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Book ; Audio / Video ; Thesis: Genetic analysis of yeast gene expression that depends on the RNA PolII holoenzyme complex

Badi, Laura

2001

Author's details	Laura Badi
Language	English
Size	1 CD-ROM, CD-R, 12 cm
Edition	[Elektronische Ressource]
Document type	Book ; Audio / Video ; Thesis
Thesis / German Habilitation thesis	Univ., Diss.--Zürich, 2001
Note	Dateiformat: PDF
Accompanying material	2 Beil.
Database	Former special subject collection: coastal and deep sea fishing

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Article ; Online: Using OWL reasoning to support the generation of novel gene sets for enrichment analysis.

Osumi-Sutherland, David J / Ponta, Enrico / Courtot, Melanie / Parkinson, Helen / Badi, Laura

Journal of biomedical semantics

2018 Volume 9, Issue 1, Page(s) 10

Abstract: Background: The Gene Ontology (GO) consists of over 40,000 terms for biological processes, cell components and gene product activities linked into a graph structure by over 90,000 relationships. It has been used to annotate the functions and cellular ... ...

Abstract	Background: The Gene Ontology (GO) consists of over 40,000 terms for biological processes, cell components and gene product activities linked into a graph structure by over 90,000 relationships. It has been used to annotate the functions and cellular locations of several million gene products. The graph structure is used by a variety of tools to group annotated genes into sets whose products share function or location. These gene sets are widely used to interpret the results of genomics experiments by assessing which sets are significantly over- or under-represented in results lists. F Hoffmann-La Roche Ltd. has developed a bespoke, manually maintained controlled vocabulary (RCV) for use in over-representation analysis. Many terms in this vocabulary group GO terms in novel ways that cannot easily be derived using the graph structure of the GO. For example, some RCV terms group GO terms by the cell, chemical or tissue type they refer to. Recent improvements in the content and formal structure of the GO make it possible to use logical queries in Web Ontology Language (OWL) to automatically map these cross-cutting classifications to sets of GO terms. We used this approach to automate mapping between RCV and GO, largely replacing the increasingly unsustainable manual mapping process. We then tested the utility of the resulting groupings for over-representation analysis. Results: We successfully mapped 85% of RCV terms to logical OWL definitions and showed that these could be used to recapitulate and extend manual mappings between RCV terms and the sets of GO terms subsumed by them. We also show that gene sets derived from the resulting GO terms sets can be used to detect the signatures of cell and tissue types in whole genome expression data. Conclusions: The rich formal structure of the GO makes it possible to use reasoning to dynamically generate novel, biologically relevant groupings of GO terms. GO term groupings generated with this approach can be used in. over-representation analysis to detect cell and tissue type signatures in whole genome expression data.
MeSH term(s)	Data Mining ; Databases, Genetic ; Gene Ontology ; Neurotransmitter Agents/metabolism ; Synapses/metabolism ; T-Lymphocytes/metabolism
Chemical Substances	Neurotransmitter Agents
Language	English
Publishing date	2018-02-14
Publishing country	England
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
ZDB-ID	2548651-2
ISSN	2041-1480 ; 2041-1480
ISSN (online)	2041-1480
ISSN	2041-1480
DOI	10.1186/s13326-018-0175-z
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: Sodium Iodate-Induced Degeneration Results in Local Complement Changes and Inflammatory Processes in Murine Retina.

Enzbrenner, Anne / Zulliger, Rahel / Biber, Josef / Pousa, Ana Maria Quintela / Schäfer, Nicole / Stucki, Corinne / Giroud, Nicolas / Berrera, Marco / Kortvely, Elod / Schmucki, Roland / Badi, Laura / Grosche, Antje / Pauly, Diana / Enzmann, Volker

International journal of molecular sciences

2021 Volume 22, Issue 17

Abstract: Age-related macular degeneration (AMD), one of the leading causes of blindness worldwide, causes personal suffering and high socioeconomic costs. While there has been progress in the treatments for the neovascular form of AMD, no therapy is yet available ...

Abstract	Age-related macular degeneration (AMD), one of the leading causes of blindness worldwide, causes personal suffering and high socioeconomic costs. While there has been progress in the treatments for the neovascular form of AMD, no therapy is yet available for the more common dry form, also known as geographic atrophy. We analysed the retinal tissue in a mouse model of retinal degeneration caused by sodium iodate (NaIO
MeSH term(s)	Animals ; Apoptosis/genetics ; Apoptosis/immunology ; Complement System Proteins/genetics ; Complement System Proteins/immunology ; Complement System Proteins/metabolism ; Disease Models, Animal ; Disease Susceptibility ; Fluorescent Antibody Technique ; Gene Expression Regulation/drug effects ; Immunity, Innate ; Immunohistochemistry ; Iodates/adverse effects ; Mice ; Retinal Degeneration/etiology ; Retinal Degeneration/metabolism ; Retinal Degeneration/pathology
Chemical Substances	Iodates ; Complement System Proteins (9007-36-7) ; sodium iodate (U558PCS5Z9)
Language	English
Publishing date	2021-08-26
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2019364-6
ISSN	1422-0067 ; 1422-0067 ; 1661-6596
ISSN (online)	1422-0067
ISSN	1422-0067 ; 1661-6596
DOI	10.3390/ijms22179218
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Article ; Online: Correction to: Detect tissue heterogeneity in gene expression data with BioQC.

Zhang, Jitao David / Hatje, Klas / Sturm, Gregor / Broger, Clemens / Ebeling, Martin / Burtin, Martine / Terzi, Fabiola / Pomposiello, Silvia Ines / Badi, Laura

BMC genomics

2018 Volume 19, Issue 1, Page(s) 558

Abstract: After the publication of this work [1], a mistake was noticed in the Eq. 1. Given an m × n expression matrix with m genes and samples of n tissues, the correct definition of the Gini index for gene i is. ...

Abstract	After the publication of this work [1], a mistake was noticed in the Eq. 1. Given an m × n expression matrix with m genes and samples of n tissues, the correct definition of the Gini index for gene i is.
Language	English
Publishing date	2018-07-30
Publishing country	England
Document type	Journal Article ; Published Erratum
ISSN	1471-2164
ISSN (online)	1471-2164
DOI	10.1186/s12864-018-4940-2
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: Besca, a single-cell transcriptomics analysis toolkit to accelerate translational research.

Mädler, Sophia Clara / Julien-Laferriere, Alice / Wyss, Luis / Phan, Miroslav / Sonrel, Anthony / Kang, Albert S W / Ulrich, Eric / Schmucki, Roland / Zhang, Jitao David / Ebeling, Martin / Badi, Laura / Kam-Thong, Tony / Schwalie, Petra C / Hatje, Klas

NAR genomics and bioinformatics

2021 Volume 3, Issue 4, Page(s) lqab102

Abstract: Single-cell RNA sequencing (scRNA-seq) revolutionized our understanding of disease biology. The promise it presents to also transform translational research requires highly standardized and robust software workflows. Here, we present the ... ...

Abstract	Single-cell RNA sequencing (scRNA-seq) revolutionized our understanding of disease biology. The promise it presents to also transform translational research requires highly standardized and robust software workflows. Here, we present the toolkit
Language	English
Publishing date	2021-11-08
Publishing country	England
Document type	Journal Article
ISSN	2631-9268
ISSN (online)	2631-9268
DOI	10.1093/nargab/lqab102
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Article ; Online: Cardiac spheroids as promising in vitro models to study the human heart microenvironment.

Polonchuk, Liudmila / Chabria, Mamta / Badi, Laura / Hoflack, Jean-Christophe / Figtree, Gemma / Davies, Michael J / Gentile, Carmine

Scientific reports

2017 Volume 7, Issue 1, Page(s) 7005

Abstract: Three-dimensional in vitro cell systems are a promising alternative to animals to study cardiac biology and disease. We have generated three-dimensional in vitro models of the human heart ("cardiac spheroids", CSs) by co-culturing human primary or iPSC- ... ...

Abstract	Three-dimensional in vitro cell systems are a promising alternative to animals to study cardiac biology and disease. We have generated three-dimensional in vitro models of the human heart ("cardiac spheroids", CSs) by co-culturing human primary or iPSC-derived cardiomyocytes, endothelial cells and fibroblasts at ratios approximating those present in vivo. The cellular organisation, extracellular matrix and microvascular network mimic human heart tissue. These spheroids have been employed to investigate the dose-limiting cardiotoxicity of the common anti-cancer drug doxorubicin. Viability/cytotoxicity assays indicate dose-dependent cytotoxic effects, which are inhibited by the nitric oxide synthase (NOS) inhibitor L-NIO, and genetic inhibition of endothelial NOS, implicating peroxynitrous acid as a key damaging agent. These data indicate that CSs mimic important features of human heart morphology, biochemistry and pharmacology in vitro, offering a promising alternative to animals and standard cell cultures with regard to mechanistic insights and prediction of toxic effects in human heart tissue.
MeSH term(s)	Antineoplastic Agents/toxicity ; Cell Survival/drug effects ; Doxorubicin/toxicity ; Endothelial Cells/drug effects ; Endothelial Cells/physiology ; Fibroblasts/drug effects ; Fibroblasts/physiology ; Heart/drug effects ; Heart/physiology ; Humans ; Models, Biological ; Myocytes, Cardiac/drug effects ; Myocytes, Cardiac/physiology ; Spheroids, Cellular/drug effects ; Spheroids, Cellular/physiology
Chemical Substances	Antineoplastic Agents ; Doxorubicin (80168379AG)
Language	English
Publishing date	2017-08-01
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2615211-3
ISSN	2045-2322 ; 2045-2322
ISSN (online)	2045-2322
ISSN	2045-2322
DOI	10.1038/s41598-017-06385-8
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Article ; Online: Detect tissue heterogeneity in gene expression data with BioQC.

Zhang, Jitao David / Hatje, Klas / Sturm, Gregor / Broger, Clemens / Ebeling, Martin / Burtin, Martine / Terzi, Fabiola / Pomposiello, Silvia Ines / Badi, Laura

BMC genomics

2017 Volume 18, Issue 1, Page(s) 277

Abstract: Background: Gene expression data can be compromised by cells originating from other tissues than the target tissue of profiling. Failures in detecting such tissue heterogeneity have profound implications on data interpretation and reproducibility. A ... ...

Abstract	Background: Gene expression data can be compromised by cells originating from other tissues than the target tissue of profiling. Failures in detecting such tissue heterogeneity have profound implications on data interpretation and reproducibility. A computational tool explicitly addressing the issue is warranted. Results: We introduce BioQC, a R/Bioconductor software package to detect tissue heterogeneity in gene expression data. To this end BioQC implements a computationally efficient Wilcoxon-Mann-Whitney test and provides more than 150 signatures of tissue-enriched genes derived from large-scale transcriptomics studies. Simulation experiments show that BioQC is both fast and sensitive in detecting tissue heterogeneity. In a case study with whole-organ profiling data, BioQC predicted contamination events that are confirmed by quantitative RT-PCR. Applied to transcriptomics data of the Genotype-Tissue Expression (GTEx) project, BioQC reveals clustering of samples and suggests that some samples likely suffer from tissue heterogeneity. Conclusions: Our experience with gene expression data indicates a prevalence of tissue heterogeneity that often goes unnoticed. BioQC addresses the issue by integrating prior knowledge with a scalable algorithm. We propose BioQC as a first-line tool to ensure quality and reproducibility of gene expression data.
MeSH term(s)	Algorithms ; Animals ; Dogs ; Gene Expression Profiling ; Humans ; Mice ; Organ Specificity ; Reproducibility of Results ; Software ; Transcriptome
Language	English
Publishing date	2017-04-04
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2041499-7
ISSN	1471-2164 ; 1471-2164
ISSN (online)	1471-2164
ISSN	1471-2164
DOI	10.1186/s12864-017-3661-2
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Article ; Online: Functional analysis and transcriptional output of the Göttingen minipig genome

BMC Genomics

2023

Keywords	analysis ; functional analysis
Publishing date	2023-03-10T14:36:23Z
Publisher	Springer
Publishing country	fr
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: DDR1 role in fibrosis and its pharmacological targeting.

Moll, Solange / Desmoulière, Alexis / Moeller, Marcus J / Pache, Jean-Claude / Badi, Laura / Arcadu, Filippo / Richter, Hans / Satz, Alexander / Uhles, Sabine / Cavalli, Andrea / Drawnel, Faye / Scapozza, Leonardo / Prunotto, Marco

Biochimica et biophysica acta. Molecular cell research

2019 Volume 1866, Issue 11, Page(s) 118474

Abstract: Discoidin domain receptor1 (DDR1) is a collagen activated receptor tyrosine kinase and an attractive anti-fibrotic target. Its expression is mainly limited to epithelial cells located in several organs including skin, kidney, liver and lung. DDR1's ... ...

Abstract	Discoidin domain receptor1 (DDR1) is a collagen activated receptor tyrosine kinase and an attractive anti-fibrotic target. Its expression is mainly limited to epithelial cells located in several organs including skin, kidney, liver and lung. DDR1's biology is elusive, with unknown downstream activation pathways; however, it may act as a mediator of the stromal-epithelial interaction, potentially controlling the activation state of the resident quiescent fibroblasts. Increased expression of DDR1 has been documented in several types of cancer and fibrotic conditions including skin hypertrophic scars, idiopathic pulmonary fibrosis, cirrhotic liver and renal fibrosis. The present review article focuses on: a) detailing the evidence for a role of DDR1 as an anti-fibrotic target in different organs, b) clarifying DDR1 tissue distribution in healthy and diseased tissues as well as c) exploring DDR1 protective mode of action based on literature evidence and co-authors experience; d) detailing pharmacological efforts attempted to drug this subtle anti-fibrotic target to date.
MeSH term(s)	Animals ; Atherosclerosis/metabolism ; Discoidin Domain Receptor 1/drug effects ; Discoidin Domain Receptor 1/metabolism ; Epithelial Cells/metabolism ; Epithelial Cells/pathology ; Fibroblasts/metabolism ; Fibroblasts/pathology ; Fibrosis/drug therapy ; Fibrosis/metabolism ; Humans ; Kidney/metabolism ; Kidney/pathology ; Liver/metabolism ; Liver/pathology ; Lung/metabolism ; Lung/pathology ; Mice ; Neoplasms/metabolism ; Nephritis, Interstitial/pathology ; Plasma Cells ; Receptor Protein-Tyrosine Kinases ; Skin/metabolism ; Skin/pathology ; Vascular Diseases/metabolism ; Wound Healing
Chemical Substances	Discoidin Domain Receptor 1 (EC 2.7.10.1) ; Receptor Protein-Tyrosine Kinases (EC 2.7.10.1)
Language	English
Publishing date	2019-04-05
Publishing country	Netherlands
Document type	Journal Article ; Review
ZDB-ID	60-7
ISSN	1879-2596 ; 1879-260X ; 1872-8006 ; 1879-2642 ; 1879-2618 ; 1879-2650 ; 0006-3002 ; 0005-2728 ; 0005-2736 ; 0304-4165 ; 0167-4838 ; 1388-1981 ; 0167-4889 ; 0167-4781 ; 0304-419X ; 1570-9639 ; 0925-4439 ; 1874-9399
ISSN (online)	1879-2596 ; 1879-260X ; 1872-8006 ; 1879-2642 ; 1879-2618 ; 1879-2650
ISSN	0006-3002 ; 0005-2728 ; 0005-2736 ; 0304-4165 ; 0167-4838 ; 1388-1981 ; 0167-4889 ; 0167-4781 ; 0304-419X ; 1570-9639 ; 0925-4439 ; 1874-9399
DOI	10.1016/j.bbamcr.2019.04.004
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Article ; Online: Signaling pathways predisposing to chronic kidney disease progression.

Zaidan, Mohamad / Burtin, Martine / Zhang, Jitao David / Blanc, Thomas / Barre, Pauline / Garbay, Serge / Nguyen, Clément / Vasseur, Florence / Yammine, Lucie / Germano, Serena / Badi, Laura / Gubler, Marie-Claire / Gallazzini, Morgan / Friedlander, Gérard / Pontoglio, Marco / Terzi, Fabiola

JCI insight

2020 Volume 5, Issue 9

Abstract: The loss of functional nephrons after kidney injury triggers the compensatory growth of the remaining ones to allow functional adaptation. However, in some cases, these compensatory events activate signaling pathways that lead to pathological alterations ...

Abstract	The loss of functional nephrons after kidney injury triggers the compensatory growth of the remaining ones to allow functional adaptation. However, in some cases, these compensatory events activate signaling pathways that lead to pathological alterations and chronic kidney disease. Little is known about the identity of these pathways and how they lead to the development of renal lesions. Here, we combined mouse strains that differently react to nephron reduction with molecular and temporal genome-wide transcriptome studies to elucidate the molecular mechanisms involved in these events. We demonstrated that nephron reduction led to 2 waves of cell proliferation: the first one occurred during the compensatory growth regardless of the genetic background, whereas the second one occurred, after a quiescent phase, exclusively in the sensitive strain and accompanied the development of renal lesions. Similarly, clustering by coinertia analysis revealed the existence of 2 waves of gene expression. Interestingly, we identified type I interferon (IFN) response as an early (first-wave) and specific signature of the sensitive (FVB/N) mice. Activation of type I IFN response was associated with G1/S cell cycle arrest, which correlated with p21 nuclear translocation. Remarkably, the transient induction of type I IFN response by poly(I:C) injections during the compensatory growth resulted in renal lesions in otherwise-resistant C57BL6 mice. Collectively, these results suggest that the early molecular and cellular events occurring after nephron reduction determine the risk of developing late renal lesions and point to type I IFN response as a crucial event of the deterioration process.
MeSH term(s)	Animals ; Cell Proliferation ; Disease Progression ; Disease Susceptibility ; Female ; G1 Phase Cell Cycle Checkpoints ; Interferon Type I/metabolism ; Kidney/metabolism ; Kidney/pathology ; Mice ; Mice, Inbred C57BL ; Nephrons/metabolism ; Nephrons/pathology ; Renal Insufficiency, Chronic/metabolism ; Renal Insufficiency, Chronic/pathology ; Signal Transduction
Chemical Substances	Interferon Type I
Language	English
Publishing date	2020-05-07
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ISSN	2379-3708
ISSN (online)	2379-3708
DOI	10.1172/jci.insight.126183
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