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Exploring Intronic RNA-Seq Read Counts for Machine Learning Phenotype Prediction

Zuiker, Thomas (author)

The inclusion of intronic reads in the downstream analysis of RNA-sequencing (RNA-seq) data has long been controversial. Recent studies show that intronic reads do contain relevant biological signal. Additionally, studies have discovered differential expression unique to intronic reads in certain diseases. Nevertheless, most disease prediction...

master thesis 2023

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Mimicked Mixing-Induced Heterogeneities of Industrial Bioreactors Stimulate Long-Lasting Adaption Programs in Ethanol-Producing Yeasts

Minden, Steven (author), Aniolek, Maria (author), Noorman, H.J. (author), Takors, Ralf (author)

Commercial-scale bioreactors create an unnatural environment for microbes from an evolutionary point of view. Mixing insufficiencies expose individual cells to fluctuating nutrient concentrations on a second-to-minute scale while transcriptional and translational capacities limit the microbial adaptation time from minutes to hours. This...

journal article 2023

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A comprehensive mouse kidney atlas enables rare cell population characterization and robust marker discovery

Novella-Rausell, Claudio (author), Grudniewska, Magda (author), Peters, Dorien J.M. (author), Mahfouz, A.M.E.T.A. (author)

The kidney's cellular diversity is on par with its physiological intricacy; yet identifying cell populations and their markers remains challenging. Here, we created a comprehensive atlas of the healthy adult mouse kidney (MKA: Mouse Kidney Atlas) by integrating 140.000 cells and nuclei from 59 publicly available single-cell and single-nuclei...

journal article 2023

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Biomarker identification for endometriosis as a target for real-time intraoperative fluorescent imaging: A new approach using transcriptomic analysis to broaden the search for potential biomarkers

Tummers, Fokkedien H.M.P. (author), Bazelmans, Maria K. (author), Jansen, F.W. (author), Blikkendaal, Mathijs D. (author), Vahrmeijer, Alexander L. (author), Kuppen, P.J.K. (author)

Intra-operative fluorescent imaging of endometriosis could help to optimize surgical treatment. Potential biomarkers to use as target for endometriosis-binding fluorescent probes were identified using a new five-phase transcriptomics-based approach to broaden the search for biomarkers. Using publicly available datasets, a differentially...

review 2023

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Long-read direct RNA sequencing of the mitochondrial transcriptome of Saccharomyces cerevisiae reveals condition-dependent intron abundance

Koster, C.C. (author), Kleefeldt, Askar A. (author), van den Broek, M.A. (author), Luttik, M.A.H. (author), Daran, J.G. (author), Daran-Lapujade, P.A.S. (author)

Mitochondria fulfil many essential roles and have their own genome, which is expressed as polycistronic transcripts that undergo co- or posttranscriptional processing and splicing. Due to the inherent complexity and limited technical accessibility of the mitochondrial transcriptome, fundamental questions regarding mitochondrial gene...

journal article 2023

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Transcriptional and cell type profiles of cortical brain regions showing ultradian cortisol rhythm dependent responses to emotional face stimulation

Habets, Philippe C. (author), Kalafatakis, Konstantinos (author), Dzyubachyk, O. (author), van der Werff, Steven J.A. (author), Keo, D.L. (author), Thakrar, Jamini (author), Mahfouz, A.M.E.T.A. (author), Pereira, Alberto M. (author), Russell, Georgina M. (author)

The characteristic endogenous circadian rhythm of plasma glucocorticoid concentrations is made up from an underlying ultradian pulsatile secretory pattern. Recent evidence has indicated that this ultradian cortisol pulsatility is crucial for normal emotional response in man. In this study, we investigate the anatomical transcriptional and...

journal article 2023

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SpaceWalker enables interactive gradient exploration for spatial transcriptomics data

Li, Chang (author), Thijssen, Julian (author), Kroes, Thomas (author), de Boer, Mitchell (author), Abdelaal, T.R.M. (author), Höllt, T. (author), Lelieveldt, B.P.F. (author)

In spatial transcriptomics (ST) data, biologically relevant features such as tissue compartments or cell-state transitions are reflected by gene expression gradients. Here, we present SpaceWalker, a visual analytics tool for exploring the local gradient structure of 2D and 3D ST data. The user can be guided by the local intrinsic...

journal article 2023

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A gastruloid model of the interaction between embryonic and extra-embryonic cell types

Berenger-Currias, N.M.L.P. (author), Mircea, Maria (author), Adegeest, Esmée (author), van den Berg, Patrick R. (author), Feliksik, Marleen (author), Hochane, Mazène (author), Idema, T. (author), Tans, S.J. (author), Semrau, Stefan (author)

Stem-cell derived in vitro systems, such as organoids or embryoids, hold great potential for modeling in vivo development. Full control over their initial composition, scalability, and easily measurable dynamics make those systems useful for studying specific developmental processes in isolation. Here we report the formation of gastruloids...

journal article 2022

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Metabolomic predictors of phenotypic traits can replace and complement measured clinical variables in population-scale expression profiling studies

Niehues, Anna (author), Bizzarri, Daniele (author), Reinders, M.J.T. (author), Slagboom, P. Eline (author), van Gool, Alain J. (author), van den Akker, E.B. (author), 't Hoen, Peter A.C. (author)

Population-scale expression profiling studies can provide valuable insights into biological and disease-underlying mechanisms. The availability of phenotypic traits is essential for studying clinical effects. Therefore, missing, incomplete, or inaccurate phenotypic information can make analyses challenging and prevent RNA-seq or other omics...

journal article 2022

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Genome-wide effect of non-optimal temperatures under anaerobic conditions on gene expression in Saccharomyces cerevisiae

García-Ríos, Estéfani (author), Alonso-del-Real, Javier (author), Lip, K.Y.F. (author), Pinheiro, Tania (author), Teixeira, José (author), van Gulik, W.M. (author), Domingues, Lucília (author), Querol, Amparo (author), Guillamón, José Manuel (author)

Understanding of thermal adaptation mechanisms in yeast is crucial to develop better-adapted strains to industrial processes, providing more economical and sustainable products. We have analyzed the transcriptomic responses of three Saccharomyces cerevisiae strains, a commercial wine strain, ADY5, a laboratory strain, CEN.PK113-7D and a...

journal article 2022

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Correcting Differential Gene Expression Analysis for Cyto—Architectural Alterations in Substantia Nigra of Parkinson’s Disease Patients Reveals Known and Potential Novel Disease—Associated Genes and Pathways

Ferraro, F. (author), Fevga, Christina (author), Bonifati, Vincenzo (author), Mandemakers, Wim (author), Mahfouz, A.M.E.T.A. (author), Reinders, M.J.T. (author)

Several studies have analyzed gene expression profiles in the substantia nigra to better understand the pathological mechanisms causing Parkinson’s disease (PD). However, the concordance between the identified gene signatures in these individual studies was generally low. This might have been caused by a change in cell type composition as loss...

journal article 2022

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The Transcriptome in Transition: Global Gene Expression Profiles of Young Adult Fruit Flies Depend More Strongly on Developmental Than Adult Diet

May, Christina M. (author), van den Akker, E.B. (author), Zwaan, Bas J. (author)

Developmental diet is known to exert long-term effects on adult phenotypes in many animal species as well as disease risk in humans, purportedly mediated through long-term changes in gene expression. However, there are few studies linking developmental diet to adult gene expression. Here, we use a full-factorial design to address how three...

journal article 2021

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Cingulate networks associated with gray matter loss in Parkinson's disease show high expression of cholinergic genes in the healthy brain

Keo, D.L. (author), Dzyubachyk, Oleh (author), van der Grond, Jeroen (author), Hafkemeijer, Anne (author), van de Berg, Wilma D.J. (author), van Hilten, Jacobus J. (author), Reinders, M.J.T. (author), Mahfouz, A.M.E.T.A. (author)

Structural covariance networks are able to identify functionally organized brain regions by gray matter volume covariance across a population. We examined the transcriptomic signature of such anatomical networks in the healthy brain using postmortem microarray data from the Allen Human Brain Atlas. A previous study revealed that a posterior...

journal article 2021

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The Cancer SENESCopedia: A delineation of cancer cell senescence

Jochems, Fleur (author), Thijssen, Bram (author), De Conti, Giulia (author), Jansen, Robin (author), Pogacar, Ziva (author), Groot, Kelvin (author), Wang, Liqin (author), Schepers, Arnout (author), Wessels, L.F.A. (author)

Cellular senescence is characterized as a stable proliferation arrest that can be triggered by multiple stresses. Most knowledge about senescent cells is obtained from studies in primary cells. However, senescence features may be different in cancer cells, since the pathways that are involved in senescence induction are often deregulated in...

journal article 2021

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Automatic cell identification in single-cell RNA-sequencing data

Michielsen, Lieke (author)

Since the revolution of single-cell RNA-sequencing, the number of available datasets has increased enormously. In these datasets, cell identification is mainly done manually, which is subjective and time-consuming. As a consequence, most datasets are annotated at a different resolution. This is not surprising as cell types form a hierarchy, but...

master thesis 2020

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“Candidatus Galacturonibacter soehngenii” Shows Acetogenic Catabolism of Galacturonic Acid but Lacks a Canonical Carbon Monoxide Dehydrogenase/Acetyl-CoA Synthase Complex

Valk, L.C. (author), Diender, Martijn (author), Stouten, G.R. (author), Petersen, Jette F. (author), Nielsen, Per H. (author), Dueholm, Morten S. (author), Pronk, J.T. (author), van Loosdrecht, Mark C.M. (author)

Acetogens have the ability to fixate carbon during fermentation by employing the Wood-Ljungdahl pathway (WLP), which is highly conserved across Bacteria and Archaea. In a previous study, product stoichometries in galacturonate-limited, anaerobic enrichment cultures of “Candidatus Galacturonibacter soehngenii,” from a novel genus within the...

journal article 2020

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Dynamics of the transcriptome and proteome in regions of the brain differ considerably

Pourquié, Valérie (author)

Human brain research is advancing, facilitated by improved high-throughput techniques and systematically preservation of brain tissue in brain banks. Due to the complex organization and regulation of the brain, most studies only focus on a single aspect of healthy and diseased samples. This research integrates analyses of the transcriptome and...

master thesis 2019

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The Penicillium chrysogenum transporter PcAraT enables high-affinity, glucose-insensitive l-arabinose transport in Saccharomyces cerevisiae

Bracher, J.M. (author), Verhoeven, M.D. (author), Wisselink, H. Wouter (author), Crimi, B. (author), Nijland, Jeroen G. (author), Driessen, Arnold J.M. (author), Klaassen, Paul (author), van Maris, A.J.A. (author), Daran, J.G. (author), Pronk, J.T. (author)

Background: l-Arabinose occurs at economically relevant levels in lignocellulosic hydrolysates. Its low-affinity uptake via the Saccharomyces cerevisiae Gal2 galactose transporter is inhibited by d-glucose. Especially at low concentrations of l-arabinose, uptake is an important rate-controlling step in the complete conversion of these...

journal article 2018

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Molecular responses of Saccharomyces cerevisiae to near-zero growth rates

Bisschops, M.M.M. (author)

doctoral thesis 2016

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Visualizing the spatial gene expression organization in the brain through non-linear similarity embeddings

Mahfouz, A.M.E.T.A. (author), Van de Giessen, M. (author), Van der Maaten, L.J.P. (author), Huisman, S.M.H. (author), Reinders, M.J.T. (author), Hawrylycz, M.J. (author), Lelieveldt, B.P.F. (author)

The Allen Brain Atlases enable the study of spatially resolved, genome-wide gene expression patterns across the mammalian brain. Several explorative studies have applied linear dimensionality reduction methods such as Principal Component Analysis (PCA) and classical Multi-Dimensional Scaling (cMDS) to gain insight into the spatial organization...

journal article 2014