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home:publications [09.12.2019 13:01]
Juha Kekäläinen 		home:publications [01.04.2020 11:58]
Juha Kekäläinen
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 Please find below annual lists of the publications that took advantage of the services provided by Bioinformatics Center. Please find below annual lists of the publications that took advantage of the services provided by Bioinformatics Center.
  
 +## 2020
  
-### 2019+Klåvus, A.; Kokla, M.; Noerman, S.; Koistinen, V.M.; Tuomainen, M.; Zarei, I.; Meuronen, T.; Häkkinen, M.R.; Rummukainen, S.; Farizah Babu, A.; Sallinen, T.; Kärkkäinen, O.; Paananen, J.; Broadhurst, D.; Brunius, C.; Hanhineva, K. **“notame”: Workflow for Non-Targeted LC–MS Metabolic Profiling.** Metabolites 2020, 10, 135, https://doi.org/10.3390/metabo10040135
  
-Karttunen, J.; Heiskanen, M.; Lipponen, A.; Poulsen, D.; Pitkänen, A. **Extracellular Vesicles as Diagnostics and Therapeutics for Structural Epilepsies**, Int. J. Mol. Sci. 2019, 20(6), 1259; https://doi.org/10.3390/ijms20061259+## 2019
  
-Paananen, J; Fortino, V. **An omics perspective on drug target discovery platforms.**, Brief Bioinform. 2019 Nov 27. pii: bbz122. https://doi.org/10.1093/bib/bbz122.+Das Gupta, S., Lipponen, A., Paldanius, K.M.A. et al. **Dynamics of clusterin protein expression in the brain and plasma following experimental traumatic brain injury.** Sci Rep 9, 20208 (2019), https://doi.org/10.1038/s41598-019-56683-6
  
-Failli M, Paananen J, Fortino V. **Prioritizing target-disease associations with novel safety and efficacy scoring methods**, //Sci Rep// 2019, https://doi.org/10.1038/s41598-019-46293-7+Ngo Trong T, Mehtonen J, González G, Kramer R, Hautamäki V, Heinäniemi M. **Semisupervised Generative Autoencoder for Single-Cell Data.**, //J Comput Biol.// 2019 Dec, https://doi.org/10.1089/cmb.2019.0337
  
-Timonen O, Särkkä M, Fülöp T, Mattsson A, Kekäläinen J, Paananen J. **Varanto: variant enrichment analysis and annotation**, Bioinformatics 2019, https://doi.org/10.1093/bioinformatics/btz046+Paananen, J; Fortino, V. **An omics perspective on drug target discovery platforms.**, //Brief Bioinform.// 2019 Nov, https://doi.org/10.1093/bib/bbz122
  
-Lipponen A, Natunen T, Hujo M, Ciszek R, Hämäläinen E, Tohka J, Hiltunen M, Paananen J, Poulsen D, Kansanen E, Ndode-Ekane XE, Levonen AL, Pitkänen A. **In Vitro and In Vivo Pipeline for Validation of Disease-Modifying Effects of Systems Biology-Derived Network Treatments for Traumatic Brain Injury—Lessons Learned**, //Int. J. Mol. Sci.// 2019, https://doi.org/10.3390/ijms20215395+Nikkilä A, Arvela H, Mehtonen J, Raitanen J, Heinäniemi M, Lohi O, Auvinen A. **Predicting residential radon concentrations in Finland: Model development, validation, and application to childhood leukemia.**, //Scand J Work Environ Health.// 2019 Nov, https://doi.org/10.5271/sjweh.3867
  
-Pölönen P, Mehtonen J, Lin J, Liuksiala T, Häyrynen S, Teppo S, Mäkinen A, Kumar A, Malani D, Pohjolainen V, Porkka K, Heckman CA, May P, Hautamäki V, Granberg K, Lohi O, Nykter M, Heinäniemi M. **Hemap: An interactive online resource for characterizing molecular phenotypes across hematologic malignancies**, //Cancer Research// 2019, https://doi.org/10.1158/0008-5472.CAN-18-2970+Sallinen H, Janhonen S, Pölönen P, Niskanen H, Liu OH, Kivelä A, Hartikainen JM, Anttila M, Heinäniemi M, Ylä-Herttuala S, Kaikkonen MU. **Comparative transcriptome analysis of matched primary and distant metastatic ovarian carcinoma.**,  //BMC Cancer.// 2019 Nov 19, https://doi.org/10.1186/s12885-019-6339-0
  
-Mehtonen J, Pölönen P, Häyrynen S, Lin J, Liuksiala T, Granberg K, Lohi O, Hautamäki V, Nykter M, Heinäniemi M. **Data-driven characterization of molecular phenotypes across heterogenous sample collections**, +Lipponen A, Natunen T, Hujo M, Ciszek R, Hämäläinen E, Tohka J, Hiltunen M, Paananen J, Poulsen D, Kansanen E, Ndode-Ekane XE, Levonen AL, Pitkänen A. **In Vitro and In Vivo Pipeline for Validation of Disease-Modifying Effects of Systems Biology-Derived Network Treatments for Traumatic Brain Injury—Lessons Learned**, //Int. J. Mol. Sci.// 2019 Oct, https://doi.org/10.3390/ijms20215395
-//Nucleic Acids Research// 2019, https://doi.org/10.1093/nar/gkz281+
  
-Ngo Trong T, Mehtonen J, González G, Kramer R, Hautamäki V, Heinäniemi M. **Semisupervised Generative Autoencoder for Single-Cell Data.**, //J Comput Biol.// 2019, https://doi.org/10.1089/cmb.2019.0337+Pölönen P, Jawahar Deen A, Leinonen HM, Jyrkkänen HK, Kuosmanen S, Mononen M, Jain A, Tuomainen T, Pasonen-Seppänen S, Hartikainen JM, Mannermaa A, Nykter M, Tavi P, Johansen T, Heinäniemi M, Levonen AL. **Nrf2 and SQSTM1/p62 jointly contribute to mesenchymal transition and invasion in glioblastoma.**, //Oncogene.// 2019 Aug, https://doi.org/10.1038/s41388-019-0956-6
  
-Nikkilä A, Arvela H, Mehtonen J, Raitanen J, Heinäniemi M, Lohi O, Auvinen A. **Predicting residential radon concentrations in Finland: Model development, validation, and application to childhood leukemia.**, //Scand J Work Environ Health.// 2019, https://doi.org/10.5271/sjweh.3867+Benhammou JN, Ko A, Alvarez M, Kaikkonen MU, Rankin C, Garske KM, Padua D, Bhagat Y, Kaminska D, Kärjä V, Pihlajamäki J, Pisegna JR, Pajukanta P. **Novel Lipid Long Intervening Noncoding RNA, Oligodendrocyte Maturation-Associated Long Intergenic Noncoding RNA, Regulates the Liver Steatosis Gene Stearoyl-Coenzyme A Desaturase As an Enhancer RNA.**, //Hepatol Commun.// 2019 Aug, https://doi.org/10.1002/hep4.1413
  
-Sallinen H, Janhonen S, Pölönen P, Niskanen H, Liu OH, Kivelä A, Hartikainen JM, Anttila M, Heinäniemi M, Ylä-Herttuala S, Kaikkonen MU. **Comparative transcriptome analysis of matched primary and distant metastatic ovarian carcinoma.**,  //BMC Cancer.// 2019, https://doi.org/10.1186/s12885-019-6339-0+Kuusanmäki H, Leppä AM, Pölönen P, Kontro M, Dufva O, Deb D, Yadav B, Brück O, Kumar A, Everaus H, Gjertsen BT, Heinäniemi M, Porkka K, Mustjoki S, Heckman CA. **Phenotype-based drug screening reveals association between venetoclax response and differentiation stage in acute myeloid leukemia.**, //Haematologica.// 2019 Jul, https://doi.org/10.3324/haematol.2018.214882
  
-Pölönen P, Jawahar Deen A, Leinonen HM, Jyrkkänen HK, Kuosmanen S, Mononen M, Jain A, Tuomainen T, Pasonen-Seppänen S, Hartikainen JM, Mannermaa A, Nykter M, Tavi P, Johansen T, Heinäniemi M, Levonen AL. **Nrf2 and SQSTM1/p62 jointly contribute to mesenchymal transition and invasion in glioblastoma.**,  +Failli M, Paananen J, Fortino V. **Prioritizing target-disease associations with novel safety and efficacy scoring methods**, //Sci Rep// 2019 Jul, https://doi.org/10.1038/s41598-019-46293-7
-//Oncogene.// 2019, https://doi.org/10.1038/s41388-019-0956-6+
  
-Kuusanmäki H, Leppä AM, Pölönen P, Kontro M, Dufva O, Deb D, Yadav B, Brück O, Kumar A, Everaus H, Gjertsen BT, Heinäniemi M, Porkka K, Mustjoki S, Heckman CA. **Phenotype-based drug screening reveals association between venetoclax response and differentiation stage in acute myeloid leukemia.**, //Haematologica.// 2019, https://doi.org/10.3324/haematol.2018.214882.+Pölönen P, Mehtonen J, Lin J, Liuksiala T, Häyrynen S, Teppo S, Mäkinen A, Kumar A, Malani D, Pohjolainen V, Porkka K, Heckman CA, May P, Hautamäki V, Granberg K, Lohi O, Nykter M, Heinäniemi M. **Hemap: An interactive online resource for characterizing molecular phenotypes across hematologic malignancies**, //Cancer Research// 2019 May, https://doi.org/10.1158/0008-5472.CAN-18-2970
  
 +Mehtonen J, Pölönen P, Häyrynen S, Lin J, Liuksiala T, Granberg K, Lohi O, Hautamäki V, Nykter M, Heinäniemi M. **Data-driven characterization of molecular phenotypes across heterogenous sample collections**, //Nucleic Acids Research// 2019 Apr, https://doi.org/10.1093/nar/gkz281
  
-### 2018+Marttinen M, Paananen J, Neme A, Mitra V, Takalo M, Natunen T, Paldanius KMA, Mäkinen P, Bremang M, Kurki MI, Rauramaa T, Leinonen V, Soininen H, Haapasalo A, Pike I, Hiltunen M **A multiomic approach to characterize the temporal sequence in Alzheimer's disease-related pathology**, //Neurobiol Dis.// 2019 Apr, https://doi.org/10.1016/j.nbd.2018.12.009 
 + 
 +Jauhiainen S, Laakkonen JP, Ketola K, Toivanen PI, Nieminen T, Ninchoji T, Levonen AL, Kaikkonen MU, Ylä-Herttuala S. **Axon Guidance-Related Factor FLRT3 Regulates VEGF-Signaling and Endothelial Cell Function.**, //Front Physiol.// 2019 Mar, https://doi.org/10.3389/fphys.2019.00224 
 + 
 +Viiri LE, Rantapero T, Kiamehr M, Alexanova A, Oittinen M, Viiri K, Niskanen H, Nykter M, Kaikkonen MU, Aalto-Setälä K. **Extensive reprogramming of the nascent transcriptome during iPSC to hepatocyte differentiation.**, //Sci Rep.//, 2019 Mar, https://doi.org/10.1038/s41598-019-39215-0 
 + 
 +Karttunen, J.; Heiskanen, M.; Lipponen, A.; Poulsen, D.; Pitkänen, A. **Extracellular Vesicles as Diagnostics and Therapeutics for Structural Epilepsies**, //Int. J. Mol. Sci.// 2019 Mar; https://doi.org/10.3390/ijms20061259 
 + 
 +Gurzeler E, Aavik E, Laine A, Valkama T, Niskanen H, Huusko J, Kaikkonen MU, Ylä-Herttuala S. **Therapeutic effects of rosuvastatin in hypercholesterolemic prediabetic mice in the absence of low density lipoprotein receptor.**, //Biochim Biophys Acta Gen Subj.//, 2019 Feb, https://doi.org/10.1016/j.bbagen.2018.11.012 
 + 
 +Timonen O, Särkkä M, Fülöp T, Mattsson A, Kekäläinen J, Paananen J. **Varanto: variant enrichment analysis and annotation**, Bioinformatics 2019 Jan, https://doi.org/10.1093/bioinformatics/btz046 
 + 
 + 
 +## 2018
  
 Chen X, Ayala I, Shannon C, Fourcaudot M, Acharya NK, Jenkinson CP, Chen X, Ayala I, Shannon C, Fourcaudot M, Acharya NK, Jenkinson CP,
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 Lewis, JD, Evans, AC, Tohka J. **T1 white/gray contrast as a predictor of chronological age, and an index of cognitive performance** //NeuroImage// 2018, https://doi.org/10.1016/j.neuroimage.2018.02.050 Lewis, JD, Evans, AC, Tohka J. **T1 white/gray contrast as a predictor of chronological age, and an index of cognitive performance** //NeuroImage// 2018, https://doi.org/10.1016/j.neuroimage.2018.02.050
- 
-Marttinen M, Paananen J, Neme A, Mitra V, Takalo M, Natunen T, 
-Paldanius KMA, Mäkinen P, Bremang M, Kurki MI, Rauramaa T, Leinonen V, 
-Soininen H, Haapasalo A, Pike I, Hiltunen M **A multiomic approach to characterize the temporal sequence in Alzheimer's disease-related pathology**, //Neurobiol Dis.// 2019, https://doi.org/10.1016/j.nbd.2018.12.009 
  
 Martiskainen H, Takalo M, Solomon A, Stančáková A, Marttinen M, Martiskainen H, Takalo M, Solomon A, Stančáková A, Marttinen M,
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 Lakkisto P, Laivuori H. **Fetal Microsatellite in the Heme Oxygenase 1 Promoter Is Associated With Severe and Early-Onset Preeclampsia** , //Hypertension// 2018, https://doi.org/10.1161/HYPERTENSIONAHA.117.10425. Lakkisto P, Laivuori H. **Fetal Microsatellite in the Heme Oxygenase 1 Promoter Is Associated With Severe and Early-Onset Preeclampsia** , //Hypertension// 2018, https://doi.org/10.1161/HYPERTENSIONAHA.117.10425.
  
-### 2017 or earlier+## 2017 or earlier
  
 Paananen, J. **Bioinformatics in the Identification of Novel Targets and Pathways in Neurodegenerative Diseases**, Curr Genet Med Rep (2017) 5:15–21, https://doi.org/10.1007/s40142-017-0115-8 Paananen, J. **Bioinformatics in the Identification of Novel Targets and Pathways in Neurodegenerative Diseases**, Curr Genet Med Rep (2017) 5:15–21, https://doi.org/10.1007/s40142-017-0115-8
home/publications.txt · Last modified: 15.01.2024 13:53 by Administrator

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