Mehmet Gonen

Research Assistant Professor

  • 2382 Citations
  • 14 h-Index
20082020

Research output per year

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Research Output

2020

A multitask multiple kernel learning formulation for discriminating early- and late-stage cancers

Rahimi, A. & Gönen, M., Jun 1 2020, In : Bioinformatics (Oxford, England). 36, 12, p. 3766-3772 7 p.

Research output: Contribution to journalArticle

1 Scopus citations

Androgen receptor-binding sites are highly mutated in prostate cancer

Morova, T., McNeill, D. R., Lallous, N., Gönen, M., Dalal, K., Wilson, D. M., Gürsoy, A., Keskin, Ö. & Lack, N. A., Dec 1 2020, In : Nature communications. 11, 1, 832.

Research output: Contribution to journalArticle

Open Access
2 Scopus citations

A prospective prediction tool for understanding Crimean–Congo haemorrhagic fever dynamics in Turkey

Ak, Ergönül & Gönen, M., Jan 2020, In : Clinical Microbiology and Infection. 26, 1, p. 123.e1-123.e7

Research output: Contribution to journalArticle

1 Scopus citations
2019

A multitask multiple kernel learning algorithm for survival analysis with application to cancer biology

Dereli, O., Oǧuz, C. & Gönen, M., Jan 1 2019, 36th International Conference on Machine Learning, ICML 2019. International Machine Learning Society (IMLS), p. 2844-2853 10 p. (36th International Conference on Machine Learning, ICML 2019; vol. 2019-June).

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

Identification of SERPINE1 as a regulator of glioblastoma cell dispersal with transcriptome profiling

Seker, F., Cingoz, A., Sur-Erdem, İ., Erguder, N., Erkent, A., Uyulur, F., Selvan, M. E., Gümüş, Z. H., Gönen, M., Bayraktar, H., Wakimoto, H. & Bagci-Onder, T., Nov 2019, In : Cancers. 11, 11, 1651.

Research output: Contribution to journalArticle

Open Access
1 Scopus citations

Path2Surv: Pathway/gene set-based survival analysis using multiple kernel learning

Dereli, O., Oǧuz, C., Gönen, M. & Wren, J., Dec 15 2019, In : Bioinformatics. 35, 24, p. 5137-5145 9 p.

Research output: Contribution to journalArticle

1 Scopus citations

Promoters of Colistin Resistance in Acinetobacter baumannii Infections

Nurtop, E., Baylndlr Bilman, F., Menekse, S., Kurt Azap, O., Gonen, M., Ergonul, O. & Can, F., Sep 1 2019, In : Microbial Drug Resistance. 25, 7, p. 997-1002 6 p.

Research output: Contribution to journalArticle

4 Scopus citations

Protein dynamics analysis reveals that missense mutations in cancer-related genes appear frequently on hinge-neighboring residues

Sayılgan, J. F., Haliloğlu, T. & Gönen, M., Jun 2019, In : Proteins: Structure, Function and Bioinformatics. 87, 6, p. 512-519 8 p.

Research output: Contribution to journalArticle

1 Scopus citations

The fungal metabolite chaetocin is a sensitizer for pro-apoptotic therapies in glioblastoma

Ozyerli-Goknar, E., Sur-Erdem, I., Seker, F., Cingöz, A., Kayabolen, A., Kahya-Yesil, Z., Uyulur, F., Gezen, M., Tolay, N., Erman, B., Gönen, M., Dunford, J., Oppermann, U. & Bagci-Onder, T., Dec 1 2019, In : Cell Death and Disease. 10, 12, 894.

Research output: Contribution to journalArticle

Open Access
1 Scopus citations

The quality of ECG data acquisition, and diagnostic performance of a novel adhesive patch for ambulatory cardiac rhythm monitoring in arrhythmia detection

Karaoğuz, M. R., Yurtseven, E., Aslan, G., Deliormanlı, B. G., Adıgüzel, Ö., Gonen, M., Li, K. M. & Yılmaz, E. N., May 1 2019, In : Journal of Electrocardiology. 54, p. 28-35 8 p.

Research output: Contribution to journalArticle

3 Scopus citations
2018

Discriminating early- and late-stage cancers using multiple kernel learning on gene sets

Rahimi, A. & Gönen, M., Jul 1 2018, In : Bioinformatics. 34, 13, p. i412-i421

Research output: Contribution to journalArticle

9 Scopus citations

Impact of the ST101 clone on fatality among patients with colistin-resistant Klebsiella pneumoniae infection

Can, F., Menekse, S., Ispir, P., Atac, N., Albayrak, O., Demir, T., Karaaslan, D. C., Karahan, S. N., Kapmaz, M., Azap, O. K., Timurkaynak, F., Yavuz, S. S., Basaran, S., Yoruk, F., Azap, A., Koculu, S., Benzonana, N., Lack, N. A., Gönen, M. & Ergonul, O., May 1 2018, In : Journal of Antimicrobial Chemotherapy. 73, 5, p. 1235-1241 7 p.

Research output: Contribution to journalArticle

9 Scopus citations

Pan-cancer transcriptional signatures predictive of oncogenic mutations reveal that Fbw7 regulates cancer cell oxidative metabolism

Davis, R. J., Gönen, M., Margineantu, D. H., Handeli, S., Swanger, J., Hoellerbauer, P., Paddison, P. J., Gu, H., Raftery, D., Grim, J. E., Hockenbery, D. M., Margolin, A. A. & Clurman, B. E., May 22 2018, In : Proceedings of the National Academy of Sciences of the United States of America. 115, 21, p. 5462-5467 6 p.

Research output: Contribution to journalArticle

5 Scopus citations

Spatiotemporal prediction of infectious diseases using structured Gaussian processes with application to Crimean–Congo hemorrhagic fever

Ak, Ç., Ergönül, Ö., Şencan, İ., Torunoğlu, M. A. & Gönen, M., Aug 2018, In : PLoS neglected tropical diseases. 12, 8, e0006737.

Research output: Contribution to journalArticle

3 Scopus citations

Systematic review and meta-analysis of postexposure prophylaxis for crimean-congo hemorrhagic fever virus among healthcare workers

Ergönül, Ö., Keske, Ş., Çeldir, M. G., Kara, İ. A., Pshenichnaya, N., Abuova, G., Blumberg, L. & Gonen, M., Sep 1 2018, In : Emerging Infectious Diseases. 24, 9, p. 1642-1648 7 p.

Research output: Contribution to journalArticle

6 Scopus citations

The Role of AcrAB–TolC Efflux Pumps on Quinolone Resistance of E. coli ST131

Atac, N., Kurt-Azap, O., Dolapci, I., Yesilkaya, A., Ergonul, O., Gonen, M. & Can, F., Dec 1 2018, In : Current Microbiology. 75, 12, p. 1661-1666 6 p.

Research output: Contribution to journalArticle

4 Scopus citations
2017

A Community Challenge for Inferring Genetic Predictors of Gene Essentialities through Analysis of a Functional Screen of Cancer Cell Lines

Gönen, M., Weir, B. A., Cowley, G. S., Vazquez, F., Guan, Y., Jaiswal, A., Karasuyama, M., Uzunangelov, V., Wang, T., Tsherniak, A., Howell, S., Marbach, D., Hoff, B., Norman, T. C., Airola, A., Bivol, A., Bunte, K., Carlin, D., Chopra, S., Deran, A. & 60 others, Ellrott, K., Gopalacharyulu, P., Graim, K., Kaski, S., Khan, S. A., Newton, Y., Ng, S., Pahikkala, T., Paull, E., Sokolov, A., Tang, H., Tang, J., Wennerberg, K., Xie, Y., Zhan, X., Zhu, F., Afsari, B., Aittokallio, T., Boehm, J. S., Chang, Y. C., Chen, T., Chong, Z., Elmarakeby, H., Fertig, E. J., Gonçalves, E., Gong, P., Hafemeister, C., Hahn, W. C., Heath, L., Kędziorski, Ł., Khemka, N., King, E. K., Lauria, M., Liu, M., Machado, D., Mamitsuka, H., Margolin, A., Mazurkiewicz, M., Menden, M. P., Migacz, S., Nie, Z., Praveen, P., Priami, C., Rizzetto, S., Rocha, M., Root, D. E., Rudd, C., Rudnicki, W. R., Saez-Rodriguez, J., Song, L., Stolovitzky, G., Stuart, J. M., Sun, D., Szalai, B., Wang, D., Wu, L. Y., Xiao, G., Ye, J., Ye, Y. & Zhou, W., Jan 1 2017, In : Cell Systems. 5, 5, p. 485-497.e3

Research output: Contribution to journalArticle

8 Scopus citations

Cytokine response in crimean-congo hemorrhagic fever virus infection

Ergönül, Ö., Şeref, C., Eren, Ş., Çelikbaş, A., Baykam, N., Dokuzoğuz, B., Gonen, M. & Can, F., Oct 1 2017, In : Journal of Medical Virology. 89, 10, p. 1707-1713 7 p.

Research output: Contribution to journalArticle

15 Scopus citations

Modeling gene-wise dependencies improves the identification of drug response biomarkers in cancer studies

Nikolova, O., Moser, R., Kemp, C., Gonen, M. & Margolin, A., May 1 2017, In : Bioinformatics. 33, 9, p. 1362-1369 8 p.

Research output: Contribution to journalArticle

4 Scopus citations
2016

AUC Maximization in Bayesian hierarchical models

Gonen, M., 2016, Frontiers in Artificial Intelligence and Applications. IOS Press, Vol. 285. p. 21-27 7 p. (Frontiers in Artificial Intelligence and Applications; vol. 285).

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

DREAMTools: A Python package for scoring collaborative challenges

Cokelaer, T., Bansal, M., Bare, C., Bilal, E., Bot, B. M., Chaibub Neto, E., Eduati, F., de la Fuente, A., Gonen, M., Hill, S. M., Hoff, B., Karr, J. R., Küffner, R., Menden, M. P., Meyer, P., Norel, R., Pratap, A., Prill, R. J., Weirauch, M. T., Costello, J. C. & 2 others, Stolovitzky, G. & Saez-Rodriguez, J., 2016, In : F1000Research. 4, 1030.

Research output: Contribution to journalArticle

6 Scopus citations

Integrating gene set analysis and nonlinear predictive modeling of disease phenotypes using a Bayesian multitask formulation

Gönen, M., Dec 13 2016, In : BMC bioinformatics. 17, p. 123-135 13 p., 0.

Research output: Contribution to journalReview article

Open Access
2 Scopus citations

Ultrasensitive proteomic quantitation of cellular signaling by digitized nanoparticle-protein counting

Jacob, T., Agarwal, A., Ramunno-Johnson, D., O'Hare, T., Gonen, M., Tyner, J., Druker, B. & Vu, T. T., Jun 20 2016, In : Scientific Reports. 6, 28163.

Research output: Contribution to journalArticle

3 Scopus citations
2015

Understanding emotional impact of images using Bayesian multiple kernel learning

Zhang, H., Gönen, M., Yang, Z. & Oja, E., Oct 1 2015, In : Neurocomputing. 165, p. 3-13 11 p.

Research output: Contribution to journalArticle

9 Scopus citations
2014

A community effort to assess and improve drug sensitivity prediction algorithms

NCI DREAM Community, Dec 1 2014, In : Nature biotechnology. 32, 12, p. 1202-1212 11 p.

Research output: Contribution to journalArticle

290 Scopus citations

Bayesian multiview dimensionality reduction for learning predictive subspaces

Gönen, M., Gönen, G. B. & Gürgen, F., Jan 1 2014, ECAI 2014 - 21st European Conference on Artificial Intelligence, Including Prestigious Applications of Intelligent Systems, PAIS 2014, Proceedings. Schaub, T., Friedrich, G. & O'Sullivan, B. (eds.). IOS Press, p. 387-392 6 p. (Frontiers in Artificial Intelligence and Applications; vol. 263).

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

3 Scopus citations
8 Scopus citations

Drug susceptibility prediction against a panel of drugs using kernelized Bayesian multitask learning

Gönen, M. & Margoliny, A. A., Sep 1 2014, In : Bioinformatics. 30, 17, p. i556-i563

Research output: Contribution to journalArticle

37 Scopus citations

Embedding heterogeneous data by preserving multiple kernels

Gönen, M., Jan 1 2014, ECAI 2014 - 21st European Conference on Artificial Intelligence, Including Prestigious Applications of Intelligent Systems, PAIS 2014, Proceedings. Schaub, T., Friedrich, G. & O'Sullivan, B. (eds.). IOS Press, p. 381-386 6 p. (Frontiers in Artificial Intelligence and Applications; vol. 263).

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

1 Scopus citations

Integrative and personalized QSAR analysis in cancer by kernelized Bayesian matrix factorization

Ammad-Ud-Din, M., Georgii, E., Gönen, M., Laitinen, T., Kallioniemi, O., Wennerberg, K., Poso, A. & Kaski, S., Aug 25 2014, In : Journal of Chemical Information and Modeling. 54, 8, p. 2347-2359 13 p.

Research output: Contribution to journalArticle

49 Scopus citations

Kernelized Bayesian Matrix Factorization

Gonen, M. & Kaski, S., Oct 2014, In : IEEE Transactions on Pattern Analysis and Machine Intelligence. 36, 10, p. 2047-2060 14 p., 6777351.

Research output: Contribution to journalArticle

35 Scopus citations

Kernelized Bayesian transfer learning

Gönen, M. & Margolin, A. A., Jan 1 2014, Proceedings of the National Conference on Artificial Intelligence. AI Access Foundation, p. 1831-1839 9 p. (Proceedings of the National Conference on Artificial Intelligence; vol. 3).

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

14 Scopus citations

Localized data fusion for kernel k-means clustering with application to cancer biology

Gönen, M. & Margolin, A. A., Jan 1 2014, In : Advances in Neural Information Processing Systems. 2, January, p. 1305-1313 9 p.

Research output: Contribution to journalConference article

52 Scopus citations

Multi-task and multi-view learning of user state

Kandemir, M., Vetek, A., Gönen, M., Klami, A. & Kaski, S., Sep 2 2014, In : Neurocomputing. 139, p. 97-106 10 p.

Research output: Contribution to journalArticle

10 Scopus citations
2013

Affective abstract image classification and retrieval using multiple kernel learning

Zhang, H., Yang, Z., Gon̈en, M., Koskela, M., Laaksonen, J., Honkela, T. & Oja, E., Dec 1 2013, Neural Information Processing - 20th International Conference, ICONIP 2013, Proceedings. PART 3 ed. p. 166-175 10 p. (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); vol. 8228 LNCS, no. PART 3).

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

9 Scopus citations

Bayesian supervised dimensionality reduction

Gonen, M., Dec 1 2013, In : IEEE Transactions on Cybernetics. 43, 6, p. 2179-2189 11 p., 6475174.

Research output: Contribution to journalArticle

11 Scopus citations

Kernelized bayesian matrix factorization

Gönen, M., Khan, S. A. & Kaski, S., Jan 1 2013, p. 1901-1909. 9 p.

Research output: Contribution to conferencePaper

4 Scopus citations

Localized algorithms for multiple kernel learning

Gönen, M. & Alpaydin, E., Mar 1 2013, In : Pattern Recognition. 46, 3, p. 795-807 13 p.

Research output: Contribution to journalArticle

60 Scopus citations

Predicting emotional states of images using Bayesian multiple kernel learning

Zhang, H., Gönen, M., Yang, Z. & Oja, E., Dec 1 2013, Neural Information Processing - 20th International Conference, ICONIP 2013, Proceedings. PART 3 ed. p. 274-282 9 p. (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); vol. 8228 LNCS, no. PART 3).

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

2 Scopus citations

Supervised multiple kernel embedding for learning predictive subspaces

Gonen, M., Sep 5 2013, In : IEEE Transactions on Knowledge and Data Engineering. 25, 10, p. 2381-2389 9 p., 6338928.

Research output: Contribution to journalArticle

6 Scopus citations
2012

A Bayesian multiple kernel learning framework for single and multiple output regression

Gönen, M., 2012, ECAI 2012 - 20th European Conference on Artificial Intelligence, 27-31 August 2012, Montpellier, France - Including Prestigious Applications of Artificial Intelligence (PAIS-2012) System Demonstration. IOS Press, p. 354-359 6 p. (Frontiers in Artificial Intelligence and Applications; vol. 242).

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

6 Scopus citations

A localized MKL method for brain classification with known intra-class variability

Ulaş, A., Gönen, M., Castellani, U., Murino, V., Bellani, M., Tansella, M. & Brambilla, P., Nov 30 2012, Machine Learning in Medical Imaging - Third International Workshop, MLMI 2012, Held in Conjunction with MICCAI 2012, Revised Selected Papers. p. 152-159 8 p. (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); vol. 7588 LNCS).

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

1 Scopus citations

Bayesian efficient multiple kernel learning

Gönen, M., Oct 10 2012, Proceedings of the 29th International Conference on Machine Learning, ICML 2012. p. 1-8 8 p. (Proceedings of the 29th International Conference on Machine Learning, ICML 2012; vol. 1).

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

48 Scopus citations

Bayesian supervised multilabel learning with coupled embedding and classification

Gönen, M., 2012, Proceedings of the 12th SIAM International Conference on Data Mining, SDM 2012. Society for Industrial and Applied Mathematics Publications, p. 367-378 12 p. (Proceedings of the 12th SIAM International Conference on Data Mining, SDM 2012).

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

2 Scopus citations

Predicting drug-target interactions from chemical and genomic kernels using Bayesian matrix factorization

Gönen, M., Sep 1 2012, In : Bioinformatics. 28, 18, p. 2304-2310 7 p., bts360.

Research output: Contribution to journalArticle

191 Scopus citations

Probabilistic and discriminative group-wise feature selection methods for credit risk analysis

Bozkurt Gönen, G., Gönen, M. & Gürgen, F., Oct 15 2012, In : Expert Systems with Applications. 39, 14, p. 11709-11717 9 p.

Research output: Contribution to journalArticle

9 Scopus citations
2011

Combining data sources nonlinearly for cell nucleus classification of renal cell carcinoma

Gönen, M., Ulaş, A., Schüffler, P., Castellani, U. & Murino, V., Oct 5 2011, Similarity-Based Pattern Recognition - First International Workshop, SIMBAD 2011, Proceedings. p. 250-260 11 p. (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); vol. 7005 LNCS).

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

1 Scopus citations

Multiple kernel learning algorithms

Gönen, M. & Alpaydin, E., Jul 1 2011, In : Journal of Machine Learning Research. 12, p. 2211-2268 58 p.

Research output: Contribution to journalReview article

1101 Scopus citations

Multitask learning using regularized multiple kernel learning

Gönen, M., Kandemir, M. & Kaski, S., Nov 28 2011, Neural Information Processing - 18th International Conference, ICONIP 2011, Proceedings. PART 2 ed. p. 500-509 10 p. (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); vol. 7063 LNCS, no. PART 2).

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

3 Scopus citations

Regularizing multiple kernel learning using response surface methodology

Gönen, M. & Alpaydn, E., Jan 1 2011, In : Pattern Recognition. 44, 1, p. 159-171 13 p.

Research output: Contribution to journalArticle

13 Scopus citations