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.
| 2007 | ||
| 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. | ||
| Fan H, Mark A E, Zhu J, Honig B, (2007) "Comparative Study of Generalized Born Models: Protein Dynamics," PNAS 102:6760-6764 | ||
| Siggers T, Silkov A, Honig B, (2007) "Structural Alignment of Protein- DNA Interfaces: Insights into the Determinants of Binding Specificity," J. Mol. Biol.: 1027-1045 | ||
| Anastassiou, D, (2007) "Computational Analysis of the Synergy Among Multiple Interacting Genes," (Review Article), Molecular Systems Biology, Vol. 3, No. 83, February 2007 | ||
| Autism Genome Project Consortium, (2007) "Mapping autism risk loci using genetic linkage and chromosomal rearrangements," Nat. Genet. 39: 319-328 | ||
| 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 | ||
| Chen, J. L., L. Sam, et al, (2007) "High-throughput functional classification of human disease genes," BMC Bioinformatics 8(Suppl 3) (S7 ): doi:10.1186/1471-2105-8-S3-S7 | ||
| Cokol, M., Iossifov, I., Rodriguez-Esteban, R., Rzhetsky, A, (2007) "How many scientific papers should be retracted?," EMBO Rep 8, 422-423. PMID: 17471252 | ||
| 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 | ||
| Lussier, Y. A. and Y. Liu, (2007) "Computational approaches to phenotyping: high-throughput phenomics," Proc Am Thorac Soc 4(1): 18-25 | ||
| Pantazatosa, S. P., J. Li, et al. , (2007) "Cross-Scale Mapping of Gene Expression to Neuroimaging Datasets via Semantic Decomposition," MEDINFO | ||
| 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 | ||
| Ross, K. A., A. Janevski, J. Stoyanovich, (2007) "A Faceted Query Engine Applied to Archaeology," Internet Archeology 21, April 2007 | ||
| Sam, L., Y. Liu, et al., (2007) "Discovery of Protein Interaction Networks Shared by Diseases," Pacific Symposium on Biocomputing(12): 76-87 | ||
| J. Sebat, 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: 445-449 | ||
| 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 | ||
Back to Top
| 2006 | ||
| 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 | ||
| Bussemaker, H, (2006) "Modeling gene expression control using Omes Law," Molecular Systems Biology (published online), 2006. doi:10.1038(msb4100055) | ||
| 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," | ||
| Foat BC, M.A., Bussemaker HJ, (2006) "Statistical mechanical modeling of genome-wide transcription factor occupancy data by MatrixREDUCE," Proceedings of ISMB | ||
| Halasz G, Van Batenburg MF., Perusse J, Hua S, White KP, Bussemaker HJ, (2006) "Detecting Transcriptionally Active Regions Using Genomic Tiling Arrays," | ||
| Friedman, C., T. Borlawsky, et al, (2006) "Bio-Ontology and text: bridging the modeling gap," Bioinformatics 22(19): 2421-9 | ||
| Goh, C. S., T. A. Gianoulis, et al, (2006) "Integration of curated databases to identify genotype-phenotype associations," BMC Genomics 7: 257 | ||
| 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 | ||
| 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 | ||
| 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 | ||
| 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 | ||
| 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 | ||
| 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 | ||
| 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, 2006. 103(6): p. 1750-5 | ||
| Kundaje A, M Middendorf, M Shah, C Wiggins, Y Freund and C Leslie., (2006) "A classification-based framework for predicting and analyzing gene regulatory response," BMC Bioinformatics (Special issue on "New Problems and Methods in Computational Biology"), 2006. 7(Supp 1)(S5) | ||
| Liu, Y., J. Li, et a., (2006) "An integrative genomic approach to uncover molecular mechanisms of prokaryotic traits," PLoS Comput Biol 2(11): e159 | ||
| 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) | ||
| Margolin AA, Wang K, Lim WK, Kustagi M, Nemenman I, Califano A, (2006) "Reverse Engineering Cellular Networks," Nature Protocols, in press, 2006 | ||
| 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., 103:12027-32. PMID: 16880385, [Joint last authorship; highlighted in Nature; listed as "must read paper" on Faculty of 1000] | ||
| 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., 103:12027-32. PMID: 16880385, [Joint last authorship; highlighted in Nature; listed as "must read paper" on Faculty of 1000] | ||
| 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 | ||
| 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 | ||
| 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 | ||
| Rodrigues-Esteban, R., Iossifov, I., Rzhetsky, A., (2006) "Imitating manual curation of text-mined facts in biomedicine," | ||
| Ross, K.A., (2006) "Alpha Radiation is a Major Germ-Line Mutagen over Evolutionary Timescales," Evolutionary Ecology Research, 8(6), 2006, 1013-1028 | ||
| Rzhetsky, A., Zheng, T., Weinreb, C. , (2006) "Self-correcting maps of molecular pathways," PLoS ONE 1, e61. PMID: 1718369 | ||
| 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 | ||
| 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 | ||
| 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 | ||
| 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 | ||
| Weston J, Leslie C., E Ie, D Zhou, A Elisseeff, WS Noble, (2006) "Semi-Supervised Protein Classification using Cluster Kernels," Book Chapter for "Semi-Supervised Learning (Editors: O. Chapelle, B. Scholkopf and A. Zien), in press, 2006 | ||
| 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) | ||
| 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 | ||
Back to Top
| 2005 | ||
| Basso K, Margolin AA, Stolovitzky G, Klein U, Dalla-Favera R, Califano A, (2005) "Reverse engineering of regulatory networks in human B cells," Nat Genet;37(4):382-90. Epub 2005 Mar 20. | ||
| 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 | ||
| Cantor MN, Sarkar IN, Bodenreider O, Lussier YA, (2005) "Genestrace: Phenomic Knowledge Discovery Via Structured Terminology," Pac Symp Biocomput.;103-14 | ||
| 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 | ||
| 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 | ||
| 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 | ||
| 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) | ||
| Margolin A, Nemenman I, Basso K, Klein U, Wiggins C, Stolovitzky G, Dalla Favera R, and Califano A, (2005) "ARACNE: An Algorithm for the Reconstruction of Gene Regulatory Networks in a Mammalian Cellular Context," in print, BMC Bioinformatics | ||
| 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) | ||
| Nair R, Rost B, (2005) "Mimicking cellular sorting improves prediction of subcellular localization," J Mol Biol 348, 85-100 | ||
| Punta M, Rost B, (2005) "PROFcon: novel prediction of long-range contacts," Bioinformatics, 21, 2960-2968 | ||
| 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 | ||
| 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 | ||
| 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 | ||
| 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 | ||
| 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 | ||
| 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 | ||
Back to Top
| 2004 | ||
| 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 | ||
| Liu J, Rost B, (2004) "CHOP proteins into structural domain-like fragments," Proteins 55, 678-688 | ||
| Lussier YA, Li J, (2004) "Terminological Mapping For High Throughput Comparative Biology of Phenotypes," Pac Symp Biocomput;:202-13 | ||
| 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) | ||
| Nair R, Rost B, (2004) "LOCnet and LOCtarget: Sub-cellular localization for structural genomics targets," Nucl Acids Res 32 (Web server issue) , W517-W521 | ||
| Rost B, Yachdav G, Liu J, (2004) "The PredictProtein server," Nucl Acids Res , 32 (Web server issue) , W321-W326 | ||
| 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 | ||
| 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 | ||
| 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 | ||
Back to Top
| 2003 | ||
| 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. Epub 2003 Feb 25 | ||
| 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 | ||
| 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 | ||
| 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 | ||
| 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 | ||
Back to Top
| 2001 | ||
| Bussemaker HJ, Li H, Siggia ED, (2001) "Regulatory element detection using correlation with expression," Nat Genet. 2001 Feb;27(2):167-71 | ||
Back to Top
| 2000 | ||
| Anastassiou D, (2000) "Frequency-Domain Analysis of Biomolecular Sequences," Bioinformatics, vol. 16, no. 12, December 2000, pp. 1073-1081 | ||
| 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 | ||
| 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 | ||
