Mariaclaudia Nicolai

Bellinzona · Switzerland · (+41) 077 814 6305 · mariaclaudia.nicolai@gmail.com

As a research assistant in developing deep learning methods for biomedical data analysis, I am at the intersection of traditional biological and chemical laboratory practices and the forefront of computational modeling techniques. My work in computational biomedicine represents a dynamic fusion of diverse disciplines aimed at unraveling the complexities of biological systems through innovative approaches.

My role involves leveraging AI algorithms to probe intricate structures and functions within biological systems. By integrating computational methodologies, I deepen our understanding of biological phenomena, uncover hidden patterns, elucidate molecular mechanisms, and predict emergent behaviors.
In my pursuit, I navigate vast datasets from experimental observations, using computational algorithms to discern meaningful insights. I strive to elucidate underlying principles governing biological processes, from molecular interactions to systemic dynamics.
My research extends beyond traditional boundaries, embracing interdisciplinary collaboration. I aim for transformative discoveries and novel therapeutic interventions by bridging experimental methodologies and computational frameworks.
Through dedication to advancing computational biomedicine, I contribute to facing pressing healthcare challenges. From disease diagnosis to personalized medicine, my work represents scientific innovation shaping biomedical research and healthcare delivery.
My endeavors guide exploration in the dynamic realm of computational biomedicine, illuminating pathways toward understanding life's complexities and improving human health and well-being.


Research Experience

Research assistant

Università della Svizzera italiana (USI) · Faculty of Informatics

Designed a method for precise immune cell tracking through the application of convolutional neural networks to enhance tracking accuracy and efficiency to understand the intricate behaviors of cells.

July 2023 - Present
Lugano, Switzerland

Research trainee

Institute for Reseach in Biomedicine (IRB) · Computational Structural Biology Group

Evaluated resistance mechanisms to venetoclax by studying mutations in apoptosis regulators BCL2 through the analysis of protein structure using PyMol and assessment of binding affinity of the BCL-2 protein family with its inhibitor venetoclax via molecular dynamics simulations with Amber to understand resistance mechanisms.

Predicted new mutations in the SARS-CoV-2 spike protein by analyzing virus structure using PyMol and establishing a comprehensive dataset of amino acid sequences from GISAID. Implemented the artificial neural network LSTM to train on this dataset to predict novel spike protein mutations successfully.

Predicted T cell receptor (TCR) and antigen binding through implementing deep learning BERT and GPT2 models. Models trained by leveraging amino acid sequences with known or unknown TCR-antigen binding specificity, employing transfer learning or self-supervised learning methodologies to predict TCR-antigen binding successfully.

March 2021 - June 2023
Bellinzona, Switzerland

Visiting student

Delft University of Technology (TUDelft) · Faculty of Electrical Engineering, Mathematics, and Computer Science

Investigated the impact of user feedback on Android healthcare applications by applying sentiment analysis to assess the sentiments expressed in these reviews, revealing insights into the user sentiments for healthcare and non-healthcare apps to develop healthcare apps that meet customers’ needs.

July 2018 - June 2019
Delft, Netherlands

Work Experience

Social Media Assistant

Foodie Lab

Implemented daily collaboration with the manager to manage and promote social media activities effectively. Increased engagement and visibility across social media platforms by creatively presenting new content and proficiently handling customer requests.

April 2020 - April 2020
Naples, Italy

Pharmacist - Educational intern

Farmacia Dr. Italiano

Implemented responsible management of health products for ethical and deontological aspects of the pharmacist profession. Realized educational initiatives for consumers on health prevention and proper medication usage, enhancing public awareness and informed healthcare decisions.

May 2018 - November 2019
Benevento, Italy

Quality control operator

Bruitparif

Assembled and tested electronic devices using precision digital equipment for a research organization controlling environmental noise monitoring to increase data acquisition and analysis accuracy.

July 2015 - June 2018
Paris, France

Education

University of Salerno

Pharmacy and Industrial Pharmacy
Master of Science (MSc)

Thesis: Identification of antimicrobial activity models via machine learning.

March 2020
Salerno, Italy

Skills

  • Programming Languages: Python, JavaScript, R
  • Technologies/Frameworks: Linux, Git
  • Data Science and Machine Learning: TensorFlow, Keras, Pytorch, Pandas, Numpy
  • Molecular Dynamics Tools: Amber, Gromacs
  • Markup and Styling Languages: LaTeX, HTML/CSS
  • Laboratory Techniques: Medication preparation, Analytical characterization, Good Manufacturing Practices (GMP)
  • Manufactoring: Assembly, Soldering, Testing

Interests

  • Biology
  • Pharmacology
  • Immunotherapy
  • Bioinformatics
  • Data analysis
  • Machine learning
  • Deep learning
  • Artificial intelligence

Awards & Certifications

Awards
  • Scholarship and housing services at university residences\\University of Salerno (2015/2016)

Professional Service
  • Invited journal reviewer for the Health Informatics Journal (2021)

Certificates
  • Machine Learning: Politecnico di Milano, Italy (23 February 2022)
  • Imaging the immune system (IIS):EMBO Workshop, in Lugano, Switzerland (28 – 30 June 2023)

Publications

Publications