Experience

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  Artisan Bio

  • Scientist I

    • Feb 2023 - Nov 2023

    I've been an integral part of the Artisan Bio team, where I've played a key role in advancing our work in Synthetic Biology. In my current role, I take on a range of responsibilities: • I plan, design experiments, and carry out complex genome editing studies, ensuring precise execution. This includes extensive genome engineering datasets, such as high-throughput gRNA tiling, knock-out expression assays, and NGS analysis, all aimed at achieving efficient editing. • I've developed in-house high-throughput assays for gRNA prediction models, leveraging the wealth of data we've generated. • Utilizing a large plasmid library with over 10,000 components, I execute multiplexed edits (indels and knock-ins) in mammalian cells through nucleofection or lipofection of nuclease/gRNA/plasmid cargo. • Effective communication is crucial in my role, and I regularly update the Data Science and Genome Analytics teams on project progress and findings.In addition, I've achieved the following milestones: • Ensured the on-time and cost-effective accomplishment of both individual and team goals on an annual basis. • Designed integration plasmids for efficient delivery of designer payloads, ranging from 100 bp to 6kb knock-ins, at the AAVS1 safe harbor site. • Created and assembled multiple extensive plasmid libraries, each containing over 10,000 gRNAs or editing cassettes. This involved multiplex oligo synthesis of designer cassettes, pooled amplification, subcloning into custom miniplasmids, and amplification/purification of final plasmid library pools in E. coli. • Evaluated pooled indel frequencies and editing efficiencies using next-generation sequencing (NGS) and assessed knock-in efficiencies in HEK293T and Pan T cells through flow cytometry to gauge the expression of inserted cargo. • Authored approved standard operating procedures (SOP) for plasmid library generation in the context of multiplexed genome editing and for various high-throughput assays.

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  University of Colorado Anschutz Medical Campus

  • Denver, Colorado, United States

  • Postdoctoral Associate

    • Apr 2020 - Feb 2023
    • Denver, Colorado, United States

    During my tenure as a Postdoctoral Associate in Prof. Dr. Christian Mosimann's and Prof. Dr. Charles Sagerstrom's labs, I contributed significantly to our research endeavors: • I played a pivotal role in engineering mixl1 zebrafish mutants, harnessing the power of CRISPR/Cas9 genome editing, PCR, Sanger sequencing, molecular cloning, and classical genetics techniques. • I identified distinct progenitor populations within the lateral-plate mesoderm structure in zebrafish embryos by applying a single-cell RNA-sequencing protocol and meticulously analyzing scRNA-sequencing datasets, in collaboration with a bioinformatician (Prummel et al., Nat Commun, 2022). • I unearthed genetic regulatory elements, specifically developmental enhancers, by skillfully assembling, processing, analyzing, and interpreting publicly available ChIP-sequencing datasets in zebrafish (Kresoja-Rakic et al, manuscript in preparation).Some notable achievements during my time in the lab include: • Pioneering the discovery of zebrafish developmental enhancers for genes like sox32, vent/vox, and mixl1. • Revealing the genome-wide binding profile of the hand2 transcription factor through the precise execution of ChIP-seq in zebrafish embryos (Kresoja-Rakic et al., manuscript in preparation). • Receiving the esteemed Hilde Mangold Post-Doctoral Symposium Award at the 81st Society for Developmental Biology Annual Meeting 2022, in recognition of my outstanding work. • Achieving the Swiss National Science Foundation - Postdoctoral Mobility Fellowship, reflecting my dedication to a successful scientific career. • Being appointed a Gates Fellow at the University of Colorado Anschutz Medical Campus as part of the Postdoctoral Training Program in Developmental Biology. • Earning a Certificate of Recognition for Postdoc of the Month at the University of Colorado Anschutz Medical Campus, in acknowledgment of my exemplary contributions to the academic community

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  University of Zurich, Department of Molecular Mechanisms of Disease, Zurich, Switzerland

  • Zürich Area, Switzerland

  • Postdoctoral Associate

    • Oct 2018 - Feb 2020
    • Zürich Area, Switzerland

    As a Postdoctoral Associate, I conducted groundbreaking research focused on the molecular underpinnings of genome organization in embryonic stem cells (ESCs). My contributions during this period are summarized below:Research and Publications: • Experimental Work: Conducted in vitro RNA transcription of pRNA, purification, visualization, and subsequent lipofection of pRNA into mouse ESCs. Employed total RNA isolation and RT-PCR analysis to discern the impact on the global genome architecture. • Research Articles: Authored a second-author research article and a first-author review elucidating the pivotal role of the nucleolus in shaping the genome organization of ESCs. • Journal Cover Feature: The research article was featured as the cover story for the November 2019 issue of the "Trends in Genetics" journal, underscoring the significance of the study.Data Deposition: • ChIP-seq Datasets: Deposited ten curated ChIP-seq datasets at the Gene Expression Omnibus (GSE150822). This involved transfecting mouse ESCs with in vitro synthesized RNA and conducting chromatin immunoprecipitation targeting H3K9me2 and H3K9me3 modifications. • RNA-seq Datasets: Archived two comprehensive RNA-seq datasets at the Gene Expression Omnibus (GSE150822). This employed the transfection of mouse ESCs with in vitro synthesized pRNA and subsequent total RNA isolation.Methodological Advancements: • Laser Capture Microdissection: Developed a groundbreaking protocol for laser capture microdissection of the nucleolus in ESCs. This innovation paved the way for single-cell genome sequencing (MALBAC) and enabled the identification of nucleolar-associated domains (NADs). • Single-Genome Sequencing: Generated a remarkable array of seventeen single-genome sequencing datasets, shedding light on the intricate landscape of nucleolar-associated domains in mouse ESCs.Teaching: • Instructor: Instructed the "RNA biology" practical course at the University of Zurich

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  UniversitätsSpital Zürich

  • Zürich Area, Switzerland

  • Postdoctoral Associate

    • May 2017 - Oct 2018
    • Zürich Area, Switzerland

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  UniversitätsSpital Zürich, Cancer Biology, Division of Thoracic surgery

  • Zürich Area, Switzerland

  • Scientific Researcher

    • Jan 2013 - May 2017
    • Zürich Area, Switzerland

    During my tenure as a Scientific Researcher at the University Hospital Zurich, Department of Thoracic Surgery, I was dedicated to advancing our understanding of tumor biology of mesothelioma and its treatment outcomes. My responsibilities and accomplishments during this period are highlighted below:Research and Collaborative Work: • Oncology Collaboration: Collaborated closely with clinical teams in the field of oncology, contributing to groundbreaking efforts aimed at understanding mesothelioma patients. This included the extraction of RNA and the utilization of RT-PCR to measure circulating non-coding RNAs in liquid samples. • Advanced Molecular Techniques: Employed a battery of advanced molecular biology techniques, including cloning, PCR, RT-PCR, DNA/RNA isolation, and the assessment of protein expression via Western-Blot and immunofluorescence.Publications and Academic Achievements: • Research Articles: Published four first-author and two second-author research articles, unraveling intricate mechanisms that govern gene expression in mesothelioma. • Ph.D. Attainment: Attained a Ph.D. in Cancer Biology from the University of Zurich, successfully defending a doctoral thesis titled "Molecular mechanisms of calretinin expression in mesothelioma." • Life Science Graduate School: Distinguished as a Ph.D. candidate in the highly competitive Life Science Graduate School of Zurich, boasting an acceptance rate of merely 5%.Laboratory Expertise and Entrepreneurship: • Cell Line Maintenance: Maintained established mammalian cancer cell lines in culture, leveraging models for in vitro DNA/RNA delivery techniques such as transfection and siRNA-mediated gene disruption. • In Vitro Toxicology Assay: Gained a profound understanding of entrepreneurship, actively participating in the development of an in vitro toxicology assay with the support of the Swiss Innovation Agency.

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  Kinderspital Zürich

  • Scientific Researcher

    • 2011 - 2012

    As a Scientific Researcher at the University Children's Hospital of Zurich, my focus was on infectious diseases and cancer research. During this period, I engaged in a range of essential research activities, contributing to the advancement of scientific knowledge in the field. Here are some of the key responsibilities and achievements:Laboratory Work and Cell-Based Assays: • Executed various cell-based assays, including apoptosis assays, cell viability assessments, and fluorescence-activated cell sorting (FACS). These activities laid a crucial foundation for our scientific understanding. • Applied small molecule inhibitors to mammalian cell lines, which significantly contributed to our knowledge of targeted therapeutic interventions.Research Contribution: • Research Article: Contributed as a second author to a research article that shed light on the critical role of growth factor survival signaling pathways in inhibiting the AKT/mTOR pathway within rhabdomyosarcoma and breast cancer cell lines. This work added valuable insights to our understanding of cancer biology.Scholarship Recognition: • Received the prestigious "Dositeja" Scholarship from the Fund for Young Talents of Serbia, recognizing my exceptional promise and dedication to the field of research.