Raphael Kfuri-Rubens
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Two tracks, one trajectory.

Research began during medical school in 2017 — CAR T-cell therapy in Munich, cancer immunology in Boston — and moved into computational biology at Cambridge after graduation. Since 2024, a residency in hematology and oncology at TUM University Hospital has run alongside a PhD at the Technical University of Munich, in Fabian Theis’s lab at Helmholtz Munich.

Institutions

  • TUM University HospitalMunich2024 – present
  • Helmholtz MunichMunich2023 – present
  • Dana-Farber · Broad InstituteBoston2023
  • University of CambridgeCambridge, UK2022 – 23
  • Massachusetts General Hospital, Harvard Medical SchoolBoston2019 – 21
  • LMU MunichMunich2016 – 22

20 entries · 2013 – present

  1. – presentMunich, Germany

    ClinicalCurrent

    Resident physician in hematology and oncology

    TUM University Hospital, Technical University of MunichDepartment of Hematology and Oncology

    Hematologic and solid malignancies — inpatient ward and outpatient chemotherapy unit

    Resident physician in the Department of Hematology and Oncology at TUM University Hospital, rotating across the inpatient ward and outpatient chemotherapy unit and managing patients with hematologic and solid malignancies.

    People

    Director
    Prof. Florian Bassermann

    Highlights

    • Clinical rotations across the general hematology/oncology inpatient ward and outpatient chemotherapy unit
    • Diagnosis, staging, and management of a broad range of hematologic and solid malignancies
    • Supervision and administration of systemic cancer therapies, including chemotherapy, immunotherapy, and targeted treatments
    • Involvement in diagnostic workup, treatment planning, and longitudinal follow-up of patients
  2. – presentMunich, Germany

    ResearchCurrent

    PhD student

    Helmholtz Munich, Technical University of MunichInstitute of Computational Biology

    Single-cell and spatial omics · graph neural networks and transformer-based models

    PhD research at the Institute of Computational Biology (Helmholtz Munich / Technical University of Munich) involving single-cell and spatial omics data analysis and the implementation and benchmarking of deep learning architectures such as graph neural networks and transformer-based models.

    People

    Principal investigator
    Prof. Fabian Theis
    Co-supervisor
    Prof. Florian Bassermann
    Co-supervisor
    Prof. Daniel Rückert

    Highlights

    • Proficient in python-based single cell and spatial omics data analysis packages, such as scanpy, squidpy and scvi-tools
    • Experienced in implementing multiple deep learning architectures, including Graph Neural Networks and transformer-based models, and benchmarking them against other machine learning models
    • Application of machine learning frameworks, such as PyTorch, PyTorch Lightning, PyTorch Geometric, Weights and Biases and configuration managers

    Methods & tools

    • scanpy
    • squidpy
    • scvi-tools
    • PyTorch
    • PyTorch Lightning
    • PyTorch Geometric
    • Graph Neural Networks
    • Transformer-based models
    • Weights and Biases
  3. – Boston, USA

    Research

    Master's thesis in Computational Oncology

    Dana-Farber Cancer Institute and Broad Institute, Harvard Medical School

    Extending a minor histocompatibility antigen (mHAg) prediction pipeline

    Master's thesis project at Dana-Farber Cancer Institute and Broad Institute extending a minor histocompatibility antigen (mHAg) prediction software pipeline, including analysis of whole exome and transcriptomic data from allogeneic stem cell transplantation patient cohorts.

    People

    Principal investigator
    Catherine Wu, MD
    Principal investigator
    Gad Getz, PhD
    Supervising postdoc
    Nicoletta Cieri, MD PhD

    Highlights

    • Combining deep learning models with multiple computational biology tools using workflow description language (WDL)
    • Mitochondrial/nuclear variant calling for chimerism and mosaicism analysis
    • Analysis and pipeline work on whole exome and transcriptomic data of allogeneic stem cell transplantation patient cohorts at Dana-Farber Cancer Institute

    Methods & tools

    • Workflow Description Language (WDL)
    • Deep learning models
    • Mitochondrial/nuclear variant calling
    • Whole exome data analysis
    • Transcriptomic data analysis

  4. Scholarship

    Studienstiftung scholarship for Master's thesis research stay

    German Academic Scholarship Foundation (Studienstiftung) — research stay at Dana-Farber Cancer Institute and Broad Institute, USA

  5. – Cambridge, United Kingdom

    Education

    MPhil in Computational Biology

    University of Cambridge

    Scientific programming, genomics, deep learning and systems biology

    MPhil in Computational Biology at the University of Cambridge covering scientific programming, genomics, genome sequence analysis, deep learning, imaging, population genetics, biodesign and systems biology.

    Highlights

    • Completed multiple projects using Python, R and Julia
    • Implemented Hidden Markov Model and inference algorithms, such as Baum-Welch and Viterbi algorithm
    • Single-cell RNA-seq analysis, ChIP/ATAC-seq
    • Generated supervised learning models with Tensorflow/Keras and PyTorch

    Subjects

    • Scientific Programming
    • Genomics
    • Genome Sequence Analysis
    • Deep Learning
    • Biological Imaging Analysis
    • Population Genetics Analysis
    • Biodesign
    • Systems Biology

    Methods & tools

    • Python
    • R
    • Julia
    • PyTorch
    • TensorFlow/Keras
    • Hidden Markov Models

  6. Award

    National doctoral thesis award

    German Society of Hematology and Medical Oncology

  7. Talk

    Award ceremony and talk

    Congress of the German, Swiss and Austrian Cancer Societies, Vienna

  8. Scholarship

    Studienstiftung scholarship for the MPhil in Computational Biology

    German Academic Scholarship Foundation (Studienstiftung) — University of Cambridge, UK

  9. – Munich, Zürich and Heidelberg

    Clinical

    Final year rotations

    Ludwig-Maximilians-Universität Munich, University of Zürich, Heidelberg University

    Pediatric oncology, gastroenterology, nephrology · trauma ICU, emergency department, cardiac surgery · hematology, oncology, cardiology

    Rotations

    • Ludwig-Maximilians-Universität MunichMunich, GermanyPediatric Oncology, Gastroenterology, Nephrology
    • University of ZürichZürich, SwitzerlandTraumatological ICU, Accident and Emergency Department, Cardiac Surgery
    • Heidelberg UniversityHeidelberg, GermanyHematology, Oncology, Cardiology

  10. Award

    Award for outstanding grades in neuroscientific courses

    LMU Munich — Neurosurgery, Neuroradiology, Neuropathology and Neurology

  11. Award

    Best Poster award

    Retreat of the Division of Rheumatology, Allergy and Immunology, Massachusetts General Hospital, Harvard Medical School

  12. Scholarship

    Stipend of Prof. Mempel

    Continuing the research project at the Center for Immunology and Inflammatory Diseases, Massachusetts General Hospital, Harvard Medical School

  13. Fellowship

    International fellowship PROSA LMU and research scholarship

    German Academic Exchange Service and German Academic Scholarship Foundation — research project at Massachusetts General Hospital, Harvard Medical School

  14. – Boston, USA

    Research

    Research scholar

    Massachusetts General Hospital, Harvard Medical SchoolCenter for Immunology and Inflammatory Diseases

    As part of the medical doctoral thesis

    Intratumoral cytotoxic T cell migration and interactions with myeloid populations

    Research scholar at the Center for Immunology and Inflammatory Diseases, Massachusetts General Hospital, Harvard Medical School, as part of the medical doctoral thesis, studying intratumoral cytotoxic T cell migration and interactions with myeloid populations in cancer immunology.

    People

    Principal investigator and associate director
    Thorsten Mempel, MD PhD
    Supervising postdoc
    Mauro Di Pilato, PhD

    Highlights

    • Performed single-cell RNA-seq experiments of ex vivo tumors
    • Multiphoton intravital microscopy, fluorescence microscopy
    • Flow cytometry of in vitro and ex vivo cells
    • Collaborated with other labs, mainly performing intravital multiphoton microscopy experiments

    Methods & tools

    • Single-cell RNA-seq experiments
    • Multiphoton intravital microscopy
    • Flow cytometry
    • Murine bone marrow chimeras
    • Imaris
    • MATLAB
    • FlowJo
    • Fiji

  15. Grant

    Two student grants for doctoral research

    LMU Munich — material resources for the doctoral research project

  16. Scholarship

    German Academic Scholarship Foundation

    Admitted as a scholar of the Studienstiftung des deutschen Volkes

  17. Program

    i-Target: Immunotargeting of cancer

    Elite Network of Bavaria — international scientific program: seminars, journal clubs, workshops and conferences

  18. – Munich, Germany

    ResearchSumma cum laude

    Medical doctoral thesis (Doctor of Medicine)

    Ludwig-Maximilians-Universität MunichDivision of Clinical Pharmacology, Department of Internal Medicine IV

    Continued at Massachusetts General Hospital, Harvard Medical School (2019 – 21)

    Improving CAR T-cell therapy of solid tumors in preclinical models

    Medical doctoral thesis research at the Division of Clinical Pharmacology, LMU Munich, aimed at improving CAR T-cell therapy of solid tumors in preclinical models.

    People

    Director
    Prof. Stefan Endres
    Principal investigator
    Prof. Max Schnurr

    Highlights

    • Generation of CAR T cells (ex vivo T cell transduction with CAR constructs)
    • Used different assays to quantify gene/protein expression of ex vivo T cells and cell lines with immunoblotting, real-time quantitative PCR, ELISA
    • Performed different cell culture assays, e.g. xCELLigence or CytoTOX, for in vitro quantification of T cell killing
    • Validated CAR T cell efficacy with orthotopic murine tumor models

    Methods & tools

    • CAR T cell generation
    • Immunoblotting
    • Real-time quantitative PCR
    • ELISA
    • xCELLigence
    • Orthotopic murine tumor models

  19. Program

    FöFoLe research scholarship and doctoral program

    LMU Munich — research scholarship and doctoral program (similar to MD-PhD)

  20. – Munich, Germany

    Education

    Medical school

    Ludwig-Maximilians-Universität Munich

    Preclinical studies in Ulm and Marburg (2013 – 16), clinical studies in Munich (2016 – 21)

    Medical studies begun at the University of Ulm and Philipps-Universität Marburg and completed at LMU Munich, with final year rotations in Munich, Zürich and Heidelberg.

    Highlights

    • Graduated from LMU Munich

    Course of study

    • Preclinical studies2013 – 2016University of Ulm, Philipps-Universität Marburg
    • Clinical studies2016 – 2021Ludwig-Maximilians-Universität Munich
    • Final year rotations2021 – 2022Ludwig-Maximilians-Universität Munich, University of Zürich, Heidelberg University

    Clinical electives

    • Dana-Farber Cancer Institute, Harvard Medical SchoolBoston, USAMDS/AML clinic
    • FAMERP, University HospitalSão José do Rio Preto, BrazilCardiology, Internal medicine
    • Spital Graubünden (teaching hospital of the University of Zürich)Samedan, SwitzerlandGeneral Surgery, Traumatology
    • Teaching Hospitals of the Ludwig-Maximilians-Universität MunichMunich, GermanyAccident and Emergency Department, Intermediate Care Unit, Gastroenterology, Neurology