Ozgun Babur

Research Assistant Professor

  • 1649 Citations
  • 14 h-Index
20022019

Research output per year

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Research Output

  • 1649 Citations
  • 14 h-Index
  • 23 Article
  • 3 Comment/debate
  • 1 Review article
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Article
2019

Identification, Quantification, and System Analysis of Protein N-ε Lysine Methylation in Anucleate Blood Platelets

Rocheleau, A. D., Melrose, A. R., Cunliffe, J. M., Klimek, J., Babur, O., Tassi Yunga, S., Ngo, A. T. P., Pang, J., David, L., McCarty, O. & Aslan, J., Jan 1 2019, In : Proteomics. 1900001.

Research output: Contribution to journalArticle

Integrated Analysis of TP53 Gene and Pathway Alterations in The Cancer Genome Atlas

The Cancer Genome Atlas Network, Jul 30 2019, In : Cell Reports. 28, 5, p. 1370-1384.e5

Research output: Contribution to journalArticle

Open Access
8 Scopus citations
2018

Large-scale automated machine reading discovers new cancer-driving mechanisms

Valenzuela-Escárcega, M. A., Babur, Ö., Hahn-Powell, G., Bell, D., Hicks, T., Noriega-Atala, E., Wang, X., Surdeanu, M., Demir, E. & Morrison, C. T., Jan 1 2018, In : Database. 2018, 2018

Research output: Contribution to journalArticle

4 Scopus citations

Platelet procoagulant phenotype is modulated by a p38-MK2 axis that regulates RTN4/Nogo proximal to the endoplasmic reticulum: utility of pathway analysis

Babur, O., Ngo, A. T. P., Rigg, R. A., Pang, J., Rub, Z. T., Buchanan, A. E., Mitrugno, A., David, L., McCarty, O., Demir, E. & Aslan, J., May 1 2018, In : American journal of physiology. Cell physiology. 314, 5, p. C603-C615

Research output: Contribution to journalArticle

3 Scopus citations
2017

Assessment of roles for the rho-specific guanine nucleotide dissociation inhibitor Ly-GDI in platelet function: A spatial systems approach

Ngo, A. T. P., Thierheimer, M. L. D., Babur, O., Rocheleau, A. D., Huang, T., Pang, J., Rigg, R. A., Mitrugno, A., Theodorescu, D., Burchard, J., Nan, X., Demir, E., McCarty, O. & Aslan, J., Apr 7 2017, In : American Journal of Physiology - Cell Physiology. 312, 4, p. C527-C536

Research output: Contribution to journalArticle

7 Scopus citations

Integrative Analysis Identifies Four Molecular and Clinical Subsets in Uveal Melanoma

Robertson, A. G., Shih, J., Yau, C., Gibb, E. A., Oba, J., Mungall, K. L., Hess, J. M., Uzunangelov, V., Walter, V., Danilova, L., Lichtenberg, T. M., Kucherlapati, M., Kimes, P. K., Tang, M., Penson, A., Babur, O., Akbani, R., Bristow, C. A., Hoadley, K. A., Iype, L. & 150 others, Chang, M. T., Abdel-Rahman, M. H., Ally, A., Auman, J. T., Balasundaram, M., Balu, S., Benz, C., Beroukhim, R., Birol, I., Bodenheimer, T., Bowen, J., Bowlby, R., Brooks, D., Carlsen, R., Cebulla, C. M., Cherniack, A. D., Chin, L., Cho, J., Chuah, E., Chudamani, S., Cibulskis, C., Cibulskis, K., Cope, L., Coupland, S. E., Defreitas, T., Demchok, J. A., Desjardins, L., Dhalla, N., Esmaeli, B., Felau, I., Ferguson, M. L., Frazer, S., Gabriel, S. B., Gastier-Foster, J. M., Gehlenborg, N., Gerken, M., Gershenwald, J. E., Getz, G., Griewank, K. G., Grimm, E. A., Hayes, D. N., Hegde, A. M., Heiman, D. I., Helsel, C., Hobensack, S., Holt, R. A., Hoyle, A. P., Hu, X., Hutter, C. M., Jager, M. J., Jefferys, S. R., Jones, C. D., Jones, S. J. M., Kandoth, C., Kasaian, K., Kim, J., Kucherlapati, R., Lander, E., Lawrence, M. S., Lazar, A. J., Lee, S., Leraas, K. M., Lin, P., Liu, J., Liu, W., Lolla, L., Lu, Y., Ma, Y., Mahadeshwar, H. S., Mariani, O., Marra, M. A., Mayo, M., Meier, S., Meng, S., Meyerson, M., Mieczkowski, P. A., Mills, G. B., Moore, R. A., Mose, L. E., Mungall, A. J., Murray, B. A., Naresh, R., Noble, M. S., Pantazi, A., Parfenov, M., Park, P. J., Parker, J. S., Perou, C. M., Pihl, T., Pilarski, R., Protopopov, A., Radenbaugh, A., Rai, K., Ramirez, N. C., Ren, X., Reynolds, S. M., Roach, J., Roman-Roman, S., Roszik, J., Sadeghi, S., Saksena, G., Sastre, X., Schadendorf, D., Schein, J. E., Schoenfield, L., Schumacher, S. E., Seidman, J., Seth, S., Sethi, G., Sheth, M., Shi, Y., Shields, C., Shmulevich, I., Simons, J. V., Singh, A. D., Sipahimalani, P., Skelly, T., Sofia, H., Soloway, M. G., Song, X., Stern, M. H., Stuart, J., Sun, Q., Sun, H., Tam, A., Tan, D., Tang, J., Tarnuzzer, R., Taylor, B. S., Thiessen, N., Thorsson, V., Tse, K., Veluvolu, U., Verhaak, R. G. W., Voet, D., Wan, Y., Wang, Z., Weinstein, J. N., Wilkerson, M. D., Williams, M. D., Wise, L., Woodman, S. E., Wong, T., Wu, Y., Yang, L., Yang, L., Zenklusen, J. C., Zhang, J., Zhang, H. & Zmuda, E., Aug 14 2017, In : Cancer Cell. 32, 2, p. 204-220.e15

Research output: Contribution to journalArticle

164 Scopus citations

PathwayMapper: A collaborative visual web editor for cancer pathways and genomic data

Bahceci, I., Dogrusoz, U., La, K. C., Babur, O., Gao, J. & Schultz, N., Jul 15 2017, In : Bioinformatics. 33, 14, p. 2238-2240 3 p.

Research output: Contribution to journalArticle

8 Scopus citations
2016

Collaborative workspaces for pathway curation

Durupinar-Babur, F., Siper, M. C., Dogrusoz, U., Bahceci, I., Babur, O. & Demir, E., 2016, In : CEUR Workshop Proceedings. 1747

Research output: Contribution to journalArticle

PaxtoolsR: Pathway analysis in R using Pathway Commons

Luna, A., Babur, O., Aksoy, B. A., Demir, E. & Sander, C., Apr 15 2016, In : Bioinformatics. 32, 8, p. 1262-1264 3 p.

Research output: Contribution to journalArticle

9 Scopus citations
2015

Perturbation biology nominates upstream–downstream drug combinations in RAF inhibitor resistant melanoma cells

Korkut, A., Wang, W., Demir, E., Aksoy, B. A., Jing, X., Molinelli, E. J., Babur, Ö., Bemis, D. L., Sumer, S. O., Solit, D. B., Pratilas, C. A. & Sander, C., Aug 18 2015, In : eLife. 4, AUGUST2015, e04640.

Research output: Contribution to journalArticle

34 Scopus citations

SBGNViz: A tool for visualization and complexity management of SBGN process description maps

Sari, M., Bahceci, I., Dogrusoz, U., Sumer, S. O., Aksoy, B. A., Babur, Ö. & Demir, E., Jun 1 2015, In : PloS one. 10, 6, e0128985.

Research output: Contribution to journalArticle

12 Scopus citations

Systematic identification of cancer driving signaling pathways based on mutual exclusivity of genomic alterations

Babur, Ö., Gönen, M., Aksoy, B. A., Schultz, N., Ciriello, G., Sander, C. & Demir, E., Feb 26 2015, In : Genome biology. 16, 1, 45.

Research output: Contribution to journalArticle

72 Scopus citations
2014

Integrating biological pathways and genomic profiles with ChiBE 2

Babur, Ö., Dogrusoz, U., C¸akir, M., Aksoy, B. A., Schultz, N., Sander, C. & Demir, E., Aug 3 2014, In : BMC Genomics. 15, 1, 642.

Research output: Contribution to journalArticle

12 Scopus citations

Pattern search in biopax models

Babur, Ö., Aksoy, B. A., Rodchenkov, I., Sümer, S. O., Sander, C. & Demir, E., Jan 1 2014, In : Bioinformatics. 30, 1, p. 139-140 2 p.

Research output: Contribution to journalArticle

9 Scopus citations

Prediction of individualized therapeutic vulnerabilities in cancer from genomic profiles

Aksoy, B. A., Demir, E., Babur, Ö., Wang, W., Jing, X., Schultz, N. & Sander, C., Jul 15 2014, In : Bioinformatics. 30, 14, p. 2051-2059 9 p.

Research output: Contribution to journalArticle

24 Scopus citations
2013

Using Biological Pathway Data with Paxtools

Demir, E., Babur, Ö., Rodchenkov, I., Aksoy, B. A., Fukuda, K. I., Gross, B., Sümer, O. S., Bader, G. D. & Sander, C., Sep 1 2013, In : PLoS computational biology. 9, 9, e1003194.

Research output: Contribution to journalArticle

32 Scopus citations
2011

Pathway Commons, a web resource for biological pathway data

Cerami, E. G., Gross, B. E., Demir, E., Rodchenkov, I., Babur, Ö., Anwar, N., Schultz, N., Bader, G. D. & Sander, C., Jan 1 2011, In : Nucleic acids research. 39, SUPPL. 1, p. D685-D690

Research output: Contribution to journalArticle

599 Scopus citations
2010

Discovering modulators of gene expression

Babur, Ö., Demir, E., Gönen, M., Sander, C. & Dogrusoz, U., May 13 2010, In : Nucleic acids research. 38, 17, p. 5648-5656 9 p., gkq287.

Research output: Contribution to journalArticle

21 Scopus citations
2009

Algorithms for effective querying of compound graph-based pathway databases

Dogrusoz, U., Cetintas, A., Demir, E. & Babur, O., Nov 16 2009, In : BMC bioinformatics. 10, 376.

Research output: Contribution to journalArticle

17 Scopus citations
2008

PATIKAmad: Putting microarray data into pathway context

Babur, O., Colak, R., Demir, E. & Dogrusoz, U., Jun 1 2008, In : Proteomics. 8, 11, p. 2196-2198 3 p.

Research output: Contribution to journalArticle

6 Scopus citations
2006

PATIKAweb: A Web interface for analyzing biological pathways through advanced querying and visualization

Dogrusoz, U., Erson, E. Z., Giral, E., Demir, E., Babur, O., Cetintas, A. & Colak, R., Feb 1 2006, In : Bioinformatics. 22, 3, p. 374-375 2 p.

Research output: Contribution to journalArticle

43 Scopus citations
2004

An ontology for collaborative construction and analysis of cellular pathways

Demir, E., Babur, O., Dogrusoz, U., Gursoy, A., Ayaz, A., Gulesir, G., Nisanci, G. & Cetin-Atalay, R., Feb 12 2004, In : Bioinformatics. 20, 3, p. 349-356 8 p.

Research output: Contribution to journalArticle

36 Scopus citations
2002

PATIKA: An integrated visual environment for collaborative construction and analysis of cellular pathways

Demir, E., Babur, O., Dogrusoz, U., Gursoy, A., Nisanci, G., Cetin-Atalay, R. & Ozturk, M., Jan 1 2002, In : Bioinformatics. 18, 7, p. 996-1003 8 p.

Research output: Contribution to journalArticle

Open Access
93 Scopus citations