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1

Effects of thermal and enzymatic treatments and harvesting time on the microbial quality and chemical composition of fibre hemp (Cannabis sativa L.)

Minna Nykter, Hanna-Riitta Kymäläinen, Anne Belinda Thomsen, Hans Lilholt, Hilkka Koponen, Anna-Maija Sjöberg, Anders Thygesen

Journal:

Biomass and Bioenergy

Year:

2008

Language:

english

File:

PDF, 346 KB

english, 2008

2

Fusion genes and their discovery using high throughput sequencing

Annala, M.J., Parker, B.C., Zhang, W., Nykter, M.

Journal:

Year:

2013

Language:

english

File:

PDF, 837 KB

english, 2013

3

Classifieds

Lin, Jake, Kreisberg, Richard, Kallio, Aleksi, Dudley, Aimée M, Nykter, Matti, Shmulevich, Ilya, May, Patrick, Autio, Reija

Journal:

JOM Journal of the Minerals, Metals and Materials Society

Year:

2014

Language:

english

File:

PDF, 318 KB

english, 2014

4

Meet a member

Lin, Jake, Kreisberg, Richard, Kallio, Aleksi, Dudley, Aimée M, Nykter, Matti, Shmulevich, Ilya, May, Patrick, Autio, Reija

Journal:

JOM Journal of the Minerals, Metals and Materials Society

Year:

2014

Language:

english

File:

PDF, 359 KB

english, 2014

5

DOT1L-HES6 fusion drives androgen independent growth in prostate cancer

Annala, M., Kivinummi, K., Leinonen, K., Tuominen, J., Zhang, W., Visakorpi, T., Nykter, M.

Journal:

EMBO Molecular Medicine

Year:

2014

Language:

english

File:

PDF, 430 KB

english, 2014

6

Laminin α5 substrates promote survival, network formation and functional development of human pluripotent stem cell-derived neurons in vitro

Hyysalo, Anu, Ristola, Mervi, Mäkinen, Meeri E.-L., Häyrynen, Sergei, Nykter, Matti, Narkilahti, Susanna

Journal:

Stem Cell Research

Year:

2017

Language:

english

File:

PDF, 4.06 MB

english, 2017

7

Cytokeratin-supervised deep learning for automatic recognition of epithelial cells in breast cancers stained for ER, PR, and Ki-67

Valkonen, Mira, Isola, Jorma, Isola, Jorma, Ylinen, Onni, Muhonen, Ville, Saxlin, Anna, Tolonen, Teemu, Nykter, Matti, Ruusuvuori, Pekka

Journal:

IEEE Transactions on Medical Imaging

Year:

2019

Language:

english

File:

PDF, 8 KB

english, 2019

8

Integrative genomic characterization and a genomic staging system for gastrointestinal stromal tumors

Antti Ylipää, Kelly K. Hunt, Jilong Yang, Alexander J. F. Lazar, Keila E. Torres, Dina C. Lev, Matti Nykter, Raphael E. Pollock, Jonathan Trent, Wei Zhang

Journal:

Year:

2011

Language:

english

File:

PDF, 568 KB

english, 2011

9

Differential gene expression in non-malignant tumour microenvironment is associated with outcome in follicular lymphoma patients treated with rituximab and CHOP

Antti Harjunpää, Minna Taskinen, Matti Nykter, Marja-Liisa Karjalainen-Lindsberg, Heidi Nyman, Outi Monni, Samuli Hemmer, Olli Yli-Harja, Sampsa Hautaniemi, Seppo Meri, Sirpa Leppä

Journal:

British Journal of Haematology

Year:

2006

Language:

english

File:

PDF, 715 KB

english, 2006

10

A Data Integration Framework for Prediction of Transcription Factor Targets : A BCL6 Case Study

Matti Nykter, Harri Lähdesmäki, Alistair Rust, Vesteinn Thorsson, Ilya Shmulevich

Journal:

Annals of the New York Academy of Sciences

Year:

2009

Language:

english

File:

PDF, 375 KB

english, 2009

11

Biological Information as Set-Based Complexity

Galas, D.J., Nykter, M., Carter, G.W., Price, N.D., Shmulevich, I.

Journal:

IEEE Transactions on Information Theory

Year:

2010

Language:

english

File:

PDF, 421 KB

english, 2010

12

Simulation of microarray data with realistic characteristics

Matti Nykter, Tommi Aho, Miika Ahdesmäki, Pekka Ruusuvuori, Antti Lehmussola, Olli Yli-Harja

Journal:

BMC Bioinformatics

Year:

2006

Language:

english

File:

PDF, 2.60 MB

english, 2006

13

Function of C/EBPδ in a regulatory circuit that discriminates between transient and persistent TLR4-induced signals

Litvak, Vladimir, Ramsey, Stephen A, Rust, Alistair G, Zak, Daniel E, Kennedy, Kathleen A, Lampano, Aaron E, Nykter, Matti, Shmulevich, Ilya, Aderem, Alan

Journal:

Nature Immunology

Year:

2009

Language:

english

File:

PDF, 586 KB

english, 2009

14

Integrated Analyses Identify a Master MicroRNA Regulatory Network for the Mesenchymal Subtype in Serous Ovarian Cancer

Yang, Da, Sun, Yan, Hu, Limei, Zheng, Hong, Ji, Ping, Pecot, Chad V., Zhao, Yanrui, Reynolds, Sheila, Cheng, Hanyin, Rupaimoole, Rajesha, Cogdell, David, Nykter, Matti, Broaddus, Russell, Rodriguez-Ag

Journal:

Year:

2013

Language:

english

File:

PDF, 11.59 MB

english, 2013

15

Transcriptome and small RNA deep sequencing reveals deregulation of miRNA biogenesis in human glioma

Moore, Lynette M, Kivinen, Virpi, Liu, Yuexin, Annala, Matti, Cogdell, David, Liu, Xiuping, Liu, Chang-Gong, Sawaya, Raymond, Yli-Harja, Olli, Shmulevich, Ilya, Fuller, Gregory N, Zhang, Wei, Nykter,

Journal:

The Journal of Pathology

Year:

2013

Language:

english

File:

PDF, 483 KB

english, 2013

16

Gene-pair expression signatures reveal lineage control

Heinäniemi, Merja, Nykter, Matti, Kramer, Roger, Wienecke-Baldacchino, Anke, Sinkkonen, Lasse, Zhou, Joseph Xu, Kreisberg, Richard, Kauffman, Stuart A, Huang, Sui, Shmulevich, Ilya

Journal:

Year:

2013

Language:

english

File:

PDF, 2.44 MB

english, 2013

17

Next generation sequencing applications in cancer research

Zhang, Wei, Nykter, Matti, Chen, Kexin

Journal:

Year:

2013

Language:

english

File:

PDF, 333 KB

english, 2013

18

Karyotypically abnormal human ESCs are sensitive to HDAC inhibitors and show altered regulation of genes linked to cancers and neurological diseases

Lund, Riikka J., Emani, Maheswara Reddy, Barbaric, Ivana, Kivinen, Virpi, Jones, Mark, Baker, Duncan, Gokhale, Paul, Nykter, Matti, Lahesmaa, Riitta, Andrews, Peter W.

Journal:

Stem Cell Research

Year:

2013

Language:

english

File:

PDF, 2.28 MB

english, 2013

19

Loss of PTEN Is Associated with Aggressive Behavior in ERG-Positive Prostate Cancer

Leinonen, K. A., Saramaki, O. R., Furusato, B., Kimura, T., Takahashi, H., Egawa, S., Suzuki, H., Keiger, K., Ho Hahm, S., Isaacs, W. B., Tolonen, T. T., Stenman, U.-H., Tammela, T. L. J., Nykter, M.,

Journal:

Cancer Epidemiology Biomarkers & Prevention

Year:

2013

Language:

english

File:

PDF, 608 KB

english, 2013

20

POMO - PlottingOmicsanalysis results for Multiple Organisms

Lin, Jake, Kreisberg, Richard, Kallio, Aleksi, Dudley, Aimée M, Nykter, Matti, Shmulevich, Ilya, May, Patrick, Autio, Reija

Journal:

Year:

2013

Language:

english

File:

PDF, 875 KB

english, 2013

21

Characterization of aberrant pathways across human cancers

Antti Ylipää,Olli Yli-Harja,Wei Zhang,Matti Nykter

Journal:

BMC Systems Biology

Year:

2013

Language:

english

File:

PDF, 3.94 MB

english, 2013

22

Insulin-like growth factor-binding protein 2-driven glioma progression is prevented by blocking a clinically significant integrin, integrin-linked kinase, and NF- B network

Holmes, K. M., Annala, M., Chua, C. Y. X., Dunlap, S. M., Liu, Y., Hugen, N., Moore, L. M., Cogdell, D., Hu, L., Nykter, M., Hess, K., Fuller, G. N., Zhang, W.

Journal:

Proceedings of the National Academy of Sciences

Year:

2012

Language:

english

File:

PDF, 1.38 MB

english, 2012

23

Two mature products of MIR-491 coordinate to suppress key cancer hallmarks in glioblastoma

Li, X, Liu, Y, Granberg, K J, Wang, Q, Moore, L M, Ji, P, Gumin, J, Sulman, E P, Calin, G A, Haapasalo, H, Nykter, M, Shmulevich, I, Fuller, G N, Lang, F F, Zhang, W

Journal:

Year:

2015

Language:

english

File:

PDF, 2.73 MB

english, 2015

24

Integrated Analyses Identify a Master MicroRNA Regulatory Network for the Mesenchymal Subtype in Serous Ovarian Cancer

Yang, Da, Sun, Yan, Hu, Limei, Zheng, Hong, Ji, Ping, Pecot, Chad V., Zhao, Yanrui, Reynolds, Sheila, Cheng, Hanyin, Rupaimoole, Rajesha, Cogdell, David, Nykter, Matti, Broaddus, Russell, Rodriguez-Ag

Journal:

Year:

2013

Language:

english

File:

PDF, 60 KB

english, 2013

25

299 Novel prostate cancer specific transcripts identified using RNA-seq

Ylipää, A., Kivinummi, K.K., Annala, M.J., Kartasalo, K., Latonen, L., Leppänen, S-P., Scaravilli, M., Zhang, W., Tammela, T.L.J., Visakorpi, T., Nykter, M.

Journal:

European Urology Supplements

Year:

2014

Language:

english

File:

PDF, 109 KB

english, 2014

26

Cancer genome sequencing: Understanding malignancy as a disease of the genome, its conformation, and its evolution

Patel, Lalit R., Nykter, Matti, Chen, Kexin, Zhang, Wei

Journal:

Year:

2013

Language:

english

File:

PDF, 1.47 MB

english, 2013

27

MicroRNA Expression Profile of Primary Prostate Cancer Stem Cells as a Source of Biomarkers and Therapeutic Targets

Rane, Jayant K., Scaravilli, Mauro, Ylipää, Antti, Pellacani, Davide, Mann, Vincent M., Simms, Matthew S., Nykter, Matti, Collins, Anne T., Visakorpi, Tapio, Maitland, Norman J.

Journal:

European Urology

Year:

2015

Language:

english

File:

PDF, 712 KB

english, 2015

28

Critical Networks Exhibit Maximal Information Diversity in Structure-Dynamics Relationships

Nykter, Matti, Price, Nathan D., Larjo, Antti, Aho, Tommi, Kauffman, Stuart A., Yli-Harja, Olli, Shmulevich, Ilya

Journal:

Physical Review Letters

Year:

2008

Language:

english

File:

PDF, 213 KB

english, 2008

29

[IEEE 2007 29th Annual International Conference of the IEEE Engineering in Medicine and Biology Society - Lyon, France (2007.08.22-2007.08.26)] 2007 29th Annual International Conference of the IEEE Engineering in Medicine and Biology Society - Microarray Simulator as Educational Tool

Ruusuvuori, Pekka, Nykter, Matti, Makiraatikka, Eeva, Lehmussola, Antti, Korpelainen, Tomi, Erkkila, Timo, Yli-Harja, Olli

Year:

2007

Language:

english

File:

PDF, 223 KB

english, 2007

30

Microarray analysis of differentially expressed genes in ovarian and fallopian tube epithelium from risk-reducing salpingo-oophorectomies

Veskimäe, Kristina, Staff, Synnöve, Tabaro, Francesco, Nykter, Matti, Isola, Jorma, Mäenpää, Johanna

Journal:

Genes, Chromosomes and Cancer

Year:

2015

Language:

english

File:

PDF, 346 KB

english, 2015

31

RecurrentLRP1-SNRNP25andKCNMB4-CCND3fusion genes promote tumor cell motility in human osteosarcoma

Yang, Jilong, Annala, Matti, Ji, Ping, Wang, Guowen, Zheng, Hong, Codgell, David, Du, Xiaoling, Fang, Zhiwei, Sun, Baocun, Nykter, Matti, Chen, Kexin, Zhang, Wei

Journal:

Journal of Hematology & Oncology

Year:

2014

Language:

english

File:

PDF, 1.52 MB

english, 2014

32

Genomically amplified Akt3 activates DNA repair pathway and promotes glioma progression

Turner, Kristen M., Sun, Youting, Ji, Ping, Granberg, Kirsi J., Bernard, Brady, Hu, Limei, Cogdell, David E., Zhou, Xinhui, Yli-Harja, Olli, Nykter, Matti, Shmulevich, Ilya, Yung, W. K. Alfred, Fuller

Journal:

Proceedings of the National Academy of Sciences

Year:

2015

Language:

english

File:

PDF, 1.63 MB

english, 2015

33

IGFBP2 potentiates nuclear EGFR–STAT3 signaling

Chua, C Y, Liu, Y, Granberg, K J, Hu, L, Haapasalo, H, Annala, M J, Cogdell, D E, Verploegen, M, Moore, L M, Fuller, G N, Nykter, M, Cavenee, W K, Zhang, W

Journal:

Year:

2015

Language:

english

File:

PDF, 3.83 MB

english, 2015

34

MiR-1247-5p is overexpressed in castration resistant prostate cancer and targets MYCBP2

Scaravilli, Mauro, Porkka, Kati P., Brofeldt, Anniina, Annala, Matti, Tammela, Teuvo LJ., Jenster, Guido W., Nykter, Matti, Visakorpi, Tapio

Journal:

Year:

2015

Language:

english

File:

PDF, 387 KB

english, 2015

35

Genomic and Molecular Characterization of Malignant Peripheral Nerve Sheath Tumor Identifies the IGF1R Pathway as a Primary Target for Treatment

Yang, J., Ylipaa, A., Sun, Y., Zheng, H., Chen, K., Nykter, M., Trent, J., Ratner, N., Lev, D. C., Zhang, W.

Journal:

Clinical Cancer Research

Year:

2011

Language:

english

File:

PDF, 2.06 MB

english, 2011

36

Ageing-associated changes in the human DNA methylome: genomic locations and effects on gene expression

Marttila, Saara, Kananen, Laura, Häyrynen, Sergei, Jylhävä, Juulia, Nevalainen, Tapio, Hervonen, Antti, Jylhä, Marja, Nykter, Matti, Hurme, Mikko

Journal:

Year:

2015

Language:

english

File:

PDF, 929 KB

english, 2015

37

Gene expression dynamics in the macrophage exhibit criticality

Nykter, M., Price, N. D., Aldana, M., Ramsey, S. A., Kauffman, S. A., Hood, L. E., Yli-Harja, O., Shmulevich, I.

Journal:

Proceedings of the National Academy of Sciences

Year:

2008

Language:

english

File:

PDF, 321 KB

english, 2008

38

Proprotein Convertase Subtilisin/Kexin Type 7 (PCSK7) Is Essential for the Zebrafish Development and Bioavailability of Transforming Growth Factor 1a (TGF 1a)

Turpeinen, H., Oksanen, A., Kivinen, V., Kukkurainen, S., Uusimaki, A., Ramet, M., Parikka, M., Hytonen, V. P., Nykter, M., Pesu, M.

Journal:

Journal of Biological Chemistry

Year:

2013

Language:

english

File:

PDF, 5.02 MB

english, 2013

39

An Integrated Study of Aberrant Gene Copy Number and Gene Expression in GIST and LMS

Yang, D., Ylipaa, A., Yang, J., Hunt, K., Pollock, R., Trent, J., Yli-Harja, O., Shmulevich, I., Nykter, M., Zhang, W.

Journal:

Technology in Cancer Research & Treatment

Year:

2010

Language:

english

File:

PDF, 2.42 MB

english, 2010

40

Computational Methods for Estimation of Cell Cycle Phase Distributions of Yeast Cells

Niemistö, Antti, Nykter, Matti, Aho, Tommi, Jalovaara, Henna, Marjanen, Kalle, Ahdesmäki, Miika, Ruusuvuori, Pekka, Tiainen, Mikko, Linne, Marja-Leena, Yli-Harja, Olli

Journal:

EURASIP Journal on Bioinformatics and Systems Biology

Year:

2007

Language:

english

File:

PDF, 1.57 MB

english, 2007

41

Unsupervised Analysis Uncovers Changes in Histopathologic Diagnosis in Supervised Genomic Studies

Nykter, M., Hunt, K. K., Pollock, R. E., El-Naggar, A. K., Taylor, E., Shmulevich, I., Yli-Harja, O., Zhang, W.

Journal:

Technology in Cancer Research & Treatment

Year:

2006

Language:

english

File:

PDF, 1.13 MB

english, 2006

42

Construction of therapeutically relevant human prostate epithelial fate map by utilising miRNA and mRNA microarray expression data

Rane, Jayant K, Ylipää, Antti, Adamson, Rachel, Mann, Vincent M, Simms, Matthew S, Collins, Anne T, Visakorpi, Tapio, Nykter, Matti, Maitland, Norman J

Journal:

British Journal of Cancer

Year:

2015

Language:

english

File:

PDF, 574 KB

english, 2015

43

Overexpression of SNORD114-3 marks acute promyelocytic leukemia

Liuksiala, T, Teittinen, K J, Granberg, K, Heinäniemi, M, Annala, M, Mäki, M, Nykter, M, Lohi, O

Journal:

Year:

2014

Language:

english

File:

PDF, 442 KB

english, 2014

44

Twist predicts poor outcome of patients with astrocytic glioma

Nordfors, Kristiina, Haapasalo, Joonas, Mäkelä, Katri, Granberg, Kirsi J, Nykter, Matti, Korja, Miikka, Paavonen, Timo, Haapasalo, Hannu, Soini, Ylermi

Journal:

Journal of Clinical Pathology

Year:

2015

Language:

english

File:

PDF, 1.51 MB

english, 2015

45

712 Processing of stacked histological tissue sections in digital pathology

Ruusuvuori, P., Nykter, M., Latonen, L.

Journal:

European Journal of Cancer

Year:

2015

Language:

english

File:

PDF, 62 KB

english, 2015

46

[IEEE 2015 23rd European Signal Processing Conference (EUSIPCO) - Nice, France (2015.8.31-2015.9.4)] 2015 23rd European Signal Processing Conference (EUSIPCO) - Mapping dynamical states to structural classes for Boolean networks using a classification algorithm

Sarbu, Septimia, Shmulevich, Ilya, Yli-Harja, Olli, Nykter, Matti, Kesseli, Juha

Year:

2015

Language:

english

File:

PDF, 158 KB

english, 2015

47

1074 Microseminoprotein-beta expression in different stages of prostate cancer

Sjöblom, L, Saramäki, O., Annala, M., Leinonen, K., Nättinen, J., Tolonen, T., Wahlfors, T., Nykter, M., Bova, G., Schleutker, J., Tammela, T., Lilja, H., Visakorpi, T.

Journal:

European Urology Supplements

Year:

2016

Language:

english

File:

PDF, 106 KB

english, 2016

48

Integrated clinical, whole-genome, and transcriptome analysis of multisampled lethal metastatic prostate cancer

Bova, G. Steven, Kallio, Heini M.L., Annala, Matti, Kivinummi, Kati, Högnäs, Gunilla, Häyrynen, Sergei, Rantapero, Tommi, Kivinen, Virpi, Isaacs, William B., Tolonen, Teemu, Nykter, Matti, Visakorpi,

Journal:

Molecular Case Studies

Year:

2016

Language:

english

File:

PDF, 2.09 MB

english, 2016

49

165 Recurrent SKIL-activating rearrangements in ETS-negative prostate cancer

Annala, M., Kivinummi, K., Tuominen, J., Latonen, L., Ylipää, A., Saramäki, O., Kaukoniemi, K.M., Karakurt, S., Yli-Harja, O., Vessella, R.L., Tammela, T.L.J., Zhang, W., Visakorpi, T., Nykter, M.

Journal:

European Urology Supplements

Year:

2015

Language:

english

File:

PDF, 157 KB

english, 2015

50

Assessment of PARP protein expression in epithelial ovarian cancer by ELISA pharmacodynamic assay and immunohistochemistry

Veskimäe, K., Staff, S., Grönholm, A., Pesu, M., Laaksonen, M., Nykter, M., Isola, J., Mäenpää, J.

Journal:

Year:

2016

Language:

english

File:

PDF, 929 KB

english, 2016

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