J., and Hood, L. 2002. Genomic analysis of the olfactory receptor region of the mouse and human T-cell receptor a/d loci. Genome Research. 12(1):81-87. pdf

Roach, J. C. 2002. A clade of trypsins found in cold-adapted fish. Proteins: Structure, Function, and Genetics. 47(1):31-44. pdf

Glusman, G., Rowen, L., Lee, I., Boysen, C., Roach, J. C., Smit, A. F. A., Wang, K., Koop, B. F., and Hood, L. 2001. Comparative genomics of the human and mouse T cell receptor loci. Immunity. 15:337-349. pdf

Van den Engh, G., Nelson, P., and Roach, J. 2000. Numismatic gyrations. Nature 408:540. pdf

The above communication was in response to an article by Moffat.
Article featured in an interview with Ger van den Engh, "Coin Toss Physics" on National Public Radio's program "All Things Considered".
More info: Peter Watterson's spinning disk project.

Siegel, A. F, van den Engh, G., Hood, L., Trask, B., and Roach, J. C. 2000. Modeling the feasibility of whole genome shotgun sequencing using a pairwise end strategy. Genomics 68:237-46. pdf

Roach, J. C., Thorsson, V., and Siegel, A. F. 2000. Parking strategies for genome sequencing. Genome Research 10:1020-1030. pdf

Roach, J. C., Siegel, A. F., Trask, B., van den Engh, G., and Hood, L. 1999. Gaps in the Human Genome Project. Nature 401:843-845. pdf

Siegel, A. F., Trask, B., Roach, J. C., Mahairas, G. G., Hood, L., and van den Engh, G. 1999. Analysis of Sequence-Tagged-Connector Strategies for DNA Sequencing. Genome Research 9:297-307. pdf

Siegel, A. F., Roach, J. C., and van den Engh, G. 1998. Expectation and Variance of True and False Fragment Matches in DNA Restriction Mapping. Journal of Computational Biology. 5(1):101-111.

Siegel, A. F., Roach, J. C., Magness, C., Thayer, E., and van den Engh, G. 1998. Optimization of Restriction Fragment DNA Mapping. Journal of Computational Biology. 5(1):113-126.

Roach, J. C. 1998. Random subcloning, pairwise end sequencing, and the molecular evolution of the vertebrate trypsinogens. Doctoral dissertation, University of Washington. Thesis

Roach, J. C., Wang, K., Gan, L., Hood, L. 1997. The Molecular Evolution of the Vertebrate Trypsinogens. Journal of Molecular Evolution. 45(6):640-652. Article superceded by more recent thesis chapter.

Szabo, C. I., Fransisco, L. V., Roach, J. C., Argonza, R., Wagner, L. A., Ostrander, E. A., King, M.-C. 1996. Human, canine, and murine BRCA1 genes: Sequence comparison among species. Human Molecular Genetics 5(9):1289-1298. pdf

Roach, J. C. 1995. Random subcloning. Genome Research 5:464-473. Article superceded by more recent thesis chapter.

Andrei Grigoriev has provided Java graphical implementations of these equations, which I encourage you to check out at his Physical Mapping Calculators web page.

Roach, J. C., Boysen, C., Wang, K., and Hood, L. 1995. Pairwise end sequencing: a unified approach to genomic mapping and sequencing. Genomics 26:345-353. Article superceded by more recent thesis chapter

Pevzner et al. provide an interesting algorithm for pairwise assembly.

Selected Abstracts

Roach, J. C. Optimization of Fragment Length in Pairwise End Sequencing. RECOMB DNA Sequencing Technologies and Computation. May 21-22, 2005. Stanford University.

Roach, J. C. Assignment of Orthology within Fast-Evolving Multigene Families. Human Genome Meeting 2000. Vancouver, Canada, April 9-12, 2000.

Roach, J. C. Distribution models for random subcloning: Application to mapping and sequencing. DIMACS Workshop on Combinatorial Methods for DNA Mapping and Sequencing. Rutgers, October 6-9, 1994.

Rowen, L., Wang, K., Trask, B., Seto, J., Paeper, B., Ankener, M., Acharja, C., Chen, L., Ahearn, M. E., Massa, H., Roach, J. C., Nickerson, D., Koop, B. F., and Hood, L. Large scale genomic sequencing: The serendipitous discovery of a trypsinogen gene family within the T-cell receptor beta locus. Fourth Annual Cold Spring Harbor Meeting on Genome Mapping and Sequencing. Cold Spring Harbor, May 12-16, 1993.

Invited Lectures

J. C. Roach. The Role of Information Technology in Predictive, Preventive, and Personalized Medicine. WSA Micro-Briefing. September 13, 2005. Seattle, Washington.

J. C. Roach, K. D. Smith, K. Strobe, C. D. Haudenschild, D. Zhou, T. J. Vasicek, G. A. Held, K. H. Duggar, G. Stolovitzky, L. Hood, A. Aderem. Human Transcription Factor Transcriptomics: Host Response to LPS stimulation. Fifth Annual Northwest Gene Expression Conference. May 25-27, 2005. University of Washington.

Jared Roach, Gustavo Glusman, Amardeep Kaur, Brian Birditt, Ryan Nesbitt, Leroy Hood, and Lee Rowen. Fugu Immune Multigene Families from Draft Sequence to Phylogenetics. The International Symposium on Functional Genomics of Pufferfish , Tokyo University, November 3-6, 2004.

If you cannot find something, drop me a line, and I will try to get a copy for you.

The resumé of Jared Roach.

Back to the homepage of Jared Roach.