Publications & Works

Publication Network
Journal articles indexed in SCI, SSCI, and AHCI 32

1. Effective primer design for genotype and subtype detection of highly divergent viruses in large scale genome datasets

Demiralay B., Can T.
BMC Bioinformatics , vol.26, no.1, 2025 (SCI-Expanded) identifier identifier identifier

2. Phosphorylation of SNAP-25 at Ser187 is enhanced following its cleavage by Botulinum Neurotoxin Serotype A, promoting the dominant-negative effect of the resulting fragment

Koc D., EZGİN S., Kavakli E., Kota K. P., Sen E., Mahone C., et al.
PLOS Pathogens , vol.21, no.10 October, 2025 (SCI-Expanded) Creative Commons License identifier identifier

3. Differential expression of mRNA 3′-end isoforms in cervical and ovarian cancers

Döken D. N., Özgül İ., Köksal Bıçakcı G., Gol K., Can T., Erson Bensan A. E.
Heliyon , vol.9, no.9, 2023 (SCI-Expanded) Creative Commons License identifier identifier identifier

4. Targeting HIF1-alpha/miR-326/ITGA5 axis potentiates chemotherapy response in triple-negative breast cancer

Assidicky R., Tokat U. M., Tarman I. O., Saatci O., Ersan P. G., Raza U., et al.
BREAST CANCER RESEARCH AND TREATMENT , vol.193, no.2, pp.331-348, 2022 (SCI-Expanded) Sustainable Development identifier identifier identifier

5. A C-term truncated EIF2Bγ protein encoded by an intronically polyadenylated isoform introduces unfavorable EIF2Bγ-EIF2γ interactions.

Circir A., Bicakci G. K., Savas B., Doken D. N., Henden O., Can T., et al.
Proteins , vol.90, no.3, pp.889-897, 2022 (SCI-Expanded) Sustainable Development identifier identifier identifier

6. Identification of an mRNA isoform switch for HNRNPA1 in breast cancers

Erdem M., Ozgul İ., Dioken D. N., Gurcuoglu I., Guntekin Ergun S., Cetin-Atalay R., et al.
Scientific Reports , vol.11, no.1, 2021 (SCI-Expanded) Sustainable Development identifier identifier identifier

7. MotifGenie: A Python Application for Searching Transcription Factor Binding Sequences Using ChIP-Seq Datasets.

Oguztuzun C., Yasar P., Yavuz K., Muyan M., Can T.
Bioinformatics (Oxford, England) , vol.37, pp.4238-4239, 2021 (SCI-Expanded) identifier identifier identifier

8. A prelude to the proximity interaction mapping of CXXC5

Ayaz G., Turan G., OLGUN Ç. E., Kars G., Karakaya B., Yavuz K., et al.
SCIENTIFIC REPORTS , vol.11, no.1, 2021 (SCI-Expanded) identifier identifier identifier

9. A CpG island promoter drives the CXXC5 gene expression

Yasar P., Kars G., Yavuz K., Ayaz G., Oguztuzun C., Bilgen E., et al.
SCIENTIFIC REPORTS , vol.11, no.1, 2021 (SCI-Expanded) identifier identifier identifier

10. JOA: Joint Overlap Analysis of multiple genomic interval sets

Otlu B., Can T.
BMC BIOINFORMATICS , vol.20, 2019 (SCI-Expanded) Sustainable Development identifier identifier identifier

11. Alternative Polyadenylation Patterns for Novel Gene Discovery and Classification in Cancer

BEGIK O., ÖYKEN M., ALICAN T. C., CAN T., Erson-Bensan A. E.
NEOPLASIA , vol.19, no.7, pp.574-582, 2017 (SCI-Expanded) Sustainable Development identifier identifier identifier

12. A multiplex primer design algorithm for target amplification of continuous genomic regions

OZTURK A. R., CAN T.
BMC BIOINFORMATICS , vol.18, 2017 (SCI-Expanded) identifier identifier identifier

13. Comparison of tissue/disease specific integrated networks using directed graphlet signatures

Sonmez A. B., Can T.
BMC BIOINFORMATICS , vol.18, 2017 (SCI-Expanded) Creative Commons License identifier identifier identifier

14. SUMONA: A supervised method for optimizing network alignment

TUNCAY E. G., Can T.
COMPUTATIONAL BIOLOGY AND CHEMISTRY , vol.63, pp.41-51, 2016 (SCI-Expanded) identifier identifier identifier

15. Alternative Polyadenylation: Another Foe in Cancer

Erson-Bensan A. E., CAN T.
MOLECULAR CANCER RESEARCH , vol.14, no.6, pp.507-517, 2016 (SCI-Expanded) Creative Commons License Sustainable Development identifier identifier identifier

16. 3 ' UTR shortening and EGF signaling: implications for breast cancer

AKMAN H. B., ÖYKEN M., TUNCER T., CAN T., Erson-Bensan A. E.
HUMAN MOLECULAR GENETICS , vol.24, no.24, pp.6910-6920, 2015 (SCI-Expanded) Creative Commons License Sustainable Development identifier identifier identifier

17. Reconstruction of the temporal signaling network in Salmonella-infected human cells

Budak G., Ozsoy O. E., Son Y., Can T., Tunçbağ N.
FRONTIERS IN MICROBIOLOGY , vol.6, 2015 (SCI-Expanded) Sustainable Development identifier identifier identifier

18. The CHEMDNER corpus of chemicals and drugs and its annotation principles

Krallinger M., Rabal O., Leitner F., Vazquez M., Salgado D., Lu Z., et al.
JOURNAL OF CHEMINFORMATICS , vol.7, 2015 (SCI-Expanded) identifier identifier

19. Div-BLAST: Diversification of Sequence Search Results

Eser E., CAN T., Ferhatosmanoglu H.
PLOS ONE , vol.9, no.12, 2014 (SCI-Expanded) identifier identifier identifier

20. GPCRsort-Responding to the Next Generation Sequencing Data Challenge: Prediction of G Protein-Coupled Receptor Classes Using Only Structural Region Lengths

Sahın M. E., Can T., Son Ç. D.
OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY , vol.18, pp.636-644, 2014 (SCI-Expanded) Sustainable Development identifier identifier identifier

21. Identification of Novel Reference Genes Based on MeSH Categories

Ersahin T., ÇARKACIOĞLU L., CAN T., Konu O., Atalay V., Cetin-Atalay R.
PLOS ONE , vol.9, no.3, 2014 (SCI-Expanded) Creative Commons License identifier identifier identifier

22. A Divide and Conquer Approach for Construction of Large-Scale Signaling Networks from PPI and RNAi Data Using Linear Programming

Ozsoy O. E., Can T.
IEEE-ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS , vol.10, pp.869-883, 2013 (SCI-Expanded) identifier identifier identifier

23. Large-Scale Signaling Network Reconstruction

Hashemikhabir S., Ayaz E. S., Kavurucu Y., Can T., Kahveci T.
IEEE-ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS , vol.9, pp.1696-1708, 2012 (SCI-Expanded) identifier identifier identifier

24. Estrogen-induced upregulation and 3 '-UTR shortening of CDC6

AKMAN B. H., CAN T., Erson-Bensan A. E.
NUCLEIC ACIDS RESEARCH , vol.40, no.21, pp.10679-10688, 2012 (SCI-Expanded) Creative Commons License Sustainable Development identifier identifier identifier

25. Using network context as a filter for miRNA target prediction

Sualp M., Can T.
BIOSYSTEMS , vol.105, pp.201-209, 2011 (SCI-Expanded) identifier identifier identifier

26. METADATA MANAGEMENT AND SEMANTICS IN MICROARRAY REPOSITORIES

Kocabas F., CAN T., BAYKAL N.
BALKAN JOURNAL OF MEDICAL GENETICS , vol.14, no.2, pp.49-63, 2011 (SCI-Expanded) Creative Commons License identifier identifier

27. Bi-k-bi clustering: mining large scale gene expression data using two-level biclustering

Carkacioglu L., Atalay R. C., KONU KARAKAYALI Ö., Atalay V., CAN T.
INTERNATIONAL JOURNAL OF DATA MINING AND BIOINFORMATICS , vol.4, no.6, pp.701-721, 2010 (SCI-Expanded) Creative Commons License identifier identifier

28. RRW: repeated random walks on genome-scale protein networks for local cluster discovery

MACROPOL K., Can T., Singh A. K.
BMC BIOINFORMATICS , vol.10, 2009 (SCI-Expanded) Creative Commons License identifier identifier identifier

29. Integration of topological measures for eliminating non-specific interactions in protein interaction networks

BAYIR M. A., GUNEY T. D., Can T.
DISCRETE APPLIED MATHEMATICS , vol.157, no.10, pp.2416-2424, 2009 (SCI-Expanded) identifier identifier

30. Discovering functional interaction patterns in protein-protein interaction networks

Turanalp M. E., Can T.
BMC BIOINFORMATICS , vol.9, 2008 (SCI-Expanded) Creative Commons License identifier identifier identifier

31. Efficient molecular surface generation using level-set methods

Can T., Chen C., Wang Y.
JOURNAL OF MOLECULAR GRAPHICS & MODELLING , vol.25, no.4, pp.442-454, 2006 (SCI-Expanded) identifier identifier identifier

32. Integrating multi-attribute similarity networks for robust representation of the protein space

Camoglu O., Can T., Singh A. K.
BIOINFORMATICS , vol.22, no.13, pp.1585-1592, 2006 (SCI-Expanded) Creative Commons License identifier identifier identifier
Articles Published in Other Journals 1

1. Informatics Olympiads in Turkey Team Selection and Training

CAN T., SIĞIRCI İ. O., ABUL O., DEMİRCİ M. F.
OLYMPIADS IN INFORMATICS , vol.9, pp.225-232, 2015 (Peer-Reviewed Journal)
Papers Presented at Peer-Reviewed Scientific Conferences 22

1. HNRNPA1 Isoform Switch in Breast Cancer

ÖZGÜL İ., Erdem M., Döken D. N., GÜRCÜOĞLU I., GÜNTEKİN ERGÜN S., Cetin Atalay R., et al.
Frontiers in Cancer Science 2021, Singapore, 1 - 03 November 2021, vol.1, pp.28, (Summary Text)

2. Transcription Elongation in Connection to 3’UTR Ends

ÖZGÜL İ., CAN T., ERSON BENSAN A. E.
Moleküler Biyoloji Kongresi MolBiyoKON18, İzmir, Turkey, 5 - 08 September 2018, pp.20

3. Deregulated APA and cancer specific APA isoforms

Begik O., Ercan M., Cingoz H., CAN T., ÖYKEN M., Erson-Bensan A. E.
Annual Meeting of the American-Association-for-Cancer-Research (AACR), Illinois, United States Of America, 14 - 18 April 2018, vol.78 Sustainable Development identifier

4. Alternative Polyadenylation patterns for cancer classification

BEGIK O., ÖYKEN M., ÇINKILLI t., CAN T., ERSON BENSAN A. E.
HIBIT 2017, 28 - 30 June 2017, (Summary Text) Sustainable Development identifier identifier identifier

5. Alternative Polyadenylation patterns for novel gene discovery and classification in cancer

BEĞİK O., ÖYKEN M., CAN T., ERSON BENSAN A. E.
Annual Meeting of the RNA Society, 30 May - 03 June 2017 Sustainable Development

6. APA isoform diversity in triple negative breast cancers

AKMAN TUNCER H. B., ÖYKEN M., AĞUŞ H. H., ERDEM M., YAVUZ E., CAN T., et al.
AACR Annual Meeting, USA, Washington, United States Of America, 1 - 05 April 2017, vol.77, pp.3374, (Summary Text) Sustainable Development identifier

7. Identification of a potential cancer related lncRNA

BEĞİK O., cinkilli t., ÖYKEN M., CAN T., ERSON BENSAN A. E.
Functional Genomics to Systems Biology-EMBO, 12 - 15 November 2016 Sustainable Development

8. Comparison of tissue disease specific integrated networks using directed graphlet signatures

SÖNMEZ A. B., CAN T.
Proceedings of the 7th ACM International Conference on Bioinformatics, Computational Biology, and Health Informatics - BCB '16, Seattle, WA, USA, United States Of America, 2 - 05 October 2016

9. 3 UTR Length Changes In Connection With Estrogen Receptor Alpha In Breast Cancer

ÖYKEN M., CAN T., ERSON BENSAN A. E.
FEBS 2016, KUSADASI, Turkey, 3 - 08 September 2016 Sustainable Development

10. 3 ' UTR lengths change in connection with estrogen receptor-alpha in breast cancer

ÖYKEN M., CAN T., Erson-Bensan A. E.
41st FEBS Congress on Molecular and Systems Biology for a Better Life, Kusadasi, Turkey, 3 - 08 September 2016, vol.283, pp.207 Sustainable Development identifier

11. Unsupervised identification of redundant domain entries in InterPro database using clustering techniques

RİFAİOĞLU A. S., DOĞAN T., CAN T.
6th ACM Conference on Bioinformatics, Computational Biology, and Health Informatics, BCB 2015, Georgia, United States Of America, 9 - 12 September 2015, pp.505-506 identifier

12. Reconstruction of the Temporal Signaling Network in Salmonella Infected Human Cells

güngör b., EREN ÖZSOY Ö., AYDIN SON Y., CAN T., nurcan t.
23rd Annual International Conference on Intelligent Systems for Molecular Biology and the 14th European Conference on Computational Biology (ISMBECCB’2015), Dublin, Ireland, 10 - 14 July 2015

13. Dbchem A database query based solution for the chemical compound and drug name recognition task

ATA Ç., CAN T.
Proceedings of the Fourth BioCreative Challenge Evaluation Workshop, BioCreative IV,, 1 - 03 October 2013, vol.2, pp.42-46

14. M4B: A novel method for designing and ordering of the genetic devices

Hashemikhabir S., Ersoy G., Oguz G., Yaldiz B., Tuncel Y., Budak G., et al.
2012 7th International Symposium on Health Informatics and Bioinformatics, HIBIT 2012, Cappadocia, Turkey, 19 - 22 April 2012, pp.123-127 identifier

15. Parallel SPICi

Hashemikhabir S., CAN T.
6th International Symposium on Health Informatics and Bioinformatics (HIBIT), İzmir, Turkey, 2 - 05 May 2011, pp.86-90 identifier

16. CONSTRUCTING SIGNALING PATHWAYS FROM RNAI DATA USING GENETIC ALGORITHMS

Ayaz E. S., CAN T.
6th International Symposium on Health Informatics and Bioinformatics (HIBIT), İzmir, Turkey, 2 - 05 May 2011, pp.95-98 identifier

17. The effect of representative training dataset selection on the classification performance of the promoter sequences

YAMAN A. G., CAN T.
6th International Symposium on Health Informatics and Bioinformatics, HIBIT 2011, İzmir, Turkey, 2 - 05 May 2011, pp.55-58 identifier identifier

18. Coevolution based prediction of protein-protein interactions with reduced training data

Pamuk B., CAN T.
2010 5th International Symposium on Health Informatics and Bioinformatics, HIBIT 2010, Antalya, Turkey, 20 - 22 April 2010, pp.187-193, (Full Text) Creative Commons License identifier

19. Text Classification in the Turkish Marketing Domain for Context Sensitive Ad Distribution

Engin M., Can T.
24th International Symposium on Computer and Information Sciences, Güzelyurt, Cyprus (Kktc), 14 - 16 September 2009, pp.105-110 identifier identifier

20. Human Skeletal and Muscle Deformation Animation Using Motion Capture Data

Bayer A. O., Sevinc A. M., CAN T.
16th International Conference in Central Europe on Computer Graphics, Visualization and Computer Vision, Plzen, Czech Republic, 4 - 07 February 2008, pp.167-168, (Full Text) identifier

21. Analysis of protein-protein interaction networks using random walks

Can T., Orhan Ç., Singh A. K.
5th International Workshop on Bioinformatics, BIOKDD 2005 - In Conjunction with 11th ACM SIGKDD International Conference on Knowledge Discovery and Data Mining, KDD 2005, Chicago, IL, United States Of America, 21 August 2005, pp.61-68 identifier

22. CTSS: A robust and efficient method for protein structure alignment based on local geometrical and biological features

Can T., WANG Y.
2nd International Computational Systems Bioinformatics Conference, California, United States Of America, 11 - 14 August 2003, pp.169-179 identifier identifier
Books 1

1. Introduction to Bioinformatics

CAN T.
in: miRNomics MicroRNA Biology and Computational Analysis, Yousef Malik, Allmer Jens, Editor, Springer Protocols, pp.51-71, 2013
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