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
Simone Tiberi
Twitter @tiberi_simone
GitHub SimoneTiberi
Google Scholar
I am a Postdoc working on the development of cutting-edge statistical methods in bioinformatics, mostly for bulk and single-cell RNA-seq data.In particular, I am currently focusing on two methodological projects. The first one consists in developing a Bayesian hierarchical model to identify differentially spliced genes, via differential transcript usage (DTU), from bulk RNA-seq data. The second project (in its early stages) aims at creating a methodology, based on permutation tests, to perform differential state analyses from single-cell RNA-seq data. Previously, I was a PhD student at the Department of Statistics at the University of Warwick, where I worked on Bayesian hierarchical models to investigate stochastic systems in single cells. In general terms, my interests are broad and lie in the development of statistical methods for applications in biology.
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
Pierre-Luc Germain
I gradually shifted from the humanities to bioinformatics towards the end of my PhD, worked a lot in the past on linking chromatin alterations to gene expression, and currently work mostly on the analysis of short RNA-seq and single-cell RNA-seq, as well as pre- and post-transcriptional regulation of gene expression especially in the context of neurodevelopment. I have a shared position with the ETH’s D-HEST Institute for Neurosciences.
PhD in Philosophy of science (2014), SEMM and University of Milan
MA in Philosophy (2009), University of Montreal
BA in Philosophy (2007)
Will Macnair
Twitter @willmacnair
GitHub wmacnair
I am a postdoc developing statistical and computational methods for analysis of single cell data, mainly different flavours of single cell RNA-seq, but also cytometry data. I’m motivated by sharp, biologically-driven research questions, and empirically sound methods to answer them. My PhD focused on analysis of trajectories in single cell data, via testing for the presence of branchpoints (TreeTop), and identification of genes underlying sequential labels (psupertime).
PhD in Computational Biology (2018), ETH Zürich
MSc in Systems Biology (2013), University of Warwick
Certificate of Advanced Studies in Mathematics (2004), University of Cambridge
BA in Mathematics (2003), University of Cambridge
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 Zürich
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 Zürich
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 Zürich and University of Zürich
BSc in Biology (2015), Université de Lausanne
Helena Lucia Crowell
Twitter @CrowellHL
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. As a PhD student, I am currently working on extending this framework for differential discovery to scRNA-seq data with complex experimental designs.
MSc in Computational Biology & Bioinformatics (2018), ETH Zürich
BSc in Biochemistry (2015), University of Heidelberg
Almut Lütge
I’m a PhD student with a background in Molecular Biotechnology, but already during my master I focused on Bioinformatics. I’m interested in all kinds of genomic analysis, but mainly worked with transcriptomic data, so far. My PhD project is about methods in single cell RNAseq and part of a Sinergia collaboration on defining the identity and differentiation pathways of the immune-stimulating fibroblastic tumor stroma.
MSc in Molecular Biotechnology (2018), University of Heidelberg
BSc Molecular Biotechnology (2013), University of Heidelberg
Anthony Sonrel
I am a PhD student that joined the Robinson Lab as part of the Life Science Zürich Graduate School. Through my past projects in academia and industry I worked on various topics such as NGS, GWAS summary statistics, epigenetic analyses (ChIP/ATAC-seq) and deep neural networks. In my current project, I’m evaluating and developing tools (mainly R packages) for single-cell RNA sequencing datasets. More specifically, I’m interested in developing new methodologies and new effective tools.
MSc in Molecular Life Sciences - Bioinformatics (2018), University of Lausanne
BSc of Science in Biology (2015), University of Lausanne
Reto Gerber
I am a Master student in the Computational Biology & Bioinformatics study program currently working on my master thesis. The focus of this project lies on using censored predictors in single cell models (mainly for flow and mass cytometry). In past projects I worked among other things on docking of biomolecules and signalling networks in cells, before turning more to the statistical aspect of bioinformatics.
BSc of Science in Biology (2017), University of Zürich
Elyas Heidari
I am a Master student of Computational Biology & Bioinformatics at ETH university. I am interested in developing analysis pipelines for single-cell multi-omics data. Currently, I am exploring single-cell B/T-cell receptor data to understand the diversity in immune repertoire and phenotypes. Prior to joining Robinson lab, I worked on developing a number of machine/deep learning tools for biomedical data. I have developed MUVIS for general medical data analysis and SeqLearner for semi-supervised learning on protein sequences.
BSc of Science in Applied Mathematics (2019), Sharif University of Technology
BSc of Science in Computer Engineering (2019), Sharif University of Technology