Description

Leader of the group Life Sciences and Health: Leen Stougie.

Our research group creates fundamental knowledge and applied solutions in the broad field of life sciences. We promote understanding of how biological processes work in detail. Our interdisciplinary team of computer scientists, mathematicians and theoretical biologists develops new models, theories, and decision support systems in collaboration with experimental biologists and medical experts. We are motivated by applications of our work in practice

 

Watch our group video to get a glimpse of our activities or click here for more information about our group structure.

 

News

Current events

LSH Seminar Nadia Pisanti (University Pisa)

  • 2019-01-22T16:00:00+01:00
  • 2019-01-22T17:00:00+01:00
January 22 Tuesday

Start: 2019-01-22 16:00:00+01:00 End: 2019-01-22 17:00:00+01:00

room L016

Mapping Reads and Palindromic Decomposition on Pan-Genomes

An elastic-degenerate string (ED-string) has been introduced to compactly represent a multiple alignment of several closely-related sequences (a pan-genome). In this representation, substrings of these sequences that match exactly are collapsed, while in positions where the sequences differ, all possible variants observed at that location are listed. The natural problem that arises is finding all matches of a deterministic pattern in an elastic-degenerate text. We introduce an algorithm to solve this problem on-line after a pre-processing stage. Moreover, we study the same problem under the edit- and Hamming-distance model. Finally, we describe a linear time algorithm for the comparison of non elastic D-strings (a special case of ED-strings) and a consequent efficient decomposition of D-strings into palindromes.

Members

Associated Members

Publications

Software

Current projects with external funding

  • 3D dose reconstruction for children with long-term follow-up Toward improved decision making in radiation treatment for children with cancer
  • Enhancing protein-drug binding prediction
  • ICT based Innovations in the Battle against Cancer – Next - Generation Patient -Tailored Brachytherapy Cancer Treatment Planning
  • Improving Childhood Cancer Care when Parents Cannot be There - Reducing Medical Traumatic Stress in Childhood Cancer Patients by Bonding with a Robot Companion
  • Statistical Models for Structural Genetic Variants in the Genome of the Netherlands
  • Fusible Evolutionary Deep Neural Network Mixture Learning from Distributed Data for Robust Medical Image Analysis (FEDMix)
  • Multi-Objective Deformable Image Registration (MODIR) – An Innovative Synergy of Multi-Objective Optimization, Machine Learning, and Biomechanical Modeling for the Registration of Medical Images with (MODIR)

Related partners

  • AMC Medical Research
  • Elekta Limited
  • Nucletron Operations BV
  • Xomnia
  • Academisch Medisch Centrum
  • Biomedical Imaging Group Rotterdam
  • Erasmus Universiteit Rotterdam
  • KiKa
  • Technische Universiteit Delft
  • Universiteit Leiden