Select Page

TOLGA CAN’S PUBLICATIONS

Tolga Can’s research is in Bioinformatics and has published in the specific areas of protein structures, biological network analysis, and transcriptome analysis in cancer research.

Peer-Reviewed Articles

2003-2022

  • R. Assidicky, U. M. Tokat, I. O. Tarman, O. Saatci, P. G. Ersan, U. Raza, H. Ogul, Y. Riazalhosseini, T. Can, and O. Sahin, “Targeting HIF1-alpha/miR-326/ITGA5 axis potentiates chemotherapy response in triple-negative breast cancer,” Breast Cancer Research and Treatment, 2022 March 25. https://doi.org/10.1007/s10549-022-06569-5

  • M. Erdem, I. Ozgul, D. N. Doken, I. Gurcuoglu, S. G. Ergun, R. Cetin-Atalay, T. Can, and A. E. Erson-Bensan, “Identification of an mRNA isoform switch for HNRNPA1 in breast cancers,” Scientific Reports, 11, Article number: 24444 (2021). https://doi.org/10.1038/s41598-021-04007-y

  • A. Circir, G. Koksal Bicakci, B. Savas, D. N. Doken, O. Henden, T. Can, E. Karaca, and A. E. Erson-Bensan, “A C-term truncated EIF2Bγ protein encoded by an intronically polyadenylated isoform introduces unfavorable EIF2Bγ-EIF2γ interactions,” Proteins, 2021 Nov 19. Published online. https://doi.org/10.1002/prot.26284

  • G. Ayaz, G. Turan, C. E. Olgun, G. Kars, B. Karakaya, K. Yavuz, O. D. Demiralay, T. Can, M. Muyan, and P. Yasar, “A prelude to the proximity interaction mapping of CXXC5,”, Scientific Reports, 11, Article number: 17587 (2021). https://doi.org/10.1038/s41598-021-97060-6

  • P. Yasar, G. Kars, K. Yavuz, G. Ayaz, C. Oguztuzun, E. Bilgen, Z. Suvaci, O. P. Cetinkol, T. Can and M. Muyan, “A CpG island promoter drives the CXXC5 gene expression,” Scientific Reports, 11, Article number: 15655 (2021). https://doi.org/10.1038/s41598-021-95165-6

  • C. Oguztuzun, P. Yasar, K. Yavuz, M. Muyan, and T. Can, “MotifGenie: A Python Application for Searching Transcription Factor Binding Sequences Using ChIP-Seq Datasets,” Bioinformatics, Applications Note, Advanced Access, May 17, 2021. https://doi.org/10.1093/bioinformatics/btab379

  • B. Otlu and T. Can, “JOA: Joint Overlap Analysis of multiple genomic interval sets,” BMC Bioinformatics, 20:121, March 2019. https://doi.org/10.1186/s12859-019-2698-4 

  • O. Begik, M. Oyken, T.C. Alican, T. Can, and A.E. Erson-Bensan, “Alternative Polyadenylation Patterns for Novel Gene Discovery and Classification in Cancer,” Neoplasia, 19(7), 574-582, July 2017. https://doi.org/10.1016/j.neo.2017.04.008

  • A. R. Ozturk and T. Can, “A multiplex primer design algorithm for target amplification of continuous genomic regions,” BMC Bioinformatics, 18:306, June 2017. https://doi.org/10.1186/s12859-017-1716-7

  • A. B. Sonmez and T. Can, “Comparison of tissue/disease specific integrated networks using directed graphlet signatures,” BMC Bioinformatics, 18(Suppl 4):135, 2017. https://doi.org/10.1186/s12859-017-1525-z

  • A. E. Erson-Bensan and T. Can, “Alternative Polyadenylation: Another foe in cancer,” Molecular Cancer Research, Published OnlineFirst, April 13, 2016. https://doi.org/10.1158/1541-7786.MCR-15-0489

  • E. G. Tuncay and T. Can, “SUMONA: A Supervised Method for Optimizing Network Alignment,” Computational Biology and Chemistry, 63:41-51, 2016. https://doi.org/10.1016/j.compbiolchem.2016.03.003

  • H. B. Akman, M. Oyken, T. Tuncer, T. Can, and A. E. Erson-Bensan, “3′ UTR Shortening and EGF signaling: Implications for breast cancer,” Human Molecular Genetics, 2015. https://doi.org/10.1093/hmg/ddv391

  • G. Budak, O. Eren-Ozsoy, Y. Aydin-Son, T. Can, and N. Tuncbag, “Reconstruction of the temporal signaling network in Salmonella-infected human cells,” Frontiers in Microbiology, 6:00730, 2015. https://doi.org/10.3389/fmicb.2015.00730

  • T. Can, I.O. Sigirci, O. Abul, and M.F. Demirci, “Informatics Olympiads in Turkey: Team Selection and Training,” Olympiads in Informatics, 9:225-232, 2015

  • M. Krallinger et al., “The CHEMDNER corpus of chemicals and drugs and its annotation principles,” Journal of Cheminformatics. 7(Suppl 1):S2. 2015. https://doi.org/10.1186/1758-2946-7-S1-S2

  • E. Eser, T. Can, H. Ferhatosmanoglu, “Div-BLAST: Diversification of Sequence Search Results,” PLOS One. December 22, 2014. https://doi.org/10.1371/journal.pone.0115445

  • M.E. Sahin, T. Can, C. Son, “GPCRsort – Responding to the Next Generation Sequencing Data Challenge: Prediction of G Protein-Coupled Receptor Classes Using Only Structural Region Lengths,” OMICS: A Journal of Integrative Biology. 18(10):636-44. Oct 2014. https://doi.org/10.1089/omi.2014.0073

  • T. Ersahin, L. Carkacioglu, T. Can, O. Konu, V. Atalay, R. Cetin-Atalay, “Identification of Novel Reference Genes Based on MeSH Categories,” PLoS ONE 9(3): e93341, 2014. https://doi.org/10.1371/journal.pone.0093341

  • O. Eren Ozsoy and T. Can, “A divide and conquer approach for construction of large- scale signaling networks from PPI and RNAi data using linear programming,” IEEE/ACM Transactions on Computational Biology and Bioinformatics, 10(4):869-883, July 2013. https://doi.org/10.1109/TCBB.2013.80

  • S. Hashemikhabir, E. S. Ayaz, Y. Kavurucu, T. Can, and Tamer Kahveci, “Large-Scale Signaling Network Reconstruction,” IEEE/ACM Transcations on Computational Biology and Bioinformatics, Nov.-Dec. 2012 (vol. 9 no. 6), pp. 1696-1708. https://doi.org/10.1109/TCBB.2012.128

  • B. H. Akman, T. Can, and A. E. Erson-Bensan, “Estrogen-induced upregulation and 3′- UTR shortening of CDC6,” Nucl. Acids Res., September 12, 2012 https://doi.org/10.1093/nar/gks855

  • M. Sualp and T. Can, “Using network context as a filter for miRNA target prediction,” Biosystems, 105(3):201-209, 2011. https://doi.org/10.1016/j.biosystems.2011.04.002

  • L. Carkacioglu, R. C. Atalay, O. Konu, V. Atalay, and T. Can, “Bi-k-Bi Clustering: Mining Large Scale Gene Expression Data Using Two-Level Biclustering,” International Journal of Data Mining and Bioinformatics (IJDMB) , 4(6):701-721, 2010. https://doi.org/10.1504/IJDMB.2010.037548

  • O. Camoglu, T. Can, and A. K. Singh, “Accurate and Scalable Techniques for the Complex/Pathway Membership Problem in Protein Networks,” Advances in Bioinformatics, vol. 2009, Article ID 787128, 2009. https://doi.org/10.1155/2009/787128

  • K. Macropol, T. Can, and A. K. Singh, “RRW: repeated random walks on genome-scale protein networks for local cluster discovery.” BMC Bioinformatics, 10:283, 2009. https://doi.org/10.1186/1471-2105-10-283 

  • M. A. Bayir, T. D. Guney and T. Can, “Integration of topological measures for eliminating non-specific interactions in protein interaction networks,” Discrete Applied Mathematics, 157(10):2416-2424, 2009. https://doi.org/10.1016/j.dam.2008.06.034 

  • M. E. Turanalp and T. Can, “Discovering functional interaction patterns in protein- protein interaction networks,” BMC Bioinformatics, 9:276, 2008. https://doi.org/10.1186/1471-2105-9-276 

  • T. Can, C.-I. Chen, Y.-F. Wang, “Efficient molecular surface generation using level-set methods,” Journal of Molecular Graphics and Modelling (JMGM), 25(4):442-454, 2006. https://doi.org/10.1016/j.jmgm.2006.02.012 

  • O. Camoglu, T. Can, and A.K. Singh, “Integrating multi-attribute similarity networks for robust representation of the protein space,” Bioinformatics, 22(13):1585-1592, 2006. https://doi.org/10.1093/bioinformatics/btl130 

  • O. Camoglu, T. Can, A.K. Singh, and Y.-F. Wang, “Decision Tree Based Information Integration for Automated Protein Classification”, Journal of Bioinformatics and Computational Biology (JBCB), Vol. 3, No. 3 (June 2005), 717-742. https://doi.org/10.1142/S0219720005001259 

  • T. Can and Y.-F. Wang, “Protein Structure Alignment and Fast Similarity Search Using Local Shape Signatures”, Journal of Bioinformatics and Computational Biology (JBCB), Vol. 2, No. 1 (March 2004), 215-239. https://doi.org/10.1142/S0219720004000533 

  • T. Can, Y. Wang, Y.-F. Wang and J. Su, “FPV: fast protein visualization using Java 3D”, Bioinformatics, 19(8):913-922, 2003. https://doi.org/10.1093/bioinformatics/btg104 

Google Scholar

Conference Proceedings

2000-2016
  • A. B. Sonmez and T. Can, “Comparison of tissue/disease specific integrated networks using directed graphlet signatures,” in the Third International Workshop on Computational Network Biology: Modeling, Analysis, and Control (CNB-MAC 2016), October 2, 2016.
  • E. G. Tuncay and T. Can, “SUMONA: A Supervised Method for Optimizing Network Alignment,” in the Proceedings of the Fourteenth Asia Pacific Bioinformatics Conference (APBC 2016), January 11-13, 2016.
  • C. Ata and T. Can, “DBCHEM: A Database Query Based Solution for the Chemical Compound and Drug Name Recognition Task,” in the Proceedings of the Fourth BioCreative Challenge Evaluation Workshop, BioCreative IV, vol. 2, pp. 42-46, October 2013.
  • A.G. Peker and T. Can, “A design goal and design pattern based approach for development of game engines for mobile platforms,” in Proceedings of the 2011 16th International Conference on Computer Games (CGAMES), pp. 114-120, 27-30 July 2011, doi: 10.1109/CGAMES.2011.6000325.
  • E. Akkoyun and T. Can, “Parallelization of the functional flow algorithm for prediction of protein function using protein-protein interaction networks,” in Proceedings of the 2011 International Conference on High Performance Computing and Simulation (HPCS), pp.56-62, 4-8 July 2011, doi: 10.1109/HPCSim.2011.5999807.
  • B. Pamuk and T. Can, “Coevolution based prediction of protein-protein interactions with reduced training data,” in Proceedings of the 5th International Symposium on Health Informaics and Bioinformatics (HIBIT 2010), pp.187-193, 20-22 April 2010.
  • M. Engin and T. Can, “Text classification in the Turkish marketing domain for context sensitive ad distribution,” in Proceedings of the 24th International Symposium on Computer and Information Sciences (ISCIS 2009), pp.105-110, 14-16 Sept. 2009.
  • A. O. Bayer, A. M. Sevinc, and T. Can, “Human Skeletal and Muscle Deformation Animation Using Motion Capture Data,” in Proceedings of the 16th WSCG International Conference in Central Europe on Computer Graphics, Visualization and Computer Vision (WSCG 2008), pp. 167-173, ISBN 978-86943-15-2, Plzen – Bory, Czech Republic, February 2008.
  • T. Can, “ProtRank: A better measure for protein essentiality,” in Proceedings of the 3rd International Symposium on Health Informatics and Bioinformatics (HIBIT’08), Istanbul, May 2008.
  • T. Can, O. Camoglu, and A. K. Singh, “Analysis of protein-protein interaction networks using random walks,” in Proceedings of the 5th ACM SIGKDD Workshop on Data Mining in Bioinformatics, Chicago, August 2005.
  • T. Can, O. Camoglu, A.K. Singh, and Y.-F. Wang, “Automated Protein Classification Using Consensus Decision”, in Proceedings of the Third International IEEE Computer Society Computational Systems Bioinformatics Conference, CSB 2004, pp. 224-235, Stanford, CA, August, 2004.
  • A. Bhattacharya, T. Can, T. Kahveci, A. K. Singh, and Y.-F. Wang, “ProGreSS: Simultaneous Searching of Protein Databases by Sequence and Structure”, in Proceedings of the 9th Pacific Symposium on Biocomputing (PSB2004), 9:264-275, Hawaii, 2004.
  • Y. Wang, T. Can, Y.-F. Wang, and J. Su, “Personalized Annotation and Information Sharing in Protein Science with Information-Slips”, in the 2nd IASTED International Conference on Information and Knowledge Sharing (IKS 2003), pp. 299-304, Scottsdale, AZ, November, 2003.
  • T. Can and Y.-F. Wang, “CTSS: A Robust and Efficient Method for Protein Structure Alignment Based on Local Geometrical and Biological Features”, in Proceedings of the Second International IEEE Computer Society Computational Systems Bioinformatics Conference, CSB 2003, pp. 169-179, Stanford, CA, August, 2003.
  • T. Can, Y. Wang, Y.-F. Wang and J. Su, “FPV: Fast Protein Visualization Using Java 3D”, in Proceedings of the 18th Annual ACM Symposium on Applied Computing, SAC’03, pp. 88-95, Melbourne, FL, March, 2003.
  • T. Can, Y. Wang, Y.-F. Wang, and J. Su, “A Distributed Protein Visualization Application,” in Proceedings of the 3rd Georgia Tech-Emory International Conference on Bioinfomatics, Poster Presentation, Atlanta, GA, Nov., 2001.
  • T. Can, V. Isler and Z. Ipekkan, “Sensor Optimization In a Virtual Environment”, in Proceedings of the 9th Conference on Computer Generated Forces and Behavioral Representation, Orlando, FL, May, 2000.

Book Chapters

2014
  • T. Can, “Introduction to Bioinformatics,” Chapter in miRNomics: MicroRNA Biology and Computational Analysis, Methods in Molecular Biology Volume 1107, 2014, pp 51- 71, Humana Press, doi:10.1007/978-1-62703-748-8_4, ISBN:978-1-62703-748-8.
  • T. Can, “Analysis of Protein-Protein Interaction Networks for Identification of Functional Modules,” Chapter 5 in Recent Advances in Systems Biology Research, series: Systems Biology – Theory, Techniques and Applications, 2014, Nova Science Publishers, ISBN:978-1-62948-736-6/