MSc students - Bioinformatics Research Center (BiRC)

This is a list of students who have defended their Master's thesis in the Master's Program in Bioinformatics at the Bioinformatics Research Center (BiRC), Aarhus University. To get the full text of a thesis, please contact the author(s) or supervisor of the thesis. Contact information for supervisors can be found at the BiRCs www-pages.

2024

Andrés Barrena Calderón: Multi-Modality Machine Learning Prediction of Mental Health - Archetypes in Deep Phenotyped Young and Representativ SampleDefended on October 22, 2024. Supervisor: Per Quist and Jakob Grove.
Tessa Jane Davita. Thesis: Exploring Methods to Analyze and Process Spatial Proteomics Data. Defended on June 27, 2024. Supervisor: Nicolai Juul Birkbak.
Sofie Poder Jørgensen. Thesis: Exploration of Immune Cell Type Composition and How It Relates to Biological Age. Defended on June 27, 2024. Supervisor: Nicolai Juul Birkbak.
Sarah Elna Valentin. Thesis: Novel method to examine strong cancer driver mutations. Defended on June 27, 2024. Supervisor: Nicolai Juul Birkbak.
Naja Lange. Thesis: Explore the impact of immune health on cancer outcome. Defended on June 27, 2024. Supervisor: Nicolai Juul Birkbak.
Paula Rodrigo Martin. Thesis: Investigating regulatory motif perturbation during SARS-CoV-2 infection in a single-cell setup. Defended on June 27, 2024. Supervisor: Jakob Skou Pedersen.
Farhad Zamani. Thesis: miDGD: Prediction of miRNA activity levels based on gene expression data using Deep Generative Decoder model. Defended on June 27, 2024. Supervisor: Jakob Skou Pedersen.
Rasmus Freund. Thesis: Enhancing Antimicrobial Resistance Prediction with Convolutional Neural Networks. Defended on June 26, 2024. Supervisor: Palle Villesen.
Maria Eskerod Sørensen. Thesis: StructUnet - Deep Learning Based Approach for RNA Secondary Structure Prediction. Defended on June 26, 2024. Supervisor: Christian Storm Pedersen.
Ainhoa Sánchez Ramón. Thesis: QC EWAS - Quality Control Flow for Epigenome-Wide Association Studies. Defended on June 25, 2024. Supervisor: Jakob Grove. Co-supervisor: Anna Starnawska.
Francisco de Borja Campuzano Jimenez. Thesis: Prediction of Maladapation from Ecological and Genomic Data using Gennomic Offsets. Defended on June 24, 2024. Supervisor: Thomas Bataillon. Co-supervisor: Genis Garcia Erill.
Anastasia Kratschmer. Thesis: Voles apart: Implementing genetics in the ALMaSS- simulation framework and simulating genetic effects of roads on voles. Defended on June 24, 2024. Supervisor: Thomas Bataillon. Co-supervisors: Geoffrey Brian Groom, Christopher John Topping.
Peter Sørud Porsborg. Thesis: Detection of recombination and de novo mutations in PacBio HiFi reads. Defended on June 24, 2024. Part of PhD Qualification Exam. Supervisor: Mikkel Schierup
Laura Skak Rasmussen. Thesis: Using Whole-Genome Nanopore Long-Read Data to Examine Autosomal DNA Methylation in Individuals with Sex Chromosome Aneuploidies. Defended on June 21, 2024. Supervisor: Jakob Skou Pedersen. Co-supervisor: Claus Højbjerg Gravholt.
Genona Torruella Maseras. Thesis: Association between Genetic Risk (PRS) and Age-Specific Risk of Mental Disorders. Defended on June 20, 2024. Supervisor: Bjarni Vilhjálmsson. Co-supervisor: Oleguer Plana-Ripoll.

2023

Jinqi Duan. Thesis: Exploring the Association between Maternal Cardiometabolic Conditions and Autism in Offspring: A Case-Cohort Study. Defended on June 29, 2023. Supervisor: Jakob Grove.
Andreas Smedemark Hammer. Thesis: Evaluating Contemporary Minimum Free Energy Bbased Methods for RNA Folding. Defended on June 28, 2023. Supervisor: Christian Storm Pedersen.
Bernadett Mercedesz Molhar. Thesis: Quantifying Social Behaviour: Animal Tracking with DeepLabCut. Defended on June 28, 2023. Supervisor: Christian Storm Pedersen.
Samuel Martin Vargas Giagnocavo. Thesis: Hardware Accelrated Solutions for Sequence Alignment. Defended on June 28, 2023. Supervisor: Christian Storm Pedersen.
Leyi Zhang. Thesis: An Evaluation of Software for Performing GWAS Mixed-model Association Analysis. Defended on June 27, 2023. Supervisor: Doug Speed.
Cæcilia Lind Skov Jensen. Thesis: Specifying the meetings between anatomically modern humans, Neanderthals, and Denisovans. Defended on June 27, 2023. Supervisor: Mikkel Schierup.
Eamon Forster Winship. Thesis: Evolutionary Pressures In Marine Sediment Microbes. Defended on June 23, 2023. Supervisor: Thomas Bataillon.
Kristian Riis Hansen. Thesis: Inferring population genetics on sediment communities using a metagenomical approach. Defended on June 23, 2023. Supervisor: Thomas Bataillon.
Christian Bjødstrup Rygaard. Thesis: Using the GLIPH2 algorithm to analyze TCR specificity in cancer patients. Defended on June 23, 2023. Supervisor: Nicolai Juul Birkbak.
Lea Korsholm Nielsen. Thesis: Understanding the Potential Causal Effects in Alzheimer’s Disease. Defended on June 12, 2023. Supervisor: Thomas Batallon.
Mathilde Diekema. Thesis: Discovering Causal Relationships in Microbial Time Series Data. Defended on June 12, 2023. Supervisor: Thomas Batallon. Co-supervisors: Leendert Vergeynst, Williane Vieira Macêdo.
Sofie Agerbæk. Thesis: Predicting the ages of blood samples using targeted metabolomic data. Defended on January 25, 2023. Supervisor: Palle Villesen.
Astrid Christensen. Defended on January 23, 2023. Supervisor: Thomas Mailund.

2022

Johan Lassen. Thesis: Using metabolomics and robust computational methods to predict donor traits in forensics and other fields of research. Defended on June 29. Part of PhD Qualification Exam. Supervisor: Palle Villesen.
Stine Katrine Rye Østergaard. Thesis: A comparison of statistical tests in microbial ecology. Defended on June 29, 2022. Supervisor: Thomas Bataillon. Co-supervisors: Leendert Vergeyns (Biological and Chemical Engineering, AU) and Ioannis Kampouris (Biological and Chemical Engineering, AU).
Oliver Kjærlund Hansen. Thesis: A model based approach to inferring rate of genome evolution in experimental evolution lineages of E.coli. Defended on June 29. Supervisor: Thomas Bataillon. Co-supervisor: Isabel Gordo (IGC Oeiras).
Marc Solé Estragués. Thesis: Use of machine learning to study batch effect removal methods in metabolomics data. Defended on June 28. Supervisor: Palle Villesen.
Dimitrios Pediotidis-Maniatis. Thesis: Range Minimum Queries and Interval-Trees for Genome Scale String Processing. Defended on June 28. Supervisor: Thomas Mailund.
Anika Gottschalk. Thesis: A reference-free strategy for detecting circulating tumor DNA. Defended on June 28. Supervisor: Søren Besenbacher.
Carmen Oroperv. Thesis: A reference-free strategy for detecting circulating tumor DNA. Defended on June 28. Supervisor: Søren Besenbacher.
Pietro Mariani. Thesis: Algorithms for Mulitiple Sequence Aliggnments. Defended on June 28. Supervisor: Christian N. S. Pedersen.
Tommaso Ottocento. Thesis: Implementation of protein folding algorithms in the HP model on a grid lattice with diagonals. Defended on June 28. Supervisor: Christian N. S. Pedersen.
Yidan Chen. Thesis: Approximation Algorithms for Multiple Sequence Alignment based on l-stars. Defended on June 28. Supervisor: Christian N. S. Pedersen.
Sergio Galera Alquegui. Thesis: T-Cell Clonotyping from Bulk Whole Transcriptome RNA-SEQ Data. Defended on June 27. Supervisor: Christian N. S. Pedersen. Co-supervisor: Paula Tataru Bjerg (QIAGEN).
Sergio Fernández Adán. Thesis: T-Cell Clonotyping from Bulk Whole Transcriptome RNA-SEQ Data. Defended on June 27. Supervisor: Christian N. S. Pedersen. Co-supervisor: Paula Tataru Bjerg (QIAGEN).
Benjamin Lehmann Nichum. Thesis: Multiple-Target Tracking with Advanced Tracking Algorithms. Defended on June 27. Supervisor: Christian N. S. Pedersen. Co-supervisor: Lars Würtz Jochumsen (Scio+).
Ole Sahlholdt Hansen. Thesis: Understanding the genetic and causal relationship between common health outcomes and mortality. Defended on June 27. Supervisor: Bjarni Jóhann Vilhjálmsson.
Léna Bonin. Thesis: Bayesian designs for first-in-human phase I trials in oncology. Defended on June 24. Supervisor: Thomas Bataillon. Co-supervisor: David Jegou (Pierre Fabre Group).
Max Gubert Olivé. Thesis: Shared and differentiating genetics characterizing autism spectrum disorder and major depressive disorder. Defended on June 23. Supervisor: Thomas Bataillon. Co-supervisors: Anders Børglum (Biomedicine, AU) and Jakob Grove (Biomedicine, AU).
Erik Fogh Sørensen. Thesis: Admixture patterns in baboons show sex-biased admixture across million-year-old divergence. Defended on June 22. Part of PhD Qualification Exam. Supervisor: Kasper Munch Terkelsen.
Laura Andersen. Thesis: Characterizing the role of tumor growth dynamics and proliferation in ctDNA release. Defended on June 22. Supervisor: Nicolai Juul Birkbak.
Janne Auning Engestoft. Thesis: Identifying Copy Number Signatures by Latent Dirichlet Allocation. Defended on June 22. Supervisor: Nicolai Juul Birkbak.
Asbjørn Kjær. Thesis: Establishing a pipeline for analysis of T-cell receptor sequencing data and characterizing the impact of the T-cell repertoire on the clinical outcome of bladder cancer. Defended on June 22. Supervisor: Nicolai Juul Birkbak.
Rikke Myrhøj Jensen. Thesis: The human gut microbiome and its association to immunotherapy response in metastatic melanoma patients. Defended on June 16. Supervisor: Palle Villesen. Co-supervisor: Louise Bruun Thingholm (BiomCare).
Rikke Møller Larsen. Thesis: Metagenomic sample clustering enhanced by SRA metadata and NLP. Defended on June 9, 2022. Supervisor: Thomas Bataillon. Co-supervisors: Patrick Ettenhuber (QIAGEN) and Fernando Tavares (QIAGEN).
Jens Brogård Stenbye. Thesis: Sequence-based neural networks applied to denoising of single-cell RNAseq data. Defended on May 18, 2022. Supervisor: Palle Villesen. Co-supervisor: Lasse Maretty Sørensen.
Rune Wind. Thesis: Using Computer Vision Models for Image Dataset Annotation. Defended on January 24, 2022. Supervisor: Christian Storm Pedersen. Co-supervisor: René Thomsen (Scio+).

2021

Iker Rivas-González. Thesis: Pervasive incomplete lineage sorting in primates and its genomic and functional determinants. Defended on July 9, 2021. Part of PhD Qualification Exam. Supervisor: Mikkel Schierup
Ditte Torlyn. Thesis: Explore the pattern of presence, abundance and diversity of the Prevotella genus in the gut microbiome of a diverse cohort of mammals. Defended on June 24, 2021. Supervisor: Mikkel Schierup. Co-supervisors: Louise Bruun Thingholm, Malte Rühlemann and Marjolaine Rousselle.
Marie Vibeke Vestergaard. Thesis: Ulcerative colitis and its association with the microbiome across age groups. Defended on June 21, 2021. Supervisor: Thomas Bataillon.
Eirini Chatziloudi. Thesis: Missing data in questionnaires - a machine learning study. Defended on June 21, 2021. Supervisor: Palle Villesen.
Carlota Myhre de Gouveia. Thesis: Signals of selection in primates due to viruses. Defended on June 21, 2021. Supervisor: Thomas Bataillon. Co-supervisor: Marjolaine Rousselle.
Aysevil Pektas. Thesis: Evolutionary Dynamics of SARS-CoV-2 Lineages B.1.1.7, B.1.351, and P.1. Defended on June 21, 2021. Supervisor: Thomas Bataillon. Co-supervisor: Palle Villesen.
Andrea Zauli. Thesis: Detection of circulating tumor DNA using structural variants. Defended on June 21, 2021. Supervisor: Søren Besenbacher. Co-supervisor: Lasse Maretty.
Kristian Ozol. Thesis: Implementing Deep Learning Models and Optimization Techniques for Image-Based Weighing of Poultry. Defended on January 27, 2021. Supervisor: Christian Storm Pedersen. Co-supervisor: René Thomsen (Scio+).

2020

Meritxell Riera Belles. Thesis: Finding drivers of the evolution of testis expressed genes using scRNA sequencing of Great Apes’ testes. Defended on July 15, 2020. Part of PhD Qualification Exam. Supervisor: Mikkel Heide Schierup.
Adrián Gómez Repollés. Thesis: Taxonomic analysis of environmental DNA in coastal water samples from Denmark. Defended on June 29, 2020. Supervisor: Mikkel Heide Schierup. Co-supervisors: Eva Egelyng Sigsgaard, Phillip Francis Thomsen.
Mateo Sokac. Thesis: Utilization of Artificial Intelligence Towards Precision Medicine: Interplay Between Chromosomal Instability and Immune System. Defended on June 29, 2020. Part of PhD Qualification Exam. Supervisor: Nicolai Juul Birkbak. Co-supervisors: Jakob Skou Pedersen, Christian N. S. Pedersen.
Solveig Østergaard. Thesis: Preprocessing Optimization of LCMS Data from Fingerprints. Defended on June 24, 2020. Supervisor: Palle Villesen.
Stine Andersen. Thesis: Inference of Fingerprint Age using LC-MS Data and Machine Learning. Defended on June 24, 2020. Supervisor: Palle Villesen.
Andrej Baláž (together with Tomáš Sládeček). Thesis: Protein Structure Prediction with Deep Neural Networks. Defended on June 23, 2020. Supervisor: Christian N. S. Pedersen.
Tomáš Sládeček (together with Andrej Baláž). Thesis: Protein Structure Prediction with Deep Neural Networks. Defended on June 23, 2020. Supervisor: Christian N. S. Pedersen.
Mathias Byskov Nielsen. Thesis: Predicting Protein Secondary Structure using Artificial Neural Networks with a focus on RNNs. Defended on June 22, 2020. Supervisor: Christian N. S. Pedersen.
Cornelia Buus (together with Lotte Hindhede). Thesis: Analysis of the Coevolution of Bacteriophages to a Diverse Bacterial Population. Defended on June 16, 2020. Supervisor: Thomas Bataillon.
Lotte Hindhede (together with Cornelia Buus). Thesis: Analysis of the Coevolution of Bacteriophages to a Diverse Bacterial Population. Defended on June 16, 2020. Supervisor: Thomas Bataillon.
Carl Mathias Kobel. Thesis: GC-biased gene conversion in a Rhizobium leguminosarum species complex. Defended on June 16, 2020. Supervisor: Thomas Bataillon. Co-supervisor: Maria Izabel Cavassim Alves.
Tobias Bovbjerg Røikjer. Thesis: Designing and implementing a coalescence tool based on phase-type distributions. Defended on June 8, 2020. Supervisor: Kasper Munch Terkelsen.