Publications

The activities of the Center build upon the substantial research record of the Center's Faculty members. The following is a select list of publications related to planned deliverables.


List publications by year:

   

List of Publications in 2011


1. Mugler, A., B. Grinshpun, R. Franks, C. H. Wiggins, (2011) Statistical method for revealing form-function relations in biological networks, Proceedings of the National Academy of Sciences of the United States of America

2. Pe'er, D., N. Hacohen , (2011) Principles and strategies for developing network models in cancer, Cell

3. Pasqualucci, L., D. Dominguez-Sola, A. Chiarenza, G. Fabbri, A. Grunn, V. Trifonov, L. H. Kasper, S. Lerach, H. Tang, J. Ma, D. Rossi, A. Chadburn, V. V. Murty, C. G. Mullighan, G. Gaidano, R. Rabadan, P. K. Brindle, R. Dalla-Favera, (2011) Inactivating mutations of acetyltransferase genes in B-cell lymphoma, Nature

4. Harpaz, R., H. Perez, H. S. Chase, R. Rabadan, G. Hripcsak, C. Friedman, (2011) Biclustering of adverse drug events in the FDA's spontaneous reporting system, Clinical pharmacology and therapeutics

5. Slattery, M, Riley, T, Liu, P, Abe, N, Gomez-Alcala, P, Dror, I, Zhou, T, Rohs, R, Honig, B, Bussemaker, H. J, Mann, R. S., (2011) Cofactor Binding Evokes Latent Differences in DNA Binding Specificity between Hox Proteins, Cell

6. Gusev, A, Shah, M. J, Kenny, E. E, Ramachandran, A, Lowe, J. K, Salit, J, Lee, C. C, Levandowsky, E. C, Weaver, T. N, Doan, Q. C, Peckham, H. E, McLaughlin, S. F, Lyons, M. R, Sheth, V. N, Stoffel, M, De La Vega, F. M, Friedman, J. M, Breslow, J. L, Pe'er, I., (2011) Low-pass Genomewide Sequencing and Variant Inference Using Identity-by-descent in an Isolated Human Population, Genetics

7. Birsoy, K, Berry, R, Wang, T, Ceyhan, O, Tavazoie, S, Friedman, J. M, Rodeheffer, M. S., (2011) Analysis of gene networks in white adipose tissue development reveals a role for ETS2 in adipogenesis, Development

8. Dewal, N, Hu, Y, Freedman, M. L, Laframboise, T, Pe'er, I., (2011) Calling amplified haplotypes in next generation tumor sequence data, Genome Res

9. Freddolino, P. L, Amini, S, Tavazoie, S., (2011) Newly identified genetic variations in common MG1655 stock cultures, J Bacteriol

10. Floratos, A, Honig, B, Pe'er, D, Califano, A., (2011) Using systems and structure biology tools to dissect cellular phenotypes, J Am Med Inform Assoc

11. Luan, B, Martyna, G, Stolovitzky, G., (2011) Characterizing and Controlling the Motion of ssDNA in a Solid-State Nanopore, Biophys J

12. Luan, B, Stolovitzky, G, Martyna, G., (2011) Slowing and controlling the translocation of DNA in a solid-state nanopore, Nanoscale

13. Amini, S, Hottes, A. K, Smith, L. E, Tavazoie, S., (2011) Fitness landscape of antibiotic tolerance in Pseudomonas aeruginosa biofilms, PLoS Pathog

14. Sumazin, P, Yang, X, Chiu, H. S, Chung, W. J, Iyer, A, Llobet-Navas, D, Rajbhandari, P, Bansal, M, Guarnieri, P, Silva, J, Califano, A., (2011) An extensive microRNA-mediated network of RNA-RNA interactions regulates established oncogenic pathways in glioblastoma, Cell

15. Kuziemko, A, Honig, B, Petrey, D., (2011) Using structure to explore the sequence alignment space of remote homologs, PLoS Comput Biol

16. Shen, Y, Gu, Y, Pe'er, I., (2011) A hidden Markov model for copy number variant prediction from whole genome resequencing data, BMC Bioinformatics

17. Basso, K, Mussolin, L, Lettieri, A, Brahmachary, M, Lim, W. K, Califano, A, Basso, G, Biondi, A, Cazzaniga, G, Rosolen, A., (2011) T-cell lymphoblastic lymphoma shows differences and similarities with T-cell acute lymphoblastic leukemia by genomic and gene expression analyses, Genes Chromosomes Cancer

18. Inigo, S, Alvarez, M. J, Strasser, B, Califano, A, Cerdan, P. D., (2011) PFT1, the MED25 subunit of the plant Mediator complex, promotes flowering through CONSTANS dependent and independent mechanisms in Arabidopsis, Plant J

19. Gusev, A, Palamara, P. F, Aponte, G, Zhuang, Z, Darvasi, A, Gregersen, P, Pe'er, I., (2011) The Architecture of Long-Range Haplotypes Shared within and across Populations, Mol Biol Evol

20. Califano, A., (2011) Striking a balance between feasible and realistic biological models, Sci Transl Med

21. Vilar, S, Harpaz, R, Chase, H. S, Costanzi, S, Rabadan, R, Friedman, C., (2011) Facilitating adverse drug event detection in pharmacovigilance databases using molecular structure similarity: application to rhabdomyolysis, J Am Med Inform Assoc

22. Meyer, P, Alexopoulos, L. G, Bonk, T, Califano, A, Cho, C. R, de la Fuente, A, de Graaf, D, Hartemink, A. J, Hoeng, J, Ivanov, N. V, Koeppl, H, Linding, R, Marbach, D, Norel, R, Peitsch, M. C, Rice, J. J, Royyuru, A, Schacherer, F, Sprengel, J, Stolle, K, Vitkup, D, Stolovitzky, G., (2011) Verification of systems biology research in the age of collaborative competition, Nat Biotechnol

23. Prill, R. J, Saez-Rodriguez, J, Alexopoulos, L. G, Sorger, P. K, Stolovitzky, G., (2011) Crowdsourcing network inference: the DREAM predictive signaling network challenge, Sci Signal

24. Wolpaw, A. J, Shimada, K, Skouta, R, Welsch, M. E, Akavia, U. D, Pe'er, D, Shaik, F, Bulinski, J. C, Stockwell, B. R., (2011) Modulatory profiling identifies mechanisms of small molecule-induced cell death, Proc Natl Acad Sci U S A

25. Kruithof-de Julio, M, Alvarez, M. J, Galli, A, Chu, J, Price, S. M, Califano, A, Shen, M. M., (2011) Regulation of extra-embryonic endoderm stem cell differentiation by Nodal and Cripto signaling, Development

26. Amini, S, Tavazoie, S., (2011) Antibiotics and the post-genome revolution, Curr Opin Microbiol

27. Hottes, A. K, Tavazoie, S., (2011) Microarray-based genetic footprinting strategy to identify strain improvement genes after competitive selection of transposon libraries, Methods Mol Biol

28. Pasqualucci, L, Trifonov, V, Fabbri, G, Ma, J, Rossi, D, Chiarenza, A, Wells, V. A, Grunn, A, Messina, M, Elliot, O, Chan, J, Bhagat, G, Chadburn, A, Gaidano, G, Mullighan, C. G, Rabadan, R, Dalla-Favera, R., (2011) Analysis of the coding genome of diffuse large B-cell lymphoma, Nature Genetics

29. Wu, Y, Vendome, J, Shapiro, L, Ben-Shaul, A, Honig, B., (2011) Transforming binding affinities from three dimensions to two with application to cadherin clustering, Nature

30. Holmes, A. B, Hawson, A, Liu, F, Friedman, C, Khiabanian, H, Rabadan, R., (2011) Discovering disease associations by integrating electronic clinical data and medical literature, Plos One

31. Oskarsson, T, Acharyya, S, Zhang, X. H, Vanharanta, S, Tavazoie, S. F, Morris, P. G, Downey, R. J, Manova-Todorova, K, Brogi, E, Massague, J., (2011) Breast cancer cells produce tenascin C as a metastatic niche component to colonize the lungs, Nat Med

32. Fischer, M, Zhang, Q. C, Dey, F, Chen, B. Y, Honig, B, Petrey, D., (2011) MarkUs: a server to navigate sequence-structure-function space, Nucleic Acids Res

33. Fabbri, G, Rasi, S, Rossi, D, Trifonov, V, Khiabanian, H, Ma, J, Grunn, A, Fangazio, M, Capello, D, Monti, S, Cresta, S, Gargiulo, E, Forconi, F, Guarini, A, Arcaini, L, Paulli, M, Laurenti, L, Larocca, L. M, Marasca, R, Gattei, V, Oscier, D, Bertoni, F, Mullighan, C. G, Foa, R, Pasqualucci, L, Rabadan, R, Dalla-Favera, R, Gaidano, G., (2011) Analysis of the chronic lymphocytic leukemia coding genome: role of NOTCH1 mutational activation, J Exp Med

34. Gilman, S. R, Iossifov, I, Levy, D, Ronemus, M, Wigler, M, Vitkup, D., (2011) Rare de novo variants associated with autism implicate a large functional network of genes involved in formation and function of synapses, Neuron

35. Zhu, J, Yu, Y, Ulbrich, M. H, Li, M. H, Isacoff, E. Y, Honig, B, Yang, J., (2011) Structural model of the TRPP2/PKD1 C-terminal coiled-coil complex produced by a combined computational and experimental approach, Proc Natl Acad Sci U S A

36. Shen, Y, Song, R, Pe'er, I., (2011) Coverage tradeoffs and power estimation in the design of whole-genome sequencing experiments for detecting association, Bioinformatics

37. Gusev, A, Kenny, E. E, Lowe, J. K, Salit, J, Saxena, R, Kathiresan, S, Altshuler, D. M, Friedman, J. M, Breslow, J. L, Pe'er, I., (2011) DASH: a method for identical-by-descent haplotype mapping uncovers association with recent variation, Am J Hum Genet

38. Zhang, Q. C, Deng, L, Fisher, M, Guan, J, Honig, B, Petrey, D., (2011) PredUs: a web server for predicting protein interfaces using structural neighbors, Nucleic Acids Res

39. Harrer, S, Waggoner, P. S, Luan, B, Afzali-Ardakani, A, Goldfarb, D. L, Peng, H, Martyna, G, Rossnagel, S. M, Stolovitzky, G. A., (2011) Electrochemical protection of thin film electrodes in solid state nanopores, Nanotechnology

40. Rudin, C, Waltz, D, Anderson, R, Boulanger, A, Salleb-Aouissi, A, Chow, M, Dutta, H, Gross, P, Huang, B, Ierome, S., (2011) Machine Learning for the New York City Power Grid, IEEE Trans Pattern Anal Mach Intell

41. Vendome, J, Posy, S, Jin, X, Bahna, F, Ahlsen, G, Shapiro, L, Honig, B., (2011) Molecular design principles underlying beta-strand swapping in the adhesive dimerization of cadherins, Nat Struct Mol Biol

42. Kim, H, Watkinson, J, Anastassiou, D., (2011) Biomarker discovery using statistically significant gene sets, J Comput Biol

43. Pe'er, D, Hacohen, N., (2011) Principles and strategies for developing network models in cancer, Cell

44. Pasqualucci, L, Dominguez-Sola, D, Chiarenza, A, Fabbri, G, Grunn, A, Trifonov, V, Kasper, L. H, Lerach, S, Tang, H, Ma, J, Rossi, D, Chadburn, A, Murty, V. V, Mullighan, C. G, Gaidano, G, Rabadan, R, Brindle, P. K, Dalla-Favera, R., (2011) Inactivating mutations of acetyltransferase genes in B-cell lymphoma, Nature

45. Harrison, O. J, Jin, X, Hong, S, Bahna, F, Ahlsen, G, Brasch, J, Wu, Y, Vendome, J, Felsovalyi, K, Hampton, C. M, Troyanovsky, R. B, Ben-Shaul, A, Frank, J, Troyanovsky, S. M, Shapiro, L, Honig, B., (2011) The extracellular architecture of adherens junctions revealed by crystal structures of type I cadherins, Structure

46. Png, K. J, Yoshida, M, Zhang, X. H, Shu, W, Lee, H, Rimner, A, Chan, T. A, Comen, E, Andrade, V. P, Kim, S. W, King, T. A, Hudis, C. A, Norton, L, Hicks, J, Massague, J, Tavazoie, S. F., (2011) MicroRNA-335 inhibits tumor reinitiation and is silenced through genetic and epigenetic mechanisms in human breast cancer, Genes Dev

47. Brasch, J, Harrison, O. J, Ahlsen, G, Carnally, S. M, Henderson, R. M, Honig, B, Shapiro, L., (2011) Structure and binding mechanism of vascular endothelial cadherin: a divergent classical cadherin, J Mol Biol

48. Shechtman, C. F, Henneberry, A. L, Seimon, T. A, Tinkelenberg, A. H, Wilcox, L. J, Lee, E, Fazlollahi, M, Munkacsi, A. B, Bussemaker, H. J, Tabas, I, Sturley, S. L., (2011) Loss of subcellular lipid transport due to ARV1 deficiency disrupts organelle homeostasis and activates the unfolded protein response, J Biol Chem

49. Shen, Y, Nicoletti, P, Floratos, A, Pirmohamed, M, Molokhia, M, Geppetti, P, Benemei, S, Giomi, B, Schena, D, Vultaggio, A, Stern, R, Daly, M. J, John, S, Nelson, M. R, Pe'er, I., (2011) Genome-wide association study of serious blistering skin rash caused by drugs, Pharmacogenomics J

50. Harpaz, R, Perez, H, Chase, H. S, Rabadan, R, Hripcsak, G, Friedman, C., (2011) Biclustering of adverse drug events in the FDA's spontaneous reporting system, Clin Pharmacol Ther

51. Behnke-Parks, W. M, Vendome, J, Honig, B, Maliga, Z, Moores, C, Rosenfeld, S. S., (2011) Loop L5 acts as a conformational latch in the mitotic kinesin Eg5, J Biol Chem

52. Kenny, E. E, Kim, M, Gusev, A, Lowe, J. K, Salit, J, Smith, J. G, Kovvali, S, Kang, H. M, Newton-Cheh, C, Daly, M. J, Stoffel, M, Altshuler, D. M, Friedman, J. M, Eskin, E, Breslow, J. L, Pe'er, I., (2011) Increased power of mixed models facilitates association mapping of 10 loci for metabolic traits in an isolated population, Human Molecular Genetics

53. Roberts, R. J, Chang, Y. C, Hu, Z, Rachlin, J. N, Anton, B. P, Pokrzywa, R. M, Choi, H. P, Faller, L. L, Guleria, J, Housman, G, Klitgord, N, Mazumdar, V, McGettrick, M. G, Osmani, L, Swaminathan, R, Tao, K. R, Letovsky, S, Vitkup, D, Segre, D, Salzberg, S. L, Delisi, C, Steffen, M, Kasif, S., (2011) COMBREX: a project to accelerate the functional annotation of prokaryotic genomes, Nucleic Acids Res

54. Cheung, Y. H, Watkinson, J, Anastassiou, D., (2011) Conditional meta-analysis stratifying on detailed HLA genotypes identifies a novel type 1 diabetes locus around TCF19 in the MHC, Human Genetics

55. Cadeiras, M, von Bayern, M, Sinha, A, Shahzad, K, Latif, F, Lim, W. K, Grenett, H, Tabak, E, Klingler, T, Califano, A, Deng, M. C., (2011) Drawing networks of rejection - a systems biological approach to the identification of candidate genes in heart transplantation, J Cell Mol Med

List of Publications in 2010


56. Bu, D. X., Rai, V., Shen, X., Rosario, R., Lu, Y., D'Agati, V., Yan, S. F., Friedman, R. A., Nuglozeh, E., Schmidt, A. M., (2010) Activation of the ROCK1 branch of the transforming growth factor-beta pathway contributes to RAGE-dependent acceleration of atherosclerosis in diabetic ApoE-null mice, Circ Res

57. Zhou, X., Sumazin, P., Rajbhandari, P., Califano, A., (2010) A systems biology approach to transcription factor binding site prediction, PLoS One

58. Chastanet, A. Vitkup, D. Yuan, G. C. Norman, T. M. Liu, J. S. Losick, R. M., (2010) Broadly heterogeneous activation of the master regulator for sporulation in Bacillus subtilis, Proc Natl Acad Sci U S A

59. Chen, J. Sam, L. Huang, Y. Lee, Y. Li, J. Liu, Y. Xing, H. R. Lussier, Y. A., (2010) Protein interaction network underpins concordant prognosis among heterogeneous breast cancer signatures, J Biomed Inform

60. Ciatto, C. Bahna, F. Zampieri, N. VanSteenhouse, H. C. Katsamba, P. S. Ahlsen, G. Harrison, O. J. Brasch, J. Jin, X. Posy, S. Vendome, J. Ranscht, B. Jessell, T. M. Honig, B. Shapiro, L., (2010) T-cadherin structures reveal a novel adhesive binding mechanism, Nat Struct Mol Biol

61. Harrison, O. J. Bahna, F. Katsamba, P. S. Jin, X. Brasch, J. Vendome, J. Ahlsen, G. Carroll, K. J. Price, S. R. Honig, B. Shapiro, L., (2010) Two-step adhesive binding by classical cadherins, Nat Struct Mol Biol

62. Hsiao, T. L. Revelles, O. Chen, L. Sauer, U. Vitkup, D., (2010) Automatic policing of biochemical annotations using genomic correlations, Nat Chem Biol

63. Kitayner, M. Rozenberg, H. Rohs, R. Suad, O. Rabinovich, D. Honig, B. Shakked, Z., (2010) Diversity in DNA recognition by p53 revealed by crystal structures with Hoogsteen base pairs, Nat Struct Mol Biol

64. Klein, U. Lia, M. Crespo, M. Siegel, R. Shen, Q. Mo, T. Ambesi-Impiombato, A. Califano, A. Migliazza, A. Bhagat, G. Dalla-Favera, R., (2010) The DLEU2/miR-15a/16-1 cluster controls B cell proliferation and its deletion leads to chronic lymphocytic leukemia, Cancer Cell

65. Lee, Y. Yang, X. Huang, Y. Fan, H. Zhang, Q. Wu, Y. Li, J. Hasina, R. Cheng, C. Lingen, M. W. Gerstein, M. B. Weichselbaum, R. R. Xing, H. R. Lussier, Y. A., (2010) Network modeling identifies molecular functions targeted by miR-204 to suppress head and neck tumor metastasis, PLoS Comput Biol

66. Lu, X. J. Olson, W. K. Bussemaker, H. J., (2010) The RNA backbone plays a crucial role in mediating the intrinsic stability of the GpU dinucleotide platform and the GpUpA/GpA miniduplex, Nucleic Acids Res

67. Rohs, R. Jin, X. West, S. M. Joshi, R. Honig, B. Mann, R. S., (2010) Origins of Specificity in Protein-DNA Recognition, Annu Rev Biochem

68. Sanchez-Garcia, F. Akavia, U. D. Mozes, E. Pe'er, D., (2010) JISTIC: Identification of Significant Targets in Cancer, BMC Bioinformatics

69. Swapneel Sheth, Nipun Arora, Christian Murphy, Gail Kaiser, (2010) weHelp: A Reference Architecture for Social Recommender Systems, 3rd International Workshop on Social Software Engineering

70. van Batenburg, M. F. Li, H. Polman, J. A. Lachize, S. Datson, N. A. Bussemaker, H. J. Meijer, O. C., (2010) Paired hormone response elements predict caveolin-1 as a glucocorticoid target gene, PLoS One

71. Yang, X. Huang, Y. Crowson, M. Li, J. Maitland, M. L. Lussier, Y. A., (2010) Kinase inhibition-related adverse events predicted from in vitro kinome and clinical trial data, J Biomed Inform

72. Akavia, U. D., O. Litvin, J. Kim, F. Sanchez-Garcia, D. Kotliar, H. C. Causton, P. Pochanard, E. Mozes, L. A. Garraway and D. Pe'er, (2010) An integrated approach to uncover drivers of cancer., Cell

73. Basso, K., M. Saito, P. Sumazin, A. A. Margolin, K. Wang, W. K. Lim, Y. Kitagawa, C. Schneider, M. J. Alvarez, A. Califano R. Dalla-Favera, (2010) Integrated biochemical and computational approach identifies BCL6 direct target genes controlling multiple pathways in normal germinal center B cells, Blood

74. Carro, M. S., W. K. Lim, M. J. Alvarez, R. J. Bollo, X. Zhao, E. Y. Snyder, E. P. Sulman, S. L. Anne, F. Doetsch, H. Colman, A. Lasorella, K. Aldape, A. Califano, A. Iavarone, (2010) The transcriptional network for mesenchymal transformation of brain tumours, Nature

75. Koehnke, J., P. S. Katsamba, G. Ahlsen, F. Bahna, J. Vendome, B. Honig, L. Shapiro, X. Jin, (2010) Splice form dependence of beta-neurexin/neuroligin binding interactions, Neuron

76. Lee, H., Z. Li, A. Silkov, M. Fischer, D. Petrey, B. Honig, D. Murray, (2010) High-throughput computational structure-based characterization of protein families: START domains and implications for structural genomics, J Struct Funct Genomics

77. Lefebvre, C., P. Rajbhandari, M. J. Alvarez, P. Bandaru, W. K. Lim, M. Sato, K. Wang, P. Sumazin, M. Kustagi, B. C. Bisikirska, K. Basso, P. Beltrao, N. Krogan, J. Gautier, R. Dalla-Favera, A. Califano, (2010) A human B-cell interactome identifies MYB and FOXM1 as master regulators of proliferation in germinal centers, Molecular Systems Biology

78. Li, X., C. Panea, C. H. Wiggins, V. Reinke, C. Leslie, (2010) Learning "graph-mer" motifs that predict gene expression trajectories in development, PLoS computational biology

79. Norel, R., D. Petrey, B. Honig, (2010) PUDGE: a flexible, interactive server for protein structure prediction, Nucleic Acids Res

80. West, S. M., R. Rohs, R. S. Mann, B. Honig, (2010) Electrostatic interactions between arginines and the minor groove in the nucleosome, J Biomol Struct Dyn

81. Zhang, Q. C., D. Petrey, R. Norel, B. H. Honig , (2010) Protein interface conservation across structure space, Proc Natl Acad Sci U S A

82. Chen, B. Y., B. Honig, (2010) VASP: a volumetric analysis of surface properties yields insights into protein-ligand binding specificity, PLoS Comput Biol

83. Cheng, L., J. Zhu, W. H. Hui, X. Zhang, B. Honig, Q. Fang, Z. H. Zhou, (2010) Backbone model of an aquareovirus virion by cryo-electron microscopy and bioinformatics, J Mol Biol

84. Mugler, A., A. M. Walczak, C. H. Wiggins , (2010) Information-optimal transcriptional response to oscillatory driving, Physical review letters

85. Love, J., F. Mancia, L. Shapiro, M. Punta, B. Rost, M. Girvin, D. N. Wang, M. Zhou, J. F. Hunt, T. Szyperski, E. Gouaux, R. MacKinnon, A. McDermott, B. Honig, M. Inouye, G. Montelione, W. A. Hendrickson, (2010) The New York Consortium on Membrane Protein Structure (NYCOMPS): a high-throughput platform for structural genomics of integral membrane proteins, J Struct Funct Genomics

86. Singarapu, K. K., J. L. Mills, R. Xiao, T. Acton, M. Punta, M. Fischer, B. Honig, B. Rost, G. T. Montelione, T. Szyperski , (2010) Solution NMR structures of proteins VPA0419 from Vibrio parahaemolyticus and yiiS from Shigella flexneri provide structural coverage for protein domain family PFAM 04175, Proteins

87. Trifonov, V., L. Pascualucci, R. Dalla-Favera, R. Rabadan , (2010) Fractal-like Distributions over the Rational Numbers in High-throughput Biological and Clinical Data, Nature Precedings

88. Van Vlierberghe, P., T. Palomero, H. Khiabanian, J. Van der Meulen, M. Castillo, N. Van Roy, B. De Moerloose, J. Philippe, S. Gonzalez-Garcia, M. L. Toribio, T. Taghon, L. Zuurbier, B. Cauwelier, C. J. Harrison, C. Schwab, M. Pisecker, S. Strehl, A. W. Langerak, J. Gecz, E. Sonneveld, R. Pieters, E. Paietta, J. M. Rowe, P. H. Wiernik, Y. Benoit, J. Soulier, B. Poppe, X. Yao, C. Cordon-Cardo, J. Meijerink, R. Rabadan, F. Speleman, A. Ferrando , (2010) PHF6 mutations in T-cell acute lymphoblastic leukemia, Nature genetics

89. Wu, Y., X. Jin, O. Harrison, L. Shapiro, B. H. Honig, A. Ben-Shaul , (2010) Cooperativity between trans and cis interactions in cadherin-mediated junction formation, Proc Natl Acad Sci U.S.A

90. Zhu, J., L. Cheng, Q. Fang, Z. H. Zhou, B. Honig , (2010) Building and refining protein models within cryo-electron microscopy density maps based on homology modeling and multiscale structure refinement, J Mol Biol

List of Publications in 2009


91. Basso, K. Sumazin, P. Morozov, P. Schneider, C. Maute, R. L. Kitagawa, Y. Mandelbaum, J. Haddad, J., Jr. Chen, C. Z. Califano, A. Dalla-Favera, R., (2009) Identification of the human mature B cell miRNome, Immunity. 30(5):744-52.

92. Chen, B.J., Causton, H.C., Goddard, N.L., Perlstein, E.O., Pe’er, D., (2009) Harnessing gene expression to identify the genetic basis of drug resistance, Mol Syst Biol. 5:310.

93. Compagno, M. Lim, W. K. Grunn, A. Nandula, S. V. Brahmachary, M. Shen, Q. Bertoni, F. Ponzoni, M. Scandurra, M. Califano, A. Bhagat, G. Chadburn, A. Dalla-Favera, R. Pasqualucci, L., (2009) Mutations of multiple genes cause deregulation of NF-kappaB in diffuse large B-cell lymphoma, Nature 459(7247):717-21.

94. Gusev A, Lowe JK, Stoffel M, Daly MJ, Altshuler D, Breslow JL, Friedman JM, Pe'er I., (2009) Whole population, genome-wide mapping of hidden relatedness, Genome Res. 19(2):318-26.

95. Katsamba, P. S., Carroll, K., Ahlsen, G., Bahna, F., Vendome, J., Posy, S., Rajebhosale, M., Price, S., Jessell, T. M., Ben-Shaul, A., Shapiro, L., B. Honig, (2009) Linking molecular affinity and cellular specificity in cadherin-mediated adhesion, Proc Natl Acad Sci U S A. 106(28):11594-9. PMID: 19553217

96. Khan, A. A., Betel, D., Miller, M. L., Sander, C., Leslie, C. S., Marks, D. S., (2009) Transfection of small RNAs globally perturbs gene regulation by endogenous microRNAs, Nat Biotechnol. 27(6):549-55. PMID: 19465925

97. Lee, S. I., Dudley, A. M., Drubin, D., Silver, P. A., Krogan, N. J., Pe'er, D., Koller, D., (2009) Learning a prior on regulatory potential from eQTL data, PLoS Genet. 5(1):e1000358. PMID: 19180192

98. Lim, W. K., Lyashenko, E., Califano, A., (2009) Master regulators used as breast cancer metastasis classifier, Pac Symp Biocomput. 2009:504-15. PMID: 19209726

99. Litvin, O., Causton, H. C., Chen, B. J., Pe'er, D., (2009) Modularity and interactions in the genetics of gene expression, Proc Natl Acad Sci U S A. 106(16):6441-6. PMID: 19223586

100. Liu, J., Ghanim, M., Xue, L., Brown, C. D., Iossifov, I., Angeletti, C., Hua, S., Negre, N., Ludwig, M., Stricker, T., Al-Ahmadie, H. A., Tretiakova, M., Camp, R. L., Perera-Alberto, M., Rimm, D. L., Xu, T., Rzhetsky, A., White, K. P., (2009) Analysis of Drosophila segmentation network identifies a JNK pathway factor overexpressed in kidney cancer, Science 323(5918):1218-22. PMID: 19164706

101. Liu, Y. Sam, L. Li, J. Lussier, Y. A., (2009) Robust methods for accurate diagnosis using pan-microbiological oligonucleotide microarrays, BMC Bioinformatics 10(Suppl 2):S11. PMID: 19208186

102. Lowe, J. K. Maller, J. B. Pe'er, I. Neale, B. M. Salit, J. Kenny, E. E. Shea, J. L. Burkhardt, R. Smith, J. G. Ji, W. Noel, M. Foo, J. N. Blundell, M. L. Skilling, V. Garcia, L. Sullivan, M. L. Lee, H. E. Labek, A. Ferdowsian, H. Auerbach, S. B. Lifton, R. P. Newton-Cheh, C. Breslow, J. L. Stoffel, M. Daly, M. J. Altshuler, D. M. Friedman, J. M., (2009) Genome-wide association studies in an isolated founder population from the Pacific Island of Kosrae, PLoS Genet. 5(2):e1000365. PMID: 19197348

103. Lussier, Y.A., Lee, Y., Radivojac, P., Ofran, Y., Butte, A., Kann, M. , (2009) Molecular Bioinformatics for Disease - Session Introduction, Pacific Symposium on Biocomputing

104. Melvin, I., Weston, J., Leslie, C., Noble, W. S., (2009) RANKPROP: a web server for protein remote homology detection, Bioinformatics 25(1):121-2. PMID: 18990723

105. Meyer, N. J. Huang, Y. Singleton, P. A. Sammani, S. Moitra, J. Evenoski, C. L. Husain, A. N. Mitra, S. Moreno-Vinasco, L. Jacobson, J. R. Lussier, Y. A. Garcia, J. G., (2009) GADD45a is a novel candidate gene in inflammatory lung injury via influences on Akt signaling, FASEB J. 23(5):1325-37. PMID: 19124556

106. Murphy, C., G. Kaiser, I. Vo, M. Chu , (2009) Quality Assurance of Software Applications Using the In Vivo Testing Approach., 2nd IEEE International Conference on Software Testing, Verification and Validation

107. Murphy, C., G. Kaiser, K. Loveland, S. Hasan, (2009) Retina: Helping Students and Instructors Based on Observed Programming Activities., 40th ACM Technical Symposium on Computer Science Education

108. Nimrod, G., Szilagyi, A., Leslie, C., Ben-Tal, N., (2009) Identification of DNA-binding proteins using structural, electrostatic and evolutionary features, J Mol Biol. 387(4):1040-53. PMID: 19233205

109. Prabhu, S., Pe'er, I., (2009) Overlapping pools for high-throughput targeted resequencing, Genome Res. 19(7):1254-61. PMID: 19447964

110. Raj, A., Wiggins, C. H., (2009) An information-theoretic derivation of min-cut based clustering., IEEE Transactions on Information Theory

111. Sachs, K., Itani, S., Carlisle, J., Nolan, G. P., Pe'er, D., Lauffenburger, D. A., (2009) Learning signaling network structures with sparsely distributed data, J Comput Biol. 16(2):201-12. PMID: 19193145

112. Sam, L. T. Mendonca, E. A. Li, J. Blake, J. Friedman, C. Lussier, Y. A., (2009) PhenoGO: an integrated resource for the multiscale mining of clinical and biological data, BMC Bioinformatics. 10 Suppl 2:S8. PMID: 19208196

113. Sethumadhavan, S., Kaiser, G.E., (2009) COMPASS: A Community-Drive Parallelization Advisor for Sequential Software., 2nd International Workshop on Multicore Software Engineering

114. Walczak, A. M., Mugler, A., Wiggins, C. H, (2009) A stochastic spectral analysis of transcriptional regulatory cascades, Proc Natl Acad Sci U S A. 106(16):6529-34. PMID: 19351901

115. Waltz, D., Buchanan, B. G., (2009) Computer science. Automating science, Science. 324(5923):43-4. PMID: 19342574

116. Wang, K. Alvarez, M. J. Bisikirska, B. C. Linding, R. Basso, K. Dalla Favera, R. Califano, A., (2009) Dissecting the interface between signaling and transcriptional regulation in human B cells, Pac Symp Biocomput. 2009:264-75. PMID: 19209707

117. Wang K, Saito M, Bisikirska BC, Alvarez MJ, Lim WK, Rajbhandari P, Shen Q, Nemenman I, Basso K, Margolin AA, Klein U, Dalla-Favera R, Califano A., (2009) Genome-wide identification of post-translational modulators of transcription factor activity in human B cells., Nat Biotechnol. 27(9):829-39. PMID: 19741643

118. Zhao X, D' Arca D, Lim WK, Brahmachary M, Carro MS, Ludwig T, Cardo CC, Guillemot F, Aldape K, Califano A, Iavarone A, Lasorella A., (2009) The N-Myc-DLL3 Cascade Is Suppressed by the Ubiquitin Ligase Huwe1 to Inhibit Proliferation and Promote Neurogenesis in the Developing Brain., Dev Cell. 17(2):210-21. PMID: 19686682

119. Rohs R, West SM, Liu P, Honig B., (2009) Nuance in the double-helix and its role in protein-DNA recognition., Curr Opin Struct Biol. 19(2):171-7. PMID: 19362815

120. Petrey D, Honig B., (2009) Is protein classification necessary? Toward alternative approaches to function annotation., Curr Opin Struct Biol. 19(3):363-8. PMID: 19269161

121. Saito M, Novak U, Piovan E, Basso K, Sumazin P, Schneider C, Crespo M, Shen Q, Bhagat G, Califano A, Chadburn A, Pasqualucci L, Dalla-Favera R., (2009) BCL6 suppression of BCL2 via Miz1 and its disruption in diffuse large B cell lymphoma., Proc Natl Acad Sci U S A. 106(27):11294-9. PMID: 19549844

122. Alvarez, M. J., Sumazin, P., Rajbhandari, P., Califano, A., (2009) Correlating measurements across samples improves accuracy of large-scale expression profile experiments, Genome Biol

List of Publications in 2008


123. Murphy, C., Kim, E., Kaiser, G., Cannon, A., (2008) Backstop: Debugging Tools for Novice Java Programmers, 39th ACM SIGCSE Technical Symposium on Computer Science Education, March 2008

124. Jabado, O. J., Liu, Y., Conlan, S., Quan, P. L., Hegyi, H., Lussier, Y., Briese, T., Palacios, G., Lipkin, W. I. , (2008) Comprehensive viral oligonucleotide probe design using conserved protein regions., Nucleic Acids Res 36(1): e3. PMID: 18079152

125. Koehnke, J., Jin, X., Budreck, E.C., Posy, S., Scheiffele, P., Honig, B., Shapiro, L., (2008) Crystal structure of the extracellular cholinesterase-like domain from neuroligin-2, Proc Natl Acad Sci U S A 105(6): 1873-8. PMID: 18250328

126. Koehnke, J., Jin, X., Trbovic, N., Katsamba, P. S., Brasch, J., Ahlsen, G., Scheiffele, P., Honig, B., Palmer, A.G., Shapiro, L. , (2008) Crystal structures of beta-neurexin 1 and beta-neurexin 2 ectodomains and dynamics of splice insertion sequence 4, Structure 16(3): 410-21. PMID: 18334216

127. Murphy, C., Phung, D., Kaiser, G. , (2008) A Distance Learning Approach to Teaching eXtreme Programming, 13th ACM Annual Conference on Innovation and Technology in Computer Science Education, June

128. Chu, M., Murphy, C., Kaiser, G. , (2008) Distributed In Vivo Testing of Software Applications, 1st IEEE International Conference on Software Testing, Verification, and Validation

129. Pe'er I, Yelensky R, Altshuler D, Daly MJ., (2008) Estimation of the multiple testing burden for genomewide association studies of nearly all common variants, Genet Epidemiol 32(4): 381-5. PMID: 18348202

130. Iossifov, I., Zheng, T., Baron, M., Gilliam, T.C., Rzhetsky, A., (2008) Genetic-linkage mapping of complex hereditary disorders to a whole-genome molecular-interaction network, Genome Res. 2008 Jul;18(7):1150-62. PMID: 18417725

131. Moreno-Vinasco, L., Gomberg-Maitland, M., Maitland, M.L., Desai, A.A., Singleton, P.A., Sammani, S., Sam, L., Liu, Y., Husain, A.N., Lang, R.M., Ratain, M.J., Lussier, Y.A., and Garcia, J., (2008) Genomic Assessment of a Multi-Kinase Inhibitor, Sorafenib, in a Rodent Model of Pulmonary Hypertension, Physiol Genomics. 33(2):278-91. PMID: 18303084.

132. de Wit, E., Braunschweig, U., Greil, F., Bussemaker, H.J., van Steensel, B. , (2008) Global chromatin domain organization of the Drosophila genome, PLoS Genet 4(3): e1000045

133. Hung, C., Madduri, R., Keshav, K., Oster, S., Langella, S., Martin, S., Mock, S., (2008) Integrating caGrid and TeraGrid, TeraGrid Conference Proceedings, TeraGrid Conference Proceedings, 2008

134. Lussier, Y. A., Lee,Y., Radivojac, P., Ofran, Y., Punta, M., Butte, A., Kann, M., (2008) Molecular Bioinformatics for Disease: Protein Interactions and and Phenomics, Pacific Symposium on Biocomputing 13: 228-230

135. Stoyanovich, J., Pe’er, I., (2008) MutaGeneSys: estimating individual disease susceptibility based on genome-wide SNP array data, Bioinformatics. 24(3):440-2. PMID: 18048395

136. Feldman, I., Rzhetsky, A., Vitkup, D., (2008) Network properties of genes harboring inherited disease mutations, Proc Natl Acad Sci U S A 105(11): 4323-8

137. Christian, S. L., C. W. Brune, et al., (2008) Novel submicroscopic chromosomal abnormalities detected in autism spectrum disorder, Biol Psychiatry 63(12): 1111-7

138. Yao, L., Rzhetsky, A., (2008) Quantitative systems-level determinants of human genes targeted by successful drugs, Genome Res 18(2): 206-13. PMID: 18083776

139. Kumar RA, KaraMohamed S, Sudi J, Conrad DF, Brune C, Badner JA, Gilliam TC, Nowak NJ, Cook EH Jr, Dobyns WB, Christian SL., (2008) Recurrent 16p11.2 microdeletions in autism, Hum Mol Genet 17(4): 628-38. PMID: 18156158

140. Ross, K. A., Stoyanovich, J., (2008) Schema Polynomials and Applications, International Conference on Extending Database Technology

141. Posy, S., Shapiro, L., Honig, B. , (2008) Sequence and structural determinants of strand swapping in cadherin domains: do all cadherins bind through the same adhesive interface?, J Mol Biol 378(4): 952-66. PMID: 18395225

142. Rodriguez-Esteban, R., Rzhetsky, A., (2008) Six senses in the literature. The bleak sensory landscape of biomedical texts, EMBO Rep 9(3): 212-5. PMID: 18311168

143. Mani, K. M., Lefebvre, C., Wang, K., Lim, W.K., Basso, K., Dalla-Favera, R., Califano, A., (2008) A systems biology approach to prediction of oncogenes and molecular perturbation targets in B-cell lymphomas, Mol Syst Biol 4:169. PMID: 18277385

144. Piccaluga PP, Califano A, Klein U, Agostinelli C, Bellosillo B, Gimeno E, Serrano S, Solè F, Zang Y, Falini B, Zinzani PL, Pileri SA., (2008) Gene expression analysis provides a potential rationale for revising the histological grading of follicular lymphomas, Haematologica. 93(7):1033-8. PMID: 18492688

145. Dinov ID, Rubin D, Lorensen W, Dugan J, Ma J, Murphy S, Kirschner B, Bug W, Sherman M, Floratos A, Kennedy D, Jagadish HV, Schmidt J, Athey B, Califano A, Musen M, Altman R, Kikinis R, Kohane I, Delp S, Parker DS, Toga AW., (2008) iTools: A Framework for Classification, Categorization and Integration of Computational Biology Resources, PLoS One, 3(5): p. e2265

146. Cadeiras M, Bayern M, Burke E, Dedrick R, Gangadin A, Latif F, Shazad K, Sinha A, Tabak EG, Marboe CC, Califano A, and Deng MC, (2008) Gene expression profiles of patients with antibody-mediated rejection after cardiac transplantation, J Heart Lung Transplant. Aug;27(8):932-4.

147. Amer-Yahia, S., M. Benedikt, Lakshmanan, L., J. Stoyanovich , (2008) Efficient Network-Aware Search in Collaborative Tagging Sites., Proceedings of the VLDB Conference

148. Boorsma, A., Lu, X.-J., Zakrzewska, A., Snyder, B., Klis, F.M., Bussemaker, H.J., (2008) Inferring condition-specific modulation of transcription factor activity through regulon-based analysis of genomewide expression., PLoS One. 3(9):e3112.

149. Hong, S.B. Huang, Y. Moreno-Vinasco, L. Sammani, S. Moitra, J. Barnard, J. W. Ma, S. F. Mirzapoiazova, T. Evenoski, C. Reeves, R. R. Chiang, E. T. Lang, G. D. Husain, A. N. Dudek, S. M. Jacobson, J. R. Ye, S. Q. Lussier, Y. A. Garcia, J. G., (2008) Essential role of pre-B-cell colony enhancing factor in ventilator-induced lung injury, Am J Respir Crit Care Med. 178(6):605-17. PMID: 18658108

150. Kundaje, A. Xin, X. Lan, C. Lianoglou, S. Zhou, M. Zhang, L. Leslie, C., (2008) A predictive model of the oxygen and heme regulatory network in yeast, PLoS Comput Biol. 4(11):e1000224. PMID: 19008939

151. Melvin, I., Weston, J., Leslie, C. S., Noble, W. S., (2008) Combining classifiers for improved classification of proteins from sequence or structure, BMC Bioinformatics 9:389. PMID: 18808707

152. Murphy, C., S. Sheth, G. Kaiser and L. Wilcox , (2008) genSpace: Exploring Social Networking Metaphors for Knowledge Sharing and Scientific Collaborative Work., 1st International Workshop on Social Software Engineering and Applications

153. Murphy, C., G. Kaiser, L. Hu and L. Wu, (2008) Properties of Machine Learning Applications for Use in Metamorphic Testing., 20th International Conference on Software Engineering and Knowledge Engineering

154. Murphy, C., K. Shen, G. Kaiser, (2008) Using JML Runtime Assertion Checking to Perform Metamorphic Testing in Applications without Test Oracles., 2nd IEEE International Conference on Software Testing, Verification and Validation

155. Murphy, C., Shen, K., Kaiser, G.E. , (2008) Automatic System Testing of Programs without Test Oracles, International Symposium on Testing and Analysis

156. Rzhetsky, A., Seringhaus, M., Gerstein, M., (2008) Seeking a new biology through text mining, Cell. 134(1):9-13. PMID: 18614002

157. Sarin, S., Prabhu, S., O'Meara, M. M., Pe'er, I., Hobert, O., (2008) Caenorhabditis elegans mutant allele identification by whole-genome sequencing, Nat Methods. 5(10):865-7. PMID: 18677319

158. Shatkay, H., Pan, F., Rzhetsky, A., Wilbur, W. J., (2008) Multi-dimensional classification of biomedical text: toward automated, practical provision of high-utility text to diverse users, Bioinformatics. 24(18):2086-93. PMID: 18718948

159. Shen, Y., Sarin, S., Liu, Y., Hobert, O., Pe'er, I., (2008) Comparing platforms for C. elegans mutant identification using high-throughput whole-genome sequencing, PLoS One. 3(12):e4012. PMID: 19107202

160. Stoyanovich, J., Yahia, S. A., Marlow, C., Yu, C., (2008) Leveraging Tagging to Model User Interests in del.icio.us., Proceeding of the AAAI Spring Symposium on Social Information Processing

161. Wang, T., Moreno-Vinasco, L., Huang, Y., Lang, G.D., Linares, J.D., Goonewardena, S.N., Grabavoy, A., Samet, J.M., Geyh, A.S., Breysse, P.N., Lussier, Y.A., Natarajan, V., Garcia, J.G.N., (2008) Murine Lung Responses to Ambient Baltimore Particulate Matter: Genomic Analysis and Contribution to Airway Hyperresponsiveness., Environ Health Perspect. 116(11):1500-8. PMID: 19057703

162. Ward, L.D., Bussemaker, H.J., (2008) Predicting functional transcription factor binding through alignment-free, affinity-based analysis of orthologous promoter sequences, Bioinformatics 24(13):i165-71. PMID: 18586710

List of Publications in 2007


163. Anastassiou D, Liu H, Varadan V, (2007) Variable Window Binding for Mutually Exclusive Alternative Splicing, Genome Biology, Vol. 7, Issue 1, pp. R2.1-R2.12.

164. Fan H, Mark A E, Zhu J, Honig B, (2007) Comparative Study of Generalized Born Models: Protein Dynamics, PNAS 102:6760-6764

165. Anastassiou, D, (2007) Computational Analysis of the Synergy Among Multiple Interacting Genes, (Review Article), Molecular Systems Biology, Vol. 3, No. 83, February 2007

166. Autism Genome Project Consortium et al., (2007) Mapping autism risk loci using genetic linkage and chromosomal rearrangements, Nat. Genet. 39(3): 319-328

167. Bussemaker, H.J., Foat, B.C., Ward, L.D., (2007) Predictive Modeling of Genome-Wide mRNA Expression: From Modules to Molecules, Annual Reviews in Biophysics and Biomolecular Structure. 36: 329-347. PMID: 17311525

168. Chen, J.L., Liu, Y., Sam, L.T., Li, J., Lussier, Y.A., (2007) High-throughput functional classification of human disease genes, BMC Bioinformatics 8(Suppl 3) (S7 ): doi:10.1186/1471-2105-8-S3-S7 PMID: 17493290

169. Cokol, M., Iossifov, I., Rodriguez-Esteban, R., Rzhetsky, A, (2007) How many scientific papers should be retracted?, EMBO Rep 8(5), 422-423. PMID: 17471252

170. Greil, F., de Wit, E., Bussemaker, H.J., van Steensel, B, (2007) HP1 controls genomic targeting of four novel heterochromatin proteins in Drosophila, EMBO J. 26:741-51. PMID: 17255947

171. Lussier, Y. A. and Y. Liu, (2007) Computational approaches to phenotyping: high-throughput phenomics, Proc Am Thorac Soc 4(1): 18-25 PMID: 17202287

172. Pantazatosa, S. P., J. Li, et al. , (2007) Cross-Scale Mapping of Gene Expression to Neuroimaging Datasets via Semantic Decomposition, MEDINFO

173. Phung D., Valetto G., Kaiser G.E., Liu T., Kender J.R., (2007) Adaptive Synchronization of Semantically Compressed Instructional Videos for Collaborative Distance Learning, International Journal of Distance Education Technologies, Idea Group Publishing, 5(2):56-73, 2007

174. Ross, K. A., A. Janevski, J. Stoyanovich, (2007) A Faceted Query Engine Applied to Archaeology, Internet Archeology 21, April 2007

175. Sam, L., Y. Liu, et al., (2007) Discovery of Protein Interaction Networks Shared by Diseases, Pacific Symposium on Biocomputing(12): 76-87

176. Sebat, J., B. Lakshumi, D. Malhotra, C. Lese-Martin, J. Troge, T. Walsh, B. Yamrom, S. Yoon, A. Krasnitz, J. Kendall, A. Leotta, D. Pai, R. Zhang, J.Hicks, S.J. Spence, A. Lee, K. Puura, T. Lehtimaki, D. Ledbetter, P.K. Gregersen, J. Bregman, J.S. Sutcliffe, V. Jobanputra, D. Warburton, M-K. King, D. Skuse, D.H. Geschwind, T. C. Gilliam, K. Ye, and M. Wigler, (2007) Strong association of de novo copy number mutations with autism, Science 316(5823):445-9. PMID: 17363630

177. Sosinsky, A., Honig, B., Mann, R.S., Califano, A., (2007) Discovering transcriptional regulatory regions in Drosophila by a non-alignment method for phylogenetic footprinting, Proc Natl Acad Sci USA. 104:6305-10. PMID: 17395715

178. Murphy, C., Kaiser, G., Arias, M. , (2007) An Approach to Software Testing of Machine Learning Applications., 19th International Conference on Software Engineering and Knowledge Engineering, July 2007

179. Lim, W., Califano, A., (2007) Assembling a compendium of druggable apoptosis regulators, in Proc. Of the 4th Annual RECOMB Satellite on Regulatory Genomics, Boston MA.

180. Lussier, Y., Bodenreider, O., (2007) Clinical Ontologies for Discovery Applications, Knowledge Discovery in the Life Sciences. Springer Verlag 2007(XXII): 450 p.

181. Zhang, L., Leslie, C., Lee, H.C., Kundaje, A., Ie, E., Xin, X., Freund, Y. , (2007) CP motifs, Hap1 and Heme Signaling, International Proceedings of the 15th International Conference on Cytochrome P450: Biochemistry, Biophysics, Functional Genomics: 45-51.

182. Tao, Y., Sam, L., Li, J., Friedman, C., Lussier, Y.A., (2007) Information Theory Applied to the Sparse Geneontology Annotation Network to Predict Novel Gene Function,  Bioinformatics 23: i529–i538. PMID: 17646340

183. Kundaje, A., Lianoglou, S., Li, X., Quigley, D., Arias, M., Wiggins, C., Zhang, L., Leslie, C. , (2007) Learning regulatory programs that accurately predict differential expression with MEDUSA, Annals of the New York Academy of Sciences 2007, 1115:178-202. PMID: 17934055

184. Melvin, I., Ie, E., Weston, J., Noble, W. S., Leslie, C., (2007) Multi-class protein classification using adaptive codes, Journal of Machine Learning Research 8: 1557-1581

185. Murphy, C., Kaiser, G., Arias, M., (2007) Parameterizing Random Test Data According to Equivalence Classes, 2nd ACM International Workshop on Random Testing, November 2007

186. Tao, Y., Patel, C., Friedman, C., Lussier, Y.A., (2007) PIE: A Phenotype Interface Engine for Automated Representation in PATO and “Semantic Web”-Based Exchange of Clinical Data and Narratives, AMIA Annual Symposium Proceedings, 2007

187. Rzhetsky, A., D. Wajngurt, et al., (2007) Probing genetic overlap among complex human phenotypes, Proc Natl Acad Sci U S A 104(28): 11694-9. PMID: 17609372

188. Griffith, R., Virmani, R., Kaiser, G., (2007) RAS Models: A Building Block for Self-Healing Benchmarks, 8th International Workshop on Performability Modeling of Computer and Communication Systems, September

189. Cokol, M., Rodriguez-Esteban, R., Rzhetsky, A., (2007) A recipe for high impact, Genome Biology 8(5): 406

190. Griffith, R., Virmani, R., Kaiser, G., (2007) The Role of Reliability, Availability and Serviceability (RAS) Models in the Design and Evaluation of Self-Healing Systems, 3rd International Conference on Self-Organization and Autonomous Systems in Computing and Communications, September

191. Stoyanovich, J., Bedathur, S., Berberich, K., Weikum, G., (2007) Semantically Enriched Graph-Based Authority Propagation, Proceedings of the Tenth International Workshop on the Web and Databases

192. Melvin, I., Ie, E., Kuang, R., Weston, J., Noble, W. S., Leslie, C., (2007) SVM-Fold: a tool for discriminative multi-class protein fold and superfamily recognition, BMC Bioinformatics 8 Suppl 4:S2. PMID: 17570145

193. Margolin, A. A. and A. Califano, (2007) Theory and limitations of genetic network inference from microarray data, Ann N Y Acad Sci 1115: 51-72. PMID: 17925348

194. Bales, M. E., Lussier, Y.A., Johnson, S.B., (2007) Topological Analysis of Large-scale Biomedical Terminology Structures, Journal of the American Medical Informatics Association 14(6): 788-797

195. Joshi, R. Passner, J. M. Rohs, R. Jain, R. Sosinsky, A. Crickmore, M. A. Jacob, V. Aggarwal, A. K. Honig, B. Mann, R. S., (2007) Functional specificity of a Hox protein mediated by the recognition of minor groove structure, Cell. 2007 131(3):530-43. PMID: 17981120

196. Lefebvre, C., Lim, W.K., Basso, K., Dalla Favera, R., Califano, A., (2007) A context-specific network of protein-DNA and protein-protein interactions reveals new regulatory motifs in human B cells., Lecture Notes in Bioinformatics

List of Publications in 2006


197. Lussier YA, Rappaport D, Borlawsky T, Friedman C, (2006) PhenoGO: assigning phenotypic context to gene ontology annotations with natural language processing, Pacific Symposium on Biocomputing, pp. 64-75. PMID: 17094228

198. Bussemaker, H, (2006) Modeling gene expression control using Omes Law, Molecular Systems Biology 2:2006.0013

199. Dobereiner H-G, Dubin-Thaler BJ, Hofman J, Xenias HS, Sims, TN, Giannone G, Dustin ML, Wiggins CH, Sheetz, MP., (2006) Lateral Membrane Waves Constitute a Universal Dynamic Pattern of Motile Cells, Phys Rev Lett. 97(3):038102.

200. Foat BC, Morozov AV, Bussemaker HJ., (2006) Statistical mechanical modeling of genome-wide transcription factor occupancy data by MatrixREDUCE, Bioinformatics 22(14):e141-9.

201. Friedman C, Borlawsky T, Shagina L, Xing HR, Lussier YA., (2006) Bio-Ontology and text: bridging the modeling gap, Bioinformatics 22(19): 2421-9

202. Goh CS, Gianoulis TA, Liu Y, Li J, Paccanaro A, Lussier YA, Gerstein M., (2006) Integration of curated databases to identify genotype-phenotype associations, BMC Genomics 7: 257

203. Griffith R., Kaiser G, (2006) A Runtime Adaptation Framework for Native C and Byt code Applications, Proceedings of 3rd IEEE International Conference on Autonomic Computing, 2006

204. Griffith R., Hellerstein J.L., Kaiser G., Diao Y, (2006) Dynamic Adaptation of Temporal Event Correlation for QoS Management in Distributed Systems, Proceedings of 14th IEEE International Workshop on Quality of Service, 2006

205. Griffith R., Valetto G., Kaiser G, (2006) Effecting Runtime Reconfiguration in Managed Execution Environments, In Parishar M., Hariri S. (eds.), Autonomic Computing: Concepts, Infrastructure, and Applications, ch. 18, CRC, 2006

206. Gross P., Kaiser G, (2006) Automated Component Interconnection for Scaling Scale-Resistant Services, Proceedings of 21st IEEE/ACM International Conference on Automated Software Engineering, 2006

207. Gupta S., Becker H., Kaiser G., Stolfo S, (2006) Verifying Genre-based Clustering Approach to Content Extraction, Proceedings of 15th World Wide Web Conference, 2006

208. Halasz, G., van Batenburg, M.F., Perusse, J., Hua, S., White, K.P., Bussemaker, H.J., (2006) Detecting Transcriptionally Active Regions Using Genomic Tiling Arrays, Genome Biology 7:R59.1-10. PMID: 16859498

209. Koster, D.A., C.H. Wiggins, and N.H. Dekker, (2006) Multiple events on single molecules: unbiased estimation in single-molecule biophysics, Proc Natl Acad Sci U S A, 103(6): p. 1750-5. PMID: 16439482

210. Kundaje A, Middendorf M, Shah M, Wiggins CH, Freund Y, Leslie C., (2006) A classification-based framework for predicting and analyzing gene regulatory response, BMC Bioinformatics (Special issue on "New Problems and Methods in Computational Biology") 7(Supp 1)(S5). PMID: 16723008

211. Liu Y, Li J, Sam L, Goh CS, Gerstein M, Lussier YA., (2006) An integrative genomic approach to uncover molecular mechanisms of prokaryotic traits, PLoS Comput Biol 2(11): e159. PMID: 17112314

212. Margolin AA, Nemenman I, Basso K, Wiggins C, Stolovitzky G, Dalla Favera R and Califano A, (2006) ARACNE: An Algorithm for the Reconstruction of Gene Regulatory Networks in a Mammalian Cellular Context, BMC Bioinformatics, 2006. 7(Supplement 1)(S7). PMID: 16723010

213. Margolin AA, Wang K, Lim WK, Kustagi M, Nemenman I, Califano A, (2006) Reverse Engineering Cellular Networks, Nat Protoc.1(2):662-71. PMID: 17406294

214. Moorman, C., Sun, L.V., Wang, J., de Wit, E. Talhout, W., Ward, L.D., Greil, F., White, K.P.*, Bussemaker, H.J.*, van Steensel, B., (2006) Hotspots of transcription factor colocalization in the genome of Drosophila melanogaster, Proc. Natl. Acad. Sci. U S A., 103(32):12027-32. PMID: 16880385. [Joint last authorship; highlighted in Nature; listed as "must read paper" on Faculty of 1000]

215. Ofran, Y., Yachdav, G., Mozes, E., Soong, T., Rost, B., (2006) Create and assess protein networks through molecular characteristics of individual proteins, Bioinformatics (ISMB Proceedings), 22: e402-e407. PMID: 16873500

216. Palomero T., Lim, W.K., Odom, D.T., Sulis, M.L., Real, P.J., Margolin, A., Barnes, K.C., O'Neil, J., Neuberg, D., Weng, A.P., Aster, J.C., Sigaux, F. Soulier, J., Look, A.T., Young, R.A., Califano, A., Ferrando, A.A. , (2006) NOTCH1 directly regulates c-MYC and activates a feed-forward-loop transcriptional network promoting leukemic cell growth, Proc. Natl. Acad. Sci USA; 103:18261-18266. PMID: 17114293

217. parekh J., Kaiser G., Gross P., Valetto G., (2006) Retrofitting Autonomic Capabilities onto Legacy Systems, Journal of Cluster Computing, Kluwer, 9(2):141-159, 2006

218. Rodrigues-Esteban, R., Iossifov, I., Rzhetsky, A., (2006) Imitating manual curation of text-mined facts in biomedicine, PLoS Comput Biol. 2(9):e118. PMID: 16965176

219. Ross, K.A., (2006) Alpha Radiation is a Major Germ-Line Mutagen over Evolutionary Timescales, Evolutionary Ecology Research, 8(6), 2006, 1013-1028

220. Rzhetsky, A., Zheng, T., Weinreb, C. , (2006) Self-correcting maps of molecular pathways, PLoS ONE 1, e61. PMID: 17183692

221. Rzhetsky, A., Iossifov, I., Loh, J. M., White, K. P. , (2006) Microparadigms: chains of collective reasoning in publications about molecular interactions, Proc Natl Acad Sci U S A 103, 4940-4945. PMID: 16543380

222. Varadan V., Miller D. III, and Anastassiou D., (2006) Computational Inference of the Molecular Logic for Synaptic Connectivity in C. elegans, Bioinformatics, Vol. 22, Issue 14 – ISMB 2006, pp. e497-e506, July 2006. PMID: 16873513

223. Wang, K., I. Nemenman, N. Banerjee, A. A. Margolin and A. Califano, (2006) Genome-wide Discovery of Modulators of Transcriptional Interactions in Human B Lymphocytes, Proceedings of RECOMB, 2006

224. Wang, K., I. Nemenman, N. Banerjee, A. A. Margolin and A. Califano, (2006) MINDY: An Algorithm for the Genome-wide Discovery of Modulators of Transcriptional Interactions, Journal of Computational Biology, submitted, 2006

225. Weston J, K.R., Leslie C, Noble WS, (2006) Ranking by Semi-Supervised Network Propagation, BMCBioinformatics (Special issue on "New Problems and Methods in Computational Biology"). 2006. 7(Supp 1)(S10). PMID: 16723003

226. Wilbur, W. J., Rzhetsky, A., Shatkay, H. , (2006) New directions in biomedical text annotation: definitions, guidelines and corpus construction, BMC Bioinformatics 7, 356. PMID: 16867190

List of Publications in 2005


227. Boorsma A, Foat BC, Vis D, Klis F, Bussemaker HJ, (2005) T-profiler: scoring the activity of predefined groups of genes using gene expression data, Nucleic Acids Res. 2005 Jul 1;33(Web Server issue):W592-5

228. Cantor MN, Sarkar IN, Bodenreider O, Lussier YA, (2005) Genestrace: Phenomic Knowledge Discovery Via Structured Terminology, Pac Symp Biocomput.;103-14

229. Cavelier G, Anastassiou D, (2005) Phenotype Analysis Using Network Motifs Derived from Changes in Regulatory Network Dynamics, Proteins, Vol. 60, Issue 3, pp. 525-546

230. Chen CP, Posy S, Ben-Shaul A, Shapiro L, Honig B, (2005) Specificity of Cell-Cell Adhesion by Classical Cadherins: Critical Role for Low-Affinity Dimerization Through ß-strand Swapping, PNAS. 102:8531-8536

231. Ie E, Weston J, Noble WS and Leslie C, (2005) Adaptive codes for multi-class protein classification, Proceedings of the International Conference on Machine Learning , August 7-11, 2005, Bonn, Germany

232. Lussier YA, (2005) Ontologies and Natural Language Processing, Russ Altman, Shankar Subramaniam. Volume 4: Bioinformatics. Encyclopedia of Genetics, Genomics, Proteomics and Bioinformatics, John Wiley & Sons (in press)

233. Middendorf M, Kundaje A, Freund Y, Wiggins C, Leslie C, (2005) Motif discovery through predictive modeling of gene regulation, Proceedings of the Ninth Annual International Conference on Research in Computational Molecular Biology (RECOMB 2005) S. Miyano et al. (Eds.): RECOMB 2005, LNBI 3500, pp. 538–552, 2005. Springer-Verlag Berlin Heidelberg 2005

234. Nair R, Rost B, (2005) Mimicking cellular sorting improves prediction of subcellular localization, J Mol Biol 348, 85-100

235. Punta M, Rost B, (2005) PROFcon: novel prediction of long-range contacts, Bioinformatics. 21(13):2960-8. PMID: 15890748

236. Siggers T, Silkov A, Honig B, (2005) Structural Alignment of Protein- DNA Interfaces: Insights into the Determinants of Binding Specificity, J Mol Biol. 345(5):1027-45.

237. Tao Y, Friedman C, Lussier YA, (2005) Visualizing information across multidimensional post-genomic structured and textual databases, Bioinformatics ;21(8):1659-67. Epub 2004 Dec 14

238. Wang X, Anastassiou D, Guo D, (2005) Statistical Inference of Transcriptional Regulatory Networks, Genomic Signal Processing and Statistics, E. Dougherty et al. (Ed.), Hindawi Pub., New York

239. Alarcon, M., A.L. Yonan, T.C. Gilliam, R.M. Cantor, and D.H. Geschwind, (2005) Quantitative genome scan and Ordered-Subsets Analysis of autism endophenotypes support language QTLs, Mol Psychiatry, 2005. 10(8): p. 747-57

240. Basso, K., A.A. Margolin, G. Stolovitzky, U. Klein, R. Dalla-Favera, and A. Califano, (2005) Reverse engineering of regulatory networks in human B cells, Nat Genet, 2005. 37(4): p. 382-90

241. Kuang, R., J. Weston, W.S. Noble, and C. Leslie, (2005) Motif-based protein ranking by network propagation, Bioinformatics, 2005. 21(19): p. 3711-8. PMID: 16076885

242. Noble, W.S., R. Kuang, C. Leslie, and J. Weston, (2005) Identifying remote protein homologs by network propagation, Febs J, 2005. 272(20): p. 5119-28. PMID: 16218946

243. Weston J, Leslie C., E Ie, D Zhou, A Elisseeff, WS Noble, (2005) Semi-Supervised Protein Classification using Cluster Kernels, Book Chapter for "Semi-Supervised Learning (Editors: O. Chapelle, B. Scholkopf and A. Zien), in press, 2006. Bioinformatics. 2005 Aug 1;21(15):3241-7. Epub 2005 May 19.

List of Publications in 2004


244. Gao F, Foat BC, Bussemaker HJ, (2004) Defining transcriptional networks through integrative modeling of mRNA expression and transcription factor binding data, BMC Bioinformatics. 2004 Mar 18;5:31

245. Liu J, Rost B, (2004) CHOP proteins into structural domain-like fragments, Proteins 55, 678-688

246. Lussier YA, Li J, (2004) Terminological Mapping For High Throughput Comparative Biology of Phenotypes, Pac Symp Biocomput;:202-13

247. Middendorf M, Kundaje A, Wiggins C, Freund Y, Leslie C, (2004) Predicting genetic regulatory response using classification, Proceedings of the Twelfth International Conference on Intelligent Systems in Molecular Biology (ISMB 2004)

248. Nair R, Rost B, (2004) LOCnet and LOCtarget: Sub-cellular localization for structural genomics targets, Nucl Acids Res 32 (Web server issue) , W517-W521

249. Rost B, Yachdav G, Liu J, (2004) The PredictProtein server, Nucl Acids Res , 32 (Web server issue) , W321-W326

250. Stolc V, Gauhar Z, Mason C, Halasz G, van Batenburg MF, Rifkin SA, Hua S, Herreman T, Tongprasit W, Barbano PE, Bussemaker HJ, White KP, (2004) A gene expression map for the euchromatic genome of Drosophila melanogaster, Science. 2004 Oct 22;306(5696):655-60

251. Sussillo D, Kundaje A, and Anastassiou D, (2004) Spectrogram Analysis of Genomes, EURASIP Journal on Applied Signal Processing, special issue on Genomic Signal Processing, Vol. 2004, No. 1, pp. 29-42

252. Weston J, Eliseeff A, Zhou D, Leslie C, Noble WS, (2004) Protein ranking: from local to global structure in the protein similarity network, Proceedings of the National Academy of Science . 101(17):6559-6563. PMID: 15087500

List of Publications in 2003


253. Klein U, Tu Y, Stolovitzky GA, Keller JL, Haddad J Jr, Miljkovic V, Cattoretti G, Califano A, Dalla-Favera R, (2003) Gene expression dynamics during B cell germinal center reaction, Proc Natl Acad Sci U S A;100(5):2639-44. PMID: 12727636

254. Liu AH, Zhang X, Stolovitzky GA , Califano A, Firestein SJ, (2003) Motif-based construction of a functional map for mammalian olfactory receptors, Genomics;81(5):443-56

255. Petrey D, Xiang Z, Tang CL, Xie L, Gimpelev M, Mitros T, Soto CS, Goldsmith-Fischman S, Kernytsky A, Schlessinger A, Koh IYY, Alexov E, Honig B, (2003) Using Multiple Structure Alignments, Fast Model Building , and Energetic Analysis in Fold Recognition and Homology Modeling, Proteins: Struc., Func. and Genet. 53:430-435

256. Tang CL, Xie L, Koh IYY, Posy S, Alexov E, Honig B, (2003) On the Role of Structural Information in Remote Homology Detection and Sequence Alignment: New Methods Using Hybrid Sequence Profiles, J. Mol. Biol. 334:1043-1062

257. Zhang X, Heller K, Hefter I, Leslie C, Chasin L, (2003) Sequence Information for the Splicing of Human pre-mRNA Identified by Support Vector Machine Classification, Genome Research 13:2637-2650

List of Publications in 2001


258. Bussemaker HJ, Li H, Siggia ED, (2001) Regulatory element detection using correlation with expression, Nat Genet. 2001 Feb;27(2):167-71

List of Publications in 2000


259. Anastassiou D, (2000) Frequency-Domain Analysis of Biomolecular Sequences, Bioinformatics, vol. 16, no. 12, December 2000, pp. 1073-1081

260. Bussemaker HJ, Li H, Siggia ED, (2000) Building a dictionary for genomes: identification of presumptive regulatory sites by statistical analysis, Proc Natl Acad Sci U S A. 2000 Aug 29;97(18):10096-100

261. Califano A, Stolovitzky G, Tu Y, (2000) Analysis of gene expression microarrays for phenotype classification, Proc Int Conf Intell Syst Mol Biol.;8:75-85