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Authors whose works are in public domain in at least one jurisdiction

List of works by Sampsa Hautaniemi

A Functional Homologous Recombination Assay Predicts Primary Chemotherapy Response and Long-Term Survival in Ovarian Cancer Patients

scientific article published on 01 June 2018

A Subset of Secreted Proteins in Ascites Can Predict Platinum-Free Interval in Ovarian Cancer

scientific article published in 2022

A novel strategy for microarray quality control using Bayesian networks

scientific article published in November 2003

A strategy for identifying putative causes of gene expression variation in human cancers

article

AIP inactivation leads to pituitary tumorigenesis through defective Gαi-cAMP signaling

scientific article published on 24 March 2014

ALDH1A1-related stemness in high-grade serous ovarian cancer is a negative prognostic indicator but potentially targetable by EGFR/mTOR-PI3K/aurora kinase inhibitors

scientific article published on 03 December 2019

Adipocyte morphology and implications for metabolic derangements in acquired obesity

scientific article

Advanced analysis and visualization of gene copy number and expression data

scientific article

Allelic Imbalance at rs6983267 Suggests Selection of the Risk Allele in Somatic Colorectal Tumor Evolution

scientific article published on 01 January 2008

Alternative splicing discriminates molecular subtypes and has prognostic impact in diffuse large B-cell lymphoma.

scientific article published on 25 August 2017

An optimized isolation of biotinylated cell surface proteins reveals novel players in cancer metastasis

scientific article

Anagrelide for Gastrointestinal Stromal Tumor

scientific article published on 07 December 2018

Analysis of BMP4 and BMP7 signaling in breast cancer cells unveils time-dependent transcription patterns and highlights a common synexpression group of genes

scientific article

Anduril 2: upgraded large-scale data integration framework

scientific article published on 01 October 2019

Aneuploidy-associated gene expression signatures characterize malignant transformation in ulcerative colitis

scientific article published in March 2013

Anima: modular workflow system for comprehensive image data analysis

scientific article

Are data from different gene expression microarray platforms comparable?

scientific article

Author Correction: Defects in mtDNA replication challenge nuclear genome stability through nucleotide depletion and provide a unifying mechanism for mouse progerias

scientific article published on 10 August 2020

Author Correction: Immunogenomic profiling determines responses to combined PARP and PD-1 inhibition in ovarian cancer

scientific article published on 18 May 2020

Biclustering methods: biological relevance and application in gene expression analysis

scientific article

CIP2A signature reveals the MYC dependency of CIP2A-regulated phenotypes and its clinical association with breast cancer subtypes

scientific article

CNAmet: an R package for integrating copy number, methylation and expression data

scientific article

Candidate driver genes in microsatellite-unstable colorectal cancer

scientific article published on 3 August 2011

Characterising metabolically healthy obesity in weight-discordant monozygotic twins

scientific article published on 8 October 2013

Characterization of the colorectal cancer-associated enhancer MYC-335 at 8q24: the role of rs67491583

scientific article published on January 2012

Circulating tumor DNA (ctDNA) in precision oncology of ovarian cancer

scientific article published on 01 December 2019

Clinical Value of 18F-fluorodeoxyglucose Positron Emission Tomography/Computed Tomography in Response Evaluation after Primary Treatment of Advanced Epithelial Ovarian Cancer.

scientific article

Co-evolution of matrisome and adaptive adhesion dynamics drives ovarian cancer chemoresistance

scientific article published on 23 June 2021

Combined T regulatory cell and Th2 expression profile identifies children with cow's milk allergy

scientific article published on 15 March 2010

Comparative analysis of algorithms for integration of copy number and expression data

scientific article

Comparative analysis of methods for identifying somatic copy number alterations from deep sequencing data

scientific article

Comparison of Affymetrix data normalization methods using 6,926 experiments across five array generations

scientific article

Complete androgen insensitivity syndrome caused by a deep intronic pseudoexon-activating mutation in the androgen receptor gene

scientific article published on 09 September 2016

Comprehensive evaluation of coding region point mutations in microsatellite‐unstable colorectal cancer

scientific article published on 14 August 2018

Comprehensive exon array data processing method for quantitative analysis of alternative spliced variants

scientific article

Computational identification of cancer susceptibility loci.

scientific article published on January 2010

Computational identification of candidate loci for recessively inherited mutation using high-throughput SNP arrays

scientific article published on 17 May 2007

DNA methylation signature (SAM40) identifies subgroups of the Luminal A breast cancer samples with distinct survival

scientific article

Data integration to prioritize drugs using genomics and curated data.

scientific article

Data integration workflow for search of disease driving genes and genetic variants

scientific article published in 2011

Deciphering downstream gene targets of PI3K/mTOR/p70S6K pathway in breast cancer

scientific article

Decision tree modeling predicts effects of inhibiting contractility signaling on cell motility

scientific article

Dectin-1 pathway activates robust autophagy-dependent unconventional protein secretion in human macrophages

scientific article

Defects in mtDNA replication challenge nuclear genome stability through nucleotide depletion and provide a unifying mechanism for mouse progerias

scientific article published on 07 October 2019

Deltex-1 mutations predict poor survival in diffuse large B-cell lymphoma

scientific article published on 9 February 2017

Deregulation of COMMD1 is associated with poor prognosis in diffuse large B-cell lymphoma

scientific article

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

scientific article published on 22 August 2006

Distinct subtypes of diffuse large B-cell lymphoma defined by hypermutated genes

scientific article published on 11 June 2019

Drug screening approach combines epigenetic sensitization with immunochemotherapy in cancer

scientific article published on 11 December 2019

Dual role of FoxA1 in androgen receptor binding to chromatin, androgen signalling and prostate cancer

scientific article

Dynamic visualization of multi-level molecular data: The Director package in R.

scientific article published on 12 October 2017

Early Trichinella spiralis and Trichinella nativa infections induce similar gene expression profiles in rat jejunal mucosa

article

Early maternal alcohol consumption alters hippocampal DNA methylation, gene expression and volume in a mouse model

scientific article published on 13 May 2015

Early recovery from cow's milk allergy is associated with decreasing IgE and increasing IgG4 binding to cow's milk epitopes

scientific article published on 11 May 2010

Effects of HER2 overexpression on cell signaling networks governing proliferation and migration

scientific article

Effects of Herceptin treatment on global gene expression patterns in HER2-amplified and nonamplified breast cancer cell lines

scientific article published on January 2004

ErbB2-driven breast cancer cell invasion depends on a complex signaling network activating myeloid zinc finger-1-dependent cathepsin B expression.

scientific article

Evolutionary history of metastatic breast cancer reveals minimal seeding from axillary lymph nodes

scientific article

Fast gene ontology based clustering for microarray experiments

scientific article

FoxA1 specifies unique androgen and glucocorticoid receptor binding events in prostate cancer cells.

scientific article

Functional Homologous Recombination Assay on FFPE Specimens of Advanced High-Grade Serous Ovarian Cancer Predicts Clinical Outcomes

scientific article published in 2023

Functional profiling of precursor MicroRNAs identifies MicroRNAs essential for glioma proliferation

scientific article

Gene-expression profiling predicts recurrence in Dukes' C colorectal cancer

scientific article published in September 2005

Genomic instability influences the transcriptome and proteome in endometrial cancer subtypes

scientific article published on 31 October 2011

Genomic profile of pseudomyxoma peritonei analyzed using next-generation sequencing and immunohistochemistry

Genomic region operation kit for flexible processing of deep sequencing data.

scientific article

Germline variation in TP53 regulatory network genes associates with breast cancer survival and treatment outcome

scientific article

Global gene expression profile of human cord blood-derived CD133+ cells

scientific article published on 6 October 2005

Glycomic Profiling Highlights Increased Fucosylation in Pseudomyxoma Peritonei

scientific article published on 02 August 2018

Heterogeneity and Clonal Evolution of Acquired PARP Inhibitor Resistance in <i>TP53-</i> and <i>BRCA1</i>-Deficient Cells

scientific article published on 29 January 2021

High frequency of TTK mutations in microsatellite-unstable colorectal cancer and evaluation of their effect on spindle assembly checkpoint

scientific article

High-resolution analysis of gene copy number alterations in human prostate cancer using CGH on cDNA microarrays: impact of copy number on gene expression

scientific article

Human cell transformation by combined lineage conversion and oncogene expression

scientific article published on 23 July 2021

Identification of Prognostic Groups in High-Grade Serous Ovarian Cancer Treated with Platinum-Taxane Chemotherapy.

scientific article

Identification of a c-Jun N-terminal kinase-2-dependent signal amplification cascade that regulates c-Myc levels in ras transformation.

scientific article

Identification of genetic markers with synergistic survival effect in cancer

scientific article

Identification of sample-specific regulations using integrative network level analysis

scientific article published on 28 April 2015

Identification of several potential chromatin binding sites of HOXB7 and its downstream target genes in breast cancer

scientific article published on 26 May 2015

Identifying differentially methylated sites in samples with varying tumor purity

scientific article published on 01 September 2018

Immunogenomic profiling determines responses to combined PARP and PD-1 inhibition in ovarian cancer

scientific article published on 19 March 2020

Individual and combined effects of DNA methylation and copy number alterations on miRNA expression in breast tumors

scientific article

Insulin/IGF-1 signaling regulates proteasome activity through the deubiquitinating enzyme UBH-4.

scientific article published on 13 June 2013

Integrated data management and validation platform for phosphorylated tandem mass spectrometry data

scientific article

Integrated mechanistic and data-driven modelling for multivariate analysis of signalling pathways

scientific article

Integrated network analysis platform for protein-protein interactions

scientific article published on 14 December 2008

Integrative analysis of deep sequencing data identifies estrogen receptor early response genes and links ATAD3B to poor survival in breast cancer

scientific article

Integrative platform to translate gene sets to networks

scientific article

Integrative transcriptional analysis between human and mouse cancer cells provides a common set of transformation associated genes

scientific article published on 29 June 2011

KSHV-initiated notch activation leads to membrane-type-1 matrix metalloproteinase-dependent lymphatic endothelial-to-mesenchymal transition.

scientific article published in December 2011

Language-Agnostic Reproducible Data Analysis Using Literate Programming

scientific article

Large-scale data integration framework provides a comprehensive view on glioblastoma multiforme

scientific article

Let-7 microRNA controls invasion-promoting lysosomal changes via the oncogenic transcription factor myeloid zinc finger-1.

scientific article published on 3 February 2018

Longitudinal single-cell RNA-seq analysis reveals stress-promoted chemoresistance in metastatic ovarian cancer

scientific article published on 23 February 2022

Lymphatic endothelium stimulates melanoma metastasis and invasion via MMP14-dependent Notch3 and β1-integrin activation

scientific article published in May 2018

MMP16 Mediates a Proteolytic Switch to Promote Cell-Cell Adhesion, Collagen Alignment, and Lymphatic Invasion in Melanoma

scientific article

Mathematical Modeling Predicts Response to Chemotherapy and Drug Combinations in Ovarian Cancer

scientific article published on 16 May 2018

MicroRNAs regulate key cell survival pathways and mediate chemosensitivity during progression of diffuse large B-cell lymphoma.

scientific article

Modeling of signal-response cascades using decision tree analysis.

scientific article published on May 2005

Molecular characterization of subcutaneous panniculitis-like T-cell lymphoma reveals upregulation of immunosuppression- and autoimmunity-associated genes

scientific article

Mre11 inhibition by oncolytic adenovirus associates with autophagy and underlies synergy with ionizing radiation

scientific article

Multiple components of PKA and TGF-β pathways are mutated in pseudomyxoma peritonei

scientific article

Multiple reaction monitoring for robust quantitative proteomic analysis of cellular signaling networks

scholarly article

Mutations in the circadian gene CLOCK in colorectal cancer

scientific article

NAV3 copy number changes and target genes in basal and squamous cell cancers

scientific article

Netrin-1-induced activation of Notch signaling mediates glioblastoma cell invasion

scientific article published on 2 April 2013

Netrin-4 promotes glioblastoma cell proliferation through integrin β4 signaling

scientific article published in March 2012

Neuron navigator 3 alterations in nervous system tumors associate with tumor malignancy grade and prognosis.

scientific article

Nonsense-mediated decay microarray analysis identifies mutations of EPHB2 in human prostate cancer

scientific article published on 8 August 2004

Novel Mad2-targeting miR-493-3p controls mitotic fidelity and cancer cells' sensitivity to paclitaxel

scientific article published on 02 March 2016

Novel proteomics strategy brings insight into the prevalence of SUMO-2 target sites

scientific article published on 24 February 2009

Oncogenic Herpesvirus Utilizes Stress-Induced Cell Cycle Checkpoints for Efficient Lytic Replication

scientific article published on 18 February 2016

Open Source Infrastructure for Health Care Data Integration and Machine Learning Analyses

scientific article published on 01 August 2019

Optimized LOWESS normalization parameter selection for DNA microarray data

scientific article

Origins and impacts of new mammalian exons

scientific article published on 19 March 2015

PINA v2.0: mining interactome modules.

scientific article published on 8 November 2011

PROX1 is a transcriptional regulator of MMP14.

scientific article published on 22 June 2018

Par6G suppresses cell proliferation and is targeted by loss-of-function mutations in multiple cancers.

scientific article

PerPAS: Topology-Based Single Sample Pathway Analysis Method.

scientific article

Phosphoprotein profiling predicts response to tyrosine kinase inhibitor therapy in chronic myeloid leukemia patients

scientific article

Plasticity of blood- and lymphatic endothelial cells and marker identification

scientific article (publication date: 2013)

Posttranscriptional regulation of angiotensin II type 1 receptor expression by glyceraldehyde 3-phosphate dehydrogenase

scientific article

Potential role of a navigator gene NAV3 in colorectal cancer.

scientific article published on 15 December 2011

Prognostic value of tumour budding in oesophageal cancer: a meta-analysis.

scientific article published on 16 July 2015

Prospective Longitudinal ctDNA Workflow Reveals Clinically Actionable Alterations in Ovarian Cancer

scientific article published on 03 May 2019

Prostatic acid phosphatase is the main acid phosphatase with 5'-ectonucleotidase activity in the male mouse saliva and regulates salivation.

scientific article

Rapid mobilization of cytotoxic lymphocytes induced by dasatinib therapy.

scientific article

Relationships between probabilistic Boolean networks and dynamic Bayesian networks as models of gene regulatory networks

scientific article published on April 2006

Reply to: Proofreading deficiency in mitochondrial DNA polymerase does not affect total dNTP pools in mouse embryos

scientific article published on 10 August 2020

Rituximab regulates signaling pathways and alters gene expression associated with cell death and survival in diffuse large B-cell lymphoma

scientific article published on 10 February 2011

Role of RNA binding protein HuR in ductal carcinoma in situ of the breast

scientific article

Rule-based induction method for haplotype comparison and identification of candidate disease loci

scientific article published on 19 March 2012

SePIA: RNA and small RNA sequence processing, integration, and analysis.

scientific article

Signal transducers and activators of transcription 5a-dependent cross-talk between follicular lymphoma cells and tumor microenvironment characterizes a group of patients with improved outcome after R-CHOP.

scientific article published on 13 April 2010

Systematic bioinformatic analysis of expression levels of 17,330 human genes across 9,783 samples from 175 types of healthy and pathological tissues

scientific article published on 19 September 2008

The gene expression signature of genomic instability in breast cancer is an independent predictor of clinical outcome

scientific article published on April 2009

The phytoestrogen genistein is a tissue-specific androgen receptor modulator

scientific article

Therapeutic targets for HIV-1 infection in the host proteome ⬇️

scientific article

Tissue-specific pioneer factors associate with androgen receptor cistromes and transcription programs

scientific article published on 22 January 2014

Transmembrane prostatic acid phosphatase (TMPAP) delays cells in G1 phase of the cell cycle

scientific article published on 30 September 2015

Transmembrane prostatic acid phosphatase (TMPAP) interacts with snapin and deficient mice develop prostate adenocarcinoma

scientific article

Use of IgE and IgG4 epitope binding to predict the outcome of oral immunotherapy in cow's milk allergy

scientific article published on 06 January 2014

Virtual clinical trials identify effective combination therapies in ovarian cancer

scientific article published on 10 December 2019

Workflow for automated quantification of cerebromicrovascular gelatinase activity.

scientific article

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