Welcome

Computational biologist and molecular geneticist with a proven track record of leading multi-omic, spatial transcriptomic, and retinal systems biology projects at the NIH/NEI. Architect of RetSeq, a dynamic web-based analytics platform for temporal retinal transcriptomes, and creator of mESAdb, a pioneering cross-species microRNA expression and motif analysis suite. Extensive experience designing and deploying high-performance pipelines for RNA-seq, ATAC-seq, and spatial omics using Nextflow, Snakemake, R, Python, C++, and advanced integration into cloud/HPC environments (AWS, Biowulf). Skilled in transforming complex biological datasets into actionable insights across photoreceptor development, stem cell modeling, and regenerative therapeutics. Also experienced in full-stack web application development (PHP, Java, JavaScript, MySQL) and scientific UI/UX design for interactive data exploration. Combining innovation with rigor, I deliver scalable, production-ready solutions at the intersection of computation and translational genomics.

QUALIFICATIONS SUMMARY

  • Molecular biologist/geneticist with over 10 years of experience in bioinformatics, specializing in high-throughput data analysis and computational tool development.
  • Strong background in gene regulation, transcription, and epigenetics.
  • Deep expertise in NGS and expression/genomic data analysis using advanced programming languages.
  • Expert in efficient data retrieval from biological databases via Bioperl, Biopython, and BioJava.
  • Exceptional creativity in integrating diverse computational frameworks to mine and visualize large-scale omics datasets with precision and scientific impact.
  • Extensive experience with scalable cloud computing solutions for data-intensive biological workflows.

COMPUTING SKILLS

  • Demonstrated mastery of NGS data analysis tools, including Bowtie2, BWA, NovoAlign, Trimmomatic, deepTools, samtools, bedtools, UCSC tools, Picard, MACS2, HOMER, Galaxy, and GATK
  • Advanced expertise in programming languages, combining high-level scripting (Python, R, Perl) with performance-optimized development in C++, Java, and Bash
  • In-depth experience with web technologies and databases: HTML, PHP, JavaScript, CSS, JQuery, AngularJS, and MySQL
  • Expert-level command of regular expressions for robust text parsing and data manipulation
  • Preferred development environments: Jupyter Notebook and Vim, optimized for bioinformatics workflows
  • Strong foundation in classical algorithms and problem-solving paradigms, including sorting, divide-and-conquer, greedy, and dynamic programming
  • Extensive experience with structured data formats, especially XML and its parsing for biological applications
  • Well-versed in Linux system administration, including workstation provisioning, web hosting, storage, and database services
  • Skilled in Microsoft Office tools for scientific documentation, reporting, and data presentation
  • Experienced with high-performance and cloud-based computing platforms, including Biowulf (HPC), AWS, and Google Cloud
  • Working knowledge of the PostScript language, applied in advanced document rendering and formatting scenarios

Education

Ph.D. in Molecular Biology and Genetics

Bilkent University, Ankara, Turkey
Advisor: Asst. Prof. Özlen Konu
Dissertation: Development of a web application/database for the integrative analysis of microRNA expression patterns
Degree Awarded: August 2011

M.Sc. in Molecular Biology and Genetics

Bilkent University, Ankara, Turkey
Advisor: Asst. Prof. Özlen Konu
Thesis: Evaluation of microRNA sequence composition and expression
Degree Awarded: August 2005

B.Sc. in Molecular Biology and Genetics (Hons)

Boğaziçi University, Istanbul, Turkey
Degree Awarded: July 2003

Research Experience

  • 2024–2025: Led spatial transcriptomics analysis using MERFISH in Alzheimer’s disease models, developing Python-based tools for segmentation and integration with scRNA-seq.
  • 2022–2024: Led Bioinformatics Research for GECKO project on fovea development; conducted large-scale Ensembl mining and co-led manuscript efforts; recognized with the Kelly Distinguished Research Award.
  • 2021–2024: Led multiomic analysis of developing RPE using Hi-C, ATAC-seq, and RNA-seq; co-author on submitted paper describing novel SERPINE3+ adult RPE subpopulation.
  • 2020–2021: Identified gene expression patterns and novel isoforms specific to uveitis and its subtypes.
  • 2015–2020: Led multiple transcriptomic studies on human retina development, organoids, and mouse models in NEI’s Neurobiology Laboratory.
  • 2013–2016: Developed RetSeq database integrating retina-specific high-throughput data(https://retseq.nei.nih.gov) Now it is integrated to that is now a part of NEI Commons (https://neicommons.nei.nih.gov). Studied photoreceptor development in 3D retina cultures.
  • 2011–2013: Applied machine learning tools via JAVA on RPPA datasets at VCU to study effects of memantine treatment in Down syndrome mice models

Teaching Experience

  • 2010-2011 Spring, TA responsible for the lab of Genomics, MBG 418. Senior level course.
  • 2010-2011 Fall, TA responsible for the lab of Bioinformatics, MBG 326, Junior level course
  • 2009-2010 Fall, TA responsible for the lab of Bioinformatics, MBG 326, Junior level course.

Conferences and Courses Attended

  • 2016: Systems Biology - Global Regulation of Gene Expression, Cold Spring Harbor Labaratory, Cold Spring Harbor, NY, USA
  • 2010: Bioinformatics Roadshow, İzmir Dokuz Eylül University, Izmir, Turkiye
  • 2008: Receptors Meeting, Wellcome Trust Campus, UK
  • 2007: BioSysBio 2007, Manchester, UK
  • 2006: FEBS Congress, Istanbul, Turkiye
  • 2005: EBI Systems Biology Workshop, Sheffield, UK

Honors & Awards

  • Kelly Distinguished Research Award 2023, 2024
  • NEI Director’s Award for Technology Innovation
  • Boğaziçi University Rector’s Special Recognition Award
  • Haci Omer Sabanci Scholarship, Turkey

Publications

  1. Kaya KD, Chen HY, Brooks MJ, Kelley RA, et al. Transcriptome-based molecular staging of human stem cell-derived retinal organoids uncovers accelerated photoreceptor differentiation by 9-cis retinal. Mol Vis. 2019 Nov 11;25:663-678.

  2. Kaya KD, Karakülah G, Yakicier CM, Acar AC, Konu O. mESAdb: microRNA expression and sequence analysis database. Nucleic Acids Res. 2011 Jan;39(Database issue):D170-80. doi:10.1093/nar/gkq1256.

  3. Mahato B, Kaya KD, Fan Y, et al. Pharmacologic fibroblast reprogramming into photoreceptors restores vision. Nature. 2020 May;581(7806):83-88.

  4. Nath PR, Maclean M, Nagarajan V, Lee JW, Yakin M, Kumar A, Nadali H, Schmidt B, Kaya KD, Kodati S, Young A, Caspi RR, Kuiper JJW, Sen HN. Single-cell profiling identifies a CD8bright CD244bright Natural Killer cell subset that reflects disease activity in HLA-A29-positive birdshot chorioretinopathy. Nature Communications. 2024 Jul 31;15(1):6443. doi:10.1038/s41467-024-50472-0. PMID: 39085199.

  5. Wang L, Kaya KD, Kim S, Brooks MJ, et al. Retinal pigment epithelium transcriptome analysis in chronic smoking reveals a suppressed innate immune response and activation of differentiation pathways. Free Radic Biol Med. 2020 Aug 20;156:176-189.

  6. Lukovic D, Artero Castro A, Kaya KD, et al. Retinal Organoids derived from hiPSCs of an AIPL1-LCA Patient Maintain Cytoarchitecture despite Reduced levels of Mutant AIPL1. Sci Rep. 2020 Mar 25;10(1):5426.

  7. Assawachananont J, Kim SY, Kaya KD, et al. Cone-rod homeobox CRX controls presynaptic active zone formation in photoreceptors of mammalian retina. Hum Mol Genet. 2018 Oct 15;27(20):3555-3567.

  8. DiStefano TJ, Chen HY, Panebianco C, Kaya KD, et al. Accelerated and Improved Differentiation of Retinal Organoids from Pluripotent Stem Cells in Rotating-Wall Vessel Bioreactors. Stem Cell Reports. 2021 Jan 12;16(1):224.

  9. Kim JW, Yang HJ, Brooks MJ, et al. Kaya KD, et al. NRL-Regulated Transcriptome Dynamics of Developing Rod Photoreceptors. Cell Rep. 2016 Nov 22;17(9):2460-2473.

  10. May-Simera HL, Gumerson JD, Gao C, et al. Kaya KD, et al. Loss of MACF1 Abolishes Ciliogenesis and Disrupts Apicobasal Polarity Establishment in the Retina. Cell Rep. 2016 Oct 25;17(5):1399-1413.

  11. Chen HY, Kaya KD, Dong L, Swaroop A. Three-dimensional retinal organoids from mouse pluripotent stem cells mimic in vivo development with enhanced stratification and rod photoreceptor differentiation. Mol Vis. 2016 Sep 9;22:1077-1094.

  12. Kaewkhaw R, Swaroop M, Homma K, et al. Kaya KD, et al. Treatment Paradigms for Retinal and Macular Diseases Using 3-D Retina Cultures Derived From Human Reporter Pluripotent Stem Cell Lines. Invest Ophthalmol Vis Sci. 2016 Apr 1;57(5):ORSFl1-ORSFl11.

  13. Kaewkhaw R, Kaya KD, Brooks M, et al. Transcriptome Dynamics of Developing Photoreceptors in Three-Dimensional Retina Cultures Recapitulates Temporal Sequence of Human Cone and Rod Differentiation Revealing Cell Surface Markers and Gene Networks. Stem Cells. 2015 Dec;33(12):3504-18.