Curriculum Vitae

Contact

• Name : Ridzky A. A. Yuda, Ph.D. (he/him)
• Work Address : 720 Rutland Ave. Baltimore, Maryland, 21210, USA
• Contact information : ryuda1@jhmi.edu

Research Interest

My research focuses on understanding how cellular and molecular mechanisms, including transcriptional and epigenetic regulation, govern hematopoietic stem cell (HSC) fate decisions and macrophage self-renewal in the context of inflammation and aging. I combine in vivo mouse models, molecular biology, and bulk and single-cell omics to investigate how environmental exposures and aging influence stem cell lineage commitment. I am particularly interested in how epigenetic regulators and transposable elements shape hematopoiesis via immune signaling. My long-term goal is to define and test candidate pathways using high-throughput gain- and loss-of-function approaches to rejuvenate aging stem cell and macrophage function.

Education

• Ph.D in Regenerative Biology, Medizinische Fakultät Carl Gustav Carus, Technische Universität Dresden, Germany Thesis: Zellzyklusaktivierung induziert Verjüngung der Gensignaturen in alten Alveolarmakrophagen (Cell cycle activation induces rejuvenated gene signatures in aging alveolar macrophages). Advisor (Doktorvater): Prof. Michael Sieweke, Ph.D. Co-advisor: Prof. Dr. Federico Calegari and Prof. Dr. med Triantafyllos Chavakis.

• M.S. in Regenerative Biology and Medicine, Center for Molecular and Cellular Bioengineering (CMCB), Technische Universität Dresden, Germany Thesis: Oligodendrocytes-preferring adeno-associated virus for studying Sox2-mediated reprogramming in oligodendrocytes progenitor cells (OPCs) Advisor: Prof. Dr. Federico Calegari & Prof. Jared Sterneckert, Ph.D.

• B.S. in Biology, Faculty of Science and Technology, Airlangga University, Indonesia Thesis: Isolasi Bakteri Selulolitik Termofilik dari Sumber Air Panas Gunung Kelud dan Karakterisasi Crude Enzim Selulase (Thermophilic bacteria isolation from Mt. Kelud’s hotspring and its crude celulase enzyme characterization) Advisor: Prof. Dr. Ni’matuzahroh and Prof. Dr. Sri Pudjiastuti

Scientific Appointment

• Postdoctoral Fellow, Division of Hematology, Johns Hopkins University School of Medicine, USA (2023-present).
• Research Associate (Wissenschaftlicher Mitarbeiter), Technische Universität Dresden, Germany (2018-2023)
• Student technical assistant (Studentische Hilfskraft) at the Electron Microscopy Facility, Center for Molecular and Cellular Bioengineering, Technische Universität Dresden, Germany (2017-2018)
• Summer School Student in Cancer Research, German Cancer Research Center (Deutsches Krebsforschungszentrum, DKFZ), Germany (2017)
• Molecular Biology Lab Technician, Hospital for Infectious Diseases, Airlangga University, (2014-2016)

Publications

• Ridzky A. A. Yuda, Habin Bea, Valerie Kellett, Jungwoo Kim, Fan Yang, Haruna B. Choijilsuren, Yejie Park, Yaojie Fu, Zewen Ha, Juhye Choi, Zhaoli Sun, Bin Gao, Sangmoo Jeong, Linda M. S. Resar, Moonjung Jung., “Chronic alcohol consumption drives inflammaging and transposon derepression in hematopoietic stem and progenitor cells”., bioRxiv., 2025. doi: https://doi.org/10.64898/2025.12.25.696246

• Dev, S., Wang, Y., Jung, M., Ma, Y., Mani, S., Kabin, E., Yuda, R., Dong, Y., Ralle, M., Hamilton, J.P., Lutsenko, S., ATP7B-maintained copper stores in myeloid progenitors are required for functional maturation of neutrophils., Cell Reports., 2026 (Accepted Manuscript in Press)

• Mallikarjun Reddy, Alli Abolarin, Valerie Kellet, Michaela Eleanor Bhoorasingh, Rodger Black, Bradley Priem, Fan Yang, Ridzky A. A. Yuda, Michael Betenbaugh, Moonjung Jung, Sangmoo Jeong., “Dietary serine restriction increases venetoclax efficacy in acute myeloid leukemia”., Blood, Volume 146 Supplement 1., Page 5046., 2025., doi: https://doi.org/10.1182/blood-2025-5046

• Ridzky A. A. Yuda, Valerie Kellet, Fan Yang, Moonjung Jung., Chronic alcohol consumption epigenetically reactivates transposable elements in aged hematopoietic stem cells., Blood, Volume 146 Supplement 1., Page 1378., 2025., doi: https://doi.org/10.1182/blood-2025-1378

• Ridzky A. A. Yuda, Valerie Kellet, Haruna B. Choijilsuren, Zewen Ha, Fan Yang, Moonjung Jung. Combinatorial Effect of Chronic Alcohol Drinking and Age Perpetuates Myeloid-Biased Hematopoiesis Via Hematopoietic Stem Cell Senescence. Blood Volume 144 Supplement 1 . Page 2672., 2024., doi: https://doi.org/10.1182/blood-2024-211006

• Busch, C.JL., Subramanian, S., Linares, J., Favret, J., Yuda, R.A.A., Sieweke, M.H. “Isolation, Ex Vivo Expansion, and Lentiviral Transduction of Alveolar Macrophages. In: Mass, E. (eds) Tissue-Resident Macrophages.” Methods in Molecular Biology, vol 2713. 231-251(2024). doi: https://link.springer.com/protocol/10.1007/978-1-0716-3437-0_16

• Sethuraman Subramanian, Clara Jana-Lui Busch, Kaaweh Molawi, Laufey Geirsdottir, Julien Maurizio, Stephanie Vargas Aguilar, Hassiba Belahbib, Gregory Gimenez, Ridzky Anis Advent Yuda, Michaela Burkon, Jérémy Favret, Sara Gholamhosseinian Najjar, Bérengère de Laval, Prashanth Kumar Kandalla, Sandrine Sarrazin, Lena Alexopoulou, Michael H. Sieweke., “Long-term culture-expanded alveolar macrophages restore their full epigenetic identity after transfer in vivo.” Nature Immunology 23. 458-468(2022)., doi: https://doi.org/10.1038/s41590-022-01146-w

Link for each publication is in the below hyperlinks

ATP7B-maintained copper stores in myeloid progenitors are required for functional maturation of neutrophils

Chronic alcohol consumption drives inflammaging and transposon derepression in hematopoietic stem and progenitor cells

Yuda, R.A.A., et al. "Chronic alcohol consumption drives inflammaging and transposon derepression in hematopoietic stem and progenitor cells." bioRxiv 2025..

Dietary serine restriction increases venetoclax efficacy in Acute Myeloid Leukemia

Malikarjun, Reddy et al. (2025). "Dietary serine restriction increases venetoclax efficacy in Acute Myeloid Leukemia." Blood 2025 vol 146 supplement 1 . Page 5046.

Chronic alcohol consumption epigenetically reactivates transposable elements in aged hematopoietic stem cells

Yuda, Ridzky et al. (2025). "Chronic alcohol consumption epigenetically reactivates transposable elements in aged hematopoietic stem cells." Blood 2025 vol 146 supplement 1 . Page 1378.

Combinatorial Effect of Chronic Alcohol Drinking and Age Perpetuates Myeloid-Biased Hematopoiesis Via Hematopoietic Stem Cell Senescence

Yuda, Ridzky et al. (2024). "Combinatorial Effect of Chronic Alcohol Drinking and Age Perpetuates Myeloid-Biased Hematopoiesis Via Hematopoietic Stem Cell Senescence." Blood Volume 144 Supplement 1 . Page 2672.

Isolation, Ex Vivo Expansion, and Lentiviral Transduction of Alveolar Macrophages. In: Mass, E. (eds) Tissue-Resident Macrophages

Busch, C.JL., Subramanian, S., Linares, J., Favret, J., Yuda, R.A.A., Sieweke, M.H. "Isolation, Ex Vivo Expansion, and Lentiviral Transduction of Alveolar Macrophages. In: Mass, E. (eds) Tissue-Resident Macrophages." Methods in Molecular Biology, vol 2713. 231-251(2024).

Long-term culture-expanded alveolar macrophages restore their full epigenetic identity after transfer in vivo

Subramanian, S., Busch, C.JL., Molawi, K. et al. "Long-term culture-expanded alveolar macrophages restore their full epigenetic identity after transfer in vivo." Nat Immunol 23. 458-468(2022).

Succesful Funding Acquisition

• Maryland Stem Cell Research Fund (MSCRF) Award (Awarded 2024-2026). Role: Principal Investigator (PI). A competitive and prestigious fellowship supporting my independent studying epigenetic regulation of alcohol-induced dsRNA accumulation and inflammation in hematopoietic stem/progenitor cells at Johns Hopkins University. link https://www.mscrf.org/awardees#2024

Honors and Awards

• Abstract Achievement Award from American Society of Hematology (ASH) for abstract with title Chronic alcohol consumption epigenetically reactivates transposable elements in aged hematopoietic stem cells. December 2025.

• 2nd Best Poster Award at the 2nd Annual Maryland Stem Cell Research Symposium. October 2025

• Training Award Grant from Dresden International School for Biomedicine and Bioengineering. October 2021

• SUPERSEMAR Excellent Student Scholarship. Supersemar Foundation (2012)

• Gold medal for Biology, National Olympiad for Mathematics and Natural Sciences for Undergraduate Students (2012). Ministry of Higher Education, Indonesia

• Gold medal for Biology, National Olympiad for Mathematics and Natural Sciences for Undergraduate Students (2011). Ministry of Higher Education, Indonesia

• First Prize for Biology, National Olympiad for Mathematics and Natural Sciences for Undergraduate Students (2011). Ministry of Education, Yogyakarta Province.

• Bronze medal for Biology at the National Selection Level for International Biology Olympiad (2008). Ministry of Education, Indonesia

Profesional service

• Peer-reviewer for a manuscript submitted to Blood

Trainings and Courses

• Single-cell Transcriptomics Data Analysis. Joint training between Sydney Kimmel Comprehensive Cancer Center at Johns Hopkins University and Cornel University Genome Center (2023)
• Writing a Winning NIH Grant Proposal by John. D. Robertson, Ph.D. Grant Writters’ Seminar and Workshop (2023).
• Bioinformatics Training RNA-seq data analysis by ECSeq GmbH, Germany (2022).
• Autumn School for Microbiome Analysis using next generation seqeuncing by Germany

Skills

• Cellular and molecular biology
  • Isolation and culture of alveolar macrophages (liquid and semisolid medium)
  • Human and murine hematopoietic stem cell culture (liquid and semisolid medium)
  • Lentiviral plasmid design and cloning, lentivirus production, titration, and transduction
  • Nucleic acid extraction (DNA and RNA)
  • Molecular cloning by restriction enzyme and ligation method
  • RNA Immunoprecipitation
  • ATAC tagmentation
  • Library preparation and quantification for next generation sequencing (NGS)
• Immunology and proteomics
  • Multicolor flow-cytometry (> 16 colors) using conventional and spectral flow cytometer
  • Enzyme-linked immunosorbent assay (ELISA)
  • Immunofluorescence staining and imaging
• In vivo mouse work
  • FELASA B certification
  • Wild-type and transgenic mouse colony management: breeding, genotyping, and cage management.
  • Bone marrow reconstitution experiment: lethal irradiation, transplantation, retroorbital bleeding, and bone marrow analysis
  • Macrophage isolation from mouse organs: lung, liver, spleen, bone-marrow.
  • Stereotactic injection of lentivirus into mouse brain.
  • Mouse surgery.
• Microscopy Imaging
  • Transmission electron microscope (TEM) sample preparation and operation of TEM
  • Correlative light and electron microscopy (CLEM)
  • Confocal fluorescence microscopy imaging
  • Wide-field fluorescence microscopy imaging with optical sectioning in Zeiss Axio Observer.
• Bioinformatics of Omics Data
  • Transcriptomics: Bulk and single-cell RNA-seq: DESeq2, Seurat, CellRanger, TEtranscript, FeatureCounts, scTE, STAR and Bowtie genome alignment
  • Epigenomics: Bulk and single-cell ATAC-seq: ArchR, MACS2, ChiPseeker
• Programming skills
  • Shell scripting in LINUX/UNIX environment
  • R programming language
  • FIJI/ImageJ macro
  • GitHub repository and documentation.
• Language skills (CEFR level)
  • Indonesian (native/C2)
  • English (C1)
  • German (B1)
  • Dutch (A1)
• Leadership skills
  • Strong interpersonal and leadership skills
  • Proven track record in managing organization from student bodies to research project

Leadership

• PI of MSCRF-funded research project to study HSC epigenome in response to alcohol and aging. Activities involved: Research project administration, design, conceptualization, investigation, data curation, analysis, visualization, and reporting to funding agency and manuscript preparation.
• Head of Student Executive Organization of the Faculty of Science and Technology, Airlangga University, (2012): Activities involved: Leadership and administration of the organization to representing students’ interests and aims for extracurricular activities, as well as active involvement of student bodies into political movement to
• Head of Microbiology Study Club, Biology Student Association, Faculty of Science and Technology, Airlangga University, (2011). Activities involved: Leadership and management of microbiology study activities including workshop and tutorials.