Emek Demir

Assistant Professor

  • 2368 Citations
  • 18 h-Index
20022019
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Research Output 2002 2019

  • 2368 Citations
  • 18 h-Index
  • 37 Article
  • 1 Conference contribution
2019
1 Citation (Scopus)

Cancer-associated mutations in DICER1 RNase IIIa and IIIb domains exert similar effects on miRNA biogenesis

Vedanayagam, J., Chatila, W. K., Aksoy, B. A., Majumdar, S., Skanderup, A. J., Demir, E., Schultz, N., Sander, C. & Lai, E. C., Dec 1 2019, In : Nature communications. 10, 1, 3682.

Research output: Contribution to journalArticle

Open Access
biological evolution
Ribonucleases
mutations
MicroRNAs
cancer
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
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)
137 Citations (Scopus)

Human SRMAtlas: A Resource of Targeted Assays to Quantify the Complete Human Proteome

Kusebauch, U., Campbell, D. S., Deutsch, E. W., Chu, C. S., Spicer, D. A., Brusniak, M. Y., Slagel, J., Sun, Z., Stevens, J., Grimes, B., Shteynberg, D., Hoopmann, M. R., Blattmann, P., Ratushny, A. V., Rinner, O., Picotti, P., Carapito, C., Huang, C. Y., Kapousouz, M., Lam, H. & 7 others, Tran, T., Demir, E., Aitchison, J. D., Sander, C., Hood, L., Aebersold, R. & Moritz, R. L., Jul 28 2016, In : Cell. 166, 3, p. 766-778 13 p.

Research output: Contribution to journalArticle

Proteome
Assays
docetaxel
Peptides
Proteins
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
17 Citations (Scopus)

Crosstalk between signaling pathways provided by single and multiple protein phosphorylation sites

Nishi, H., Demir, E. & Panchenko, A. R., Jan 30 2015, In : Journal of Molecular Biology. 427, 2, p. 511-520 10 p.

Research output: Contribution to journalArticle

Phosphorylation
Proteins
Phosphotransferases
Protein Stability
Computer Simulation
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
27 Citations (Scopus)

Promoting coordinated development of community-based information standards for modeling in biology: The COMBINE initiative

Hucka, M., Nickerson, D. P., Bader, G. D., Bergmann, F. T., Cooper, J., Demir, E., Garny, A., Golebiewski, M., Myers, C. J., Schreiber, F., Waltemath, D. & Le Novère, N. L., Jan 1 2015, In : Frontiers in Bioengineering and Biotechnology. 3, FEB, 19.

Research output: Contribution to journalArticle

Computational Biology
Standardization
Research
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
6 Citations (Scopus)

Systems Biology Graphical Notation: Process Description language Level 1 Version 1.3

Moodie, S., Le Novère, N., Demir, E., Mi, H. & Villéger, A., 2015, In : Journal of integrative bioinformatics. 12, 2, p. 263 1 p.

Research output: Contribution to journalArticle

Systems Biology
Language
Biological Phenomena
Textbooks
Metabolic Networks and Pathways
7 Citations (Scopus)

Systems Biology Graphical Notation: Activity Flow language Level 1 Version 1.2

Mi, H., Schreiber, F., Moodie, S., Czauderna, T., Demir, E., Haw, R., Luna, A., Le Novère, N., Sorokin, A. & Villéger, A., 2015, In : Journal of integrative bioinformatics. 12, 2, p. 265 1 p.

Research output: Contribution to journalArticle

Systems Biology
Language
Gene Ontology
Textbooks
Semantics
4 Citations (Scopus)

Systems Biology Graphical Notation: Entity Relationship language Level 1 Version 2

Sorokin, A., Le Novère, N., Luna, A., Czauderna, T., Demir, E., Haw, R., Mi, H., Moodie, S., Schreiber, F. & Villéger, A., 2015, In : Journal of integrative bioinformatics. 12, 2, p. 264 1 p.

Research output: Contribution to journalArticle

Systems Biology
Language
Protein Interaction Maps
Textbooks
Semantics
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
3 Citations (Scopus)

The BioPAX validator

Rodchenkov, I., Demir, E., Sander, C. & Bader, G. D., Oct 15 2013, In : Bioinformatics. 29, 20, p. 2659-2660 2 p.

Research output: Contribution to journalArticle

Informatics
Critical Pathways
Licensure
Semantics
Inconsistency
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
2012
41 Citations (Scopus)

Software support for SBGN maps: SBGN-ML and LibSBGN

Van Iersel, M. P., Villéger, A. C., Czauderna, T., Boyd, S. E., Bergmann, F. T., Luna, A., Demir, E., Sorokin, A., Dogrusoz, U., Matsuoka, Y., Funahashi, A., Aladjem, M. I., Mi, H., Moodie, S. L., Kitano, H., Le novère, N. & Schreiber, F., Aug 2012, In : Bioinformatics. 28, 15, p. 2016-2021 6 p., bts270.

Research output: Contribution to journalArticle

Systems Biology
Notation
Software
Libraries
Bioinformatics
2011
11 Citations (Scopus)

BioPAX support in CellDesigner

Mi, H., Muruganujan, A., Demir, E., Matsuoka, Y., Funahashi, A., Kitano, H. & Thomas, P. D., Dec 2011, In : Bioinformatics. 27, 24, p. 3437-3438 2 p., btr586.

Research output: Contribution to journalArticle

Pathway
Software
Databases
Biological Phenomena
Information Storage and Retrieval
9 Citations (Scopus)

Meeting report from the first meetings of the Computational Modeling in Biology Network (COMBINE)

le Novère, N., Hucka, M., Anwar, N., Bader, G. D., Demir, E., Moodie, S. & Sorokin, A., 2011, In : Standards in Genomic Sciences. 5, 2, p. 230-242 13 p.

Research output: Contribution to journalArticle

Software
Systems Biology
Computational Biology
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
221 Citations (Scopus)

Automated network analysis identifies core pathways in glioblastoma

Cerami, E., Demir, E., Schultz, N., Taylor, B. S. & Sander, C., Feb 12 2010, In : PLoS One. 5, 2, e8918.

Research output: Contribution to journalArticle

Glioblastoma
Electric network analysis
Genes
neoplasms
Neoplasms
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
33 Citations (Scopus)

A layout algorithm for undirected compound graphs

Dogrusoz, U., Giral, E., Cetintas, A., Civril, A. & Demir, E., Mar 15 2009, In : Information Sciences. 179, 7, p. 980-994 15 p.

Research output: Contribution to journalArticle

Layout
Pathway
Graph in graph theory
Arbitrary
Vertex of a graph
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
1 Citation (Scopus)

Erratum: The systems biology graphical notation (Nature Biotechnology (2009) 27 (735-741))

Le Novère, N., Hucka, M., Mi, H., Moodie, S., Schreiber, F., Sorokin, A., Demir, E., Wegner, K., Aladjem, M. I., Wimalaratne, S. M., Bergman, F. T., Gauges, R., Ghazal, P., Kawaji, H., Li, L., Matsuoka, Y., Villéger, A., Boyd, S. E., Calzone, L., Courtot, M. & 19 others, Dogrusoz, U., Freeman, T. C., Funahashi, A., Ghosh, S., Jouraku, A., Kim, S., Kolpakov, F., Luna, A., Sahle, S., Schmidt, E., Watterson, S., Wu, G., Goryanin, I., Kell, D. B., Sander, C., Sauro, H., Snoep, J. L., Kohn, K. & Kitano, H., Sep 2009, In : Nature Biotechnology. 27, 9, p. 864 1 p.

Research output: Contribution to journalArticle

480 Citations (Scopus)

The Systems Biology Graphical Notation

Novère, N. L., Hucka, M., Mi, H., Moodie, S., Schreiber, F., Sorokin, A., Demir, E., Wegner, K., Aladjem, M. I., Wimalaratne, S. M., Bergman, F. T., Gauges, R., Ghazal, P., Kawaji, H., Li, L., Matsuoka, Y., Villéger, A., Boyd, S. E., Calzone, L., Courtot, M. & 19 others, Dogrusoz, U., Freeman, T. C., Funahashi, A., Ghosh, S., Jouraku, A., Kim, S., Kolpakov, F., Luna, A., Sahle, S., Schmidt, E., Watterson, S., Wu, G., Goryanin, I., Kell, D. B., Sander, C., Sauro, H., Snoep, J. L., Kohn, K. & Kitano, H., Aug 2009, In : Nature Biotechnology. 27, 8, p. 735-741 7 p.

Research output: Contribution to journalArticle

Systems Biology
Visual languages
Language
Cell signaling
Unified Modeling Language
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
24 Citations (Scopus)

A compound graph layout algorithm for biological pathways

Dogrusoz, U., Giral, E., Cetintas, A., Civril, A. & Demir, E., 2004, Lecture Notes in Computer Science. Pach, J. (ed.). Vol. 3383. p. 442-447 6 p.

Research output: Chapter in Book/Report/Conference proceedingConference contribution

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