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Alper Kucukural PhD

TitleAssistant Professor
InstitutionUniversity of Massachusetts Medical School
DepartmentProgram in Molecular Medicine
AddressUniversity of Massachusetts Medical School
55 Lake AVenue North
Worcester MA 01655
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    Other Positions
    InstitutionUMMS - School of Medicine
    DepartmentProgram in Molecular Medicine

    InstitutionUMMS - Programs, Centers and Institutes
    DepartmentBioinformatics and Integrative Biology


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    Istanbul Technical University, Istanbul, , TurkeyBSMathematics Engineering
    Istanbul Technical University, Istanbul, , TurkeyMSSytems Analysis
    Sabanci University, Istanbul, , TurkeyPHDBiological Sciences

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    Dr. Kucukural designs and implements reusable, robust and production grade bioinformatics analysis pipelines and pipeline generation tools for processing next-generation sequencing data. 



    He mainly works on NGS data analysis; RNA-Seq, RIP-Seq, Chip-Seq, CLIP-Seq and derivatives. He implemented algorithms to reduce noise by calling the peaks caused by experimental and alignment biases especially for RIP and CLIP-Seq data.



    Dr. Kucukural worked on analyzing deep sequencing data to discover key elements of splicing of pre-mRNAs to have better understanding of post-transcriptional regulations of RNAs. Moreover, he has deep knowledge of finding genome wide mRNA targets of RNA binding proteins (RBPs). Analyzing RNA targets of tdp43 RBP with deep sequencing on Rat and human was another focus of his research to understand the mechanisms of neuro-degenerative diseases such as Alzheimer and ALS. 



    He also worked for protein structure characterization and prediction. He applied techniques from graph theory on protein structure analysis and implemented the theories from computer sciences to biology to find solutions in drug design and small molecular docking fields. He developed applications using genetic algorithms to discover biomarkers and implemented feature detection methods using various clustering, classification and machine learning algorithms such as hidden markov models and support vector machines. 




    Collapse Bibliographic 
    Collapse selected publications
    Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications. Faculty can login to make corrections and additions.
    List All   |   Timeline
    1. Fazzalari A, Basadonna G, Kucukural A, Tanriverdi K, Koupenova M, Pozzi N, Kakuturu J, Friedrich AU, Korstanje R, Fowler N, Belant JL, Beyer DE, Brooks MB, Dickson EW, Blackwood M, Mueller C, Palesty JA, Freedman JE, Cahan MA. A Translational Model for Venous Thromboembolism: MicroRNA Expression in Hibernating Black Bears. J Surg Res. 2020 Aug 25; 257:203-212. PMID: 32858321.
      View in: PubMed
    2. Lawson ND, Li R, Shin M, Grosse A, Yukselen O, Stone OA, Kucukural A, Zhu L. An improved zebrafish transcriptome annotation for sensitive and comprehensive detection of cell type-specific genes. Elife. 2020 Aug 24; 9. PMID: 32831172.
      View in: PubMed
    3. Li HJ, Ray SK, Kucukural A, Gradwohl G, Leiter AB. Reduced Neurog3 Gene Dosage Shifts Enteroendocrine Progenitor Towards Goblet Cell Lineage in the Mouse Intestine. Cell Mol Gastroenterol Hepatol. 2020 Aug 18. PMID: 32822913.
      View in: PubMed
    4. Kucukural A, Garber M, Yukselen O, Turkyilmaz O, Ozturk A, Girard I, Martin R. DolphinNext: A graphical user interface for creating, deploying and executing Nextflow pipelines. J Biomol Tech. 2020 Aug; 31(Suppl):S25-S26. PMID: 32831734.
      View in: PubMed
    5. Rinaldi VD, Donnard E, Gellatly K, Rasmussen M, Kucukural A, Yukselen O, Garber M, Sharma U, Rando OJ. An atlas of cell types in the mammalian epididymis and vas deferens. Elife. 2020 Jul 30; 9. PMID: 32729827.
      View in: PubMed
    6. Dragon JA, Gates C, Sui SH, Hutchinson JN, Karuturi RKM, Kucukural A, Polson S, Riva A, Settles ML, Thimmapuram J, Levine SS. Bioinformatics Core Survey Highlights the Challenges Facing Data Analysis Facilities. J Biomol Tech. 2020 Apr 29. PMID: 32382253.
      View in: PubMed
    7. Yukselen O, Turkyilmaz O, Ozturk AR, Garber M, Kucukural A. DolphinNext: a distributed data processing platform for high throughput genomics. BMC Genomics. 2020 Apr 19; 21(1):310. PMID: 32306927.
      View in: PubMed
    8. Sissaoui S, Yu J, Yan A, Li R, Zhu LJ, Kucukural A, Yukselen O, Lawson ND. Genomic Characterization of Endothelial Enhancers Reveals a Multifunctional Role for NR2F2 in Regulation of Arteriovenous Gene Expression. Circ Res. 2020 Feb 17. PMID: 32065070.
      View in: PubMed
    9. Wang Y, Lifshitz L, Gellatly K, Vinton CL, Busman-Sahay K, McCauley S, Vangala P, Kim K, Derr A, Jaiswal S, Kucukural A, McDonel P, Hunt PW, Greenough T, Houghton J, Somsouk M, Estes JD, Brenchley JM, Garber M, Deeks SG, Luban J. HIV-1-induced cytokines deplete homeostatic innate lymphoid cells and expand TCF7-dependent memory NK cells. Nat Immunol. 2020 Feb 17. PMID: 32066947.
      View in: PubMed
    10. Özata DM, Yu T, Mou H, Gainetdinov I, Colpan C, Cecchini K, Kaymaz Y, Wu PH, Fan K, Kucukural A, Weng Z, Zamore PD. Evolutionarily conserved pachytene piRNA loci are highly divergent among modern humans. Nat Ecol Evol. 2020 Jan; 4(1):156-168. PMID: 31900453.
      View in: PubMed
    11. Redick SD, Leehy L, Rittenhouse AR, Blodgett DM, Derr AG, Kucukural A, Garber MG, Shultz LD, Greiner DL, Wang JP, Harlan DM, Bortell R, Jurczyk A. Recovery of viable endocrine-specific cells and transcriptomes from human pancreatic islet-engrafted mice. FASEB J. 2020 Jan; 34(1):1901-1911. PMID: 31914605.
      View in: PubMed
    12. Kucukural A. DolphinNext: A Graphical User Interface for Distributed Data Processing of High Throughput Genomics. J Biomol Tech. 2019 Dec; 30(Suppl):S47-S48. PMID: 31896982.
      View in: PubMed
    13. Min SY, Desai A, Yang Z, Sharma A, DeSouza T, Genga RMJ, Kucukural A, Lifshitz LM, Nielsen S, Scheele C, Maehr R, Garber M, Corvera S. Diverse repertoire of human adipocyte subtypes develops from transcriptionally distinct mesenchymal progenitor cells. Proc Natl Acad Sci U S A. 2019 Aug 16. PMID: 31420514.
      View in: PubMed
    14. Mou H, Ozata DM, Smith JL, Sheel A, Kwan SY, Hough S, Kucukural A, Kennedy Z, Cao Y, Xue W. CRISPR-SONIC: targeted somatic oncogene knock-in enables rapid in vivo cancer modeling. Genome Med. 2019 Apr 16; 11(1):21. PMID: 30987660.
      View in: PubMed
    15. Russell MA, Redick SD, Blodgett DM, Richardson SJ, Leete P, Krogvold L, Dahl-Jørgensen K, Bottino R, Brissova M, Spaeth JM, Babon JAB, Haliyur R, Powers AC, Yang C, Kent SC, Derr AG, Kucukural A, Garber MG, Morgan NG, Harlan DM. HLA Class II Antigen Processing and Presentation Pathway Components Demonstrated by Transcriptome and Protein Analyses of islet ß-Cells from Donors with Type 1 Diabetes. Diabetes. 2019 Mar 04. PMID: 30833470.
      View in: PubMed
    16. Kucukural A, Yukselen O, Ozata DM, Moore MJ, Garber M. DEBrowser: interactive differential expression analysis and visualization tool for count data. BMC Genomics. 2019 Jan 05; 20(1):6. PMID: 30611200.
      View in: PubMed
    17. Donnard E, Vangala P, Afik S, McCauley S, Nowosielska A, Kucukural A, Tabak B, Zhu X, Diehl W, McDonel P, Yosef N, Luban J, Garber M. Comparative Analysis of Immune Cells Reveals a Conserved Regulatory Lexicon. Cell Syst. 2018 Jan 30. PMID: 29454939.
      View in: PubMed
    18. Zhu LJ, Lawrence M, Gupta A, Pagès H, Kucukural A, Garber M, Wolfe SA. GUIDEseq: a bioconductor package to analyze GUIDE-Seq datasets for CRISPR-Cas nucleases. BMC Genomics. 2017 May 15; 18(1):379. PMID: 28506212.
      View in: PubMed
    19. Diehl WE, Lin AE, Grubaugh ND, Carvalho LM, Kim K, Kyawe PP, McCauley SM, Donnard E, Kucukural A, McDonel P, Schaffner SF, Garber M, Rambaut A, Andersen KG, Sabeti PC, Luban J. Ebola Virus Glycoprotein with Increased Infectivity Dominated the 2013-2016 Epidemic. Cell. 2016 Nov 03; 167(4):1088-1098.e6. PMID: 27814506.
      View in: PubMed
    20. Tanriverdi K, Kucukural A, Mikhalev E, Tanriverdi SE, Lee R, Ambros VR, Freedman JE. Comparison of RNA isolation and associated methods for extracellular RNA detection by high-throughput quantitative polymerase chain reaction. Anal Biochem. 2016 May 15; 501:66-74. PMID: 26969789.
      View in: PubMed
    21. Beaulieu LM, Vitseva O, Tanriverdi K, Kucukural A, Mick E, Hamburg N, Vita J, Freedman JE. Platelet functional and transcriptional changes induced by intralipid infusion. Thromb Haemost. 2016 Jun 2; 115(6):1147-56. PMID: 26940969.
      View in: PubMed
    22. Sharma U, Conine CC, Shea JM, Boskovic A, Derr AG, Bing XY, Belleannee C, Kucukural A, Serra RW, Sun F, Song L, Carone BR, Ricci EP, Li XZ, Fauquier L, Moore MJ, Sullivan R, Mello CC, Garber M, Rando OJ. Biogenesis and function of tRNA fragments during sperm maturation and fertilization in mammals. Science. 2016 Jan 22; 351(6271):391-6. PMID: 26721685.
      View in: PubMed
    23. Shea JM, Serra RW, Carone BR, Shulha HP, Kucukural A, Ziller MJ, Vallaster MP, Gu H, Tapper AR, Gardner PD, Meissner A, Garber M, Rando OJ. Genetic and Epigenetic Variation, but Not Diet, Shape the Sperm Methylome. Dev Cell. 2015 Dec 21; 35(6):750-8. PMID: 26702833.
      View in: PubMed
    24. Blodgett DM, Nowosielska A, Afik S, Pechhold S, Cura AJ, Kennedy NJ, Kim S, Kucukural A, Davis RJ, Kent SC, Greiner DL, Garber MG, Harlan DM, diIorio P. Novel Observations From Next-Generation RNA Sequencing of Highly Purified Human Adult and Fetal Islet Cell Subsets. Diabetes. 2015 Sep; 64(9):3172-81. PMID: 25931473.
      View in: PubMed
    25. Shishkin AA, Giannoukos G, Kucukural A, Ciulla D, Busby M, Surka C, Chen J, Bhattacharyya RP, Rudy RF, Patel MM, Novod N, Hung DT, Gnirke A, Garber M, Guttman M, Livny J. Simultaneous generation of many RNA-seq libraries in a single reaction. Nat Methods. 2015 Apr; 12(4):323-5. PMID: 25730492.
      View in: PubMed
    26. Ricci EP, Kucukural A, Cenik C, Mercier BC, Singh G, Heyer EE, Ashar-Patel A, Peng L, Moore MJ. Staufen1 senses overall transcript secondary structure to regulate translation. Nat Struct Mol Biol. 2014 Jan; 21(1):26-35. PMID: 24336223.
      View in: PubMed
    27. Kucukural A, Özadam H, Singh G, Moore MJ, Cenik C. ASPeak: an abundance sensitive peak detection algorithm for RIP-Seq. Bioinformatics. 2013 Oct 1; 29(19):2485-6. PMID: 23929032.
      View in: PubMed
    28. Singh G, Kucukural A, Cenik C, Leszyk JD, Shaffer SA, Weng Z, Moore MJ. The Cellular EJC Interactome Reveals Higher-Order mRNP Structure and an EJC-SR Protein Nexus. Cell. 2012 Nov 09; 151(4):915-916. PMID: 30360293.
      View in: PubMed
    29. Singh G, Kucukural A, Cenik C, Leszyk JD, Shaffer SA, Weng Z, Moore MJ. The cellular EJC interactome reveals higher-order mRNP structure and an EJC-SR protein nexus. Cell. 2012 Nov 9; 151(4):750-64. PMID: 23084401.
      View in: PubMed
    30. Ozdemir Ozgenturk N, Oruç F, Sezerman U, Kuçukural A, Vural Korkut S, Toksoz F, Un C. Generation and Analysis of Expressed Sequence Tags from Olea europaea L. Comp Funct Genomics. 2010; 2010:757512. PMID: 21197085.
      View in: PubMed
    31. Sephton CF, Cenik C, Kucukural A, Dammer EB, Cenik B, Han Y, Dewey CM, Roth FP, Herz J, Peng J, Moore MJ, Yu G. Identification of neuronal RNA targets of TDP-43-containing ribonucleoprotein complexes. J Biol Chem. 2011 Jan 14; 286(2):1204-15. PMID: 21051541.
      View in: PubMed
    32. Roy A, Kucukural A, Zhang Y. I-TASSER: a unified platform for automated protein structure and function prediction. Nat Protoc. 2010 Apr; 5(4):725-38. PMID: 20360767.
      View in: PubMed
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