2.7k citations · 3k across the 13 of their papers we have counts for
15 papers
Noise transfer for unsupervised domain adaptation of retinal OCT images
Valentin Koch, Olle Holmberg, Hannah Spitzer +4
Optical coherence tomography (OCT) imaging from different camera devices causes challenging domain shifts and can cause a severe drop in accuracy for machine learning models. In th…
Beyond Predictions in Neural ODEs: Identification and Interventions
Hananeh Aliee, Fabian J. Theis, Niki Kilbertus
Spurred by tremendous success in pattern matching and prediction tasks, researchers increasingly resort to machine learning to aid original scientific discovery. Given large amount…
A field guide to cultivating computational biology
Anne E Carpenter, Casey S Greene, Piero Carnici +11
Biomedical research centers can empower basic discovery and novel therapeutic strategies by leveraging their large-scale datasets from experiments and patients. This data, together…
SARS-CoV-2 Entry Genes Are Most Highly Expressed in Nasal Goblet and Ciliated Cells within Human Airways
Waradon Sungnak, Ni Huang, Christophe Bécavin +2
The SARS-CoV-2 coronavirus, the etiologic agent responsible for COVID-19 coronavirus disease, is a global threat. To better understand viral tropism, we assessed the RNA expression…
Conditional out-of-sample generation for unpaired data using trVAE
Mohammad Lotfollahi, Mohsen Naghipourfar, Fabian J. Theis +1
While generative models have shown great success in generating high-dimensional samples conditional on low-dimensional descriptors (learning e.g. stroke thickness in MNIST, hair co…
Single-cell eQTLGen Consortium: a personalized understanding of disease
Monique G. P. van der Wijst, Dylan H. de Vries, Hilde E. Groot +11
In recent years, functional genomics approaches combining genetic information with bulk RNA-sequencing data have identified the downstream expression effects of disease-associated…
Fully integrative data analysis of NMR metabolic fingerprints with comprehensive patient data: a case report based on the German Chronic Kidney Disease (GCKD) study
Helena U. Zacharias, Michael Altenbuchinger, Stefan Solbrig +11
Omics data facilitate the gain of novel insights into the pathophysiology of diseases and, consequently, their diagnosis, treatment, and prevention. To that end, it is necessary to…
Mitosis Detection in Intestinal Crypt Images with Hough Forest and Conditional Random Fields
Gerda Bortsova, Michael Sterr, Lichao Wang +6
Intestinal enteroendocrine cells secrete hormones that are vital for the regulation of glucose metabolism but their differentiation from intestinal stem cells is not fully understo…
A simulation-based approach for solving optimisation problems with ODE-type steady state constraints
Anna Fiedler, Fabian J. Theis, Jan Hasenauer
Ordinary differential equations (ODEs) are widely used to model biological, (bio-)chemical and technical processes. The parameters of these ODEs are often estimated from experiment…
Data-driven modelling of biological multi-scale processes
Jan Hasenauer, Nick Jagiella, Sabrina Hross +1
Biological processes involve a variety of spatial and temporal scales. A holistic understanding of many biological processes therefore requires multi-scale models which capture the…
MCA: Multiresolution Correlation Analysis, a graphical tool for subpopulation identification in single-cell gene expression data
Justin Feigelman, Fabian J. Theis, Carsten Marr
Background: Biological data often originate from samples containing mixtures of subpopulations, corresponding e.g. to distinct cellular phenotypes. However, identification of disti…
Separation of uncorrelated stationary time series using autocovariance matrices
Jari Miettinen, Katrin Illner, Klaus Nordhausen +3
Blind source separation (BSS) is a signal processing tool, which is widely used in various fields. Examples include biomedical signal separation, brain imaging and economic time se…
Joining Forces of Bayesian and Frequentist Methodology: A Study for Inference in the Presence of Non-Identifiability
Andreas Raue, Clemens Kreutz, Fabian Joachim Theis +1
Increasingly complex applications involve large datasets in combination with non-linear and high dimensional mathematical models. In this context, statistical inference is a challe…
Stability and multi-attractor dynamics of a toggle switch based on a two-stage model of stochastic gene expression
Michael K. Strasser, Fabian J. Theis, Carsten Marr
A toggle switch consists of two genes that mutually repress each other. This regulatory motif is active during cell differentiation and is thought to act as a memory device, being…
Patterns of subnet usage reveal distinct scales of regulation in the transcriptional regulatory network of Escherichia coli
Carsten Marr, Fabian J. Theis, Larry S. Liebovitch +1
The set of regulatory interactions between genes, mediated by transcription factors, forms a species' transcriptional regulatory network (TRN). By comparing this network with measu…