Luke Research / Asiantuntija

A1 Alkuperäisartikkeli tieteellisessä aikakauslehdessä

Fischer, Daniel; Tapio, Miika; Bitz, Oliver; Iso-Touru, Terhi; Kause, Antti; Tapio, Ilma. 2025. Fine-tuning GBS data with comparison of reference and mock genome approaches for advancing genomic selection in less studied farmed species. Bmc genomics 26 1: 17 p.

Pokharel, Kisun; Fischer, Daniel; Iso-Touru, Terhi; Tapio, Ilma; Tapio, Miika; Leinonen, Tuomas; Kause, Antti. 2025. The genome assembly of the farmed European whitefish Coregonus lavaretus L. from the Finnish selective breeding programme. BMC genomic data 26 1: 3 p.

Vargas Jurado, Napoleon; Kärkkäinen, Hanni; Fischer, Daniel; Bitz, Oliver; Manninen, O.; Pärssinen, P.; Isolahti, Mika; Strandén, Ismo; Mäntysaari, Esa A. 2025. Genetic architecture and genomic prediction for yield, winter damage, and digestibility traits in timothy (Phleum pratense L.) using genotyping-by-sequencing data. Theoretical and applied genetics 138 4: 17 s.

Chitneedi, Praveen Krishna; Hadlich, Frieder; Moreira, Gabriel C M; Espinosa-Carrasco, Jose; Li, Changxi; Plastow, Graham; Fischer, Daniel; Charlier, Carole; Rocha, Dominique; Chamberlain, Amanda J; Kuehn, Christa. 2024. eQTL-Detect: nextflow-based pipeline for eQTL detection in modular format with sharable and parallelizable scripts. NAR genomics and bioinformatics 6 3:

Iso-Touru, Terhi; Panitz, Frank; Fischer, Daniel; Kyläniemi, Minna K.; Taponen, Suvi; Tabell, Jonna; Virta, Anneli; Vilkki, Johanna. 2024. Genes and pathways revealed by whole transcriptome analysis of milk derived bovine mammary epithelial cells after Escherichia coli challenge. Veterinary research 55 1: 10 p.

Rehman, Attiq ur; Iso‐Touru, Terhi; Junkers, Jakob; Rantanen, Marja; Karhu, Saila; Fischer, Daniel; Alsheikh, Muath; Hjeltnes, Stein Harald; Mezzetti, Bruno; Davik, Jahn; Schulman, Alan H.; Hytönen, Timo; Haikonen, Tuuli. 2024. Multi‐model GWAS reveals key loci for horticultural traits in reconstructed garden strawberry. Physiologia plantarum 176 4:

Calboli, Federico C F; Iso-Touru, Terhi; Bitz, Oliver; Fischer, Daniel; Nousiainen, Antti; Koskinen, Heikki; Tapio, Miika; Tapio, Ilma; Kause, Antti. 2023. Genomic selection for survival under naturally occurring Saprolegnia oomycete infection in farmed European whitefish Coregonus lavaretus. Journal of Animal Science 101: 1-16.

Shanthi, Keerthanaa Balasubramanian; Fischer, Daniel; Sharma, Abhishek; Kiviniemi, Antti; Kaakinen, Mika; Vainio, Seppo J.; Bart, Geneviève. 2023. Human Adult Astrocyte Extracellular Vesicle Transcriptomics Study Identifies Specific RNAs Which Are Preferentially Secreted as EV Luminal Cargo. Genes 14 4: 49 p.

Tapio, Miika; Fischer, Daniel; Mäntysaari, Päivi; Tapio, Ilma. 2023. Rumen Microbiota Predicts Feed Efficiency of Primiparous Nordic Red Dairy Cows. Microorganisms 11 5: 21 p.

Bart, Geneviève; Fischer, Daniel; Samoylenko, Anatoliy; Zhyvolozhnyi, Artem; Stehantsev, Pavlo; Miinalainen, Ilkka; Kaakinen, Mika; Nurmi, Tuomas; Singh, Prateek; Kosamo, Susanna; Rannaste, Lauri; Viitala, Sirja; Hiltunen, Jussi; Vainio, Seppo J. 2021. Characterization of nucleic acids from extracellular vesicle-enriched human sweat. BMC genomics 22 1:

Fischer, Daniel; Mosler, Karl; Möttönen, Jyrki; Nordhausen, Klaus; Pokotylo, Oleksii; Vogel, Daniel. 2020. Computing the Oja Median in R: The Package OjaNP. Journal of Statistical Software 92 8: 36 p.

Fischer, Daniel; Nordhausen, Klaus; Oja, Hannu. 2020. On linear dimension reduction based on diagonalization of scatter matrices for bioinformatics downstream analyses. Heliyon 6 12: 8 p.

Fischer, Daniel; Berro, Alain; Nordhausen, Klaus; Ruiz-Gazen, Anne. 2019. REPPlab: An R package for detecting clusters and outliers using exploratory projection pursuit. Communications in Statistics - Simulation and Computation: 23 p.

Dillard, Kati J.; Hytönen, Marjo K.; Fischer, Daniel; Tanhuanpää, Kimmo; Lehti, Mari S.; Vainio-Siukola, Katri; Sironen, Anu; Anttila, Marjukka. 2018. A splice site variant in INPP5E causes diffuse cystic renal dysplasia and hepatic fibrosis in dogs. PLoS ONE 13 9: e0204073.

Iso-Touru, Terhi; Pesonen, Maiju; Fischer, Daniel; Huuskonen, Arto; Sironen, Anu. 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.

Tuiskula-Haavisto, Maria; Honkatukia, Mervi; Cunn, I. C.; Bain, M. M.; Koning, D. J. De; Preisinger, R.; Schmutz, M.; Arango, J.; Fischer, Daniel; Vilkki, Johanna. 2018. Validated quantitative trait loci for eggshell quality in experimental and commercial laying hens. Animal Genetics:

Da Ros, Matteo; Lehtiniemi, Tiina; Olotu, Opeyemi; Fischer, Daniel; Zhang, Fu-Ping; Vihinen, Helena; Jokitalo, Eija; Sironen, Anu; Toppari, Jorma; Kotaja, Noora. 2017. FYCO1 and autophagy control the integrity of the haploid male germ cell-specific RNP granules. Autophagy 13 2: 302-321.

Fischer, Daniel. 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.

Fischer, Daniel; Honkatukia, Mervi; Tuiskula-Haavisto, Maria; Nordhausen, Klaus; Cavero, David; Preisinger, Rudolf; Vilkki, Johanna. 2017. Subgroup detection in genotype data using invariant coordinate selection. BMC Bioinformatics 18:

Tapio, Ilma; Fischer, Daniel; Blasco, Lucia; Tapio, Miika; Wallace, R. John; Bayat, Ali R.; Ventto, Laura; Kahala, Minna; Negussie, Enyew; Shingfield, Kevin J.; Vilkki, Johanna. 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.

Nurminen, R.; Rantapero, T.; Wong, Sw. C.; Fischer, Daniel; 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.

Spiliopoulos, S.; Hergesell, V.; Fischer, Daniel; Dapunt, O.; Krueger, U.; 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 23 6: 976-978.

Tapio, Ilma; Shingfield, Kevin J.; McKain, Nest; Bonin, Aurelie; Fischer, Daniel; Bayat, Ali R.; Vilkki, Johanna; Taberlet, Pierre; Snelling, Timothy J.; Wallace, R. John. 2016. Oral samples as non-invasive proxies for assessing the composition of the rumen microbial community. PLoS ONE 11 3:

Bruford, Michael W.; Ginja, Catarina; Hoffmann, Irene; Joost, Stephane; Orozco-terWengel, Pablo; Alberto, Florian J.; Amaral, Andreia J.; Barbato, Mario; Biscarini, Filippo; Colli, Licia; Costa, Mafalda; Curik, Ino; Duruz, Solange; Ferencakovic, Maja; Fischer, Daniel; Fitak, Robert; Groeneveld, Linn F.; Hall, Stephen J. G.; Hanotte, Olivier; Hassan, Faiz-ul; Helsen, Philippe; Iacolina, Laura; Kantanen, Juha; Leempoel, Kevin; Lenstra, Johannes A.; Ajmone-Marsan, Paolo; Masembe, Charles; Megens, Hendrik-Jan; Miele, Mara; Neuditschko, Markus; Nicolazzi, Ezequiel L.; Pompanon, Francois; Roosen, Jutta; Sevane, Natalia; Smetko, Anamarija; Stambuk, Anamaria; Streeter, Ian; Stucki, Sylvie; Supakorn, China; Telo Da Gama, Luis; Tixier-Boichard, Michele; Wegmann, Daniel; Zhan, Xiangjiang. 2015. Prospects and challenges for the conservation of farm animal genomic resources, 2015-2025. Frontiers in Genetics 6: 11 p.

Fischer, Daniel; Laiho, Asta; Gyenesei, Attila; Sironen, Anu. 2015. Identification of reproduction-related gene polymorphisms using whole transcriptome sequencing in the Large White pig population. G3: Genes, Genomes, Genetics 5: 1351-1360.

Fischer, Daniel; Oja, Hannu. 2015. Mann-Whitney type tests for microarray experiments: the R package gMWT. Journal of Statistical Software 65 9: 19 p.

Fischer, Daniel; Wahlfors, Tiina; Mattila, Henna; Oja, Hannu; Tammela, Teuvo L. J.; Schleutker, Johanna. 2015. MiRNA profiles in lymphoblastoid cell lines of Finnish prostate cancer families. PLoS ONE 10 5:

Fischer, Daniel; Oja, Hannu; Schleutker, Johanna; Sen, Pranab K.; Wahlfors, Tiina. 2014. Generalized Mann-Whitney type tests for microarray experiments. Scandinavian Journal of Statistics 41 3: 672-692.

Laitinen, Virpi H.; Rantapero, Tommi; Fischer, Daniel; Vuorinen, Elisa M.; Tammela, Teuvo L. J.; Wahlfors, Tiina; Schleutker, Johanna. 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.

Sironen, Anu; Fischer, Daniel; Laiho, A.; Gyenesei, A.; Vilkki, Johanna. 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.

Siltanen, Sanna; Fischer, Daniel; Rantapero, Tommi; Laitinen, Virpi; Mpindi, John Patrik; Kallioniemi, Olli; Wahlfors, Tiina; Schleutker, Johanna. 2013. ARLTS1 and prostate cancer risk : analysis of expression and regulation. PLoS ONE 8 8: 10 p.

A3 Kirjan tai muun kokoomateoksen osa

Fischer, Daniel; Nordhausen, Klaus; Yi, Mengxi. 2022. An Analysis of David E. Tyler’s Publication and Coauthor Network. In: Robust and Multivariate Statistical Methods : Festschrift in Honor of David E. Tyler. Springer Cham. 3-21.

Fischer, Daniel; Nordhausen, Klaus; Taskinen, Sara. 2015. Publication and coauthorship networks of Hannu Oja. In: Modern nonparametric, robust and multivariate methods : Festschrift in honour of Hannu Oja / Eds. Klaus Nordhausen and Sara Taskinen. Springer International Publishing. p. 7-27.

A4 Artikkeli konferenssijulkaisussa

Gredler-Grandl, B.; Raymond, B.; Schopen, G.C.B.; Chitneedi, P.K.; Cai, Z.; Manzanilla-Pech, C.I.V.; Iso-Touru, T.; Fischer, D.; Bolormaa, S.; Chud, T.S.; Schenkel, F.S.; Wang, Y.; Li, C.; Hailemariam, D.; Villanueva, B.; Fernandez, A.; Kuehn, C.; Sahana, G.; Lidauer, M.H.; Pryce, J.E.; González-Recio, O.; Plastow, G.; Baes, C.F.; Charfeddine, N.; de Haas, Y.; Veerkamp, R.F.; Bouwman, A.C. 2022. Accuracy of genomic prediction of dry matter intake in Dutch Holsteins using sequence variants from meta-analyses. In: Proceedings of 12th World Congress on Genetics Applied to Livestock Production (WCGALP). Wageningen academic publishers. 1181-1184.

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. In: Proceedings of 12th World Congress on Genetics Applied to Livestock Production (WCGALP). Wageningen academic publishers. 2830-2833.

B1 Kirjoitus tieteellisessä aikakauslehdessä (Unrefereed journal articles)

Fischer, Daniel. 2024. Book review: An Introduction to R and Python for Data Analysis: A Side‐by‐Side ApproachTaylorR. Brown Chapman and Hall/CRC, 2023, 246 pages (hardback $99.95, ebook $74.96) ISBN 978‐10322032‐56. International Statistical Review 92 1: 132-134.

Fischer, Daniel. 2022. Population Genomics with R , , Chapman & Hall/CRC, 2020, 394 pages, $120, hardback ISBN: 978-1-1386-0818-4. International Statistical Review:

Fischer, Daniel. 2019. Data Science with Julia, Paul D. McNicholas and Peter A. Tait, CRC Press, 2019, 220 pages, £37.59, paperback, ISBN: 978‐1‐138‐49998‐0. International Statistical Review 87 2: 445-446.

Fischer, Daniel. 2018. Correspondence Analysis–Theory, Practice and New Strategies : Eric J. Beh and Rosaria Lombardo, Wiley Series in Probability and Statistics, 2014, 592 pages, 82.20EUR, hardcover, ISBN: 978‐1‐119‐95324‐1. In: Book Reviews, International Statistical Review (2018), 86, 3, 598–605 / editor Ananda Sen. International Statistical Review 86 3: 603-604.

Fischer, Daniel. 2010. Applied Statistical Genetics with R: For Population-based Association Studies : Andrea S. Foulkes, Springer, 2009, xxiv + 252 pages, £ 35.99 / € 44.95 / US$ 59.95, softcover, ISBN: 978-0-387-89553-6. In: Short Book Reviews, International Statistical Review (2010), 78, 1, 134–159 / editor Simo Puntanen. International Statistical Review 78 1: 151-152.

B2 Kirjan tai muun kokoomateoksen osa (Book section)

Fischer, Daniel. 2020. Performing QTL and eQTL Analyses with the R-Package GenomicTools. In: eQTL Analysis: Methods and Protocols. Methods in Molecular Biology: 15-38.

D5 Oppikirja, ammatillinen käsi- tai opaskirja taikka sanakirja

Fischer, Daniel. 2018. GenomicTools.fileHandler: File Handlers for Genomic Data Analysis.

Fischer, Daniel; Mosler, Karl; Möttönen, Jyrki; Nordhausen, Klaus; Pokotylo, Oleksii; Vogel, Daniel. 2018. OjaNP: Multivariate Methods Based on the Oja Median and Related Concepts.26 p.

Fischer, Daniel. 2017. GenomicTools: Collection of Tools for Genomic Data Analysis.

Fischer, Daniel; Berro, Alain; Nordhausen, Klaus; Ruiz-Gazen, Anne. 2016. REPPlab: R Interface to 'EPP-Lab', a Java Program for Exploratory Projection Pursuit.

Fischer, Daniel; Oja, Hannu. 2016. gMWT: Generalized Mann-Whitney Type Tests.

Fischer, Daniel; Sironen, Anu. 2016. hoardeR: Collect and Retrieve Annotation Data for Various Genomic Data Using Different Webservices.

G5 Artikkeliväitöskirja

Fischer, Daniel. 2017. On statistical methods in prostate cancer genomics. Acta Electronica Universitatis Tamperensis 1750: 178 p. Diss. : Tampereen yliopisto, 2017.

M2 Konferenssiabstraktit

Iso-Touru, Terhi; Fischer, Daniel; Kyläniemi, Minna; Vilkki, Johanna. 2018. Enhancing mastitis resistance in dairy cattle.1 p.

Iso-Touru, Terhi; Fischer, Daniel; Strandén, Ismo; Vilkki, Johanna; Tapio, Miika. 2017. Genomic comparison of Western Finncattle and Nordic Red Cattle in Finland. In: Book of Abstracts of the 68th Annual Meeting of the European Federation of Animal Science, Tallinn, Estonia, 28 August - 1 September 2017 / ed. EAAP scientific committee. EAAP Book of Abstracts 2017 23: p. 316.

Iso-Touru, Terhi; Sevón-Aimonen, Marja-Liisa; Fischer, Daniel; Serenius, Timo; Uimari, Pekka; Sironen, Anu. 2017. Copy number variations in two Finnish pig breeds. In: Book of Abstracts of the 68th Annual Meeting of the European Federation of Animal Science, Tallinn, Estonia, 28 August - 1 September 2017 / ed. EAAP scientific committee. EAAP Book of Abstracts 23: p. 108.

Viitala, Sirja; Fischer, Daniel; Ventto, Laura; Leskinen, Heidi; Bayat, Alireza R.; Shingfield, Kevin J.; Vilkki, Johanna. 2015. Diet induced milk fat depression alters the mammary transcriptome in lactating dairy cows. In: 6 th ISAFG, International Symposium on Animal Functional Genomics, Piacenza : ISAFG 2015 proceedings. Universita Cattolica del Sacro Cuore. p. 72.

Viitala, Sirja; Fischer, Daniel; Ventto, Laura; Bayat, Ali; Leskinen, Heidi; Shingfield, Kevin; Vilkki, Johanna. 2014. Changes in the mammary gland transcriptome due to diet-induced milk fat depression in dairy cows. In: Book of abstracts of the 65th annual meeting of the european federation of animal science. EAAP Book of Abstracts 20: 456.

Fischer Daniel