Finished reports: Master of Science in Bioinformatics
2025
MSc BIOINF 25 001 - Anika Thordarson
”Improving Accessibility and Confidence Assessment of the TT-Method”
Uppsala University
Report
MSc BIOINF 25 002 - Muhamed Khatib
”Predicting Shunt Surgery Outcomes in Idiopathic Normal pressure Hydrocephalus using Machine Learning”
Uppsala University
Report
MSc BIOINF 25 003 - Raziyeh Mohseni
”Developing a Machine Learning Model to Estimate Within-Species DNA Contamination”
Karolinska Institutet
Report
MSc BIOINF 25 004 - Denise Ravinale
”WCX2CytoSure - visualization of structural variants in prenatal samples”
Karolinska Institutet
Report
MSc BIOINF 25 005 - Santhosh Rajakumar
”Clustering and prediction of autism based on genomic and brain single cell expression data”
Karolinska Institutet
Report
MSc BIOINF 25 006 - Sofia Hernandez Valenzuela
”Uncertainty Quantification in Predicting Kinase Inhibitor Families: A Conformal Prediction Approach on Cell Painting Data”
Uppsala University
Report
MSc BIOINF 25 007 - Silvija Subotic
”Multimodal Contrastive Learning for Mechanism of Action Prediction in Cancer Drug Profiling”
Uppsala University
Report
MSc BIOINF 25 008 - Wenjie Ouyang
”Investigating the Effect of BMI on Cardiometabolic Diseases Risk Mediated Through Metabolites”
Uppsala University
Report
MSc BIOINF 25 009 - Solomon Asnake
”Pangenomic and Phylogenomic Analysis of Segmented Filamentous Bacteria for Phylogenetic Construction and Potential Biomarkers Identification”
Uppsala University
Report
MSc BIOINF 25 010 - Kürsat Birgin
”Multi-omics identification of accessible chromatin markers for nucleosome footprinting”
University of Zurich
Report
MSc BIOINF 25 011 - Ahamefula Izuike
”Developing Machine Learning Models for Sequence-Based Diagnostics in Antimicrobial Resistance and Virulence Factor Identification”
Akademiska sjukhuset
Report
MSc BIOINF 25 012 - Jakob Siljebo
”Towards Personalised Multiple Sclerosis Diagnostics and Prognostics: A Deep Learning Framework using Serum Metabolomics and Lipidomics”
Uppsala University
Archiving only.
MSc BIOINF 25 013 - Yuyan Teng
”Phylogenetic and Environmental Distribution of NirB-Ammonifiers”
Swedish University of Agricultural Sciences (SLU)
Report
MSc BIOINF 25 014 - Deeksha Kurthkoti
”Immunoprofiling of Hodgkin Lymphoma using multiplex immunofluorescence(mIF)”
Uppsala University
Delayed publication until 2030-08-02.
MSc BIOINF 25 015 - Matias Becker Burgos
”Genome-Microbiome Interactions in Feral Chicken Populations”
Uppsala University
Archiving only.
MSc BIOINF 25 016 - Ioannis Alexopoulos
”Characterization of small RNAs derived from extracellular vesicles released by Toxoplasma infected neuronal cells”
SciLifeLab, Stockholm University
Report
MSc BIOINF 25 017 - Emma Dizdarevic
”Acute pediatric leukemia subtype classification with machine learning using DNA methylation data”
Uppsala University
Delayed publication until 2026-10-31.
MSc BIOINF 25 018 - Bela Soares De Almeida Dutta
”An evaluation study of molecular docking tools: comparing pose accuracy, computational efficiency and affinity prediction”
Göteborg University
Report
MSc BIOINF 25 019 - Agapi Eleni Simaiaki
”Machine Learning and Genetic Algorithm-based Analyses of Time-Lapse Movies and Viability Readouts from a Large-Scale Brain Cancer Drug Combination Experiment”
Place
Report
MSc BIOINF 25 020 - Athanasios Toros
”Evolutionary Genomics of Longevity in Experimentally Evolved Insects”
Place
Report
2024
MSc BIOINF 24 001 – Sybil A. Herrera Foessel
Delayed publication until 2026-01-10.
MSc BIOINF 24 002 – Bonita van Waardenburg
Archiving only.
MSc BIOINF 24 003 – Victoria Giffin
"Identification of target genes for collateral lethality-based cancer treatment"
Uppsala University
Report
MSc BIOINF 24 004 – Bernat Xandri Zaragoza
"Network Analysis Techniques for Transcriptomics Data in Colorectal Cancer"
Uppsala University
Report
MSc BIOINF 24 005 – Yasemin Utkueri
Delayed publication until 2026-06-01.
MSc BIOINF 24 006 – Cristian Catalin Pop
"Using ADME/PK models to improve generative molecular design with reinforcement learning"
Uppsala University
Report
MSc BIOINF 24 007 – Matias Wanntorp
"The Evolutionary History of Picozoa : Phylogenomic inquiries into the plastid-lacking Archaeplastids"
Uppsala University
Report
MSc BIOINF 24 008 – Lei Zhao
"Creating pipeline for linkage analysis using whole genome sequencing data in rare diseases"
Uppsala University
Report
MSc BIOINF 24 009 – Benjamin Frey
"A framework for single-cell morphological data"
Uppsala University
Report
MSc BIOINF 24 010 – Michael Kinsella
"Developing an Image Analysis Pipeline for Insights into Symbiodiniaceae Growth and Morphology"
Uppsala University
Report
MSc BIOINF 24 011 – Maria Dada-Olorunwa
Delayed publication until 2027-07-01.
MSc BIOINF 24 012 – Neh Eyong Langsi
Archiving only.
MSc BIOINF 24 013 – Supraja Sathya Prakash
Delayed publication until 2029-07-06.
MSc BIOINF 24 014 – Miguel Alonso
"Development of an automated pipeline for monitoring spatial metabolic dynamics in disease models"
Uppsala University
Report
MSc BIOINF 24 015 – Linnea Ekström
Archiving only.
MSc BIOINF 24 016 – Arisa Kitagishi
Delayed publication until 2025-08-31.
MSc BIOINF 24 017 – Praissy Zefi
"Studying Copy Number Variations pattern in selfing vs. outcrossing species - in a single species: A study in Capsella bursa-pastoris"
Uppsala University
Report
MSc BIOINF 24 018 – Dongxiao Chen
"Data-driven interpretation, assessment and prioritization of immune escape strategies in human tumors"
SciLifeLab and Karolinska institutet (KI)
Report
MSc BIOINF 24 019 - Prasanna Venkataramanan
”Investigating the genetics of comb mass in commercial laying hens”
Swedish University of Agricultural Sciences (SLU)
Report
MSc BIOINF 24 020 - Eleni Aretaki
”Mining of drug sensitivity screens to explore implications of chromatin remodeling complexes in genome stability”
Institute of Molecular Biology, Germany
Report
MSc BIOINF 24 021 - Sarah Lideus
”Analysis of long-read sequencing data to uncover variants causing rare disorders”
Uppsala University
Report
MSc BIOINF 24 022 - Jinyu Peng
Confidential.
MSc BIOINF 24 023 - Sethuraman Narayanan
”Activating Transcription Factor 6 (ATF6): Structure, Interactions and Inhibition”
Göteborg University
Report
2023
MSc BIOINF 23 001 – Choi Tsang
Archiving only.
MSc BIOINF 23 002 – Emilie Laurent
Archiving only.
MSc BIOINF 23 003 – Erik Everett Palm
“Combining Cell Painting, Gene Expression and Structure-Activity Data for Mechanism of Action Prediction”
Uppsala University
Report
MSc BIOINF 23 004 – Milena Doroszko
Archiving only.
MSc BIOINF 23 005 – Ho Yeung Chim
“Modelling Large Protein Complexes”
Stockholm University
Report
MSc BIOINF 23 006 – Ashwini Jatti
“Panacea: Predicting anti-aging combinations from expression analysis”
Karolinska institutet (KI)
Report
MSc BIOINF 23 007 – Paula Camargo Romera
“Computational prediction of cell-cell interactions in the brain-tumour microenvironment”
Uppsala University
Report
MSc BIOINF 23 008 – Linn Zetterberg Huser
”Allelic Diversity and Signs of Natural Selection Associated with Environmental Adaptation in European Aspen”
Swedish University of Agricultural Sciences (SLU)
Report
MSc BIOINF 23 009 – Kaavya Venkateswaran
”Comparative genomics of Central Arctic Ocean microbiota for observation of Alternative Carbon Fixation Pathways”
Swedish University of Agricultural Sciences (SLU)
Report
MSc BIOINF 23 010 – Lars Huson
“Detecting structural variants in the DNA of the inbred Scandinavian wolf”
Uppsala University
Report
MSc BIOINF 23 011 – Jay Håkansson
“Metagenomic insights into AMR distributions in freshwaters and soils”
Swedish University of Agricultural Sciences (SLU)
Report
MSc BIOINF 23 012 – Melina Toni Marie Martin
“Developing a reproducible bioinformatics workflow for canine inherited retinal disease”
Uppsala University and Swedish University of Agricultural Sciences (SLU)
Report
MSc BIOINF 23 013 – Carl Bogstedt
”Predicting and classifying atrial fibrillation from ECG recordings using machine learning”
Uppsala University
Report
MSc BIOINF 23 014 – Erkin Alacamli
“Developing an Advanced Method for Kinship from Ancient DNA Data”
Uppsala University
Report
MSc BIOINF 23 015 – Claudia Gonzalez Valdivia
"The gut microbiome and nausea in pregnancy"
Uppsala University
Report
MSc BIOINF 23 016 – Nanxing Liu
"A Rank Score Model of Variants Prioritization for Rare Disease"
Karolinska institutet (KI)
Report
MSc BIOINF 23 017 – Tiscar Graells Fernandez
Delayed publication until 2024-01.
MSc BIOINF 23 018 – Torbjörn Larsson
"CRISPR-Drawr, a tool to design mutagenic primer"
Karolinska institutet (KI)
Report
MSc BIOINF 23 019 – Girish Pulinkala
"Predicting Biomarkers/ Candidate Genes involved in iALL, using Rough Sets based Interpretable Machine Learning Model"
Uppsala University
Report
MSc BIOINF 23 020 – Chiara Dalla Santa
"Diagnosing intraventricular hemorrhage from brain ultrasound images using machine learning"
Uppsala University
Report
2022
MSc BIOINF 22 001 - Nadia Hassan Shamas
”System level analysis of Immune system in children with solid tumors”
Karolinska Institutet
Report
MSc BIOINF 22 002 - Tomas Cumlin
“Filtering of Clinical NGS Data to Improve Low Allele Frequency Variant Calling”
Uppsala University
Report
MSc BIOINF 22 003 - Milena Regina Trabert
”Large-scale pan-genome analysis of Campylobacter jejuni: with a special focus on virulence factors in the accessory genome”
National Veterinary Institute (SVA)
Report
MSc BIOINF 22 004 - Janek Sendrowski
“Demography of Birch Populations across Scandinavia”
Uppsala University
Report
MSc BIOINF 22 005 - Melih Öten
Delayed publication until 2023-07.
MSc BIOINF 22 006 - Ziqi Kang
Delayed publication until 2024-07.
MSc BIOINF 22 007 - Greta Buinovskaja
“Identifying structural variants from plant short-read sequencing data”
Swedish University of Agricultural Sciences (SLU)
Report
MSc BIOINF 22 008 - Siqi Li
”Identification of de novo Transcription Factor Binding Motifs Created by Cancer-related Mutations”
Uppsala University
Report
MSc BIOINF 22 009 - Selma Bozorgpana
Confidential.
MSc BIOINF 22 010 - Xinyao Sun
”Genetics of complement proteins among Swedish newborns”
Karolinska Institutet
Report
MSc BIOINF 22 011 - Patrick Hennig
”Super-resolution 3D dot localization in Escherichia Coli using a convolutional neural network”
Uppsala University
Report
MSc BIOINF 22 012 - Harshal Kunal Bhawe
”Phylogenomics of Ascetosporea”
Uppsala University
Report
MSc BIOINF 22 013 - Ines Martins Borges
Delayed publication until 2025-10.
2021
MSc BIOINF 21 001 - Margus Veanes
“Identification of novel loss of heterozygosity collateral lethality genes for potential applications in cancer”
Uppsala University
Report
MSc BIOINF 21 002 - Karthik Nair
”Optimisation of autoencoders for prediction of SNPs determining phenotypes in wheat”
Uppsala University
Report
MSc BIOINF 21 003 - Yuen Ting Cheung
“Investigation of the gene expression landscape of human skin wounds”
Karolinska Institutet
Report
MSc BIOINF 21 004 - Abhishekapriya Ganesan
“The role of RFX-target genes in neurodevelopmental and psychiatric disorders”
Karolinska Institutet
Report
MSc BIOINF 21 005 - Akshai Parakkal Sreenivasan
“Deep learning prediction of Quantmap clusters”
Uppsala University
Report
MSc BIOINF 21 006 - Shrija Srinivasan
“Effects of Environmental Pollutants on Gene Expression and Cellular Pathways in Model Organism”
Uppsala University
Report
MSc BIOINF 21 007 - Karl Nyrén
“Phylogenetic analysis of secretion systems in Francisellaceae and Legionellales: Investigating events of intracellularization”
Uppsala University
Report
MSc BIOINF 21 008 - Raphaela Pensch
“Non-coding constraint mutations impact the gene regulatory system in osteosarcoma”
Uppsala University
Report
MSc BIOINF 21 009 - Mei Wu
“Detection of aberrant events in RNA for clinical diagnostics”
Karolinska Institutet
Report
MSc BIOINF 21 010 - Camille Humbert
Archiving only.
MSc BIOINF 21 011 - Marina Mota Merlo
“Evolutionary evidence of chromosomal rearrangements through SNAP: Selection during Niche AdaPtation”
Uppsala University
Report
MSc BIOINF 21 012 – María del Carmen Abaurre
Archiving only.
MSc BIOINF 21 013 - Mirela Balan
“Integrative bioinformatic analysis of SARs-CoV-2 data”
Uppsala University
Report
MSc BIOINF 21 014 - Alva Annett
"Single Cell Methods and Cell Hashing forHigh Throughput Drug Screens"
Uppsala University
Report
MSc BIOINF 21 015 - Cristina Díaz Ubieta
"Chemistry Data Mining to Discover Molecular Interactions"
Uppsala University
Report
MSc BIOINF 21 016 - Yiwen Chen
”Genome-wide association studies on body weight and component traits in an intercross of two divergently selected chicken lines”
Uppsala University
Report
MSc BIOINF 21 017 - Satya Krishna Prasanna Kolluri
”Evaluation of performance of MSI detection tools using targeted sequencing data”
Uppsala University
Report
2020
MSc BIOINF 20 001 – Amanj Bajalan
"Improved methods for virus detection and discovery in metagenomic sequence data"
Karolinska Institutet
Report
MSc BIOINF 20 002 - Arnar Kári Sigurðarson Sandholt
"Dual RNA-seq analysis of host-pathogen interaction in Eimeria infection in chickens"
Statens Veterinärmedicinska Anstalt
Report
MSc BIOINF 20 003 - Holly Halstead
"ARG-MATEE Automated Pipeline for Detection of Antimicrobial Resistance in WGS Data Collected from Pig Farms and Surrounding Communities"
Uppsala University
Report
MSc BIOINF 20 004 - Claudio Novella Rausell
"The transcriptional landscape of B cells upon mucosal healing in experimental colitis: A single cell transcriptomics analysis"
Karolinska Institutet
Report
MSc BIOINF 20 005 - Roberto Rossini
"Development and validation of bioinformatic methods for GRC assembly and annotation"
Uppsala University
Report
MSc BIOINF 20 006 - Silvia Yahel Bahena Hernández
"Computational Methods for the structural and dynamical understanding of GPCR-RAMP interactions"
ScilifeLab Stockholm
Report
MSc BIOINF 20 007 - Markella-Achilleia Zacharouli
"Characterization of immune infiltrate in early breast cancer based on a multiplex imaging method"
Karolinska Institutet
Report
MSc BIOINF 20 008 - Carolina Pita Barros
"Causality in Coexpression"
Uppsala University
Report
MSc BIOINF 20 009 - Leonard Sparring
"Conquering Chamical Space: Optimization of docking Libraries through Interconnected Molecular Features"
Uppsala University
Report
MSc BIOINF 20 010 - Katharina Waury
"A pipeline for the identification and examination of proteins implicated in frontotemporal dementia"
Karolinska Institutet
Report
MSc BIOINF 20 011 - Rajmund Csombordi
"Metabolomics database resolver"
Uppsala University
Report
MSc BIOINF 20 012 - Erik Zhivkoplias
"Comparing the performance of different methods to estimate selection coefficient across parameter space using time-series genomic data"
Stockholm University
Report
MSc BIOINF 20 013 - Jiarong Liang
"Federated Learning for Bioimage Classification"
Uppsala University
Report
MSc BIOINF 20 014 - Yuvarani Masarapu
Delayed publication until 2026-01.
MSc BIOINF 20 015 - Alina Orozco
"A spatial analysis of Norwegian spruce cone developmental stages"
SLU / SciLifeLab KTH
Report
MSc BIOINF 20 016 - Ismini-Christina Stamatelou
"Clustering approaches for extracting structural determinants of enzyme active sites"
University of Athens
Report
MSc BIOINF 20 017 - Ylva Jondelius
Archiving only.
MSc BIOINF 20 018 - Xiao Yuan
"Graph neural networks for spatial gene expression analysis of the developing human heart"
Uppsala University
Report
MSc BIOINF 20 019 - Georgios Nikiforos Pyrounakis
Archiving only.