Mark D Robinson
Twitter @markrobinsonca
GitHub markrobinsonuzh
Google Scholar
My research interests are diverse, but more-or-less encompass the general application of statistical methods and data science to experimental data with biological applications. Often, this is within the context of genomics data types, but we are interested in methodological challenges and robust solutions in data, generally. We also try to be modern scientists, with a focus on reproducibility (repos for code) and open science (preprints).
PhD in Medical Biology (2008), University of Melbourne (Walter and Eliza Hall Institute)
MSc in Statistics (2001), University of British Columbia
BSc in Applied Mathematics and Statistics (1999), University of Guelph
Charlotte Soneson
Twitter @CSoneson
GitHub csoneson
Google Scholar
As a postdoctoral research associate, one of my main interests is the development and improvement of statistical methods and workflows, currently mainly in the field of RNA-seq. I am also interested in the process of evaluating and comparing methods in an objective, robust and reproducible manner.
PhD in Mathematics (2011), Lund University
MSc in Engineering Physics (2005), Lund University
Simone Tiberi
I am a postdoctoral research associate working on the development of cutting-edge statistical methods for RNA-seq data. In particular, I am currently focusing on a Bayesian hierarchical model to detect genes showing differential transcript usage (DTU); the method accounts for the subject-to-subject variability in the transcripts proportions and for the uncertainty in the allocation of each fragment to the corresponding transcript, which is treated as a latent variable. In general terms, my interests are quite broad and lie in the development of statistical methods for applications in the medical and biological fields.
PhD in Statistics (2017), The University of Warwick
MSc in Statistics (2012), The University of Padua
BSc in Statistics (2010), Sapienza University of Rome
Izaskun Mallona
Google Scholar
I am mainly interested in gene expression modulation, as it lays the ground for any cell fate. The questions which excite my curiosity the most are: How are gene expression programs coded? and maintained? how do they adapt during development? and disease? To mine the regulation metastructure genome-wide I’m fond of integrating gene expression and epigenomic data, and to develop methods for doing so.
BSc in Computer Engineering (2014), Open University of Catalonia
PhD (2012), Technical University of Cartagena
MSc in Agriculture Engineering (2008), Technical University of Cartagena
MSc in Biology (2007), University of Murcia
Lukas Weber
Twitter @lmwebr
GitHub lmweber
Google Scholar
I am a PhD student in biostatistics, working on the development of statistical and computational methods for analysis of various types of high-throughput biological data. The main focus of my project is on methods for differential discovery in high-dimensional single-cell flow and mass cytometry data. These methods are now available in the diffcyt R package from Bioconductor. I also enjoy teaching, especially R programming and data analysis skills as an instructor for Software and Data Carpentry.
MSc in Statistics (2014), ETH Zurich
Katharina Hembach
I have a background in bioinformatics and I am a shared PhD student with the Polymenidou lab. They focus on understanding the molecular mechanisms of neurodegenerative diseases such as Amyotrophic Lateral Sclerosis (ALS) and Frontotemporal Lobar Degeneration (FTLD). I help with the analysis and interpretation of different sequencing data, such as RNA-seq, CLIP-seq, and iCLIP. My main project is the development of a pipeline for the identification and quantification of alternative splicing events, specifically microexons and cryptic exons, from RNA-seq data.
MSc in Bioinformatics (2015), LMU and TU Munich
BSc in Bioinformatics (2012), LMU and TU Munich
Stephan Schmeing
Twitter @StephanSchmeing
GitHub schmeing
As a PhD student coming from a particle physics background I am currently working on a more realistic Illumina sequence simulator called ReSequenceR. It is able to create a profile from a bam file that is then used to simulate paired-read fastq files. Furthermore I will work on an assembly and population genomics of the Indo-Pacific bottlenose dolphin (tursiops aduncus).
MSc in Astro, Particle and Nuclear physics (2014), TU Munich
BSc in Physics (2011), TU Munich
Ruizhu Huang
My major research interest is in the development and application of statistical methods in biological data. Currently, I am working on the project about tree signal aggregation.
MSc in Biostatistics (2015), University of Zurich
BSc in Applied Chemsitry (2010), Wuhan University
Vladimir Barbosa C. de Souza
I am a PhD candidate in Bioinformatics, and I am working with PacBio data (third-generation sequencing). As there is just few documentation about the data, one of the focus of my research is to figure out their features, mainly about quality scores. At the moment I am working on a project to develop a new fast and accurate method to create CCS reads (circular consensus sequences).
MSc in Applied Statistics (2015), University of Vicosa
BSc in Biology, specialization Genetics (2013), University of Vicosa
Stephany Orjuela
GitHub sorjuela
I have a shared PhD position with the Marra lab, which focuses on studying the molecular mechanisms underlying the development and progression of Colorectal Cancer. Most of my work focuses on analyzing and developing methods to process methylation data obtained from Bisulfite-seq. I am currently developing a method to identify differential allele-specific methylation.
MSc in Biology (2017), University of Zurich
BSc in Biology (2015), Universidad Nacional de Colombia
Stefan Milosavljevic
GitHub supermaxiste
I have a shared PhD position with the Shimizu lab. I’ve got a background in biology and bioinformatics and I’m currently working on the rapid evolution of a plant species called Arabidopsis kamchatica. My project focuses on epigenetic modifications over short timescales and my general aim is to assess the impact and the importance of DNA methylation in evolution over short periods (rapid evolution).
MSc in Computational Biology and Bioinformatics (2017), ETH Zurich and University of Zurich
BSc in Biology (2015), Université de Lausanne
Helena Lucia Crowell
In collaboration with the Bodenmiller lab lab, I have worked on correcting for spillover in CyTOF data. The preprint to this project is available on bioRxiv and has been published in cell systems. Alongside our compensation approach, I have made Finck et al.’s bead-based normalization and Zunder et al.’s single-cell deconvolution available in CATALYST (Cytometry dATa anALYSis Tools): a Bioconductor package providing tools for preprocessing and analysis of cytometry data; and have further integrated M. Nowicka’s CyTOF workflow for differential analysis into the package. Currently, I am working my MSc thesis project, which is predicated on differential discovery for scRNA-seq data.
MSc in Computational Biology & Bioinformatics (present), ETH Zurich
BSc in Biochemistry (2015), University of Heidelberg