Mehmet Gonen

Research Assistant Professor

  • 2382 Citations
  • 14 h-Index
20082020

Research output per year

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Research Output

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Article
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

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

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

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
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

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

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

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

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

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

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

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
2010

Cost-conscious multiple kernel learning

Gönen, M. & Alpaydin, E., Jul 1 2010, In : Pattern Recognition Letters. 31, 9, p. 959-965 7 p.

Research output: Contribution to journalArticle

14 Scopus citations

Supervised learning of local projection kernels

Gönen, M. & Alpaydn, E., Jun 1 2010, In : Neurocomputing. 73, 10-12, p. 1694-1703 10 p.

Research output: Contribution to journalArticle

5 Scopus citations
2009

Machine learning integration for predicting the effect of single amino acid substitutions on protein stability

Özen, A., Gönen, M., Alpaydn, E. & Haliloǧlu, T., Dec 28 2009, In : BMC Structural Biology. 9, 66.

Research output: Contribution to journalArticle

17 Scopus citations
2008

Multiclass posterior probability support vector machines

Gönen, M., Tanuǧur, A. G. & Alpaydin, E., Jan 1 2008, In : IEEE Transactions on Neural Networks. 19, 1, p. 130-139 10 p.

Research output: Contribution to journalArticle

53 Scopus citations