Degree Projects in Bioinformatics
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- 2024
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Mark
The Analysis of Human Protein Deletion
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- Master (Two yrs)
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Mark
Evaluating Variant Calling Pipelines for RNA-seq Data
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- Master (Two yrs)
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Mark
Workflows for the analysis of transcriptomic data at single-cell and spatial resolutions: T cells in lymphoma
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- Master (Two yrs)
- 2023
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Mark
Developing a method to study the effect of germline variants and somatic mutations in breast cancer patients on mRNA splicing
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- Master (Two yrs)
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Mark
Investigation of age-related changes in neuroblast populations using RNA velocity
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- Master (Two yrs)
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Mark
Assessment of Alphafold methods in structural prediction of toxin-antitoxin systems with a focus on interface analysis
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- Master (Two yrs)
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Mark
Application of molecular barcoding and engineered viral vectors for the determination of causative transcriptomic changes in Parkinson’s disease and generation of a fluorescent reporter model for studying cell-cell communication in the brain
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- Master (Two yrs)
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Mark
Multi-omics integration of spatially resolved transcriptome and proteome data in mantle cell lymphoma
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- Master (Two yrs)
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Mark
SubKluster: Novel method to bin scaffolds from cereal genomes into subgenomes using substring frequency analysis
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- Master (Two yrs)
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Mark
Exploring the sex and gender differences in the human brain at single cell level
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- Master (Two yrs)
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Mark
Early Stage LPS Injection Causes Long-term Effects on Microglial Heterogeneity in Alzheimer's Mouse Model
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- Master (Two yrs)
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Mark
Applying Large-Scale Transcriptomic Data to Analyze In Vitro Human Hypothalamic Differentiation Protocols
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- Master (Two yrs)
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Mark
The genomic basis and gene expression of adaptation to a novel host plant in the peacock fly Tephritis conura
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- Master (Two yrs)
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Mark
Host and graft glial composition in a stem cell transplantation model of Parkinson’s disease
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- Master (Two yrs)
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Mark
Gene expression-based classification of urothelial carcinoma for research and clinical applications
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- Master (Two yrs)
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Mark
Pseudomonas aeruginosa gene expression analysis using pangenome and PAO1 reference genomes
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- Master (Two yrs)
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Mark
Straight-line orientation in the brain of a ball-rolling dung beetle: an interdisciplinary investigation
(
- Master (Two yrs)
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Mark
Comparative Genomics and Transcriptomic Profiling of Mycobacterium avium’s morphotypes
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- Master (Two yrs)
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Mark
Genome assembly and annotation of seven litter decomposing fungi
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- Master (Two yrs)
- 2022
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Mark
Development and comparison of feature-selection pipelines for predicting patient outcome from RNA-seq data in breast cancer
(
- Master (Two yrs)
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Mark
Fly Tephritis conura´s adaption to new host plant
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- Master (Two yrs)
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Mark
Explore the biogeographic characteristics of the microbiome in diverse datasets and predict its geographical sources
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- Master (Two yrs)
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Mark
A Single-Nucleus RNA Sequencing Analysis of HERVs and LINE1s in Alzheimer's and Parkinson's Disease
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- Master (Two yrs)
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Mark
Diversification of predators in multi-trophic communities: A trait-based theoretical approach
(
- Master (Two yrs)
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Mark
Identification of functional synonymous variants in familial breast cancer
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- Master (Two yrs)
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Mark
Molecular and clinicopathological characterization of luminal HER2-enriched breast cancer
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- Master (Two yrs)
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Mark
Metatranscriptomics and multi-omics exploration of the phyllosphere and rhizosphere of potato and cassava
(
- Master (Two yrs)
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Mark
Classification of sequence tags from tandem mass spectrometry spectra using machine learning models
(
- Master (Two yrs)
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Mark
Comparing the efficacy of algorithmic approaches to the functional annotation of proteins in Trichomonad parasites
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- Master (Two yrs)
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Mark
The Geographic Coordinate Prediction of Ancestral Origin for Individuals Worldwide with Less Markers
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- Master (Two yrs)
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Mark
Insect Diversity Estimation in Entomological Lidar
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- Master (Two yrs)
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Mark
Optimal peptide quantification via machine learning enhanced fragment ion ranking in DIA-MS proteomics
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- Master (Two yrs)
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Mark
Lateral gene transfer from protists could enable freshwater sponges to adapt to hypoxia
(
- Master (Two yrs)
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Mark
EPTA: A User-friendly Protein Phylogenetic Tree Generation and Annotating Toolkit
(
- Master (Two yrs)
- 2021
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Mark
Ten weeks of mindfulness training leads to no structural brain changes in adolescents
(
- Master (Two yrs)
-
Mark
A mixed clinicopathological and molecular proxy of homologous recombination deficiency in triple negative breast cancer
(
- Master (Two yrs)
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Mark
Epigenetic regulation of Cancer Testis Antigens: candidate drivers of genomic instability in Triple Negative Breast Cancer
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- Master (Two yrs)
-
Mark
Functional annotation of synonymous genetic variants in breast cancer
(
- Master (Two yrs)
-
Mark
Epigenetic and transcriptional effects of full-length LINE-1 retrotransposons in human neural progenitor cells
(
- Master (Two yrs)
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Mark
Differential expression of small RNAs in human and chimpanzee and the role of transposable elements
(
- Master (Two yrs)
-
Mark
Application of machine learning algorithms in analysing single cell/nuclei RNA sequencing datasets in rat model of Parkinson's disease
(
- Master (Two yrs)
-
Mark
Dissecting the genetic basis of familial multiple myeloma
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- Master (Two yrs)
-
Mark
DLBCL Patient stratification using serum protein profiling
(
- Master (Two yrs)
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Mark
Functional connectivity analysis in the human brain using ultra-high field MRI
(
- Master (Two yrs)
-
Mark
Automated pipeline for processing fluorescence calcium imaging microscopy data and electrophysiological measurements from 3D brain organoids
(
- Master (Two yrs)
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Mark
Biomedical image analysis with artificial intelligence
(
- Master (Two yrs)
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Mark
Transcriptional Bursting Kinetics of Incomplete Dosage Compensation in ZW Sex Determining System
(
- Master (Two yrs)
-
Mark
Computational analysis of high throughput flow cytometry data of blood cells in cord blood
(
- Master (Two yrs)
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Mark
Identifying a fine genetic structure across Ashkenazic Jews
(
- Master (Two yrs)
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Mark
Genome-wide microscopic image analysis of potential regulators of lysosomes and cell death
(
- Master (Two yrs)
- 2020
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Mark
Searching for a link between AID-mediated mutations and patterns of transcription initiation and pausing in activated B cells
(
- Master (Two yrs)
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Mark
Pan-cancer validation of a lung-adenocarcinoma-derived gene-expression-based prognostic predictor
(
- Master (Two yrs)
-
Mark
Identification of Causal Variants underlying Febrile seizures following Genome-Wide Association Studies
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- Master (Two yrs)
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Mark
Pipeline for metagenomics-based population genomics
(
- Master (Two yrs)
-
Mark
Computational inference and analysis of 5’UTR-leader sequence of alleles of immunoglobulin heavy chain genes
(
- Master (Two yrs)
-
Mark
NIB - A visualization tool for feature-level multi-omic data based on global metrics
(
- Master (Two yrs)
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Mark
Understanding DNA double-strand breaks and genome fragility across neurodifferentiation
(
- Master (Two yrs)
-
Mark
Development of Tools to Classify Poor Quality Images from High Content Screening results for Cell Death and Lysosome Studies
(
- Master (Two yrs)
-
Mark
Building a bioinformatic workflow to study methane metabolism in a capture metagenomics dataset of peatland soil
(
- Master (Two yrs)
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Mark
Analysis of a genome-wide microscopy screen for regulators of lysosomal stability
(
- Master (Two yrs)
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Mark
Automated inference of cell type hierarchies for single-cell RNA-seq data
(
- Master (Two yrs)
-
Mark
TaxSeedo: An energy-saving ANI alternative for rapid classification of bacteria
(
- Master (Two yrs)
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Mark
The 3D genome of the frog Xenopus laevis
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- Master (Two yrs)
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Mark
3D Image Analysis of Oat Seeds using Deep Learning
(
- Master (Two yrs)
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Mark
Optimization in the analysis of social interaction test in rodents - development of a new complex vision-based tool for the detection of complex behaviors
(
- Master (Two yrs)
- 2019
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Mark
GhostMS: An error-controlled machine learning approach to efficient alignment and quantification of multi-sample experiments in Mass Spectrometry-based Proteomics
(
- Master (Two yrs)
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Mark
Predicting zinc finger-DNA interactions using a scoring function based on statistic potentials
(
- Master (Two yrs)
-
Mark
Deciphering glucocorticoid-mediated stress responses in the pancreatic beta cell using bioinformatics methods
(
- Master (Two yrs)
-
Mark
The human gut microbiota and type 2 diabetes: comparison of several methodological approaches to analyzing microbiome sequence data
(
- Master (Two yrs)
-
Mark
Selection on proteins during the transition to multicellularity - A study on volvocine algae
(
- Master (Two yrs)
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Mark
Monogenic causes of neurological movement disorders - a case study of a family with hereditary ataxia
(
- Master (Two yrs)
-
Mark
Quantative Omics Discovery Base - A web-based workflow for improved functional enrichment analysis of comparative proteomic expression data
(
- Master (Two yrs)
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Mark
Finding the underlying genotype behind a familial embolic stroke of unknown origin
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- Master (Two yrs)
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Mark
Transposable elements as alternative gene promoters and their silencing mechanisms
(
- Master (Two yrs)
-
Mark
Whole-Genome Sequencing of two Swedish Individuals on PromethION
(
- Master (Two yrs)
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Mark
Exploring the genomic landscape of gene flow between willow warblers (Phylloscopus trochilus) and chiffchaffs (P. collybita)
(
- Master (Two yrs)
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Mark
New approach to investigate the relationships between Denisovan and human populations
(
- Master (Two yrs)
-
Mark
Evolution of the aerobic iron oxidation metabolism
(
- Master (Two yrs)
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Mark
A Pan-Cancer guide to cancer-related alterations of pro-survival and -apoptotic BCL-2 proteins
(
- Master (Two yrs)
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Mark
Dissecting mechanisms underlying dendritic cell epigenetic reprogramming
(
- Master (Two yrs)
-
Mark
Evaluation of haplotype imputation as a new method to improve genetic variant information from great apes low-coverage whole genome sequencing (lcWGS) data
(
- Master (Two yrs)
- 2018
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Mark
Looking for CLUes and Motifes in mRNA Transcripts
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- Master (Two yrs)
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Mark
PhyloPyPruner: Tree-based Orthology Inference for Phylogenomics with New Methods for Identifying and Excluding Contamination
(
- Master (Two yrs)
-
Mark
Machine Learning Prediction of Cardiovascular Complications
(
- Master (Two yrs)
-
Mark
Use of solid-state NMR and MD simulations for the study of tissue engineering scaffolds
(
- Master (Two yrs)
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Mark
Exploring Breast Cancer Associated Fibroblast Subpopulations By Using Single-Cell RNA Sequencing
(
- Master (Two yrs)
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Mark
Disease susceptibility may be increased by accumulation of genetic variants in chromatin loops from disease-relevant cell-types
(
- Master (Two yrs)
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Mark
Optimization of mutation detection from breast cancer RNA-seq data and prediction of patient outcome
(
- Master (Two yrs)
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Mark
A 'multiscale' assessment of the molecular mechanisms underlying the pro-survival Bcl-2 protein members in cancer
(
- Master (Two yrs)
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Mark
Elucidating the molecular mechanisms behind the behavioural manipulation of ‘zombie’-flies by the entomopathogenic fungus, Entomophthora muscae
(
- Master (Two yrs)
-
Mark
SVenX: A highly parallelized pipeline for structural variation detection using linked read whole genome sequencing data
(
- Master (Two yrs)
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Mark
SeqCapAnalyst, a pipeline for analyzing Sequence Capture data in avian malaria
(
- Master (Two yrs)
-
Mark
Gene regulation of avian malaria during its life-cycle in the vector
(
- Master (Two yrs)
- 2017
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Mark
Web-Interface to browse, filter and visualize plant genotyping data
(
- Master (Two yrs)
-
Mark
A Novel Method for Predicting Ribosomal RNA Genes in Prokaryotic Genomes
(
- Master (Two yrs)
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Mark
Zebrash larva action sequence analysis
(
- Master (Two yrs)
-
Mark
Captured metagenomics of fungi in agricultural soils
(
- Master (Two yrs)
-
Mark
Comparative Evolutionary Genomics of Toll-like Receptors in True Geese (Anserini)
(
- Master (Two yrs)
-
Mark
Retinal transcriptome analysis of four owl species: Longeared owl (Asio otus), Short-eared owl (Asio flammeus), Tawny owl (Strix aluco) and Boreal owl (Aegolius funereus)
(
- Master (Two yrs)
-
Mark
Finding candidate genes underlying early flowering barley mat-e mutants
(
- Master (Two yrs)
-
Mark
Evolution of sex chromosomes and sex-biased gene expression
(
- Master (Two yrs)
-
Mark
Analysis of the genetic contribution to the persistent resistance to an obesogenic lifestyle influence on BMI
(
- Master (Two yrs)
-
Mark
A novel pipeline for protein level quantification using peptide mass spectrometry data
(
- Master (Two yrs)
-
Mark
Methods for structural variation detection and improved theory prediction for densely labeled DNA barcodes
(
- Master (Two yrs)
- 2016
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Mark
Dialysis patients’ hospital readmission prediction using artificial neural networks
(
- Master (Two yrs)
-
Mark
Are Restriction Enzymes Recognition Sites Underrepresented in the Organisms That Host Them?
(
- Master (Two yrs)
-
Mark
Development of an exome pipeline for the identification of single nucleotide variants and indels from ovarian cancer tissue
(
- Bach. Degree
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Mark
Fast method to find sterically possible amino acid substitutions
(
- Master (Two yrs)
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Mark
Performance testing of in silico HLA typing tools using a validated next generation sequencing data set, and identification of HLA allele restricted tumour neo-antigens
(
- Master (Two yrs)
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Mark
THESES db - The Algae 18S rDNA Sequence-Structure Database for Inferring Phylogenies
(
- Master (Two yrs)
-
Mark
FibSim, a web application to refine fibrillar macromolecular models
(
- Master (Two yrs)
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Mark
Identication, analysis and prediction of frequent hitters from high-throughput screening
(
- Master (Two yrs)
- 2015
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Mark
Transcriptional profiling analysis of clear cell ovarian cancer
(
- Master (Two yrs)
-
Mark
Statistical power considerations in genotype-based recall randomized controlled trials
(
- Master (Two yrs)
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Mark
Identification & evaluation of the within host variation in Plasmodium relictum, a cosmopolite avian malaria parasite
(
- Master (Two yrs)
-
Mark
Optimizing Diabetes Simulation Model Parameters using an Evolutionary Computing Approach
(
- Master (Two yrs)
-
Mark
BaCON: A Google Chrome extension for sequence analysis
(
- Master (Two yrs)
-
Mark
Bioinformatics analysis of human epigenetic data
(
- Master (Two yrs)
-
Mark
Evolution of Major Histocompatibility Complex (MHC) Genes in Songbirds
(
- Master (Two yrs)
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Mark
Finalizing a rapid algorithm to describe community structure using next generation amplicon sequencing data
(
- Master (Two yrs)
- 2014
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Mark
Variant Calling and Microarray Expression Analysis in Pancreatic Islet Samples
(
- Master (Two yrs)
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Mark
OrthoGroup SEARCH: Identification of Orthologous genes using Synteny
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- Master (Two yrs)
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Mark
Secondary metabolite prediction in Dactylellina haptotyla
(
- Master (Two yrs)
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Mark
Computational Simulations of Evolutionary Dynamics: The Fate of Deleterious Alleles
(
- Master (Two yrs)
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Mark
Transcriptome analysis to elucidate the radiation of endemic finches (Nesospiza acunhae) on the islands of Tristan da Cunha
(
- Master (Two yrs)
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Mark
Building predictive unbound brain-to-plasma concentration ratio (Kp,uu,brain) models
(
- Master (Two yrs)
- 2013
-
Mark
Investigation into the Aberrant Pathways of Hodgkin’s Lymphoma
(
- Master (Two yrs)
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Mark
Protein shape similarity assessment
(
- Master (Two yrs)
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Mark
Analysis of the domain superfamily composition in unicellular and multicellular fungi
(
- Master (Two yrs)
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Mark
Quality Control and Analysis of RNA-seq Data from Breast Cancer Tumor Samples
(
- Master (Two yrs)
- 2012
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Mark
Limitation of algorithms for quantitative label-free LC-MS-based proteomics
(
- Master (Two yrs)
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Mark
Genomics of the wine yeast Dekkera bruxellensis
(
- Master (Two yrs)
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Mark
Molecular topology, a novel descriptor for compound quality assessment
(
- Master (Two yrs)
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Mark
Estimates of Evolutionary Rate, Date and Migration of Hepatitis B Virus Genotypes A and D
(
- Master (Two yrs)