Alexandru I. Tomescu - Teaching and Supervision

Courses

• Models of Computation, Spring 2025, University of Helsinki
• Research Seminar in Life Science Informatics (with Andrey Prjibelski), Fall 2024, University of Helsinki
• Elements of Bioinformatics (with Ville Mustonen), Fall 2024, University of Helsinki
• Models of Computation, Spring 2024, University of Helsinki
• Elements of Bioinformatics (with Ville Mustonen), Fall 2023, University of Helsinki
• Models of Computation, Spring 2023, University of Helsinki
• Elements of Bioinformatics (with Ville Mustonen), Fall 2022, University of Helsinki
• Models of Computation, Spring 2022, University of Helsinki
• Elements of Bioinformatics (with Ville Mustonen), Fall 2021, University of Helsinki
• Models of Computation, Spring 2021, University of Helsinki
• Elements of Bioinformatics (with Ville Mustonen), Fall 2020, University of Helsinki
• Seminar on Genomic Data Science, Fall 2019, University of Helsinki, Finland
• Design and Analysis of Algorithms, Fall 2017, University of Helsinki, Finland, co-teaching with Veli Mäkinen
• Seminar on High-throughput Sequencing Data Analysis, Spring 2016, University of Helsinki, Finland
• Design and Analysis of Algorithms, Fall 2015, University of Helsinki, Finland, co-teaching with Veli Mäkinen
• In May 2015 I've taught three lectures on minimum-cost flows at the University of Primorska, in Koper, Slovenia,
  in the courses Bioinformatics, Graph Algorithms and Optimization Methods
• Algorithms for Bioinformatics, Fall 2013, University of Helsinki, Finland
• Advanced Algorithms (14-hour module), Fall 2013, University of Udine, Italy

PhD Students

• Francisco Sena, 2023 -
• Andreas Grigorjew, Algorithms and Graph Structures for Splitting Network Flows, in Theory and Practice, main supervisor, defended February 2025
• Manuel (Ariel) Cáceres, Parameterized and Safe & Complete Graph Algorithms for Bioinformatics, main supervisor, defended October 2023
• Sebastian Schmidt, Unitigs Are Not Enough: the Advantages of Superunitig-Based Algorithms in Bioinformatics, main supervisor, defended August 2023
• Massimo Equi, Lower and Upper Bounds for String Matching in Labelled Graphs, secondary supervisor (main supervisor Veli Mäkinen), University of Helsinki, defended June 2022
• Anna Kuosmanen, Third-generation RNA-sequencing analysis: graph alignment and transcript assembly with long reads, secondary supervisor (main supervisor Veli Mäkinen), University of Helsinki, defended December 2017

Master Students

• Rael Huizenga, Minimum Flow Decomposition for Haplotype-Aware Genome Assembly, 2025, at TU Delft, external advisor role
• Eliel Ingervo, Safe walks for flow decompositions with subpath constraints, in general graphs, graduated 2024 (co-supervised with Sebastian Schmidt and Manuel Cáceres)
• Andrea Cracco, Creating compacted de Brujin graphs from raw sequencing data, graduated 2021 (at University of Verona, co-supervision with Romeo Rizzi). Resulted in a paper in RECOMB 2023 / Genome Research
• Jun Ma, Chaining on Graphs with Cycles, graduated 2021 (co-supervision with Manuel Cáceres). Resulted in a paper in Bioinformatics
• Nicola Rizzo, The Longest Repeated String Problem on Graphs, graduated 2021 (at University of Udine, co-supervision with Alberto Policriti). Resulted in a paper in Algorithmica. Received the prize Best Italian MSc Thesis in Theoretical Computer Science 2022, by the Italian Chapter of EATCS.
• Niko Kiirala, Safe and Complete Prediction of RNA Secondary Structure, University of Helsinki, co-supervision with Leena Salmela and Veli Mäkinen, graduated 2019. Resulted in a paper in CPM 2019
• Nidia Obscura Acosta, Safe solutions for walks on graphs, University of Helsinki, co-supervision with Veli Mäkinen, graduated 2018. Resulted in two papers in: CPM 2017, and Algorithms for Molecular Biology
• Topi Paavilainen, Faster algorithms for minimum path cover by graph decomposition, University of Helsinki, co-supervision with Veli Mäkinen, graduated 2017. Resulted in a paper in RECOMB 2018
• Xinyue Li, Data simulation of tumor phylogenetic trees and evaluation of phylogenetic reconstructing tools, co-supervision with Veli Mäkinen and Juho Rousu, Aalto University, graduated 2017. Resulted in paper in Bioinformatics
• Ahmed Sobih, MetaFlow: Metagenomics taxonomic analysis using network flows, University of Helsinki, co-supervision with Veli Mäkinen, graduated 2016. Resulted in a paper in RECOMB 2016