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List of works by Matti Nykter

A data integration framework for prediction of transcription factor targets

scientific article

A linear model for transcription factor binding affinity prediction in protein binding microarrays

scientific article

A systems biological approach to identify key transcription factors and their genomic neighborhoods in human sarcomas ⬇️

scientific article published on January 1, 2011

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

scientific article published on 14 March 2015

Analysis of spatial heterogeneity in normal epithelium and preneoplastic alterations in mouse prostate tumor models.

scientific article published on 20 March 2017

Androgen Receptor Deregulation Drives Bromodomain-Mediated Chromatin Alterations in Prostate Cancer

scientific article published on June 2017

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

scientific article published on 07 May 2016

Balance between noise and information flow maximizes set complexity of network dynamics ⬇️

scientific article

Bioinformatics Assembling and Assessment of Novel Coxsackievirus B1 Genome

scientific article published on 01 January 2018

Biological Information as Set-Based Complexity

scientific article published on 25 February 2010

Bone morphogenetic protein 4 regulates microRNA expression in breast cancer cell lines in diverse fashion

scientific article published on 18 December 2015

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

scientific article

Characterization of aberrant pathways across human cancers

scientific article

Chromatin accessibility is associated with CRISPR-Cas9 efficiency in the zebrafish (Danio rerio).

scientific article published on 23 April 2018

Circulating Tumor DNA Abundance and Potential Utility in De Novo Metastatic Prostate Cancer

scientific article published on 10 January 2019

Circulating Tumor DNA Reveals Clinically Actionable Somatic Genome of Metastatic Bladder Cancer.

scientific article published on 31 July 2017

Circulating mutational portrait of cancer: manifestation of aggressive clonal events in both early and late stages.

scientific article

Circulating plasma MiR-141 is a novel biomarker for metastatic colon cancer and predicts poor prognosis

scientific article

Circulating tumor DNA genomics correlate with resistance to abiraterone and enzalutamide in prostate cancer

scientific article published on 24 January 2018

Clinical association analysis of ependymomas and pilocytic astrocytomas reveals elevated FGFR3 and FGFR1 expression in aggressive ependymomas.

scientific article

Comparative Analysis of Tissue Reconstruction Algorithms for 3D Histology.

scientific article published on 19 April 2018

Comparative analysis of osteoblast gene expression profiles and Runx2 genomic occupancy of mouse and human osteoblasts in vitro

scientific article published on 11 May 2017

Comparison of iTRAQ and SWATH in a clinical study with multiple time points

scholarly article by Antti Jylhä published in January 2018

Computational Characterization of Suppressive Immune Microenvironments in Glioblastoma

scientific article published on 19 June 2018

Computational methods for estimation of cell cycle phase distributions of yeast cells

scientific article published on January 2007

Concordance of Circulating Tumor DNA and Matched Metastatic Tissue Biopsy in Prostate Cancer.

scientific article published in December 2017

Constitutively active androgen receptor splice variants AR-V3, AR-V7 and AR-V9 are co-expressed in castration-resistant prostate cancer metastases

scientific article published on 10 July 2018

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

scientific article

Crosstalk between ROR1 and BCR pathways defines novel treatment strategies in mantle cell lymphoma

scientific article published on 09 November 2017

DOT1L-HES6 fusion drives androgen independent growth in prostate cancer

scientific article

Driver Fusions and Their Implications in the Development and Treatment of Human Cancers.

scientific article published in April 2018

Epigenetically altered miR-193b targets cyclin D1 in prostate cancer

scientific article

Erratum: Whole-exome sequencing identifies germline mutation in TP53 and ATRX in a child with genomically aberrant AT/RT and her mother with anaplastic astrocytoma.

scientific article

Essential Physiological Differences Characterize Short- and Long-Lived Strains of Drosophila melanogaster

scientific article published on 01 November 2019

Expression Analysis of Platinum Sensitive and Resistant Epithelial Ovarian Cancer Patient Samples Reveals New Candidates for Targeted Therapies

scientific article published on 26 July 2018

Expressional profiling of prostate cancer risk SNPs at 11q13.5 identifies DGAT2 as a new target gene.

scientific article

Extensive reprogramming of the nascent transcriptome during iPSC to hepatocyte differentiation

scientific article published on 05 March 2019

Feasibility of Prostate PAXgene Fixation for Molecular Research and Diagnostic Surgical Pathology: Comparison of Matched Fresh Frozen, FFPE, and PFPE Tissues.

scientific article published on 3 October 2017

Feature-based analysis of mouse prostatic intraepithelial neoplasia in histological tissue sections.

scientific article published on 29 January 2016

Frequent mutation of the untranslated region in prostate cancer

article

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

scientific article published on 8 March 2009

Gene expression dynamics in the macrophage exhibit criticality

scholarly article

Gene-pair expression signatures reveal lineage control

scientific article

Genome-wide repression of eRNA and target gene loci by the ETV6-RUNX1 fusion in acute leukemia

scientific article published on 12 September 2016

Genomic Alterations in Cell-Free DNA and Enzalutamide Resistance in Castration-Resistant Prostate Cancer.

scientific article

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

scientific article published on October 31, 2011

Genomically amplified Akt3 activates DNA repair pathway and promotes glioma progression

scientific article

Hemap: An Interactive Online Resource for Characterizing Molecular Phenotypes across Hematologic Malignancies

scientific article published on 02 April 2019

Independent and cumulative coeliac disease-susceptibility loci are associated with distinct disease phenotypes

scientific article published on 15 January 2021

Information diversity in structure and dynamics of simulated neuronal networks

scientific article published on June 2011

Information-theoretic analysis of the dynamics of an executable biological model

scientific article

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

scientific article published on 15 February 2012

Integrated RNA-seq and DNase-seq analyses identify phenotype-specific BMP4 signaling in breast cancer.

scientific article

Integrated analyses identify a master microRNA regulatory network for the mesenchymal subtype in serous ovarian cancer

scientific article published on February 2013

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

scientific article published on May 2016

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

scientific article

Integrative proteomics in prostate cancer uncovers robustness against genomic and transcriptomic aberrations during disease progression.

scientific article published on 21 March 2018

Interleukin 10 mutant zebrafish have an enhanced interferon gamma response and improved survival against a Mycobacterium marinum infection

scientific article published on 09 July 2018

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

scientific article published on 18 July 2013

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

scientific article published on 12 September 2017

Leukemia prediction using sparse logistic regression

scientific article

Loss of PTEN is associated with aggressive behavior in ERG-positive prostate cancer

scientific article

Metastasis detection from whole slide images using local features and random forests.

scientific article published on 20 April 2017

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

scientific article

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

scientific article published on 23 February 2015

Microseminoprotein-Beta Expression in Different Stages of Prostate Cancer

scientific article

Modes of immunosuppression in glioblastoma microenvironment

scientific article published on 29 January 2019

Mutational Landscapes of Smoking-Related Cancers in Caucasians and African Americans: Precision Oncology Perspectives at Wake Forest Baptist Comprehensive Cancer Center

scientific article

Myeloid cell expressed proprotein convertase FURIN attenuates inflammation

scientific article published on 05 August 2016

NRF2, DJ1 and SNRX1 and their prognostic impact in astrocytic gliomas

scientific article published on 14 February 2018

Oncogenic K-Ras upregulates ITGA6 expression via FOSL1 to induce anoikis resistance and synergizes with αV-Class integrins to promote EMT.

scientific article published on 12 June 2017

Overexpression of PTP4A3 in ETV6-RUNX1 acute lymphoblastic leukemia.

scientific article published on 26 December 2016

POMO--Plotting Omics analysis results for Multiple Organisms

scientific article

Proprotein convertase subtilisin/kexin type 7 (PCSK7) is essential for the zebrafish development and bioavailability of transforming growth factor β1a (TGFβ1a).

scientific article published on 31 October 2013

Proteomics of prostate cancer - revealing how cancer cells master their messy genomes

scientific article published on 31 July 2018

Quantitative analysis of colony morphology in yeast

scientific article

RNA Polymerase III Subunit POLR3G Regulates Specific Subsets of PolyA+ and SmallRNA Transcriptomes and Splicing in Human Pluripotent Stem Cells

scientific article published on May 2017

Recurrent LRP1-SNRNP25 and KCNMB4-CCND3 fusion genes promote tumor cell motility in human osteosarcoma

scientific article

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

scientific article published on March 2015

Segmentum: a tool for copy number analysis of cancer genomes

scientific article

Simulation of microarray data with realistic characteristics.

scientific article

Single-cell ATAC and RNA sequencing reveal pre-existing and persistent cells associated with prostate cancer relapse

scientific article published on 06 September 2021

Strong FGFR3 staining is a marker for FGFR3 fusions in diffuse gliomas.

scientific article published on April 2017

The evolutionary history of lethal metastatic prostate cancer

scientific article published on April 2015

The expression of AURKA is androgen regulated in castration-resistant prostate cancer.

scientific article published on 21 December 2017

The tumorigenic FGFR3-TACC3 gene fusion escapes miR-99a regulation in glioblastoma

scientific article published on 9 January 2013

Topical fluorometholone treatment and desiccating stress change inflammatory protein expression in tears.

scientific article published on 13 September 2017

Transcriptional analysis reveals gender-specific changes in the aging of the human immune system.

scientific article published on 11 June 2013

Transcriptome Sequencing Reveals PCAT5 as a Novel ERG-Regulated Long Noncoding RNA in Prostate Cancer.

scientific article published on 17 August 2015

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

scientific article published on February 2013

Treatment Outcomes and Tumor Loss of Heterozygosity in Germline DNA Repair-deficient Prostate Cancer

scientific article

Twist predicts poor outcome of patients with astrocytic glioma

scientific article published on 10 July 2015

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

scientific article

Unsupervised analysis uncovers changes in histopathologic diagnosis in supervised genomic studies

scientific article

Vipie: web pipeline for parallel characterization of viral populations from multiple NGS samples.

scientific article

Virtual cell imaging: A review on simulation methods employed in image cytometry

scientific article

Whole-exome sequencing identifies germline mutation in TP53 and ATRX in a child with genomically aberrant AT/RT and her mother with anaplastic astrocytoma.

scientific article

Whole-exome sequencing of Finnish hereditary breast cancer families

scientific article published on 26 October 2016

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