Alper Kucukural

Assistant Professor
Program in Molecular Medicine
UMass Medical School





Publications

  1. Simultaneous generation of many RNA-seq libraries in a single reaction
    Alexander A Shishkin, Georgia Giannoukos, Alper Kucukural, ...
    Nature Methods (2015),doi:10.1038/nmeth.3313

  2. Staufen1 senses overall transcript secondary structure to regulate translation
    EP Ricci, A Kucukural, C Cenik, BC Mercier, G Singh, EE Heyer, ...
    Nature structural & molecular biology 21 (1), 26-35, 2014

  3. ASPeak: an abundance sensitive peak detection algorithm for RIP-Seq
    A Kucukural*, H Özadam*, G Singh, MJ Moore, C Cenik
    Bioinformatics, 2013

    *Authors have equal contribution

  4. Protein Homology Analysis for Function Prediction with Parallel Sub—Graph lsomorphism
    A Kucukural, A Szilagyi, OU Sezerman, Y Zhang
    Bioinformatics: Concepts, Methodologies, Tools, and Applications, 386, 2013

  5. The cellular EJC interactome reveals higher-order mRNP structure and an EJC-SR protein nexus
    G Singh*, A Kucukural*, C Cenik, JD Leszyk, SA Shaffer, Z Weng, MJ Moore
    Cell 151 (4), 750-764, 2012

    *Authors have equal contribution

  6. Abundance sensitive diferentially expressed cluster detection for RIP-Seq
    A Kucukural, C Cenik, G Singh, Z Weng, M Moore
    FEBS JOURNAL 279, 510-511, 2012

  7. Identification of neuronal RNA targets of TDP-43-containing ribonucleoprotein complexes
    CF Sephton*, C Cenik*, A Kucukural*, EB Dammer, B Cenik, YH Han, ...
    Journal of Biological Chemistry, 2010

    *Authors have equal contribution

  8. I-TASSER: a unified platform for automated protein structure and function prediction
    A Roy, A Kucukural, Y Zhang
    Nature protocols 5 (4), 725-738, 2010

  9. Generation and analysis of expressed sequence tags (ESTs) from olea europaea L.
    N Özdemir Özgentürk, F Oruç, U Sezerman, A Kucukural, Ş Vural Korkut, ...
    Comparative and Functional Genomics, 2010

  10. mRNAs with a complex: The long-term consequences of a nuclear upbringing
    MJ Moore, G Singh, A Kucukural, Z Weng
    The FASEB Journal, 2010

  11. Discovery of biomarkers for hexachlorobenzene toxicity using population based methods on gene expression data
    C Meydan, A Kucukural, D Yörükoğlu, OU Sezerman
    Pattern Recognition in Bioinformatics, 412-423, 2008

  12. Biomarker detection for hexachlorobenzene toxicity using genetic algorithms on gene expression data
    C Meydan, A Kucukural, D Yörükoğlu, OU Sezerman
    International Symposium on Health Informatics and Bioinformatics (HIBIT ‘08 ..., 2008

  13. Discrimination of Native Folds Using Network Properties of Protein Structures.
    A Kucukural, OU Sezerman, A Ercil
    APBC, 59-68, 2008

  14. Evolutionary selection of minimum number of features for classification of gene expression data using genetic algorithms
    A Kucukural, R Yeniterzi, S Yeniterzi, OU Sezerman
    Proceedings of the 9th annual conference on Genetic and evolutionary ..., 2007

  15. Potential use of graph theoretical properties of protein structures in structural alignment
    A Kucukural, U Sezerman
    CSREA Press, 2007

  16. Discrimination of proteins using graph theoretic properties
    A Kucukural, OU Sezerman
    BMC Systems Biology 1 (Suppl 1), P49, 2007

  17. Feature selection with genetic algorithms on cardiac arrhytnua database
    S Yeniterzi, R Yeniterzi, A Kucukural, U Sezerman
    HIBIT, 2007

  18. Protein Fold Prediction Using Attributed Graph Matching with Parallel Computing
    A Kucukural, U Sezerman
    HIBIT, 2007

  19. Modified association rule mining approach for the MHC-Peptide binding problem
    GG Yardımcı, A Kucukural, Y Saygın, U Sezerman
    Computer and Information Sciences–ISCIS 2006, 165-173, 2006