Finished reports: Master of Science in Bioinformatics

Table of contents:

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
Delayed publication until 2020-11

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
Delayed publication until 2021-01

MSc BIOINF 20 011 - Rajmund Csombordi
"Metabolomics database resolver"
Uppsala University