Hasso-Plattner-Institut
Prof. Dr. Bernhard Renard
 

Ferdous Nasri, M.Sc.

Research Scientist, PhD Candidate

 Phone:+49 (0)331 5509 - 4969
 E-mail:Ferdous.Nasri(at)hpi.de
 Organization:Hasso Plattner Institute, University of Potsdam
 Address:August-Bebel-Str. 88, 14482 Potsdam, Germany
 Room:HPI Campus I, K-E.09/10
 LinkedIn (CV):https://www.linkedin.com/in/ferbsx/
 Twitter:@ferbsx

Research

Developing Machine Learning and Algorithmic Approaches for Detecting Pathogen Outbreaks

As genome sequencing data increases with the improving NGS machines, new algorithms and methods need to be developed to analyse, process and make use of the data to better detect pathogens and their outbreaks. I started working on such projects already during my Master's and continue in pursuit of optimized algorithms and better suited machine learning methods to computationally detect a disease-causing agent and predict its spread. I have focused on different projects and topics until now, including developing and implementing an efficient indexing and aligning algorithm, which can align and analyse sequences as they are being sequenced (more details). Followed by a focus on curating a fungi-hosts database and using ResNets to detect fungal pathogenic potential from short DNA samples (see published paper and more details on the project). I am now more focused on analysing and predicting the spread of emerging diseases and their mutations (more details).

Keywords:

Machine Learning, Epidemiology, Genomic Surveillance, Pathogenicity Prediction, Live-DREAM Analysis

 

Teaching

Summer Term 2023

Summer Term 2022

Winter Term 2021/2022

Publications and achievements

  • Won 2nd place at the MobiDataLab Codagon in Leuven, Belgium (link) with "AI-driven analytics transforming existing urban data into accessibility plans".
  • Won 2nd place at the MobiDataLab Hackathon in Paris, France (link) with "Transforming urban pedestrian mobility: a data-driven solution for city planning". (POLIS network)
  • Ferdous Nasri*, Simon Cyrani*, Lukas Wenner, and Bernhard Y. Renard. "Immunity score calibration based on vaccination rebalancing", ICLR - MLGH Workshop, 2023; https://openreview.net/forum?id=1VMoclIsQEe
  • Won 1st Place at the MobiDataLab Datathon in Berlin, Germany (link) with "An environmental approach to disability data" (Datathon post, 'here' post).
  • Ferdous Nasri, Kunaphas Kongkitimanon, Alice Wittig, Jorge Sánchez Cortés, Annika Brinkmann, Andreas Nitsche, Anna-Juliane Schmachtenberg, Bernhard Y Renard, Stephan Fuchs. "MpoxRadar: a worldwide MPXV genomic surveillance dashboard", Nucleic Acids Research, 2023;, gkad325, https://doi.org/10.1093/nar/gkad325
  • Bartoszewicz, Jakub M.*, Ferdous Nasri*, Melania Nowicka, and Bernhard Y. Renard. "Detecting DNA of novel fungal pathogens using ResNets and a curated fungi-hosts data collection." Bioinformatics 38, no. Supplement_2 (2022): ii168-ii174. https://doi.org/10.1093/bioinformatics/btac495

Scientific community participation

2024

  • The 16th Great Lakes Bioinformatics (GLBIO) conference in Pittsburgh, USA (link), Talk presenting my work titled: "Graph-based Linear Optimization for Spatial-temporal Population Immunity Calculation".


2023

  • The 31st annual Intelligent Systems For Molecular Biology (ISMB) and the 22nd annual European Conference on Computational Biology (ECCB) in Lyon, France (link), Talk presenting my work titled: "Platform for global genomic surveillance of emerging diseases applied to Mpox",
  • The Eleventh International Conference on Learning Representations (ICLR) in Kigali, Rwanda (link), Poster presentation with the title: "Immunity score calibration based on vaccination rebalancing",
  • The 20th Basel Computational Biology Conference (BC2) in Basel, Switzerland (link). Poster presented with the title: "High-resolution spatial and temporal immunity scores based on vaccination, recoveries and accounting for immunity waning".
  • Organised the one-day symposium named: Data Analytics and Computational Statistics & Future Research Ideas and ENDeavors Symposium (DACS&Friends), in Potsdam, Germany.

2022

  • First International Summer School on Data Science for Mobility in Santorini (Kamari village), Greece (link),
  • 21st European Conference on Computational Biology (ECCB 2022) in Barcelona (Sitges), Spain, Poster presentation with the title: "LIVE-DREAM: Live analysis of NGS data using an optimized hierarchical inter-leaved Bloom Filter index" (link),
  • German Conference on Bioinformatics 2022 (GCB 2022) in Halle, Germany, Poster presentation with the title: "Integration of contact, mobility, vaccination, and SARS-CoV-2 incidence data for prediction using statistical and machine learning models" (link),
  • "Workshop: The future of compressed data structures, 20 years after the FM-index" in Lipari, Italy (link),
  • Lipari School Computational Complex and Social Systems with the topic: "Data Science: Models, Algorithms, AI and Beyond" in Lipari, Italy (link).

2021

  • German Conference on Bioinformatics 2021 (GCB 2021), Poster presentation with the title: "Pathogenic potential prediction of novel fungal DNA based on a newly curated fungi-host database" (link),
  • International Society for Computational Biology (ISCB) Student Council Symposium (SCS) 2021 (link),
  • 29th Intelligent Systems for Molecular Biology and 20th European Conference on Computational Biology (ISMB/ECCB 2021), Poster presentation with the title: "Pathogenic potential prediction of novel fungal DNA using ResNets based on a newly curated fungi-host database" (link).