Computer-Aided Identification and Design of Ligands for Multi-Targeting Inhibition of a Molecular Acute Myeloid Leukemia Network

Asfa S. S., Bonab R. A., Önder O., Uça Apaydın M., Döşeme H., Küçük C., et al.

CANCERS , vol.16, pp.3607, 2024 (SCI-Expanded)  

Potential diagnostic and prognostic biomarkers of pediatric Burkitt lymphoma identified through miRNA expression profiling.

Küçük C., Sönmez E. E., Hatipoğlu T., Yuan H., Hu X., Ceylan A., et al.

Pediatric research , no.Advanced online, 2024 (SCI-Expanded)    

Whole-exome sequencing reveals genetic variants in low-risk and high-risk neuroblastoma.

Altun Z. S., Yuan H., Baran B., Aktaş S., Esmeray Sönmez E., Küçük C., et al.

Gene , vol.860, pp.147233, 2023 (SCI-Expanded)    

Genetic and epigenetic analyses reveal transcriptional silencing of SOX7 due to deletion in a multiple myeloma case with double relapse

Şeyhanlı A., Hatipoğlu T., Akman B., Hu X., Özsan G. H., Küçük C.

UHOD - ULUSLARARASI HEMATOLOJI-ONKOLOJI DERGISI , vol.33, no.1, pp.54-56, 2023 (SCI-Expanded)  

New insights into epigenetic regulation of resistance to PD-1/PD-L1 blockade cancer immunotherapy: mechanisms and therapeutic opportunities

Dai M., Liu M., Yang H., Küçük A. P. D. C., You H.

EXPERIMENTAL HEMATOLOGY & ONCOLOGY , vol.11, pp.101, 2022 (SCI-Expanded)     

Whole Transcriptome Sequencing Reveals Cancer-Related, Prognostically Significant Transcripts and Tumor-Infiltrating Immunocytes in Mantle Cell Lymphoma.

Esmeray Sönmez E., Hatipoğlu T., Kurşun D., Hu X., Akman B., Yuan H., et al.

Cells , vol.11, no.21, 2022 (SCI-Expanded)     

Plasma Concentrations and Cancer-Associated Mutations in Cell-Free Circulating DNA of Treatment-Naive Follicular Lymphoma for Improved Non-Invasive Diagnosis and Prognosis.

Hatipoğlu T., Esmeray Sönmez E., Hu X., Yuan H., Danyeli A. E., Şeyhanlı A., et al.

Frontiers in oncology , vol.12, pp.870487, 2022 (SCI-Expanded)   

In Silico Methods for the Identification of Diagnostic and Favorable Prognostic Markers in Acute Myeloid Leukemia.

Yilmaz H., Toy H. I., Marquardt S., KARAKÜLAH G., KÜÇÜK C., Kontou P., et al.

International journal of molecular sciences , vol.22, no.17, 2021 (SCI-Expanded)   

PRDM1 decreases sensitivity of human NK cells to IL2-induced cell expansion by directly repressing CD25 (IL2RA)

Akman B., Hu X., Liu X., Hatipoglu T., You H., Chan W. C., et al.

JOURNAL OF LEUKOCYTE BIOLOGY , vol.109, no.5, pp.901-914, 2021 (SCI-Expanded)   

A prognostic model for melanoma patients on the basis of immune-related lncRNAs

Wang Y., Ba H., Wen X., Zhou M., KÜÇÜK C., Tamagnone L., et al.

AGING-US , vol.13, no.5, pp.6554-6564, 2021 (SCI-Expanded)   

Ultra-Deep Targeted Sequencing Reveals Cancer-Associated, Prognostically Significant Mutations in Circulating Cell-Free DNA in Treatment-Naive Patients with Follicular Lymphoma

Hatipoglu T., Esmeray E., Hu X., Yuan H., Danyeli A. E., Seyhanli A., et al.

BLOOD , vol.136, 2020 (SCI-Expanded)   

Indolent T-Cell Lymphoproliferative Disease of the GI Tract: Insights for Better Diagnosis, Prognosis, and Appropriate Therapy

KÜÇÜK C., Wei L., You H.

FRONTIERS IN ONCOLOGY , vol.10, 2020 (SCI-Expanded)   

Genetic susceptibility to natural killer T-cell lymphoma

KÜÇÜK C.

LANCET ONCOLOGY , vol.21, no.2, pp.196-197, 2020 (SCI-Expanded)  

Epigenetic aberrations in natural killer/T-cell lymphoma: diagnostic, prognostic and therapeutic implications

KÜÇÜK C., Wang J., Xiang Y., You H.

THERAPEUTIC ADVANCES IN MEDICAL ONCOLOGY , vol.12, 2020 (SCI-Expanded)    

Genetic alterations in B cell lymphoma subtypes as potential biomarkers for noninvasive diagnosis, prognosis, therapy, and disease monitoring

Esmeray E., Küçük C.

TURKISH JOURNAL OF BIOLOGY , vol.44, no.1, pp.1-14, 2020 (SCI-Expanded)    

Systematic analysis of the frequently amplified 2p15-p16.1 locus reveals PAPOLG as a potential proto-oncogene in follicular and transformed follicular lymphoma

Kursun D., KÜÇÜK C.

TURKISH JOURNAL OF BIOLOGY , vol.43, no.2, pp.124-133, 2019 (SCI-Expanded)   

Primary cardiac diffuse large B-cell lymphoma with concurrent high MYC and BCL2 expression in an immunocompetent Chinese elderly woman

Wan Y., He D., Ye Y., Zhang W., Zhao S., Long Y., et al.

CARDIOVASCULAR PATHOLOGY , vol.31, pp.54-56, 2017 (SCI-Expanded)    

Whole transcriptome analysis reveals dysregulated oncogenic lncRNAs in natural killer/T-cell lymphoma and establishes MIR155HG as a target of PRDM1

Baytak E., Gong Q., Akman B., Yuan H., Chan W. C., KÜÇÜK C.

TUMOR BIOLOGY , vol.39, no.5, 2017 (SCI-Expanded)    

The relationship of REL proto-oncogene to pathobiology and chemoresistance in follicular and transformed follicular lymphoma

Hu X., Baytak E., Li J., Akman B., Okay K., Hu G., et al.

LEUKEMIA RESEARCH , vol.54, pp.30-38, 2017 (SCI-Expanded)    

Clinicopathologic Characterization of Aggressive Natural Killer Cell Leukemia Involving Different Tissue Sites

Gao L., Zhao S., Liu W., Zhang W., Li G., KÜÇÜK C., et al.

AMERICAN JOURNAL OF SURGICAL PATHOLOGY , vol.40, no.6, pp.836-846, 2016 (SCI-Expanded)   

Diagnostic and Biological Significance of KIR Expression Profile Determined by RNA-Seq in Natural Killer/T-Cell Lymphoma

KÜÇÜK C., Hu X., Gong Q., Jiang B., Cornish A., Gaulard P., et al.

AMERICAN JOURNAL OF PATHOLOGY , vol.186, no.6, pp.1435-1441, 2016 (SCI-Expanded)    

Lack of Evidence that HACE1 Is Not a Tumor Suppressor Gene in NKTCL

Kuecuek C., Hu X., McKeithan T., Chan W. 

AMERICAN JOURNAL OF PATHOLOGY , vol.185, no.4, pp.1167-1168, 2015 (SCI-Expanded)  

Global Promoter Methylation Analysis Reveals Novel Candidate Tumor Suppressor Genes in Natural Killer Cell Lymphoma

Kuecuek C., Hu X., Jiang B., Klinkebiel D., Geng H., Gong Q., et al.

CLINICAL CANCER RESEARCH , vol.21, no.7, pp.1699-1711, 2015 (SCI-Expanded)    

Activating mutations of  STAT5B and  STAT3 in lymphomas derived from γδ-T or NK cells

Kucuk C., Jiang B., Hu X., Zhang W., Chan J. K. C., Xiao W., et al.

NATURE COMMUNICATIONS , 2015 (SCI-Expanded)    

Genome-wide copy-number analyses reveal genomic abnormalities involved in transformation of follicular lymphoma

Bouska A., McKeithan T. W., Deffenbacher K. E., Lachel C., Wright G. W., Iqbal J., et al.

BLOOD , vol.123, no.11, pp.1681-1690, 2014 (SCI-Expanded)   

Indolent T-cell lymphoproliferative disease of the gastrointestinal tract

Perry A. M., Warnke R. A., Hu Q., Gaulard P., Copie-Bergman C., Alkan S., et al.

BLOOD , vol.122, no.22, pp.3599-3606, 2013 (SCI-Expanded)    

microRNA expression profiling identifies molecular signatures associated with anaplastic large cell lymphoma

Liu C., Iqbal J., Teruya-Feldstein J., Shen Y., Dabrowska M. J., Dybkaer K., et al.

BLOOD , vol.122, no.12, pp.2083-2092, 2013 (SCI-Expanded)   

HACE1 Is a Tumor Suppressor Gene Candidate in Natural Killer Cell Neoplasms

Kuecuek C., Hu X., Iqbal J., Gaulard P., Klinkebiel D., Cornish A., et al.

AMERICAN JOURNAL OF PATHOLOGY , vol.182, no.1, pp.49-55, 2013 (SCI-Expanded)   

IDH2 mutations are frequent in angioimmunoblastic T-cell lymphoma

Cairns R. A., Iqbal J., Lemonnier F., KÜÇÜK C., de Leval L., Jais J., et al.

BLOOD , vol.119, no.8, pp.1901-1903, 2012 (SCI-Expanded)    

PRDM1 is a tumor suppressor gene in natural killer cell malignancies

Kuecuek C., Iqbal J., Hu X., Gaulard P., De Leval L., Srivastava G., et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA , vol.108, no.50, pp.20119-20124, 2011 (SCI-Expanded)    

Natural killer cell lymphoma shares strikingly similar molecular features with a group of non-hepatosplenic gamma delta T-cell lymphoma and is highly sensitive to a novel aurora kinase A inhibitor in vitro

Iqbal J., Weisenburger D. D., Chowdhury A., Tsai M. Y., Srivastava G., Greiner T. C., et al.

LEUKEMIA , vol.25, no.2, pp.348-358, 2011 (SCI-Expanded)    

Synaptic Development of the Mouse Dorsal Lateral Geniculate Nucleus

Bickford M. E., Slusarczyk A., Dilger E. K., Krahe T. E., KÜÇÜK C., Guido W.

JOURNAL OF COMPARATIVE NEUROLOGY , vol.518, no.5, pp.622-635, 2010 (SCI-Expanded)    

Molecular signatures to improve diagnosis in peripheral T-cell lymphoma and prognostication in angioimmunoblastic T-cell lymphoma

Iqbal J., Weisenburger D. D., Greiner T. C., Vose J. M., McKeithan T., KÜÇÜK C., et al.

BLOOD , vol.115, no.5, pp.1026-1036, 2010 (SCI-Expanded)   

Genomic analyses reveal global functional alterations that promote tumor growth and novel tumor suppressor genes in natural killer-cell malignancies

Iqbal J., KÜÇÜK C., deLeeuw R. J., Srivastava G., Tam W., Geng H., et al.

LEUKEMIA , vol.23, no.6, pp.1139-1151, 2009 (SCI-Expanded)    

Clinical implication of genome-wide profiling in diffuse large B-cell lymphoma and other subtypes of B-cell lymphoma.

Iqbal J., Joshi S., Patel K. N., Javed S. I., Kucuk C., Aabida A., et al.

Indian journal of cancer , vol.44, no.2, pp.72-86, 2007 (SCI-Expanded)   

Articles Published in Other Journals

Generation of a Genetically Engineered Aggressive Nk Cell Leukemia Cell Line with Stable IL2 Expression

Hu X., Chan W. C., KÜÇÜK C.

Acta Medica International , vol.2, no.2, pp.78-84, 2015 (Peer-Reviewed Journal)

Refereed Congress / Symposium Publications in Proceedings

1. Potential diagnostic and prognostic biomarkers of pediatric Burkitt lymphoma identified through miRNA-Seq of tumor tissue and plasma

Küçük C., Esmeray Sönmez E., Hatipoğlu T., Yuan H., Hu X., Ceylan A., et al.

EHA2024 Hybrid Congress, 13 - 16 June 2024, pp.4005  

2. PRDM1 Promotes Primary Human Circulating CD56dim NK-Cell Differentiation

Liu X., Zhang J., Shi Y., Shetty K., Küçük C., Esmeray Sönmez E., et al.

65. Amerika Hematoloji Derneği (ASH) yıllık toplantısı , California, United States Of America, 9 - 12 December 2023, pp.1177  

3.Genetik ve epigenetik olarak sessizleşen SOX7’nin multipl miyelomdaki tümör baskılayıcı gen potansiyeli

Ceylan A., Hu X., Anar Arıcı A., Hatipoğlu T., Payzın K. B., Özsan G. H., et al.

49. Ulusal Hematoloji Kongresi, Antalya, Turkey, 1 - 05 November 2023, pp.102 

4. Sox7 is a candidate tumor suppressor gene in multiple myeloma

Ceylan A., Hu X., Anar A., Hatipoğlu T., Payzın K. B., Özsan G. H., et al.

6th Edition of International Cancer Conference, London, England, 17 - 19 August 2023, pp.72-73 

5. Pediatrik Burkitt lenfomalarda miRNA-seq ile belirlenen miRNA seviyelerinin noninvazif tanı biyobelirteç potansiyelleri

Esmeray Sönmez E., Hu X., Yuan H., Anar A., Hatipoğlu T., Önder Siviş Z., et al.

48. Ulusal Hematoloji Kongresi, Antalya, Turkey, 1 - 05 November 2022  

6. THERAPEUTIC IMPLICATIONS OF TARGETED SEQUENCING AND miRNA-SEQ OF B CELL LYMPHOMAS

Esmeray Sönmez E., Hatipoğlu ., Hu X., Yuan H., Erşen Danyeli A., Anar Arici ., et al.

1st International Basic Oncology Congress, 2 - 04 June 2022, vol.5, pp.31   

7. Mantle Hücreli Lenfoma Prognozuyla İlişkili Proto-OnkogenAdaylarının Transkriptomik Analizlerle Belirlenmesi

Esmeray E., Kurşun D., Akman B., Hu X., Yuan H., Erşen Danyeli A., et al.

46. Ulusal Hematoloji Kongresi, 28 - 31 October 2020

8. SOX7 tümör baskılayıcı gen adayının multipl myelom olgularında tanı ve nüks esnasındaki rolünün incelenmesi

Akman B., Şeyhanlı A., Hu X., TÜRKYILMAZ D., Olgun A., Yuan H., et al.

45. Ulusal Hematoloji Kongresi, Turkey, 30 October - 02 November 2019

9. Foliküler lenfoma dolaşımsal serbest DNA’sındaki kanser ilişkili mutasyon varlığının hedefli derin dizilemeyle araştırılması

KÜÇÜK C.

IV. YAŞAM BİLİMLERİ KONGRESİ, Kayseri, Turkey, 22 - 23 February 2019 

10. Foliküler lenfoma dolaşımsal serbest DNA’sının invazif olmayan tanı amaçlı genomik profil analizi

KÜÇÜK C.

44. Ulusal Hematoloji Kongresi, Turkey, 31 October - 03 November 2018

11. CD25 (IL2RA) Is a Direct Transcriptional Target of PRDM1 in Activated Human Natural Killer Cells

Akman B., Kursun D., Hatipoglu T., Hu X., Chan W. C., Kucuk C.

60th Annual Meeting of the American-Society-of-Hematology (ASH), California, United States Of America, 1 - 04 December 2018, vol.132  

12. Doğal öldürücü/T hücre lenfomalarında tüm transkriptom analizi sonucu disregüle olan kanser ilişkili uzun kodlamayan RNA’ların ve ilişkili oldukları sinyal yolaklarının belirlenmesi

KÜÇÜK C.

XV. Ulusal Tıbbi Biyoloji ve Genetik Kongresi, Turkey, 26 - 29 October 2017  

13. Diagnostic and therapeutic implications of omic approaches in lymphoid malignancies towards personalized medicine

KÜÇÜK C.

5th International Bahçeşehir University (BAU) Drug Design Congress, 19 - 21 October 2017 

14. THE ROLE OF REL PROTO ONCOGENE IN FOLLICULAR LYMPHOMA DEVELOPMENT

Baytak E., Hu X., Li J., Okay K., Hu G., Scuto A., et al.

6. Multidisipliner Kanser Araştırma Kongresi, Turkey, 27 - 30 October 2016

15. Lenfoid Kanser Genomiği

KÜÇÜK C.

EKOG Hacettepe Biyoloji ve Uygulamaları Kongresi, Turkey, 27 - 29 June 2016 

16. Doğal öldürücü hücrelerde ChIp Seq ve mikrodizin analizi yoluyla PRDM1 transkripsiyon faktörünün hedef genlerinin belirlenmesi

KÜÇÜK C.

8. Geleneksel Bilim ve Teknoloji Sempozyumu- Omik Bilimler ve Teknolojileri, Turkey, 24 April 2016

17. Functional genomics of NK and T cell lymphomas therapeutic and diagnostic implications

KÜÇÜK C.

Bilkent Üniversitesi Moleküler Biyoloji ve Genetik Bölümü Semineri, Turkey, 17 February 2016

18. RNA Seq analysis reveals KIR2DL4 expression as a clonal diagnostic marker and potential therapeutic target in natural killer T cell lymphoma

KÜÇÜK C., Hu X., Gong Q., Cornish A., Gaulard P., McKeithan T., et al.

9th International Symposium on Health Informatics and Bioinformatics HIBIT 2015, 16 - 17 October 2015

19. Global promoter methylation analysis of natural killer cell lymphoma

KÜÇÜK C.

iBG-izmir Genom Konferansı, 20 April 2015

20. Frequent activating mutations of JAK STAT pathway genes in natural killer cell lymphomas

KÜÇÜK C., Jiang B., Hu X., Gaulard P., Zhang W., Xiao W., et al.

Amerika Hematoloji Topluluğu (ASH)- Uluslararası Yıllık 55. ASH toplantısı, 10 December 2013 

21. Global Methylation Analysis Reveals Novel Candidate Tumor Suppressor Genes In Natural Killer Cell Lymphomas

KÜÇÜK C., Hu X., Jiang B., Gaulard P., Klinkebiel D., Geng H., et al.

Amerika Hematoloji Topluluğu- Uluslarası Yıllık 55. ASH toplantısı, 07 December 2013 

22. Global methyation analysis reveals novel candidate tumor supressor genes in natural killer cell lymphomas

KÜÇÜK C., Hu X., Jiang B., Gaulard P., Klinkebiel D., Geng H., et al.

Nebraska Üniversitesi Tıp Merkezi Eppley Kanser Merkezi, Lösemi ve Lenfoma Araştırma Merkezi (CRLL), United States Of America, 02 May 2013

23. Novel fusion transcripts identified in angioimmunoblastic T cell lymphoma

Guo S., KÜÇÜK C., Iqbal J., Rohr J., Bi C., Wang C., et al.

102nci Amerika Birleşik Devletleri ve Kanada Patoloji Akademisi, 2 - 08 March 2013

24. MicroRNA expression profiling identifies molecular diagnostic signatures for anaplastic large cell lymphoma

Liu C., Iqbal J., TeruyaFeldstein J., Shen Y., Dabrowska M. J., Dybkr K., et al.

102inci Amerika Birleşik Devletleri ve Kanada Patoloji Akademisi (102nd USCAP Annual Meeting), 2 - 08 March 2013 

25. Genetic Abnormalities in Follicular Lymphoma and Transformed Follicular Lymphoma

Bouska A., McKeithan T., Deffenbacher K. E., Lachel C., Wright G. W., Iqbal J., et al.

Amerika Hematoloji Topluluğu (ASH)-Yıllık Uluslarası ASH toplantısı, 8 - 10 December 2012 

26. The role of IDH2 and TET2 mutations in the pathogenesis of angioimmunoblastic T cell lymphoma

Wang C., KÜÇÜK C., Chan W. C.

Sekizinci Uluslarası Öğrenci Araştırma Forumu, 7 - 09 August 2012

27. HACE1 is a tumor supressor gene candidate in natural killer cell malignancies

KÜÇÜK C., Hu X., Iqbal J., Gaulard P., Klinkebiel D., Cornish A., et al.

43’üncü Yıllık Ortabatı Öğrenci Biyomedikal Araştırma Forumu (MSBRF), 18 February 2012

28. PRDM1 is a tumor supressor gene in natural killer cell malignancies

KÜÇÜK C.

Losemi ve Lenfoma Araştırma Merkezi (CRLL), United States Of America, 03 February 2011

29. NK cell lymphoma shares strikingly similar molecular features with a distinct set of T cell lymphoma and identification of Aurora Kinase A Inhibitor as a novel therapeutic agent

Iqbal J., Weisenburger D. D., Chowdhury A., Srivastava G., Greiner T. C., Deffenbacher K. E., et al.

Amerika Hematoloji Topluluğu- Uluslarası Yıllık 51. ASH toplantisi, 5 - 08 December 2009 

30. Molecular signatures to improve diagnosis prognostication and identification of oncogenic pathways in peripheral T and NK cell lymphoma

Iqbal J., Weisenburger D., Greiner T. C., Nakamura S., Vose J. M., Seto M., et al.

Amerika Hematoloji Topluluğu- Uluslarası Yıllık 50. ASH toplantısı, 5 - 08 December 2008 

31. Genomic analyses reveal global functional alterations that promote tumor growth and novel tumor supressor genes in natural killer cell malignancies

KÜÇÜK C., Iqbal J., deLeeuw R. J., Gopesh S., Tam W., Klinkebiel D., et al.

Kanser Markerlerinin Değerlendirilmesi Amaçlı Stratejik Toplantı (SPECS), United States Of America, 3 - 05 December 2008

32. Genomic Analyses Reveal Global Functional Alterations That Promote Tumor Growth and Novel Tumor Suppressor Genes in Natural Killer-Cell Malignancies.

KÜÇÜK C., Iqbal J., deLeeuw R. J., Srivastava G., Tam W., Klinkebiel D., et al.

50th Annual Meeting of the American-Society-of-Hematology, San-Francisco, Costa Rica, 6 - 09 December 2008, vol.112, pp.1298 

33. Synaptic organization of the adult and neonatal mouse dorsal lateral geniculate nucleus

Slusarczyk A., KÜÇÜK C., Chomsung R., Eisenback M. A., Guido W., Bickford M. E.

Sinirbilim Topluluğu (Society for Neuroscience) Yıllık Toplantı, 14 - 18 October 2006 

Books & Book Chapters

1. Genomics and Epigenomics of Natural Killer/T Cell Lymphoma: Diagnostic, Prognostic, and Therapeutic Implications

Tan Y., Küçük C., Cui L.

in: Interdisciplinary Cancer Research, Nima Rezaei, Editor, Springer, London/Berlin , Edinburgh, pp.1-32, 2024  

2. Genomic and Its Applications

Küçük C.

in: Molecular Biology and Genetics-Advanced Applications in Health and Biotechnology, Prof. Dr. Mustafa Solak, Editor, Tüba Basın Yayın, Ankara, pp.235-258, 2023  

3. Lenfoma Genetiği (HL, B-hücre NHL, KLL)

KÜÇÜK C.

in: HematoLog, Güner Hayri Özsan, Müge Sayitoğlu, Editor, Galenos Yayınevi, pp.102-111, 2019