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Alper Kucukural PhD

TitleAssociate Professor
InstitutionUMass Chan Medical School
DepartmentGenomics and Computational Biology
AddressUMass Chan Medical School
55 Lake AVenue North
Worcester MA 01655
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    InstitutionT.H. Chan School of Medicine
    DepartmentGenomics and Computational Biology

    InstitutionT.H. Chan School of Medicine
    DepartmentProgram in Molecular Medicine

    Collapse Biography 
    Collapse education and training
    Istanbul Technical University, Istanbul, , TurkeyBSMathematics Engineering
    Istanbul Technical University, Istanbul, , TurkeyMSSytems Analysis
    Sabanci University, Istanbul, , TurkeyPHDBiological Sciences

    Collapse Overview 
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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. 

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    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.
    Newest   |   Oldest   |   Most Cited   |   Most Discussed   |   Timeline   |   Field Summary   |   Plain Text
    PMC Citations indicate the number of times the publication was cited by articles in PubMed Central, and the Altmetric score represents citations in news articles and social media. (Note that publications are often cited in additional ways that are not shown here.) Fields are based on how the National Library of Medicine (NLM) classifies the publication's journal and might not represent the specific topic of the publication. Translation tags are based on the publication type and the MeSH terms NLM assigns to the publication. Some publications (especially newer ones and publications not in PubMed) might not yet be assigned Field or Translation tags.) Click a Field or Translation tag to filter the publications.
    1. Dominov JA, Madigan LA, Whitt JP, Rademacher KL, Webster KM, Zhang H, Banno H, Tang S, Zhang Y, Wightman N, Shychuck EM, Page J, Weiss A, Kelly K, Kucukural A, Brodsky MH, Jaworski A, Fallon JR, Lipscombe D, Brown RH. Up-regulation of cholesterol synthesis pathways and limited neurodegeneration in a knock-in Sod1 mutant mouse model of ALS. bioRxiv. 2023 May 05. PMID: 37205335.
    2. Whittaker CA, Kucukural A, Gates C, Wilkins OM, Bell GW, Hutchinson JN, Polson SW, Dragon J. Functional Annotation Routines Used by ABRF Bioinformatics Core Facilities - Observations, Comparisons, and Considerations. J Biomol Tech. 2023 03 31; 34(1). PMID: 37089874.
      Citations:    Fields:    
    3. Mou H, Eskiocak O, ?zler KA, Gorman M, Yue J, Jin Y, Wang Z, Gao Y, Janowitz T, Meyer HV, Yu T, Wilkinson JE, Kucukural A, Ozata DM, Beyaz S. CRISPR-induced exon skipping of ?-catenin reveals tumorigenic mutants driving distinct subtypes of liver cancer. J Pathol. 2023 04; 259(4):415-427. PMID: 36641763.
      Citations: 1     Fields:    Translation:Animals
    4. Wang J, Zhang Y, Mendonca CA, Yukselen O, Muneeruddin K, Ren L, Liang J, Zhou C, Xie J, Li J, Jiang Z, Kucukural A, Shaffer SA, Gao G, Wang D. AAV-delivered suppressor tRNA overcomes a nonsense mutation in mice. Nature. 2022 04; 604(7905):343-348. PMID: 35322228.
      Citations: 25     Fields:    Translation:HumansAnimalsCells
    5. Qaisar N, Arowosegbe A, Derr AG, Kucukural A, Satish B, Racicot R, Guo Z, Trombly MI, Wang JP. Type I IFN-Driven Immune Cell Dysregulation in Rat Autoimmune Diabetes. Immunohorizons. 2021 10 26; 5(10):855-869. PMID: 34702762.
      Citations: 2     Fields:    Translation:HumansAnimalsCells
    6. Beyaz S, Chung C, Mou H, Bauer-Rowe KE, Xifaras ME, Ergin I, Dohnalova L, Biton M, Shekhar K, Eskiocak O, Papciak K, Ozler K, Almeqdadi M, Yueh B, Fein M, Annamalai D, Valle-Encinas E, Erdemir A, Dogum K, Shah V, Alici-Garipcan A, Meyer HV, ?zata DM, Elinav E, Kucukural A, Kumar P, McAleer JP, Fox JG, Thaiss CA, Regev A, Roper J, Orkin SH, Yilmaz ?H. Dietary suppression of MHC class II expression in intestinal epithelial cells enhances intestinal tumorigenesis. Cell Stem Cell. 2021 11 04; 28(11):1922-1935.e5. PMID: 34529935.
      Citations: 37     Fields:    Translation:HumansCells
    7. 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. 2021 01; 257:203-212. PMID: 32858321.
      Citations: 5     Fields:    Translation:HumansAnimalsCells
    8. 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 08 24; 9. PMID: 32831172.
      Citations: 27     Fields:    Translation:AnimalsCells
    9. 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. 2021; 11(2):433-448. PMID: 32822913.
      Citations: 7     Fields:    Translation:AnimalsCells
    10. 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 mouse epididymis and vas deferens. Elife. 2020 07 30; 9. PMID: 32729827.
      Citations: 30     Fields:    Translation:Animals
    11. 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 07; 31(2):66-73. PMID: 32382253.
      Citations: 1     Fields:    Translation:Humans
    12. 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.
      Citations: 40     Fields:    
    13. Sissaoui S, Yu J, Yan A, Li R, Yukselen O, Kucukural A, Zhu LJ, Lawson ND. Genomic Characterization of Endothelial Enhancers Reveals a Multifunctional Role for NR2F2 in Regulation of Arteriovenous Gene Expression. Circ Res. 2020 03 27; 126(7):875-888. PMID: 32065070.
      Citations: 17     Fields:    Translation:HumansCells
    14. 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 03; 21(3):274-286. PMID: 32066947.
      Citations: 43     Fields:    Translation:HumansCells
    15. ?zata 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 01; 4(1):156-168. PMID: 31900453.
      Citations: 37     Fields:    Translation:HumansAnimals
    16. 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 01; 34(1):1901-1911. PMID: 31914605.
      Citations: 5     Fields:    Translation:HumansAnimalsCells
    17. 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 09 03; 116(36):17970-17979. PMID: 31420514.
      Citations: 56     Fields:    Translation:HumansCells
    18. 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 04 16; 11(1):21. PMID: 30987660.
      Citations: 10     Fields:    Translation:HumansAnimalsCells
    19. Russell MA, Redick SD, Blodgett DM, Richardson SJ, Leete P, Krogvold L, Dahl-J?rgensen 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 ?-Cells From Donors With Type 1 Diabetes. Diabetes. 2019 05; 68(5):988-1001. PMID: 30833470.
      Citations: 52     Fields:    Translation:HumansCells
    20. 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.
      Citations: 100     Fields:    Translation:HumansCells
    21. 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 Mar 28; 6(3):381-394.e7. PMID: 29454939.
      Citations: 12     Fields:    Translation:HumansAnimalsCells
    22. Zhu LJ, Lawrence M, Gupta A, Pag?s H, Kucukural A, Garber M, Wolfe SA. GUIDEseq: a bioconductor package to analyze GUIDE-Seq datasets for CRISPR-Cas nucleases. BMC Genomics. 2017 05 15; 18(1):379. PMID: 28506212.
      Citations: 18     Fields:    
    23. 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 11 03; 167(4):1088-1098.e6. PMID: 27814506.
      Citations: 99     Fields:    Translation:HumansAnimalsCells
    24. 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.
      Citations: 13     Fields:    Translation:Humans
    25. 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 06 02; 115(6):1147-56. PMID: 26940969.
      Citations: 4     Fields:    Translation:HumansCells
    26. 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):391-396. PMID: 26721685.
      Citations: 526     Fields:    Translation:AnimalsCells
    27. 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.
      Citations: 69     Fields:    Translation:AnimalsCells
    28. 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.
      Citations: 162     Fields:    Translation:HumansCells
    29. 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.
      Citations: 138     Fields:    Translation:Cells
    30. 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.
      Citations: 82     Fields:    Translation:HumansCells
    31. Kucukural A, ?zadam H, Singh G, Moore MJ, Cenik C. ASPeak: an abundance sensitive peak detection algorithm for RIP-Seq. Bioinformatics. 2013 Oct 01; 29(19):2485-6. PMID: 23929032.
      Citations: 26     Fields:    
    32. 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 11 09; 151(4):915-916. PMID: 30360293.
      Citations: 11     Fields:    
    33. 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):750-764. PMID: 23084401.
      Citations: 183     Fields:    Translation:HumansCells
    34. Ozdemir Ozgenturk N, Oru? F, Sezerman U, Ku?ukural 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.
    35. 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.
      Citations: 237     Fields:    Translation:HumansAnimalsCells
    36. 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.
      Citations: 2896     Fields:    Translation:Cells
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