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Gökhan Karakülah
Bronze Contributor
5,140 Points

Contributions by role

Author 840
Reviewer 30
Editor 4,270

Contributions by subject area

Bioinformatics
Computational Biology
Evolutionary Studies
Genomics
Virology
Statistics
Oncology
Neurology
Medical Genetics
Cognitive Disorders
Translational Medicine
Women's Health
Microbiology
Dentistry
Ophthalmology
Biochemistry
Cell Biology
Molecular Biology
Geriatrics
Data Mining and Machine Learning
Data Science
Epidemiology
Infectious Diseases
Pediatrics
Public Health
Cardiology
Radiology and Medical Imaging
Surgery and Surgical Specialties
Metabolic Sciences
Genetics
Diabetes and Endocrinology
Agricultural Science
Veterinary Medicine
Zoology
Allergy and Clinical Immunology
Gastroenterology and Hepatology
COVID-19
Paleontology
Computational Science
Plant Science
Gynecology and Obstetrics
Immunology
Drugs and Devices
Animal Behavior
Biodiversity
Developmental Biology
Neuroscience
Obesity
Pharmacology
Taxonomy
Bronze Contributor

Gökhan Karakülah

PeerJ Author & Reviewer

Summary

Dr. Gökhan Karakülah currently works at Dokuz Eylül University, Izmir International Biomedicine and Genome Institute in Turkey as an associate professor. He obtained BSc (2005) from Ege University, and MSc (2009) and PhD (2014) degrees from Dokuz Eylül University, Health Sciences Institute in Turkey. Between October 2014 and April 2016, he joined Dr. Anand Swaroop’s research group as a postdoctoral researcher at National Eye Institute, NIH, US. The main focus of his current research has been to develop tools and algorithms for the better analysis and integration of diverse “omics” data sets generated with next generation sequencing technologies.

Bioinformatics Computational Biology Data Mining & Machine Learning Data Science Genetics Genomics Molecular Biology

Past or current institution affiliations

Dokuz Eylül University

Work details

Prof.

Dokuz Eylül University
Izmir International Biomedicine and Genome Institute

Websites

  • Google Scholar

PeerJ Contributions

  • Articles 8
  • Edited 31
February 12, 2025
PGSXplorer: an integrated nextflow pipeline for comprehensive quality control and polygenic score model development
Tutku Yaraş, Yavuz Oktay, Gökhan Karakülah
https://doi.org/10.7717/peerj.18973 PubMed 39959831
March 17, 2023
“In the light of evolution:” keratins as exceptional tumor biomarkers
Işıl Takan, Gökhan Karakülah, Aikaterini Louka, Athanasia Pavlopoulou
https://doi.org/10.7717/peerj.15099 PubMed 36949761
March 16, 2023
An in silico approach to the identification of diagnostic and prognostic markers in low-grade gliomas
Melih Özbek, Halil Ibrahim Toy, Yavuz Oktay, Gökhan Karakülah, Aslı Suner, Athanasia Pavlopoulou
https://doi.org/10.7717/peerj.15096 PubMed 36945359
October 3, 2022
Identification of neoplasm-specific signatures of miRNA interactions by employing a systems biology approach
Reza Arshinchi Bonab, Seyedehsadaf Asfa, Panagiota Kontou, Gökhan Karakülah, Athanasia Pavlopoulou
https://doi.org/10.7717/peerj.14149 PubMed 36213495
October 12, 2020
Mutations of SARS-CoV-2 nsp14 exhibit strong association with increased genome-wide mutation load
Doğa Eskier, Aslı Suner, Yavuz Oktay, Gökhan Karakülah
https://doi.org/10.7717/peerj.10181 PubMed 33083157
August 19, 2020
Mutation density changes in SARS-CoV-2 are related to the pandemic stage but to a lesser extent in the dominant strain with mutations in spike and RdRp
Doğa Eskier, Aslı Suner, Gökhan Karakülah, Yavuz Oktay
https://doi.org/10.7717/peerj.9703 PubMed 32879797
July 21, 2020
RdRp mutations are associated with SARS-CoV-2 genome evolution
Doğa Eskier, Gökhan Karakülah, Aslı Suner, Yavuz Oktay
https://doi.org/10.7717/peerj.9587 PubMed 32742818
December 5, 2019
TEffectR: an R package for studying the potential effects of transposable elements on gene expression with linear regression model
Gökhan Karakülah, Nazmiye Arslan, Cihangir Yandım, Aslı Suner
https://doi.org/10.7717/peerj.8192 PubMed 31824778

Academic Editor on

August 12, 2025
RpNGS: an automated platform for pathogen identification and monitoring in clinical metagenomics data
Jing Zhou, Yao Tian, Min Yang, Ting Hao, Jun Ma, Shengyu Wang
https://doi.org/10.7717/peerj.19849 PubMed 40821992
February 12, 2025
pandasPGS: a Python package for easy retrieval of Polygenic Score Catalog data
Zheyu Zhang, Jintong Zhou, Tianze Cao, Yuexia Huang, Chu Huang, Yu Xia
https://doi.org/10.7717/peerj.18985 PubMed 39959838
August 28, 2024
Kinome state is predictive of cell viability in pancreatic cancer tumor and cancer-associated fibroblast cell lines
Matthew E. Berginski, Madison R. Jenner, Chinmaya U. Joisa, Gabriela Herrera Loeza, Brian T. Golitz, Matthew B. Lipner, Jack R. Leary, Naim Rashid, Gary L. Johnson, Jen Jen Yeh, Shawn M. Gomez
https://doi.org/10.7717/peerj.17797 PubMed 39221276
June 12, 2024
Use of machine learning to identify protective factors for death from COVID-19 in the ICU: a retrospective study
Lander Dos Santos, Lincoln Luis Silva, Fernando Castilho Pelloso, Vinicius Maia, Constanza Pujals, Deise Helena Borghesan, Maria Dalva Carvalho, Raíssa Bocchi Pedroso, Sandra Marisa Pelloso
https://doi.org/10.7717/peerj.17428 PubMed 38881861
May 18, 2023
Characterization of gut microbiota in adults with coronary atherosclerosis
Yu Dong, Rui Xu, Xiaowei Chen, Chuanli Yang, Fei Jiang, Yan Shen, Qiong Li, Fujin Fang, Yongjun Li, Xiaobing Shen
https://doi.org/10.7717/peerj.15245 PubMed 37220524
May 16, 2023
Assessment of multi-population polygenic risk scores for lipid traits in African Americans
Domenica E. Drouet, Shiying Liu, Dana C. Crawford
https://doi.org/10.7717/peerj.14910 PubMed 37214096
April 20, 2023
Effects of leptin on the viability of human ovarian cancer cells and changes in cytokine expression levels
Fatih Dincer, Harika Atmaca, Levent Akman, Latife Merve Oktay, Burcak Karaca, Mustafa Cosan Terek
https://doi.org/10.7717/peerj.15246 PubMed 37155466
March 29, 2023
Gram-negative ESKAPE bacteria bloodstream infections in patients during the COVID-19 pandemic
María Dolores Alcántar-Curiel, Manuel Huerta-Cedeño, Ma Dolores Jarillo-Quijada, Catalina Gayosso-Vázquez, José Luis Fernández-Vázquez, María Luisa Hernández-Medel, Manuelita Zavala-Pineda, Miguel Ángel Morales-Gil, Verónica Alejandra Hernández-Guzmán, Manuel Ismael Bolaños-Hernández, Silvia Giono-Cerezo, José Ignacio Santos-Preciado
https://doi.org/10.7717/peerj.15007 PubMed 37013147
March 24, 2023
Baseline gene expression in subcutaneous adipose tissue predicts diet-induced weight loss in individuals with obesity
Ali Oghabian, Birgitta W. van der Kolk, Pekka Marttinen, Armand Valsesia, Dominique Langin, W. H. Saris, Arne Astrup, Ellen E. Blaak, Kirsi H. Pietiläinen
https://doi.org/10.7717/peerj.15100 PubMed 36992941
March 20, 2023
Wastewater monitoring of SARS-CoV-2 RNA at K-12 schools: comparison to pooled clinical testing data
Sooyeol Kim, Alexandria B. Boehm
https://doi.org/10.7717/peerj.15079 PubMed 36967994
January 23, 2023
A clustering method for small scRNA-seq data based on subspace and weighted distance
Zilan Ning, Zhijun Dai, Hongyan Zhang, Yuan Chen, Zheming Yuan
https://doi.org/10.7717/peerj.14706 PubMed 36710872
December 21, 2022
Future stem cell analysis: progress and challenges towards state-of-the art approaches in automated cells analysis
Nurul Syahira Mohamad Zamani, Wan Mimi Diyana Wan Zaki, Zariyantey Abd Hamid, Aqilah Baseri Huddin
https://doi.org/10.7717/peerj.14513 PubMed 36573241
November 8, 2022
ScanFold 2.0: a rapid approach for identifying potential structured RNA targets in genomes and transcriptomes
Ryan J. Andrews, Warren B. Rouse, Collin A. O’Leary, Nicholas J. Booher, Walter N. Moss
https://doi.org/10.7717/peerj.14361 PubMed 36389431
October 17, 2022
Comparison of reference gene expression stability in mouse skeletal muscle via five algorithms
Jianfeng Ma, Jingyun Chen, Mailin Gan, Lei Chen, Ye Zhao, Lili Niu, Yan Zhu, Shunhua Zhang, Xuewei Li, Zongyi Guo, Jinyong Wang, Li Zhu, Linyuan Shen
https://doi.org/10.7717/peerj.14221 PubMed 36275473
September 21, 2022
Association between EPHA5 methylation status in peripheral blood leukocytes and the risk and prognosis of gastric cancer
Xu Han, Tianyu Liu, Jiabao Zhai, Chang Liu, Wanyu Wang, Chuang Nie, Qi Wang, Xiaojie Zhu, Haibo Zhou, Wenjing Tian
https://doi.org/10.7717/peerj.13774 PubMed 36164608
August 4, 2022
The COVID-19 infodemic in Brazil: trends in Google search data
Maria da Penha Harb, Lena Veiga e Silva, Nandamudi Vijaykumar, Marcelino Silva da Silva, Carlos Renato Lisboa Frances
https://doi.org/10.7717/peerj.13747 PubMed 35945937
May 26, 2022
Dementia-related user-based collaborative filtering for imputing missing data and generating a reliability scale on clinical test scores
Savas Okyay, Nihat Adar
https://doi.org/10.7717/peerj.13425 PubMed 35642196
March 30, 2022
Long non-coding RNA SPRY4-IT1 promotes proliferation and metastasis in nasopharyngeal carcinoma cell
Yanfei Li, Zhenpeng Liao, Rong Wang, Zibin Liang, Zhihe Lin, Shiqi Deng, Lei Chen, Zhigang Liu, Shaoyan Feng
https://doi.org/10.7717/peerj.13221 PubMed 35378932
January 19, 2022
Reconstructing the transmission dynamics of varicella in Japan: an elevation of age at infection
Ayako Suzuki, Hiroshi Nishiura
https://doi.org/10.7717/peerj.12767 PubMed 35111401
September 24, 2021
Quantitative trait locus mapping analysis of multiple traits when using genotype data with potential errors
Liang Tong, Ying Zhou, Yixing Guo, Hui Ding, Donghai Ji
https://doi.org/10.7717/peerj.12187 PubMed 34631317
August 4, 2021
Optimization of change in epicardial fat thickness for obese patients who lost weight via the bariatric surgery method using central composite and Box-Behnken experimental designs
Ferhan Elmalı, Mustafa Agâh Tekindal, Cihan Altın, Can Ateş, Varlık Erol
https://doi.org/10.7717/peerj.11831 PubMed 34430075
May 3, 2021
The autistic-like behaviors development during weaning and sexual maturation in VPA-induced autistic-like rats is accompanied by gut microbiota dysbiosis
Qingmin Kong, Peijun Tian, Jianxin Zhao, Hao Zhang, Gang Wang, Wei Chen
https://doi.org/10.7717/peerj.11103 PubMed 33986978
December 4, 2020
Identification and characterization of critical genes associated with tamoxifen resistance in breast cancer
Kai Zhang, Kuikui Jiang, Ruoxi Hong, Fei Xu, Wen Xia, Ge Qin, Kaping Lee, Qiufan Zheng, Qianyi Lu, Qinglian Zhai, Shusen Wang
https://doi.org/10.7717/peerj.10468 PubMed 33335811
October 27, 2020
Integrated transcriptome meta-analysis of pancreatic ductal adenocarcinoma and matched adjacent pancreatic tissues
Sevcan Atay
https://doi.org/10.7717/peerj.10141 PubMed 33194391
October 16, 2020
A robust semi-supervised NMF model for single cell RNA-seq data
Peng Wu, Mo An, Hai-Ren Zou, Cai-Ying Zhong, Wei Wang, Chang-Peng Wu
https://doi.org/10.7717/peerj.10091 PubMed 33088619
September 29, 2020
Identification of hub genes and small molecule therapeutic drugs related to breast cancer with comprehensive bioinformatics analysis
Mingqian Hao, Wencong Liu, Chuanbo Ding, Xiaojuan Peng, Yue Zhang, Huiying Chen, Ling Dong, Xinglong Liu, Yingchun Zhao, Xueyan Chen, Sadia Khatoon, Yinan Zheng
https://doi.org/10.7717/peerj.9946 PubMed 33083112
September 21, 2020
Identification of NUF2 and FAM83D as potential biomarkers in triple-negative breast cancer
Xiuming Zhai, Zhaowei Yang, Xiji Liu, Zihe Dong, Dandan Zhou
https://doi.org/10.7717/peerj.9975 PubMed 33005492
August 20, 2020
Further evaluation of differential expression of keratoconus candidate genes in human corneas
Justyna A. Karolak, Barbara Ginter-Matuszewska, Katarzyna Tomela, Michal Kabza, Dorota M. Nowak-Malczewska, Malgorzata Rydzanicz, Piotr Polakowski, Jacek P. Szaflik, Marzena Gajecka
https://doi.org/10.7717/peerj.9793 PubMed 32879808
May 15, 2020
Personalized analysis of breast cancer using sample-specific networks
Ke Zhu, Cong Pian, Qiong Xiang, Xin Liu, Yuanyuan Chen
https://doi.org/10.7717/peerj.9161 PubMed 32461838
May 4, 2020
Transcriptional profiling to identify the key genes and pathways of pterygium
Yihui Chen, Haoyu Wang, Yaping Jiang, Xiaoyan Zhang, Qingzhong Wang
https://doi.org/10.7717/peerj.9056 PubMed 32411530
April 8, 2020
Transcriptome analysis revealed key prognostic genes and microRNAs in hepatocellular carcinoma
Xi Ma, Lin Zhou, Shusen Zheng
https://doi.org/10.7717/peerj.8930 PubMed 32296612