Publications

  1. Korbel, J. O.; Urban, A. E.; Affourtit, J. P.; Godwin, B.; Grubert, F.; Simons, J. F.; Kim, P. M.; Palejev, D.; Carriero, N. J.; Du, L.; Taillon, B. E.; Chen, Z.; Tanzer, A.; Saunders, A. C.; Chi, J.; Yang, F.; Carter, N. P.; Hurles, M. E.; Weissman, S. M.; Harkins, T. T.; Gerstein, M. B.; Egholm, M.; Snyder, M., Paired-end mapping reveals extensive structural variation in the human genome. Science 2007, 318, (5849), 420-6.
  2. Korbel, J. O.; Urban, A. E.; Grubert, F.; Du, J.; Royce, T. E.; Starr, P.; Zhong, G.; Emanuel, B. S.; Weissman, S. M.; Snyder, M.; Gerstein, M. B., Systematic prediction and validation of breakpoints associated with copy-number variants in the human genome. Proceedings of the National Academy of Sciences of the United States of America 2007, 104, (24), 10110-5.
  3. Frost, A.; Perera, R.; Roux, A.; Spasov, K.; Destaing, O.; Egelman, E. H.; De Camilli, P.; Unger, V. M., Structural basis of membrane invagination by F-BAR domains. [see comment]. Cell 2008, 132, (5), 807-17.
  4. Weinberg, Z.; Regulski, E. E.; Hammond, M. C.; Barrick, J. E.; Yao, Z.; Ruzzo, W. L.; Breaker, R. R., The aptamer core of SAM-IV riboswitches mimics the ligand-binding site of SAM-I riboswitches. Rna-A Publication of the Rna Society 2008, 14, (5), 822-8.
  5. Weinberg, Z.; Barrick, J. E.; Yao, Z.; Roth, A.; Kim, J. N.; Gore, J.; Wang, J. X.; Lee, E. R.; Block, K. F.; Sudarsan, N.; Neph, S.; Tompa, M.; Ruzzo, W. L.; Breaker, R. R., Identification of 22 candidate structured RNAs in bacteria using the CMfinder comparative genomics pipeline. Nucleic Acids Research 2007, 35, (14), 4809-19.
  6. Ma, S.; Song, X.; Huang, J., Supervised group Lasso with applications to microarray data analysis. BMC Bioinformatics 2007, 8, 60.
  7. Leng, C.; Ma, S., Path consistent model selection in additive risk model via Lasso. Statistics in Medicine 2007, 26, (20), 3753-70.
  8. Rosengarten, R. D.; Sperling, E. A.; Moreno, M. A.; Leys, S. P.; Dellaporta, S. L., The mitochondrial genome of the hexactinellid sponge Aphrocallistes vastus: evidence for programmed translational frameshifting. BMC Genomics 2008, 9, 33.
  9. Zhou, X.; Tuck, D. P., MSVM-RFE: extensions of SVM-RFE for multiclass gene selection on DNA microarray data.[erratum appears in Bioinformatics. 2007 Aug;23(15):2029]. Bioinformatics 2007, 23, (9), 1106-14.
  10. Leng, C.; Ma, S., Accelerated failure time models with nonlinear covariates effects. Australian and New Zealand Journal of Statistics 2007, 49, (2), 155-172.
  11. Sudarsan N., L. E., Weinberg Z., Moy R., Kim J., Link K., Breaker, R., Riboswitches in Eubacteria Sense the Second Messenger Cyclic Di-GMP. Science 2008, 321, (5887), 411-413.
  12. Braithwaite, R. S.; Roberts, M. S.; Chang, C. C.; Goetz, M. B.; Gibert, C. L.; Rodriguez-Barradas, M. C.; Shechter, S.; Schaefer, A.; Nucifora, K.; Koppenhaver, R.; Justice, A. C., Influence of alternative thresholds for initiating HIV treatment on quality-adjusted life expectancy: a decision model. Annals of Internal Medicine 2008, 148, (3), 178-85.
  13. Carriero, N.; Osier, M. V.; Cheung, K.-H.; Miller, P. L.; Gerstein, M.; Zhao, H.; Wu, B.; Rifkin, S.; Chang, J.; Zhang, H.; White, K.; Williams, K.; Schultz, M., A high productivity/low maintenance approach to high-performance computation for biomedicine: four case studies. Journal of the American Medical Informatics Association 2005, 12, (1), 90-8.
  14. Bjornson, R. D.; Carriero, N. J.; Colangelo, C.; Shifman, M.; Cheung, K. H.; Miller, P. L.; Williams, K., X!!Tandem, an improved method for running X!tandem in parallel on collections of commodity computers. Journal of Proteome Research 2008, 7, (1), 293-9.
  15. Weinberg, Z., Perreault, J., Meyer, M.M., Breaker, R.R. Exceptional structured noncoding RNAs revealed by bacterial metagenome analysis. Nature, December 2009, 462, (7273), 656-9.