Mario Fasold

Mario Fasold
University of Leipzig

Dr.rer.nat.

About

31
Publications
10,135
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1,593
Citations

Publications

Publications (31)
Article
Full-text available
Background Calling germline SNP variants from bisulfite-converted sequencing data poses a challenge for conventional software, which have no inherent capability to dissociate true polymorphisms from artificial mutations induced by the chemical treatment. Nevertheless, SNP data is desirable both for genotyping and to understand the DNA methylome in...
Article
Full-text available
The expanding scope and scale of next generation sequencing experiments in ecological plant epigenetics brings new challenges for computational analysis. Existing tools built for model data may not address the needs of users looking to apply these techniques to non-model species, particularly on a population or community level. Here we present a to...
Article
Full-text available
Research in evolutionary biology has been progressively influenced by big data such as massive genome and transcriptome sequencing data, scalar measurements of several phenotypes on tens to thousands of individuals, as well as from collecting worldwide environmental data at an increasingly detailed scale. The handling and analysis of such data requ...
Article
The spotted gar genome illuminates vertebrate evolution and facilitates human-teleost comparisons (vol 48, pg 427, 2016)
Article
Full-text available
To connect human biology to fish biomedical models, we sequenced the genome of spotted gar (Lepisosteus oculatus), whose lineage diverged from teleosts before teleost genome duplication (TGD). The slowly evolving gar genome has conserved in content and size many entire chromosomes from bony vertebrate ancestors. Gar bridges teleosts to tetrapods by...
Article
Full-text available
Contents 79 The Chicken Leads the Way in Avian Genomics. Prepared by J. Smith. 80 The Chicken Genome: Current Status of Genome Assembly and Annotations. Prepared by D.W. Burt, L. Eöry, A.L. Archibald, B.L. Aken, P. Flicek, K. Howe, W. Chow, M. Dunn, J.M.D. Wood, R. Nag, and W.C. Warren. 83 The Avian RNAseq Consortium: A Community Effort to Annot...
Article
Full-text available
Here we present the results of a large-scale bioinformatics annotation of non-coding RNA loci in 48 avian genomes. Our approach uses probabilistic models of hand-curated families from the Rfam database to infer conserved RNA families within each avian genome. We supplement these annotations with predictions from the tRNA annotation tool, tRNAscan-S...
Article
Full-text available
Large-scale RNA sequencing has revealed a large number of long mRNA-like transcripts (lncRNAs) that do not code for proteins. The evolutionary history of these lncRNAs has been notoriously hard to study systematically due to their low level of sequence conservation that precludes comprehensive homology-based surveys and makes them nearly impossible...
Article
Full-text available
High-throughput sequencing techniques have made it possible to assay an organism's entire repertoire of small non-coding RNAs (ncRNAs) in an efficient and cost-effective manner. The moderate size of small RNA-seq datasets makes it feasible to provide free web services to the research community that provide many basic features of a small RNA-seq ana...
Article
Full-text available
The great utility of microarrays for genome-scale expression analysis is challenged by the widespread presence of batch effects, which bias expression measurements in particular within large data sets. These unwanted technical artifacts can obscure biological variation and thus significantly reduce the reliability of the analysis results. It is lar...
Article
Full-text available
Calcium ions (Ca2+) play important roles in neuroplasticity and the regeneration of nerves. Intracellular Ca2+ concentrations are regulated by Ca2+ channels, among them L-type voltage-gated Ca2+ channels, which are inhibited by dihydropyridines like nimodipine. The purpose of this study was to investigate the effect of nimodipine on neurite growth...
Article
Full-text available
There is a critical need for standard approaches to assess, report, and compare the technical performance of genome-scale differential gene expression experiments. We assess technical performance with a proposed "standard" dashboard of metrics derived from analysis of external spike-in RNA control ratio mixtures. These control ratio mixtures with d...
Article
Full-text available
We present primary results from the Sequencing Quality Control (SEQC) project, coordinated by the US Food and Drug Administration. Examining Illumina HiSeq, Life Technologies SOLiD and Roche 454 platforms at multiple laboratory sites using reference RNA samples with built-in controls, we assess RNA sequencing (RNA-seq) performance for junction disc...
Article
Full-text available
Here we present the results of a large-scale bioinformatic annotation of non-coding RNA loci in 48 avian genomes. Our approach uses probabilistic models of hand-curated families from the Rfam database to infer conserved RNA families within each avian genome. We supplement these annotations with predictions from the tRNA annotation tool, tRNAscan-SE...
Conference Paper
Full-text available
Mastitis is a major animal welfare problem and the most costly disease in dairy cattle worldwide. Within the EU FP7 Quantomics project, we aimed at validating quantitative trait loci affecting mastitis resistance at the molecular level. Eight chromosome regions with major effects on resistance to mastitis were identified by GWAS using high-density...
Conference Paper
Full-text available
Mastitis is a major animal welfare problem and the most costly disease in dairy cattle worldwide. Within the EU FP7 Quantomics project, we aimed at validating quantitative trait loci affecting mastitis resistance at the molecular level. Eight chromosome regions with major effects on resistance to mastitis were identified by GWAS using high­density...
Article
Full-text available
Self-organizing maps (SOM) portray molecular phenotypes with individual resolution. We present an analysis pipeline based on SOM machine learning which allows the comprehensive study of large scale clinical data. The potency of the method is demonstrated in selected applications studying the diversity of gene expression in Glioblastoma Multiforme (...
Article
Full-text available
Self organizing maps (SOMs) portrait molecular phenotypes with individual resolution. We demonstrate the potency of the method in selected applications characterizing the diversity of gene expression in different tissues and cancer subtypes, mRNA and miRNA fingerprints of stem cells, the proteome landscape of algae and genomic relations between hum...
Article
Full-text available
Motivation: Gene expression experiments aim to accurately quantify thousands of transcripts in parallel. Factors posterior to RNA extraction can, however, impair their accurate representation. RNA degradation and differences in the efficiency of amplification affect raw intensity measurements using Affymetrix expression arrays. The positional inten...
Article
Full-text available
Background Microarrays are a powerful tool for transcriptome analysis. Best results are obtained using high-quality RNA samples for preparation and hybridization. Issues with RNA integrity can lead to low data quality and failure of the microarray experiment. Results Microarray intensity data contains information to estimate the RNA quality of the...
Article
Full-text available
Small non-coding RNAs (ncRNAs) such as microRNAs, snoRNAs and tRNAs are a diverse collection of molecules with several important biological functions. Current methods for high-throughput sequencing for the first time offer the opportunity to investigate the entire ncRNAome in an essentially unbiased way. However, there is a substantial need for met...
Data
Full-text available
The additional text provides a list of the datasets studied, the frequencies of triple motifs on selected array types and the positional sensitivity profiles of specific and nonspecific hybridization for three selected hybridizations.
Article
Full-text available
The brightness of the probe spots on expression microarrays intends to measure the abundance of specific mRNA targets. Probes with runs of at least three guanines (G) in their sequence show abnormal high intensities which reflect rather probe effects than target concentrations. This G-bias requires correction prior to downstream expression analysis...
Data
Hybridization modes and base pairings for probe selection. The supporting text provides an overview about the hybridization modes, probe attributes and interaction groups;about base pairings in probe/target duplexes at the middle and SNP position of the probe sequences; and how probes are selected for triple-averaging (including the ‘hook’ criteria...
Article
Full-text available
Single nucleotide polymorphism (SNP) arrays are important tools widely used for genotyping and copy number estimation. This technology utilizes the specific affinity of fragmented DNA for binding to surface-attached oligonucleotide DNA probes. We analyze the variability of the probe signals of Affymetrix GeneChip SNP arrays as a function of the pro...
Article
Full-text available
Microarrays aim at measuring the expression degree of thousands of genes in a single experiment. The measured intensities of the probe spots are unfortu- nately affected by parasitic interferences, which in many cases prohibit the direct translation into the target RNA concentrations. The calibration of raw intensity data is therefore a fundamental...
Article
Full-text available
Self organizing maps (SOMs) portrait molecular phenotypes with individual resolution. We demonstrate the potency of the method in selected applications characterizing the diversity of gene expression in different tissues and cancer subtypes. SOM portraiting provides a comprehensive frame to describe development, differentiation and diversity in spa...

Questions

Questions (2)
Question
Then the following workshop is an ideal starting point:
A Beginner's Guide to NGS Data Analysis 
9 - 13 March 2015, Leipzig/Germany
Question
Points the would be interesting to know for each journal: scope, impact factor, author charges, access model, page/word limit.

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