Welcome to Kaplan's Lab

Our lab is dedicated to uncovering the genetic and molecular mechanisms driving rare diseases, with a particular focus on ciliopathies. By integrating comparative genomics, functional assays, and cutting-edge gene editing technologies, we aim to bridge the gap between genotype and phenotype, advancing our understanding of disease mechanisms and identifying potential therapeutic targets.

Research Updates

We recently identified a link between CILK1/DYF-5 and cranioectodermal dysplasia by integrating patient-derived cells and C. elegans models. Our study, titled "A homozygous frameshift variant in the CILK1 gene causes cranioectodermal dysplasia", has been submitted for publication.

Turan MG, Kantarci H, Cevik S, Kaplan OI. ARL13B regulates juxtaposed cilia-cilia elongation in BBSome dependent manner in Caenorhabditis elegans. iScience. 2025 Jan 10;28(2):111791. doi: 10.1016/j.isci.2025.111791

Pir MS, Cevik S, Kaplan OI. CilioGenics: an integrated method and database for predicting novel ciliary genes. Nucleic Acids Res. 2024 Aug 12;52(14):8127-8145. doi: 10.1093/nar/gkae554

Pir MS, Cevik S, Kaplan OI. ConVarT: a search engine for matching human genetic variants with variants from non-human species. Nucleic Acids Res. 2022 Jan 7;50(D1):D1172-D1178. doi: 10.1093/nar/gkab939 (Note: DOI may be inactive; see GitHub)

Research Overview

Our lab is dedicated to uncovering the genetic and molecular mechanisms driving rare diseases, with a particular focus on ciliopathies. By integrating comparative genomics, functional assays, and cutting-edge gene editing technologies, we aim to bridge the gap between genotype and phenotype, advancing our understanding of disease mechanisms and identifying potential therapeutic targets.

Cilia and Ciliopathies

We study ciliopathies such as Joubert syndrome, Bardet-Biedl syndrome, and cranioectodermal dysplasia to identify causative genes and understand their roles in disease pathogenesis.

Disease Modeling

Using advanced genomic technologies and CRISPR/Cas9, we identify and characterize genetic variants associated with rare diseases, aiming to improve diagnosis and treatment.

Cilia-Cilia Joining

We investigate the molecular machinery involved in cilia-cilia elongation and inter-ciliary communication, critical for ciliary function and related diseases.

Bioinformatics

We develop and maintain bioinformatics tools like ConVarT, CilioGenics, and CiliaMiner to facilitate research in ciliopathies and rare diseases.

Cilia and Ciliopathies

Cilia are microtubule-based organelles that mediate numerous cellular processes, such as motility, signaling, and development. Ciliopathies are a group of rare genetic diseases caused by structural or functional defects in cilia and lead to syndromes such as Joubert syndrome, Bardet-Biedl syndrome, Meckel syndrome, and cranioectodermal dysplasia. Though outstanding advances have been achieved, the genetic etiology of ciliopathies is still not fully understood.

Our group has newly identified CILK1 as a causative gene of cranioectodermal dysplasia. Our goal is to identify and functionally annotate ciliopathy-associated genes comprehensively with genetic models, high-resolution microscopy, and biochemical assays. By integrating patient-derived data with experimental data, we will develop improved diagnostic reagents and therapeutic approaches to these rare diseases.

Disease Modeling

Genetic variant analysis of rare diseases attempts to identify mutations responsible for such often poorly described conditions. With the help of advanced genomic technologies like whole exome sequencing and CRISPR/Cas9-based functional screening in C. elegans, our lab is able to distinguish disease-causing variants and comprehend their mechanisms better (Cevik et al., 2023). This work provides insight into the genetic architecture of rare diseases, eventually culminating in the design of tailored treatments and propelling precision medicine for such individuals.

Cilia-Cilia Joining

Our study aims to make sense of the molecular machinery in cilia-cilia elongation. We isolate the key proteins and signaling cascades involved. We are further conducting FIB-SEM analysis in a bid to deliver quantitative ultrastructural detail.

We are further contributing to understanding cilia-cilia communication, as demonstrated by Turan et al. (2025) in iScience. We shall expand on such findings by studying the molecular machinery regulating cilia-cilia interaction, including elongation and communication, and the implications for uncommon diseases.

Bioinformatics

ConVarT: A search engine for matching human genetic variants with variants from non-human species, aiding in the functional characterization of rare disease variants. (Currently unavailable at http://convart.org/; see GitHub)

CilioGenics: An integrated database and tool for predicting novel ciliary genes, supporting research into ciliopathies and ciliary biology. https://ciliogenics.com/?page=Home

CiliaMiner: A bioinformatics platform for exploring ciliopathy genes and related data, designed to accelerate discovery in rare disease research. https://kaplanlab.shinyapps.io/ciliaminer/

GitHub: Access our open-source code, protocols, and bioinformatics pipelines for rare disease and ciliopathy research. https://github.com/thekaplanlab

Current Members

Oktay I. Kaplan, Dr.
Principal Investigator

GitHub (Lab): thekaplanlab
GitHub (Personal): oktaykaplan
X: @KaplanOLab
ORCID: 0000-0002-8733-0920
Bluesky: oktaykaplan.bsky.social

Sebiha Cevik, Dr.
Principal Investigator

Ferhan Yenisert
PhD Student

Damla Puçak
Graduate Student

Sinem Güzel
Graduate Student

Fatma Güzel
Graduate Student

Zanyar Demir
Graduate Student

Former Members

Graduate Students in the Lab

Merve Gül Turan (September 2019 - June 2023)
Position in the lab: Graduate Student
Current Position: PhD student at Max Planck Institute for Biology Tübingen

Mustafa Samet Pir
Position in the lab: Graduate Student
Current Position: PhD student at Acibadem University

Fatma Nihal Yetgin
Position in the lab: Graduate Student

Ziya Zorluer
Position in the lab: Graduate Student
Current Position: PhD student, AGU, Türkiye

Undergraduate Students in the Lab

Ahsen Konaç (2018-2021)
Position in the lab: Undergraduate Student
Current Position: PhD student, Göttingen, Germany

Onur Çakıcı (2018-2023)
Position in the lab: Undergraduate Student
Current Position: PhD student, Crete, Greece

Hanife Kantarcı
Position in the lab: Undergraduate Student
Current Position: Graduate Student, Sabancı University, Türkiye

Sadiye Dilay Temtek
Position in the lab: Undergraduate Student
Current Position: TÜBİTAK, Ankara, Türkiye

Group Photos

See our lab team in action.

Lab Meeting 2025

Open Positions

We are always looking for talented undergraduate students, graduate students, and postdoctoral researchers to join our team. If you are passionate about rare diseases, ciliopathies, and innovative research, we encourage you to contact the Principal Investigator (PI) for more information.

For postdoctoral positions, we offer the opportunity to apply for prestigious fellowships such as the EMBO Postdoctoral Fellowship, Marie Curie Fellowship, and TÜBİTAK Fellowship.

Contact: Oktaykaplan(at)gmail.com

Publications

Turan MG, Kantarci H, Cevik S, Kaplan OI. ARL13B regulates juxtaposed cilia-cilia elongation in BBSome dependent manner in Caenorhabditis elegans. iScience. 2025 Jan 10;28(2):111791. doi: 10.1016/j.isci.2025.111791

Kim AH, Sakin I, Viviano S, et al. CC2D1A causes ciliopathy, intellectual disability, heterotaxy, renal dysplasia, and abnormal CSF flow. Life Sci Alliance. 2024 Oct;7(10):e202402708. doi: 10.26508/lsa.202402708

Pir MS, Begar E, Yenisert F, et al. CilioGenics: an integrated method and database for predicting novel ciliary genes. Nucleic Acids Res. 2024 Aug 12;52(14):8127-8145. doi: 10.1093/nar/gkae554

Cevik S, Zhao P, Zorluer A, et al. Matching variants for functional characterization of genetic variants. G3 (Bethesda). 2023 Dec 7;13(12):jkad227. doi: 10.1093/g3journal/jkad227

Cevik S, Peng X, Beyer T, et al. WDR31 displays functional redundancy with GTPase-activating proteins (GAPs) ELMOD and RP2 in regulating IFT complex and recruiting the BBSome to cilium. Life Sci Alliance. 2023 Aug;6(8):e202201844. doi: 10.26508/lsa.202201844

Turan MG, Orhan ME, Cevik S, Kaplan OI. CiliaMiner: an integrated database for ciliopathy genes and ciliopathies. Database (Oxford). 2023;2023:baad047. doi: 10.1093/database/baad047

Kaplan OI. RPI-1 (human DCDC2) displays functional redundancy with Nephronophthisis 4 in regulating cilia biogenesis in C. elegans. Nucleic Acids Res. 2023;47(1):74-83. doi: 10.55730/1300-0152.2642

Pir MS, Cevik S, Kaplan OI. ConVarT: Search Engine for Missense Variants Between Humans and Other Organisms. Curr Protoc. 2022 Nov;2(11):e619. doi: 10.1002/cpz1.619

Turan MG, Kantarci H, Temtek SD, et al. Protocol for determining the average speed and frequency of kinesin and dynein-driven intraflagellar transport (IFT) in C. elegans. STAR Protoc. 2022 Sep 16;3(3):101498. doi: 10.1016/j.xpro.2022.101498

Pir MS, Bilgin HI, Sayici A, et al. ConVarT: a search engine for matching human genetic variants with variants from non-human species. Nucleic Acids Res. 2022 Jan 7;50(D1):D1172-D1178. doi: 10.1093/nar/gkab939 (Note: DOI may be inactive; see GitHub)

Torun FM, Bilgin HI, Kaplan OI. MSABrowser: dynamic and fast visualization of sequence alignments, variations and annotations. Bioinform Adv. 2021;1(1):vbab009. doi: 10.1093/bioadv/vbab009

Cevik S, Kaplan OI. The Joubert syndrome protein CEP41 is excluded from the distal segment of cilia in C. elegans. MicroPubl Biol. 2021;2021:10.17912/micropub.biology.000406. doi: 10.17912/micropub.biology.000406

Cevik S, Kaplan OI. Subcellular localization of the voltage-gated K+ channel EGL-36, a member of the KV3 subfamily, in the ciliated sensory neurons in C. elegans. MicroPubl Biol. 2021;2021:10.17912/micropub.biology.000367. doi: 10.17912/micropub.biology.000367

Kimura Y, Tsutsumi K, Konno A, et al. Environmental responsiveness of tubulin glutamylation in sensory cilia is regulated by the p38 MAPK pathway. Sci Rep. 2018 Jun 8;8(1):8392. doi: 10.1038/s41598-018-26694-w

Kaplan OI, Berber B, Hekim N, Doluca O. G-quadruplex prediction in E. coli genome reveals a conserved putative G-quadruplex-Hairpin-Duplex switch. Nucleic Acids Res. 2016 Oct 20;44(19):9083-9095. doi: 10.1093/nar/gkw769

Cevik S, Sanders AA, Van Wijk E, et al. Active transport and diffusion barriers restrict Joubert Syndrome-associated ARL13B/ARL-13 to an Inv-like ciliary membrane subdomain. PLoS Genet. 2013 Dec;9(12):e1003977. doi: 10.1371/journal.pgen.1003977

Kaplan OI, Doroquez DB, Cevik S, et al. Endocytosis genes facilitate protein and membrane transport in C. elegans sensory cilia. Curr Biol. 2012 Mar 20;22(6):451-60. doi: 10.1016/j.cub.2012.01.060

Kaplan OI, Molla-Herman A, Cevik S, et al. The AP-1 clathrin adaptor facilitates cilium formation and functions with RAB-8 in C. elegans ciliary membrane transport. J Cell Sci. 2010 Nov 15;123(Pt 22):3966-77. doi: 10.1242/jcs.073908

Kimura Y, Kurabe N, Ikegami K, et al. Identification of tubulin deglutamylase among Caenorhabditis elegans and mammalian cytosolic carboxypeptidases (CCPs). J Biol Chem. 2010 Jul 23;285(30):22936-41. doi: 10.1074/jbc.C110.128280

Cevik S, Hori Y, Kaplan OI, et al. Joubert syndrome Arl13b functions at ciliary membranes and stabilizes protein transport in Caenorhabditis elegans. J Cell Biol. 2010 Mar 22;188(6):953-69. doi: 10.1083/jcb.200908133

Blacque OE, Cevik S, Kaplan OI. Intraflagellar transport: from molecular characterisation to mechanism. Front Biosci. 2008;13:2633-52. doi: 10.2741/2871

News

March 26, 2025: We recently identified a link between CILK1/DYF-5 and cranioectodermal dysplasia by integrating patient-derived cells and C. elegans. models. Our study, titled "A homozygous frameshift variant in the CILK1 gene causes cranioectodermal dysplasia" has been submitted for publication.

March 2025: New publication in iScience on cilia-cilia elongation! Read more

January 2025: Kaplan Lab receives grant for ciliopathy research.

Resources

Our lab is committed to open science, and we openly share our protocols and bioinformatics pipelines to contribute to the broader scientific community.

ConVarT: A search engine for matching human genetic variants with variants from non-human species, aiding in the functional characterization of rare disease variants. (Currently unavailable at http://convart.org/; see GitHub)

CilioGenics: An integrated database and tool for predicting novel ciliary genes, supporting research into ciliopathies and ciliary biology. https://ciliogenics.com/?page=Home

CiliaMiner: A bioinformatics platform for exploring ciliopathy genes and related data, designed to accelerate discovery in rare disease research. https://kaplanlab.shinyapps.io/ciliaminer/

GitHub: Access our open-source code, protocols, and bioinformatics pipelines for rare disease and ciliopathy research. https://github.com/thekaplanlab

CRISPR/Cas9 Protocol: A PCR-based, cost-efficient, and fast screening strategy.
Download Protocol (PDF)

Movies

Explore animated insights into our research and protocols.

STAR Protocol Animation: A visual guide to our protocol for determining the average speed and frequency of kinesin and dynein-driven intraflagellar transport (IFT) in C. elegans.

Research Animation: Worm movement comparison of wild-type and mutants, showcasing our lab’s work on ciliary biology and rare disease mechanisms.

Images

View images from our research and lab activities.

Lab Experiment 1

Lab Experiment 2