Finished reports: Master of Science in Bioinformatics

2011

MSc BIOINF 11 001 – Nagarjun Vijay
"Whole genome sequencing and assembly of an avian genome, the European crow Corvus corone spec. - A reduced representation library based approach"
Uppsala University
Report

2012

MSc BIOINF 12 001 – Md.Hasan Sahid
"Mitochondrial DNA phyleography of Norway spruce (Picea abies) in Northern Europe"
Uppsala University
Report

MSc BIOINF 12 002 – Sanea Sheikh
"Microsatellites in the flycatcher genome"
Uppsala University
Report

MSc BIOINF 12 003 – Shahina Hayat
"Whole-genome characterisation of CfERVs in dog and wolf"
Uppsala University
Confidential until 2016-03.

MSc BIOINF 12 004 – Zeeshan Khaliq
"A computational model for the pathogenicity of influenza A virus" (confidential until April 2017)
Uppsala University
Confidential until 2017-04.

MSc BIOINF 12 005 – Fan Han
"Genome-wide analysis of genetic variation in honeybee, Apis mellifera"
Uppsala University
Report

MSc BIOINF 12 006 – Weizhou Zhao
"Distribution of mobile genetic elements in bacterial metagenomes"
University of California, Merced, USA
Report

MSc BIOINF 12 007 – Anders Bergström
"Analysis of natural and artificial yeast populations by next-generation sequencing"
Institute for Research on Cancer and Aging in Nice (IRCAN), Nice, France
Report

MSc BIOINF 12 008 – Behrooz Torabi Moghadam
"Identification of genetic variations in a cancer genome"
Uppsala University
Confidential until 2017-11.

MSc BIOINF 12 009 – Nasir Mahmood Abbasi
"Adaptive evolution in birds"
Stockholm Bioinformatics Centre, SciLifeLab, Stockholm
Report

2013

MSc BIOINF 13 001 – Amin Zarif Saffari
"Exploring the diversity of unmapped reads from human deep sequencing"
Uppsala University
Report

MSc BIOINF 13 002 – Xiaodong Liu
"Prediction of drug class and adverse side effects based on induced gene expression profiles - a feasibility study"
Uppsala University
Report

MSc BIOINF 13 003 – Nicholas Baltzer
"Using Feature Synthesis to discern non-linear interactions via composites"
Uppsala University
Report

2014

MSc BIOINF 14 001 – Klev Diamanti
"A machine learning approach for whole-genome identification of enhancer regions"
Uppsala University
Confidential until 2016-03. 

MSc BIOINF 14 002 – Isam Saleh
"Global bioinformatic analyses of Chlamydia trachomatis MLST genotypes"
Uppsala University
Confidential until 2019-08.

MSc BIOINF 14 003 – Behra Phani Rama Krishna
"Identification and analysis of small noncoding RNAs in Mycobacterium phlei"
Uppsala University
Confidential until 2016-04.

2015

MSc BIOINF 15 001 – Veronika Scholz
Confidential until 2015-12.

MSc BIOINF 15 002 – Misty Attwood
Archiving only.

MSc BIOINF 15 003 – Srilakshmy L H

MSc BIOINF 15 004 – Sofia Stamouli
"Mathematical modeling of normal and cancer prostate signaling pathways"
KI / SciLifeLab, Stockholm
Report

MSc BIOINF 15 005 – Marco Capuccini
"Structure-based virtual screening in Spark"
Uppsala university
Report

2016

MSc BIOINF 16 001 – Fredrik Wrede
"An Explorative Parameter Sweep: Spatial-temporal Data Mining in Stochastic Reaction-diffusion Simulations"
Uppsala University
Report

MSc BIOINF 16 002 – Stephen Omondi
"VisuNet: Visualizing Networks of feature interactions in rule-based classifiers"
Uppsala University
Report

MSc BIOINF 16 003 – Anastasios Glaros
"Data-driven definition of cell types based on single-cell gene expression data"
SciLifeLab, Stockholm
Report

MSc BIOINF 16 004 – Athanasios Alexiou
Archiving only.

MSc BIOINF 16 005 – Huiwen Che
"Evaluation of de novo assembly using PacBio long reads"
SciLifeLab Uppsala
Report

MSc BIOINF 16 006 – Efthymia Chantzi
Archiving only.

MSc BIOINF 16 007 – Faheema Kalsoom
Archiving only.

2017

MSc BIOINF 17 001 – Jon Ander Novella
Archiving only.

MSc BIOINF 17 002 – Kristaps Bebris
"Local adaptation of Grauer's gorilla gut microbiome"
Uppsala University
Report

MSc BIOINF 17 003 – Caesar Al Jewari
Archiving only.

MSc BIOINF 17 004 – Luis Leal
"Before speciation: adaptive evolution of diapause regulation in common wood-white butterflies (Leptidea sinapis)"
Uppsala University
Report

MSc BIOINF 17 005 - Helena Ishak
”Developing a ChIP-seq pipeline that analyzes the human genome and its repetitive sequences”
KI
Report

2018

MSc BIOINF 18 001 - Tea Ammunet
”Evolution and diversification of secreted protein effectors in the order Legionellales”
Uppsala University
Report

MSc BIOINF 18 002 - Aleksei Polajev
”Selfish, mobile genes in honeybee gut bacteria”
Uppsala University
Report

MSc BIOINF 18 003 - Juan Salvador Inda Diaz

MSc BIOINF 18 004 - Dimitrios Bampalikis
"Recognizing biological and technical differences in scRNAseq: A comparison of two protocols"
Uppsala University
Report

2019

MSc BIOINF 19 001 - Turid Everitt
"Utilizing data from a new, quantitative ChIP-sequencing method to investigate the dynamics of histone H3.3"
Karolinska Institutet
Report

MSc BIOINF 19 002 - Samuel Ferrer
"STAIRS - Data reduction strategy on genomics"
SVA
Report

MSc BIOINF 19 003 - Zhiwei Li
"Characterising copy number polymorphisms using next generation sequencing data"
Uppsala University
Report

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
Archiving only.

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
Archiving only.

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
Archiving only.

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