Ozgun Babur

Research Assistant Professor

  • 1469 Citations
  • 13 h-Index
20022019
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Research Output 2002 2019

  • 1469 Citations
  • 13 h-Index
  • 26 Article
  • 1 Comment/debate
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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

Methylation
Platelets
Systems Analysis
Lysine
Identification (control systems)

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
Atlases
p53 Genes
Tumors
Genes
Genome
2018
1 Citation (Scopus)

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

Valenzuela-Escárcega, M. A., Babur, O., Hahn-Powell, G., Bell, D., Hicks, T., Noriega-Atala, E., Wang, X., Surdeanu, M., Demir, E. & Morrison, C. T., Jan 1 2018, In : Database : the journal of biological databases and curation. 2018

Research output: Contribution to journalArticle

Search engines
Reading
Throughput
Biological Phenomena
Search Engine
3 Citations (Scopus)

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

Endoplasmic Reticulum
Blood Platelets
Phenotype
Hemostatics
Systems Biology
2017
6 Citations (Scopus)

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

rho-Specific Guanine Nucleotide Dissociation Inhibitors
Guanine Nucleotide Dissociation Inhibitors
Systems Analysis
Blood Platelets
Protein Kinase C
113 Citations (Scopus)

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. & 191 others, Chang, M. T., Abdel-Rahman, M. H., Akbani, R., Ally, A., Auman, J. T., Babur, O., Balasundaram, M., Balu, S., Benz, C., Beroukhim, R., Birol, I., Bodenheimer, T., Bowen, J., Bowlby, R., Bristow, C. A., Brooks, D., Carlsen, R., Cebulla, C. M., Chang, M. T., Cherniack, A. D., Chin, L., Cho, J., Chuah, E., Chudamani, S., Cibulskis, C., Cibulskis, K., Cope, L., Coupland, S. E., Danilova, L., 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., Gibb, E. A., Griewank, K. G., Grimm, E. A., Hayes, D. N., Hegde, A. M., Heiman, D. I., Helsel, C., Hess, J. M., Hoadley, K. A., 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., Kimes, P. K., Kucherlapati, M., Kucherlapati, R., Lander, E., Lawrence, M. S., Lazar, A. J., Lee, S., Leraas, K. M., Lichtenberg, T. M., Lin, P., Liu, J., Liu, W., Mills, G., Lu, Y., Iype, L., 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., Mungall, K. L., Murray, B. A., Naresh, R., Noble, M. S., Oba, J., Pantazi, A., Parfenov, M., Park, P. J., Parker, J. S., Penson, A., Perou, C. M., Pihl, T., Pilarski, R., Protopopov, A., Radenbaugh, A., Rai, K., Ramirez, N. C., Ren, X., Reynolds, S. M., Roach, J., Robertson, A. G., 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., Shih, J., 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, M., Tang, J., Tarnuzzer, R., Taylor, B. S., Thiessen, N., Thorsson, V., Tse, K., Uzunangelov, V., Veluvolu, U., Verhaak, R. G. W., Voet, D., Walter, V., 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., Yau, C., Zenklusen, J. C., Zhang, J., Zhang, H., Zmuda, E., Cherniack, A. D., Benz, C., Mills, G. B., Verhaak, R. G. W., Griewank, K. G., Felau, I., Zenklusen, J. C., Gershenwald, J. E., Schoenfield, L., Lazar, A. J., Abdel-Rahman, M. H., Roman-Roman, S., Stern, M. H., Cebulla, C. M., Williams, M. D., Jager, M. J., Coupland, S. E., Esmaeli, B., Kandoth, C. & Woodman, S. E., Aug 14 2017, In : Cancer Cell. 32, 2, p. 204-220.e15

Research output: Contribution to journalArticle

Monosomy
DNA Methylation
Mutation
Uveal melanoma
Neoplasms
3 Citations (Scopus)

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

Genomics
Pathway
Cancer
Genes
Web browsers
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

Application programming interfaces (API)
7 Citations (Scopus)

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

Merging
Pathway
Language
Web Services
Datasets
2015
29 Citations (Scopus)

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, O., 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

Drug Combinations
Melanoma
Proto-Oncogene Proteins c-myc
MAP Kinase Signaling System
Mitogen-Activated Protein Kinase Kinases
9 Citations (Scopus)

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, O. & Demir, E., Jun 1 2015, In : PLoS One. 10, 6, e0128985.

Research output: Contribution to journalArticle

Aptitude
Visualization
Websites
Web Browser
Web browsers
66 Citations (Scopus)

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

Babur, O., 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

cancer
genomics
neoplasms
gene
Genes
2014
12 Citations (Scopus)

Integrating biological pathways and genomic profiles with ChiBE 2

Babur, O., 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

Genomics
Software
Research Personnel
Workflow
Databases
9 Citations (Scopus)

Pattern search in biopax models

Babur, O., 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

Pattern Search
Databases
Licensure
Metabolic Networks and Pathways
Computational Biology
22 Citations (Scopus)

Prediction of individualized therapeutic vulnerabilities in cancer from genomic profiles

Aksoy, B. A., Demir, E., Babur, O., 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

Vulnerability
Genomics
Cancer
Cells
Prediction
2013
28 Citations (Scopus)

Using Biological Pathway Data with Paxtools

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

Research output: Contribution to journalArticle

Medicine
Pathway
Software
software
Java
2011
549 Citations (Scopus)

Pathway Commons, a web resource for biological pathway data

Cerami, E. G., Gross, B. E., Demir, E., Rodchenkov, I., Babur, O., Anwar, N., Schultz, N., Bader, G. D. & Sander, C., Jan 2011, In : Nucleic Acids Research. 39, SUPPL. 1

Research output: Contribution to journalArticle

Databases
Catalysis
Language
Software
RNA
2010
20 Citations (Scopus)

Discovering modulators of gene expression

Babur, O., 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

Gene Expression
Transcription Factors
Co-Repressor Proteins
Proteins
Androgen Receptors
1 Citation (Scopus)

Erratum: The BioPAX community standard for pathway data sharing (Nat. Biotechnol. (2010) 28 (935-942)

Demir, E., Paley, S., Fukuda, K., Lemer, C., Vastrik, I., Wu, G., D'Eustachio, P., Schaefer, C., Luciano, J., Schacherer, F., Martinez-Flores, I., Hu, Z., Jimenez-Jacinto, V., Joshi-Tope, G., Kandasamy, K., Lopez-Fuentes, A. C., Mi, H., Pichler, E., Rodchenkov, I., Splendiani, A. & 69 others, Tkachev, S., Zucker, J., Gopinath, G., Rajasimha, H., Ramakrishnan, R., Shah, I., Syed, M., Anwar, N., Babur, O., Blinov, M., Brauner, E., Corwin, D., Donaldson, S., Gibbons, F., Goldberg, R., Hornbeck, P., Luna, A., Murray-Rust, P., Neumann, E., Reubenacker, O., Samwald, M., Van Iersel, M., Wimalaratne, S., Allen, K., Braun, B., Whirl-Carrillo, M., Cheung, K. H., Dahlquist, K., Finney, A., Gillespie, M., Glass, E., Gong, L., Haw, R., Honig, M., Hubaut, O., Kane, D., Krupa, S., Kutmon, M., Leonard, J., Marks, D., Merberg, D., Petri, V., Pico, A., Ravenscroft, D., Ren, L., Shah, N., Sunshine, M., Tang, R., Whaley, R., Letovksy, S., Buetow, K. H., Rzhetsky, A., Schachter, V., Sobral, B. S., Dogrusoz, U., McWeeney, S., Aladjem, M., Birney, E., Collado-Vides, J., Goto, S., Hucka, M., Novère, N. L., Maltsev, N., Pandey, A., Thomas, P., Wingender, E., Karp, P. D., Sander, C. & Bader, G. D., Dec 2010, In : Nature Biotechnology. 28, 12, p. 1308 1 p.

Research output: Contribution to journalArticle

366 Citations (Scopus)

The BioPAX community standard for pathway data sharing

Demir, E., Cary, M. P., Paley, S., Fukuda, K., Lemer, C., Vastrik, I., Wu, G., D'Eustachio, P., Schaefer, C., Luciano, J., Schacherer, F., Martinez-Flores, I., Hu, Z., Jimenez-Jacinto, V., Joshi-Tope, G., Kandasamy, K., Lopez-Fuentes, A. C., Mi, H., Pichler, E., Rodchenkov, I. & 70 others, Splendiani, A., Tkachev, S., Zucker, J., Gopinath, G., Rajasimha, H., Ramakrishnan, R., Shah, I., Syed, M., Anwar, N., Babur, O., Blinov, M., Brauner, E., Corwin, D., Donaldson, S., Gibbons, F., Goldberg, R., Hornbeck, P., Luna, A., Murray-Rust, P., Neumann, E., Reubenacker, O., Samwald, M., Van Iersel, M., Wimalaratne, S., Allen, K., Braun, B., Whirl-Carrillo, M., Cheung, K. H., Dahlquist, K., Finney, A., Gillespie, M., Glass, E., Gong, L., Haw, R., Honig, M., Hubaut, O., Kane, D., Krupa, S., Kutmon, M., Leonard, J., Marks, D., Merberg, D., Petri, V., Pico, A., Ravenscroft, D., Ren, L., Shah, N., Sunshine, M., Tang, R., Whaley, R., Letovksy, S., Buetow, K. H., Rzhetsky, A., Schachter, V., Sobral, B. S., Dogrusoz, U., McWeeney, S., Aladjem, M., Birney, E., Collado-Vides, J., Goto, S., Hucka, M., Novère, N. L., Maltsev, N., Pandey, A., Thomas, P., Wingender, E., Karp, P. D., Sander, C. & Bader, G. D., Sep 2010, In : Nature Biotechnology. 28, 9, p. 935-942 8 p.

Research output: Contribution to journalArticle

Information Dissemination
Databases
Gene Regulatory Networks
Metabolic Networks and Pathways
Gene expression
2009
15 Citations (Scopus)

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

Pathway
Databases
Query
Software
Graph in graph theory
26 Citations (Scopus)

ChiBE: Interactive visualization and manipulation of BioPAX pathway models

Babur, O., Dogrusoz, U., Demir, E. & Sander, C., Dec 9 2009, In : Bioinformatics. 26, 3, p. 429-431 3 p., btp665.

Research output: Contribution to journalArticle

Manipulation
Pathway
Software
Visualization
Cellular Structures
2008
6 Citations (Scopus)

PATIKAmad: Putting microarray data into pathway context

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

Research output: Contribution to journalArticle

Microarrays
Proteome
Microarray Analysis
Oligonucleotide Array Sequence Analysis
Cluster Analysis
2006
43 Citations (Scopus)

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

Pathway
Visualization
Databases
Interface Dynamics
User interfaces
2004
36 Citations (Scopus)

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

Ontology
Pathway
Software
Genome
Exploratory Behavior
2002
92 Citations (Scopus)

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., 2002, In : Bioinformatics. 18, 7, p. 996-1003 8 p.

Research output: Contribution to journalArticle

Knowledge Acquisition
Knowledge acquisition
Pathway
Genome
Genes