Emek Demir

Assistant Professor

  • 2644 Citations
  • 19 h-Index
20022020

Research output per year

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Research Output

  • 2644 Citations
  • 19 h-Index
  • 33 Article
  • 4 Comment/debate
  • 3 Review article
  • 1 Conference article
2020

COVID-19 Disease Map, building a computational repository of SARS-CoV-2 virus-host interaction mechanisms

Ostaszewski, M., Mazein, A., Gillespie, M. E., Kuperstein, I., Niarakis, A., Hermjakob, H., Pico, A. R., Willighagen, E. L., Evelo, C. T., Hasenauer, J., Schreiber, F., Dräger, A., Demir, E., Wolkenhauer, O., Furlong, L. I., Barillot, E., Dopazo, J., Orta-Resendiz, A., Messina, F., Valencia, A. & 5 others, Funahashi, A., Kitano, H., Auffray, C., Balling, R. & Schneider, R., Dec 1 2020, In : Scientific Data. 7, 1, 136.

Research output: Contribution to journalComment/debate

Open Access

Pathway Commons 2019 Update: integration, analysis and exploration of pathway data

Rodchenkov, I., Babur, O., Luna, A., Aksoy, B. A., Wong, J. V., Fong, D., Franz, M., Siper, M. C., Cheung, M., Wrana, M., Mistry, H., Mosier, L., Dlin, J., Wen, Q., O'Callaghan, C., Li, W., Elder, G., Smith, P. T., Dallago, C., Cerami, E. & 5 others, Gross, B., Dogrusoz, U., Demir, E., Bader, G. D. & Sander, C., Jan 8 2020, In : Nucleic acids research. 48, D1, p. D489-D497

Research output: Contribution to journalArticle

Open Access
6 Scopus citations
2019

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
4 Scopus citations

Systems Biology Graphical Notation: Process Description language Level 1 Version 2.0

Rougny, A., Touré, V., Moodie, S., Balaur, I., Czauderna, T., Borlinghaus, H., Dogrusoz, U., Mazein, A., Dräger, A., Blinov, M. L., Villéger, A., Haw, R., Demir, E., Mi, H., Sorokin, A., Schreiber, F. & Luna, A., Jun 13 2019, In : Journal of integrative bioinformatics. 16, 2

Research output: Contribution to journalReview article

Open Access
3 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

8 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

6 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

9 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

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

167 Scopus citations

PaxtoolsR: Pathway analysis in R using Pathway Commons

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

Research output: Contribution to journalArticle

11 Scopus citations
2015

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

25 Scopus citations

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

36 Scopus citations

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., 2015, In : Frontiers in Bioengineering and Biotechnology. 3, FEB, 19.

Research output: Contribution to journalArticle

32 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

76 Scopus citations

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

11 Scopus citations

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

9 Scopus citations

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

6 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

10 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

25 Scopus citations
2013

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

5 Scopus citations

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 2013, In : PLoS computational biology. 9, 9, e1003194.

Research output: Contribution to journalArticle

33 Scopus citations
2012

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

45 Scopus citations
2011

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

12 Scopus citations

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., Dec 15 2011, In : Standards in Genomic Sciences. 5, 2, p. 230-242 13 p.

Research output: Contribution to journalArticle

9 Scopus citations

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 2011, In : Nucleic acids research. 39, SUPPL. 1, p. D685-D690

Research output: Contribution to journalArticle

614 Scopus citations
2010

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

232 Scopus citations

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

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, Ö., 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, 1 p.

Research output: Contribution to journalComment/debate

3 Scopus citations

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, Ö., 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 journalReview article

399 Scopus citations
2009

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

37 Scopus citations

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

18 Scopus citations

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.

Research output: Contribution to journalComment/debate

29 Scopus citations

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 1 2009, In : Nature biotechnology. 27, 9, 1 p.

Research output: Contribution to journalComment/debate

2 Scopus citations

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 1 2009, In : Nature biotechnology. 27, 8, p. 735-741 7 p.

Research output: Contribution to journalReview article

515 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

A compound graph layout algorithm for biological pathways

Dogrusoz, U., Giral, E., Cetintas, A., Civril, A. & Demir, E., 2004, In : Lecture Notes in Computer Science. 3383, p. 442-447 6 p.

Research output: Contribution to journalConference article

24 Scopus citations

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

Research output: Contribution to journalArticle

Open Access
93 Scopus citations