Daniel Fischer

Daniel Fischer
Natural Resources Institute Finland (Luke) · Production Systems

PhD, Biostatistics

About

45
Publications
13,862
Reads
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352
Citations
Additional affiliations
January 2015 - April 2021
Natural Resources Institute Finland (Luke)
Position
  • Bioinformatician
January 2013 - December 2014
MTT Agrifood Research
Position
  • Bioinformatician
May 2009 - January 2017
Tampere University
Position
  • PhD Student

Publications

Publications (45)
Article
Full-text available
Background The human sweat is a mixture of secretions from three types of glands: eccrine, apocrine, and sebaceous. Eccrine glands open directly on the skin surface and produce high amounts of water-based fluid in response to heat, emotion, and physical activity, whereas the other glands produce oily fluids and waxy sebum. While most body fluids ha...
Article
Full-text available
Dimension reduction is often a preliminary step in the analysis of data sets with a large number of variables. Most classical, both supervised and unsupervised, dimension reduction methods such as principal component analysis (PCA), independent component analysis (ICA) or sliced inverse regression (SIR) can be formulated using one, two or several d...
Article
Full-text available
The Oja median is one of several extensions of the univariate median to the multivariate case. It has many desirable properties, but is computationally demanding. In this paper, we first review the properties of the Oja median and compare it to other multivariate medians. Then, we discuss four algorithms to compute the Oja median, which are impleme...
Chapter
We present the R-package GenomicTools that can be used to perform QTL and eQTL analyses in a user-friendly way. First, the theoretical backgrounds of both implemented methods are explained. These are (a) the linear model approach that is commonly used in the standard QTL/eQTL testing as well as (b) a non-parametrical directional testing method impl...
Article
The R-package REPPlab is designed to explore multivariate data sets using one-dimensional unsupervised projection pursuit. It is useful as a preprocessing step to find clusters or as an outlier detection tool for multivariate data. Except from the packages tourr and rggobi, there is no implementation of exploratory projection pursuit tools availabl...
Article
Full-text available
High meat quality and specifically meat tenderness are desired traits by the consumers, however the environmental impact of meat production is becoming a relevant factor in the industry. Therefore, breeding of dual purpose cattle breeds may answer the high demand of meat production in the future. In this study we identified statistical differences...
Article
Full-text available
Ciliopathies presenting as inherited hepatorenal fibrocystic disorders are rare in humans and in dogs. We describe here a novel lethal ciliopathy in Norwich Terrier puppies that was diagnosed at necropsy and characterized as diffuse cystic renal disease and hepatic fibrosis. The histopathological findings were typical for cystic renal dysplasia in...
Article
Compromised eggshell quality causes considerable economic losses for the egg industry. Breeding for improved eggshell quality has been very challenging. Eggshell quality is a trait that would greatly benefit from marker‐assisted selection, which would allow the selection of sires for their direct contribution to the trait and would also allow imple...
Article
Background and objective: We introduce the R-package GenomicTools to perform, among others, a Multifactor Dimensionality Reduction (MDR) for the identification of SNP-SNP interactions. The package further provides a new class of tests for an (exploratory) Quantitative Trait Loci analysis that overcomes some of the limitations of other popular (e)QT...
Article
Full-text available
The ruminal microbiome, comprising large numbers of bacteria, ciliate protozoa, archaea and fungi, responds to diet and dietary additives in a complex way. The aim of this study was to investigate the benefits of increasing the depth of the community analysis in describing and explaining responses to dietary changes. Quantitative PCR, ssu rRNA ampl...
Data
Supporting information, containing supporting methods, supporting data, and supporting references. (DOCX)
Data
Bacterial, archaeal, protozoal and fungal evenness as measured from amplicon sequence data, in four diets. Diets are as follows: high (H) or low (L) proportion of concentrates without oil, or supplemented with SO (HSO and LSO, respectively). (TIF)
Data
Rumen bacterial, archaeal, ciliate protozoa and fungal taxa average abundances per diet and Tukey test for pairwise comparisons (P values). (XLSX)
Data
Graphical network representing the interactions between rumen microorganisms within L-H diet comparison. Nodes correspond to microbial taxa while green and red edges represent positive and negative partial correlations above 0.05, respectively. Microbial taxa are colored by taxonomy: archaea—gray, ciliate protozoa—blue, fungi—dark yellow, bacteria—...
Data
Sequences of primers used for qPCR and metabarcoding amplicon sequencing. (DOCX)
Data
Bacterial, archaeal, protozoal and fungal richness as measured from amplicon sequence data, in four diets. Diets are as follows: high (H) or low (L) proportion of concentrates without oil, or supplemented with SO (HSO and LSO, respectively). (TIF)
Data
Graphical network representing the interactions between rumen microorganisms within L-LSO diet comparison. Nodes correspond to microbial taxa while green and red edges represent positive and negative partial correlations above 0.05, respectively. Microbial taxa are colored by taxonomy: archaea—gray, ciliate protozoa—blue, fungi—dark yellow, bacteri...
Data
Graphical network representing the interactions between rumen microorganisms within H-HSO diet comparison. Nodes correspond to microbial taxa while green and red edges represent positive and negative partial correlations above 0.05, respectively. Microbial taxa are colored by taxonomy: archaea—gray, ciliate protozoa—blue, bacteria—white. (PDF)
Article
Full-text available
Background The current gold standard in dimension reduction methods for high-throughput genotype data is the Principle Component Analysis (PCA). The presence of PCA is so dominant, that other methods usually cannot be found in the analyst’s toolbox and hence are only rarely applied. ResultsWe present a modern dimension reduction method called ’Inva...
Thesis
Full-text available
With the introduction of the PSA test for Prostate Cancer (PrCa) using Prostate Specific Antigen (PSA) values, the number of diagnosed PrCa cases has been growing tremendously. However, the growing number of PrCa cases is not only due to an increased PrCa risk, but also due to an overly sensitive but not cancer specific PSA test. Consequently, the...
Preprint
Full-text available
The R-package REPPlab is designed to explore multivariate data sets using one-dimensional unsupervised projection pursuit. It is useful in practice as a preprocessing step to find clusters or as an outlier detection tool for multivariate numerical data. Except from the package tourr that implements smooth sequences of projection matrices and rggobi...
Article
Full-text available
Ribonucleoprotein (RNP) granules play a major role in compartmentalizing cytoplasmic RNA regulation. Haploid round spermatids that have exceptionally diverse transcriptomes are characterized by a unique germ cell-specific RNP granule, the chromatoid body (CB). The CB shares many characteristics with somatic RNP granules but also has germline-specif...
Article
Full-text available
Currently available diagnostic modalities for the detection of graft vasculopathy following orthotopic heart transplantation are subject to various restrictions. We hypothesized that cardiogoniometry, a novel non-invasive diagnostic tool for the detection of atherosclerotic coronary vessel disease, is applicable in the graft vasculopathy setting. C...
Preprint
Full-text available
The Oja median is one of several extensions of the univariate median to the multivariate case. It has many nice properties, but is computationally demanding. In this paper, we first review the properties of the Oja median and compare it to other multivariate medians. Afterwards we discuss four algorithms to compute the Oja median, which are impleme...
Article
A total of nine non-coding variants on 11q13.5 predispose men to prostate cancer (PrCa). rs200331695 within the EMSY intron is associated with aggressive PrCa and two high linkage disequilibrium (LD) groups of single-nucleotide polymorphisms (SNPs) in the intergenic region are associated with PrCa death. Here, we investigated the cis-effect of the...
Article
Full-text available
Microbial community analysis was carried out on ruminal digesta obtained directly via rumen fistula and buccal fluid, regurgitated digesta (bolus) and faeces of dairy cattle to assess if non-invasive samples could be used as proxies for ruminal digesta. Samples were collected from five cows receiving grass silage based diets containing no additiona...
Data
Supporting information, containing five Tables and two Figures. Table A. Sequences of primers used for qPCR and amplicon sequencing. Table B. Within-diet significances of sample type in qPCR analyses shown in Fig 1. Table C. Between-diet significances of qPCR analyses shown in Fig 1. Table D. Number of filtered high quality sequences and the averag...
Article
Full-text available
Livestock conservation practice is changing rapidly in light of policy developments, climate change and diversifying market demands. The last decade has seen a step change in technology and analytical approaches available to define, manage and conserve Farm Animal Genomic Resources (FAnGR). However, these rapid changes pose challenges for FAnGR con...
Chapter
In this paper we review Hannu Oja’s publications and form coauthor networks based on them. Applying community detection methods to the network formed by all of Hannu’s publications shows that his coauthors can be classified into 13 clusters, where two large clusters refer to his methodological research. The network concerning this methodological wo...
Article
Full-text available
We present the R package gMWT which is designed for the comparison of several treatments (or groups) for a large number of variables. The comparisons are made using certain probabilistic indices (PI). The PIs computed here tell how often pairs or triples of observations coming from different groups appear in a specific order of magnitude. Classical...
Article
Full-text available
Background: Heritable factors are evidently involved in prostate cancer (PrCa) carcinogenesis, but currently, genetic markers are not routinely used in screening or diagnostics of the disease. More precise information is needed for making treatment decisions to distinguish aggressive cases from indolent disease, for which heritable factors could b...
Article
The 2q37 and 17q12-q22 loci are linked to an increased prostate cancer (PrCa) risk. No candidate gene has been localized at 2q37 and the HOXB13 variant G84E only partially explains the linkage to 17q21-q22 observed in Finland. We screened these regions by targeted DNA sequencing to search for cancer-associated variants. Altogether, four novel susce...
Article
Full-text available
Recent developments in high-throughput sequencing techniques have enabled large scale analysis of genetic variations and gene expression in different tissues and species, but gene expression patterns and genetic variations in livestock are not well characterized. In this study we have used high-throughput transcriptomic sequencing of the Finnish La...
Article
New statistical procedures are introduced to analyse typical microRNA expression data sets. For each separate microRNA expression, the null hypothesis to be tested is that there is no difference between the distributions of the expression in different groups. The test statistics are then constructed having certain type of alternatives in mind. To a...
Article
The immotile short tail sperm (ISTS) defect was recognized in the Finnish Yorkshire population at the end of the 1990s when several affected boars were identified. The causal mutation for this defect is a recent L1 insertion within the SPEF2 gene. In 2001, the insertion frequency was already 0.23. Even though all homozygous boars are eliminated fro...
Article
Full-text available
Prostate cancer (PCa) is a heterogeneous trait for which several susceptibility loci have been implicated by genome-wide linkage and association studies. The genomic region 13q14 is frequently deleted in tumour tissues of both sporadic and familial PCa patients and is consequently recognised as a possible locus of tumour suppressor gene(s). Deletio...

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Cited By

Projects

Projects (3)
Project
This project is aiming at connecting the animal genome, gastrointestinal microbiome and nutrition to improve digestion efficiency and the environmental impacts of ruminant livestock production.
Project
Connecting the animal genome, gastrointestinal microbiomes and nutrition to improve digestion efficiency and the environmental impacts of ruminant livestock production