Integrative analysis of complex cancer genomics and clinical profiles using the cBioPortal von Gao, Jianjiong, Aksoy, Bülent Arman, Dogrusoz, Ugur, Dresdner, Gideon, Gross, Benjamin, Sumer, S Onur, Sun, Yichao, Jacobsen, Anders, Sinha, Rileen, Larsson, Erik, Cerami, Ethan, Sander, Chris, Schultz, Nikolaus

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VISIBIOweb: visualization and layout services for BioPAX pathway models von Dilek, Alptug, Belviranli, Mehmet E, Dogrusoz, Ugur

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PATIKA: an integrated visual environment for collaborative construction and analysis of cellular pathways von DEMIR, E, BABUR, O, DOGRUSOZ, U, GURSOY, A, NISANCI, G, CETIN-ATALAV, R, OZTURK, M

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A layout algorithm for signaling pathways von Genc, B., Dogrusoz, U.

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Patikaweb: a Web interface for analyzing biological pathways through advanced querying and visualization von Dogrusoz, U., Erson, E. Z., Giral, E., Demir, E., Babur, O., Cetintas, A., Colak, R.

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An ontology for collaborative construction and analysis of cellular pathways von Demir, E., Babur, O., Dogrusoz, U., Gursoy, A., Ayaz, A., Gulesir, G., Nisanci, G., Cetin-Atalay, R.

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A multi-graph approach to complexity management in interactive graph visualization von Dogrusoz, U., Genc, B.

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CiSE: A Circular Spring Embedder Layout Algorithm von Dogrusoz, U., Belviranli, M. E., Dilek, A.

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Combinatorial Pattern Matching: 15th Annual Symposium, CPM 2004, Istanbul, Turkey, July 5-7, 2004, Proceedings von Sahinalp, Suleyman C, Muthukrishnan, S, Dogrusoz, Ugur

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Oncogenic signaling pathways in the cancer genome atlas von Sanchez-Vega, F, Mina, M, Armenia, J, Chatila, WK, Luna, A, La, KC, Dimitriadoy, S, Liu, DL, Kantheti, HS, Saghafinia, S, Chakravarty, D, Daian, F, Gao, Q, Bailey, MH, Liang, W-W, Foltz, SM, Shmulevich, I, Ding, L, Heins, Z, Ochoa, A, Gross, B, Gao, J, Zhang, H, Kundra, R, Kandoth, C, Bahceci, I, Dervishi, L, Dogrusoz, U, Zhou, W, Shen, H, Laird, PW, Way, GP, Greene, CS, Liang, H, Xiao, Y, Wang, C, Iavarone, A, Berger, AH, Bivona, TG, Lazar, AJ, Hammer, GD, Giordano, T, Kwong, LN, McArthur, G, Huang, C, Tward, AD, Frederick, MJ, McCormick, F, Meyerson, M, Van Allen, EM, Cherniack, AD, Ciriello, G, Sander, C, Schultz, N

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Reversal Distance without Hurdles and Fortresses von Bergeron, Anne, Mixtacki, Julia, Stoye, Jens

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Two-dimensional packing algorithms for layout of disconnected graphs von Dogrusoz, Ugur

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Patika: an integrated visual environmentfor collaborative construction and analysis of cellularpathways von Demir, E., Babur, O., Dogrusoz, U., Gursoy, A., Nisanci, G., Cetin-Atalay, R., Ozturk, M.

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A Fast Set Intersection Algorithm for Sorted Sequences von Baeza-Yates, Ricardo

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Quadratic Time Algorithms for Finding Common Intervals in Two and More Sequences von Schmidt, Thomas, Stoye, Jens

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Sorting by Reversals in Subquadratic Time von Tannier, Eric, Sagot, Marie-France

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Optimizing Multiple Spaced Seeds for Homology Search von Xu, Jinbo, Brown, Daniel G., Li, Ming, Ma, Bin

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P atika web : a Web interface for analyzing biological pathways through advanced querying and visualization von Dogrusoz, U., Erson, E. Z., Giral, E., Demir, E., Babur, O., Cetintas, A., Colak, R.

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Compressed Compact Suffix Arrays von Mäkinen, Veli, Navarro, Gonzalo

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A Constrained, Force-Directed Layout Algorithm for Biological Pathways von Genc, Burkay, Dogrusoz, Ugur

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