Finished reports: Master of Science in Bioinformatics
2020
MSc BIOINF 20 001 – Amanj Bajalan
"Improved methods for virus detection and discovery in metagenomic sequence data"
Report
Karolinska Institutet
MSc BIOINF 20 002 - Arnar Kári Sigurðarson Sandholt
"Dual RNA-seq analysis of host-pathogen interaction in Eimeria infection in chickens"
Report
Statens Veterinärmedicinska Anstalt
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"
Report
Uppsala University
MSc BIOINF 20 004 - Claudio Novella Rausell
"The transcriptional landscape of B cells upon mucosal healing in experimental colitis: A single cell transcriptomics analysis"
Report
Karolinska Institutet
MSc BIOINF 20 005 - Roberto Rossini
"Development and validation of bioinformatic methods for GRC assembly and annotation"
Report
Uppsala University
MSc BIOINF 20 006 - Silvia Yahel Bahena Hernández
"Computational Methods for the structural and dynamical understanding of GPCR-RAMP interactions"
Report
ScilifeLab Stockholm
MSc BIOINF 20 007 - Markella-Achilleia Zacharouli
"Characterization of immune infiltrate in early breast cancer based on a multiplex imaging method"
Report
Karolinska Institutet
MSc BIOINF 20 008 - Carolina Pita Barros
"Causality in Coexpression"
Report
Uppsala University
MSc BIOINF 20 009 - Leonard Sparring
"Conquering Chamical Space: Optimization of docking Libraries through Interconnected Molecular Features"
Report
Uppsala University
MSc BIOINF 20 010 - Katharina Waury
"A pipeline for the identification and examination of proteins implicated in frontotemporal dementia"
Report
Karolinska Institutet
MSc BIOINF 20 011 - Rajmund Csombordi
"Metabolomics database resolver"
Report
Uppsala University
MSc BIOINF 20 012 - Erik Zhivkoplias
"Comparing the performance of different methods to estimate selection coefficient across parameter space using time-series genomic data"
Report
Stockholm University
MSc BIOINF 20 013 - Jiarong Liang
"Federated Learning for Bioimage Classification"
Report
Uppsala University
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"
Report
SLU / SciLifeLab KTH
MSc BIOINF 20 016 - Ismini-Christina Stamatelou
"Clustering approaches for extracting structural determinants of enzyme active sites"
Report
University of Athens
MSc BIOINF 20 017 - Ylva Jondelius
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MSc BIOINF 20 018 - Xiao Yuan
"Graph neural networks for spatial gene expression analysis of the developing human heart"
Report
Uppsala University
MSc BIOINF 20 019 - Georgios Nikiforos Pyrounakis
Archiving only.
2021
MSc BIOINF 21 001 - Margus Veanes
“Identification of novel loss of heterozygosity collateral lethality genes for potential applications in cancer”
Report
Uppsala University
MSc BIOINF 21 002 - Karthik Nair
”Optimisation of autoencoders for prediction of SNPs determining phenotypes in wheat”
Report
Uppsala University
MSc BIOINF 21 003 - Yuen Ting Cheung
“Investigation of the gene expression landscape of human skin wounds”
Report
Karolinska Institutet
MSc BIOINF 21 004 - Abhishekapriya Ganesan
“The role of RFX-target genes in neurodevelopmental and psychiatric disorders”
Report
Karolinska Institutet
MSc BIOINF 21 005 - Akshai Parakkal Sreenivasan
“Deep learning prediction of Quantmap clusters”
Report
Uppsala University
MSc BIOINF 21 006 - Shrija Srinivasan
“Effects of Environmental Pollutants on Gene Expression and Cellular Pathways in Model Organism”
Report
Uppsala University
MSc BIOINF 21 007 - Karl Nyrén
“Phylogenetic analysis of secretion systems in Francisellaceae and Legionellales: Investigating events of intracellularization”
Report
Uppsala University
MSc BIOINF 21 008 - Raphaela Pensch
“Non-coding constraint mutations impact the gene regulatory system in osteosarcoma”
Report
Uppsala University
MSc BIOINF 21 009 - Mei Wu
“Detection of aberrant events in RNA for clinical diagnostics”
Report
Karolinska Institutet
MSc BIOINF 21 010 - Camille Humbert
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MSc BIOINF 21 011 - Marina Mota Merlo
“Evolutionary evidence of chromosomal rearrangements through SNAP: Selection during Niche AdaPtation”
Report
Uppsala University
MSc BIOINF 21 012 – María del Carmen Abaurre
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MSc BIOINF 21 013 - Mirela Balan
“Integrative bioinformatic analysis of SARs-CoV-2 data”
Report
Uppsala University
MSc BIOINF 21 014 - Alva Annett
"Single Cell Methods and Cell Hashing forHigh Throughput Drug Screens"
Report
Uppsala University
MSc BIOINF 21 015 - Cristina Díaz Ubieta
"Chemistry Data Mining to Discover Molecular Interactions"
Report
Uppsala University
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”
Report
Uppsala University
MSc BIOINF 21 017 - Satya Krishna Prasanna Kolluri
”Evaluation of performance of MSI detection tools using targeted sequencing data”
Report
Uppsala University
2022
MSc BIOINF 22 001 - Nadia Hassan Shamas
”System level analysis of Immune system in children with solid tumors”
Report
Karolinska Institutet
MSc BIOINF 22 002 - Tomas Cumlin
“Filtering of Clinical NGS Data to Improve Low Allele Frequency Variant Calling”
Report
Uppsala University
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”
Report
National Veterinary Institute (SVA)
MSc BIOINF 22 004 - Janek Sendrowski
“Demography of Birch Populations across Scandinavia”
Report
Uppsala University
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”
Report
Swedish University of Agricultural Sciences (SLU)
MSc BIOINF 22 008 - Siqi L
”Identification of de novo Transcription Factor Binding Motifs Created by Cancer-related Mutations”
Report
Uppsala University
MSc BIOINF 22 009 - Selma Bozorgpana
Confidential.
MSc BIOINF 22 010 - Xinyao Sun
”Genetics of complement proteins among Swedish newborns”
Report
Karolinska Institutet
MSc BIOINF 22 011 - Patrick Hennig
”Super-resolution 3D dot localization in Escherichia Coli using a convolutional neural network”
Report
Uppsala University
MSc BIOINF 22 012 - Harshal Kunal Bhawe
”Phylogenomics of Ascetosporea”
Report
Uppsala University
MSc BIOINF 22 013 - Ines Martins Borges
Delayed publication until 2025-10.
2023
MSc BIOINF 23 001 – Choi Tsang
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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”
Report
Uppsala University
MSc BIOINF 23 004 – Milena Doroszko
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MSc BIOINF 23 005 – Ho Yeung Chim
“Modelling Large Protein Complexes”
Report
Stockholm University
MSc BIOINF 23 006 – Ashwini Jatti
“Panacea: Predicting anti-aging combinations from expression analysis”
Report
Karolinska institutet (KI)
MSc BIOINF 23 007 – Paula Camargo Romera
“Computational prediction of cell-cell interactions in the brain-tumour microenvironment”
Report
Uppsala University
MSc BIOINF 23 008 – Linn Zetterberg Huser
”Allelic Diversity and Signs of Natural Selection Associated with Environmental Adaptation in European Aspen”
Report
Swedish University of Agricultural Sciences (SLU)
MSc BIOINF 23 009 – Kaavya Venkateswaran
”Comparative genomics of Central Arctic Ocean microbiota for observation of Alternative Carbon Fixation Pathways”
Report
Swedish University of Agricultural Sciences (SLU)
MSc BIOINF 23 010 – Lars Huson
“Detecting structural variants in the DNA of the inbred Scandinavian wolf”
Report
Uppsala University
MSc BIOINF 23 011 – Jay Håkansson
“Metagenomic insights into AMR distributions in freshwaters and soils”
Report
Swedish University of Agricultural Sciences (SLU)
MSc BIOINF 23 012 – Melina Toni Marie Martin
“Developing a reproducible bioinformatics workflow for canine inherited retinal disease”
Report
Uppsala University and Swedish University of Agricultural Sciences (SLU)
MSc BIOINF 23 013 – Carl Bogstedt
”Predicting and classifying atrial fibrillation from ECG recordings using machine learning”
Report
Uppsala University
MSc BIOINF 23 014 – Erkin Alacamli
“Developing an Advanced Method for Kinship from Ancient DNA Data”
Report
Uppsala University
MSc BIOINF 23 015 – Claudia Gonzalez Valdivia
"The gut microbiome and nausea in pregnancy"
Report
Uppsala University
MSc BIOINF 23 016 – Nanxing Liu
"A Rank Score Model of Variants Prioritization for Rare Disease"
Report
Karolinska institutet (KI)
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"
Report
Karolinska institutet (KI)