List of publications

List of publications

Publications in peer-reviewed journals

  1. Iso-Touru, T., Panitz, F., Fischer, D. et al. (2024): Genes and pathways revealed by whole transcriptome analysis of milk derived bovine mammary epithelial cells after Escherichia coli challenge. Vet Res 55, 13.
  2. Calboli, F.C.F., Iso-Touru, T., Bitz, O., Fischer, D., Nousiainen, A., et al. (2023): Genomic selection for survival under naturally occuring Saprolegnia oomycete infection in farmed European whitefish Coregonus lavaretus. Journal of Animal Science 101: 1-16.
  3. Tapio, M., Fischer, D., Mäntysaari, P., Tapio, I. (2023): Rumen Microbiota Predicts Feed Efficiency of Primiparous Nordic Red Dairy Cows. Microorganisms 11 (5), 1116.
  4. Shanthi, K.B., Fischer, D., Sharma, A., Kiviniemi, A., Kaakinen, M., Vainio, S.J., et al. (2023): Human Adult Astrocyte Extracellular Vesicle Transcriptomics Study Identifies Specific RNAs Which Are Preferentially Secreted as EV Luminal Cargo. Genes 14 (4), 853.
  5. Fischer, D., Nordhausen, K., Yi, M. (2023): An Analysis of David E. Tyler’s Publication and Coauthor Network. Robust and Multivariate Statistical Methods: Festschrift in Honor of David E. Tyler. Pages 3-21, Springer International Publishing.
  6. Bart, G., Fischer, D., Samoylenko, A., Zhyvolozhnyi, A., Stehantsev, P. et al (2021): Characterization of nucleic acids from extracellular vesicle-enriched human sweat. BMC genomics 22, 1-29.
  7. Fischer, D., Nordhausen, K., Oja, H. (2020): On linear dimension reduction based on diagonalization of scatter matrices for bioinformatics downstream analyses. Heliyon, 6(12), e05732.
  8. Fischer, D., Mosler, K., Nordhausen, K., Möttönen, J., Pokotylo, O., and Vogel, D. (2020): Computing the Oja Median in R: The Package OjaNP. Journal of Statistical Software, 92(8), pp. 1-36.
  9. Fischer, D., Berro, A., Nordhausen, K., Ruiz-Gazen, A. (2019): REPPLab: Detecting Groups and Outliers Using Exploratory Projection Pursuit. Communications in Statistics – Simulation and Computation.
  10. Dillard, K., Hytönen, M.K., Fischer, D., Tanhuanpää, K., Lehti, M., Sironen, A., Anttila, M. (2018): A splice site variant in INPP5E causes diffuse cystic renal dysplasia and hepatic fibrosis in dogs. PLoS ONE 13(9): e0204073.
  11. Iso-Touru, T., Pesonen, M., Fischer, D., Huuskonen, A., Sironen, A. (2018): The effect of CAPN1 and CAST gene variations on meat quality traits in Finnish Aberdeen Angus and Nordic Red Cattle populations. Agricultural and Food Science, 27(4), 227–231.
  12. Tuiskula-Haavisto, M., Honkatukia, M., Dunn, I.C., Bain, M.M., De Koning, D.J., Preisinger, R., Schmutz, M., Arango, J., Fischer, D., Vilkki, J. (2018): Validated QTL for egg shell quality in experimental and commercial laying hens. Animal Genetics.
  13. Fischer, D. (2017): The R-package GenomicTools for multifactor dimensionality reduction and the analysis of (exploratory) Quantitative Trait Loci. Computer Methods and Programs in Biomedicine, 151, 171–177.
  14. Tapio,I., Fischer,D., Blasco,L., Tapio,M., Wallace,R.J., Bayat,A.R., Ventto,L., Kahala,M., Negussie,E., Shingfield,K.J., Vilkki,J. (2017): Taxon abundance, diversity, co-occurrence and network analysis of the ruminal microbiota in response to dietary changes in dairy cows. PLoS ONE 12(7): e0180260.
  15. Fischer, D., Honkatukia,M., Tuiskula-Haavisto,M., Nordhausen,K., Cavero,D., Preisinger,R., Vilkki,J. (2017): Subgroup Detection in Genotype Data using Invariant Coordinate Selection. BMC Bioinformatics, 18(173), 1–9.
  16. Da Ros, M., Lehtiniemi, T., Olotu, O., Fischer, D., Zhang, F.-P., Vihinen, H., Jokitalo, E., Sironen, A., Toppari, J., Kotaja, N. (2017): FYCO1 and autophagy control the integrity of the haploid male germ cell-specific RNP granules. Autophagy, 13(2), 302–321.
  17. Spiliopoulos, S., Hergesell, V., Fischer, D., Koerfer, R., Tenderich, G. (2016):Applicability of Cardiogoniometry as a non- invasive Screening Tool for the Detection of Graft Vasculopathy in Heart Transplant Recipients. Interactive CardioVascular and Thoracic Surgery.
  18. Nurminen, R., Rantapero, T., Chong, W.S., Fischer, D., Lehtonen, R., Tammela, T.L.J., Nykter, M., Visakorpi, T., Wahlfors, T., Schleutker, J. (2016): Expressional profiling of prostate cancer risk SNPs at 11q13.5 identifies DGAT2 as a new target gene. Genes, Chromosomes and Cancer, 55(8), 661-673.
  19. Tapio,I., Shingfield,K.J., McKain,N., Bonin,A., Bayat,A., Fischer,D., Vilkki,J., Taberlet,P., Snelling,T.J., Wallace, R.J. (2016): Oral Samples as Non-Invasive Proxies for Assessing the Composition of the Rumen Microbial Community. PLoS ONE 11(3): e0151220.
  20. Fischer, D., Nordhausen, K. and Taskinen, S. (2015): Publication and Coauthorship Networks of Hannu Oja. Modern Nonparametric, Robust and Multivariate Methods – Festschrift in Honour of Hannu Oja. pp.7-31. Springer, Heidelberg
  21. Bruford, M.W., Ginja, C., Hoffmann, I., Joost, S., Orozco-terWengel, P. et al. (2015): Prospects and Challenges for the Conservation of Farm Animal Genomic Resources, 2015-2025. Frontiers in Genetics 6(314).
  22. Fischer, D., Laiho, A., Gyenesei, A., Sironen, A. (2015): Identification of reproduction related gene mutations using RNAseq in the Large White pig population. G3: Genes, Genomes, Genetics. July 1, 2015 vol. 5 no. 7 1351-1360.
  23. Fischer, D., Oja, H. (2015): Mann-Whitney Type Tests for Microarray Experiments: The R Package gMWT. Journal of Statistical Software, 65(9).
  24. Fischer, D., Wahlfors, T., Mattila, H., Oja, H., Tammela, T.L.J, Schleutker, J. (2015): MiRNA Profiles in Lymphoblastoid Cell Lines of Finnish Prostate Cancer Families. PLoS ONE 10(5): e0127427.
  25. Laitinen, V.H., Rantapero, T., Fischer, D., Vuorinen, E.M. , Tammela, T.L.J., Wahlfors, T., PRACTICAL Consortium, Schleutker, J. (2014): Fine-mapping the 2q37 and 17q11.2-q22 Loci for Novel Genes and Sequence Variants Associated with a Genetic Predisposition to Prostate Cancer. International Journal of Cancer, 136(10), 2316-2327.
  26. Sironen, A., Fischer, D., Laiho, A., Gyenesei, A., Vilkki, J. (2014): A recent L1 insertion within SPEF2 gene is associated with changes in PRLR expression in sow reproductive organs. Animal Genetics, 45(4), 500-507.
  27. Fischer, D., Oja, H., Schleutker, J., Sen, P.K. and Wahlfors, T. (2014): Generalized Mann-Whitney Type Tests for Microarray Experiments. Scandinavian Journal of Statistics, 41(3), 672-692.
  28. Siltanen, S., Fischer, D., Rantapero, T., Laitinen, V., Mpindi, J.P., Kallioniemi, O., Wahlfors, T., Schleutker, J. (2013): ARLTS1 and Prostate Cancer Risk – Analysis of Expression and Regulation. PLoS ONE 8(8): e72040.

Manuscripts accepted for publication

Submitted Manuscripts

  1. Fischer, D., Tapio, M., Bitz, O., Iso-Touru, T., Kause, A., Tapio, I. (XXX): Fine-Tuning GBS Data with Comparison of Reference and Mock Genome Approaches for Advancing Genomic Selection in Less Studied Farmed Species.

Manuscripts in peer-reviewed conference proceedings

  1. Iso-Touru, T., Fischer, D., Kyläniemi, M., Tabell, J., Virta, A., Vilkki, J. (2022): Genomewide transcriptome profiling of milk derived primary bovine mammary epithelial cells after pathogen challenge. Proceedings of 12th World Congress on Genetics Applied to Livestock Production (WCGALP), 2830-2833.
  2. Gredler-Grandl, B., Raymond, B., Schopen, G.C.B., Chitneedi, P.K., Cai, Z., Manzanilla-Pech, C.I.V., et al. (2022): Accuracy of genomic prediction of dry matter intake in Dutch Holsteins using sequence variants from meta-analyses. Proceedings of 12th World Congress on Genetics Applied to Livestock Production (WCGALP). 1181-1184.

Other publications

  1. Fischer, D. (2024)  An Introduction to R and Python for Data Analysis: A Side-by-Side Approach Taylor R. Brown Chapman and Hall/CRC, 2023, 246 pages (hardback $99.95, ebook $74.96) ISBN 978-10322032-56. International Statistical Review,  92:  132–134.
  2. Fischer, D.: Performing QTL and eQTL Analyses with the R-Package GenomicTools. eQTL Analysis: Methods and Protocols, p. 15-38. Springer US.
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