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List of works by Tero Aittokallio

A Community Challenge for Inferring Genetic Predictors of Gene Essentialities through Analysis of a Functional Screen of Cancer Cell Lines

scientific article published on 3 October 2017

A Two-Step Learning Approach for Solving Full and Almost Full Cold Start Problems in Dyadic Prediction

article by Tapio Pahikkala et al published 2014 in Lecture Notes in Computer Science

A community effort to assess and improve drug sensitivity prediction algorithms.

scientific article

A comparative evaluation of software for the analysis of liquid chromatography-tandem mass spectrometry data from isotope coded affinity tag experiments

scientific article

A harmonized meta-knowledgebase of clinical interpretations of somatic genomic variants in cancer

scientific article published on 03 April 2020

A human ImmunoChip cDNA microarray provides a comprehensive tool to study immune responses

article

A model of a snorer's upper airway

scientific article published in March 2001

A multilevel layout algorithm for visualizing physical and genetic interaction networks, with emphasis on their modular organization

scientific article published on 26 March 2012

A normalized drug response metric improves accuracy and consistency of anticancer drug sensitivity quantification in cell-based screening

scientific article published on 23 January 2020

A normalized drug response metric improves accuracy and consistency of drug sensitivity quantification in cell-based screening

A practical comparison of methods for detecting transcription factor binding sites in ChIP-seq experiments

scientific article

A relational database to identify differentially expressed genes in the endometrium and endometriosis lesions

scientific article published on 28 August 2020

A statistical score for assessing the quality of multiple sequence alignments

scientific article published on 3 November 2006

Abstract 5588: Functional drug sensitivity and resistance profiling of AML patient cells defines a disease-specific combination of druggable signal addictions

Accumulated Metabolites of Hydroxybutyric Acid Serve as Diagnostic and Prognostic Biomarkers of Ovarian High-Grade Serous Carcinomas

scientific article published on 18 December 2015

Adjustment of the human respiratory system to increased upper airway resistance during sleep

scientific article published in January 2002

Adrenals Contribute to Growth of Castration-Resistant VCaP Prostate Cancer Xenografts

Aggressive natural killer-cell leukemia mutational landscape and drug profiling highlight JAK-STAT signaling as therapeutic target.

scientific article published on 19 April 2018

Alignment of LC-MS images, with applications to biomarker discovery and protein identification

scientific article

An immunity and pyroptosis gene-pair signature predicts overall survival in acute myeloid leukemia

scientific article published in 2022

An update on clinical proteomics in Alzheimer's research

scientific article published on 24 December 2009

Analysis of inspiratory flow shapes in patients with partial upper-airway obstruction during sleep

scientific article published in January 2001

Analysis of similarity of electrophoretic patterns in mRNA differential display

scientific article published in August 2000

Antiandrogens Reduce Intratumoral Androgen Concentrations and Induce Androgen Receptor Expression in Castration-Resistant Prostate Cancer Xenografts

scientific article published on 7 November 2017

Anticancer compound ABT-263 accelerates apoptosis in virus-infected cells and imbalances cytokine production and lowers survival rates of infected mice

scientific article published on 25 July 2013

Antiviral Properties of Chemical Inhibitors of Cellular Anti-Apoptotic Bcl-2 Proteins

scientific article published on 25 September 2017

Automated detection of differently expressed fragments in mRNA differential display

scientific article published in June 2001

Breeze: an integrated quality control and data analysis application for high-throughput drug screening

scientific article published on 02 March 2020

C-SPADE: a web-tool for interactive analysis and visualization of drug screening experiments through compound-specific bioactivity dendrograms

scientific article published on 4 May 2017

CIP2A Promotes T-Cell Activation and Immune Response to Listeria monocytogenes Infection

scientific article (publication date: 2016)

Can carotid body perfusion act as a respiratory controller?

scientific article published on 15 September 2007

Cancer stem cell drugs target K-ras signaling in a stemness context

scientific article published on 14 March 2016

Castration induces up-regulation of intratumoral androgen biosynthesis and androgen receptor expression in an orthotopic VCaP human prostate cancer xenograft model

scientific article published on 17 June 2014

Chemogenomic Analysis of the Druggable Kinome and Its Application to Repositioning and Lead Identification Studies

scientific article published on 11 September 2019

Chk1 targeting reactivates PP2A tumor suppressor activity in cancer cells

scientific article

Classification of nasal inspiratory flow shapes by attributed finite automata

scientific article

Climacteric vasomotor symptoms do not predict nocturnal breathing abnormalities in postmenopausal women

scientific article published in July 2001

Combined ASRGL1 and p53 immunohistochemistry as an independent predictor of survival in endometrioid endometrial carcinoma

scientific article published on 24 February 2018

Comparison of PDQuest and Progenesis software packages in the analysis of two-dimensional electrophoresis gels

scientific article published in October 2003

Comprehensive Drug Testing of Patient-derived Conditionally Reprogrammed Cells from Castration-resistant Prostate Cancer

scientific article

Computational-experimental approach to drug-target interaction mapping: A case study on kinase inhibitors.

scientific article published on 07 August 2017

Computer-assisted identification of multitrace electrophoretic patterns in differential display experiments

scientific article published in March 2007

Consistency in drug response profiling

scientific article published in November 2016

Corrections: Reinstated p53 response and high anti-T-cell leukemia activity by the novel alkylating deacetylase inhibitor tinostamustine

scientific article published on 23 October 2020

Cost-effective survival prediction for patients with advanced prostate cancer using clinical trial and real-world hospital registry datasets

scientific article published on 17 November 2019

Crowdsourced assessment of common genetic contribution to predicting anti-TNF treatment response in rheumatoid arthritis

scientific article published on 23 August 2016

DNMT Inhibitors Increase Methylation in the Cancer Genome

scientific article published on 24 April 2019

Dealing with missing values in large-scale studies: microarray data imputation and beyond.

scientific article

Detection of high-frequency respiratory movements during sleep

scientific article

Discovery of novel drug sensitivities in T-PLL by high-throughput ex vivo drug testing and mutation profiling.

scientific article published on 14 August 2017

Drug Target Commons 2.0: a community platform for systematic analysis of drug-target interaction profiles

Drug Target Commons: A Community Effort to Build a Consensus Knowledge Base for Drug-Target Interactions

scientific article

Drug response prediction by inferring pathway-response associations with kernelized Bayesian matrix factorization

scientific article published on September 2016

Drug-Sensitivity Screening and Genomic Characterization of 45 HPV-Negative Head and Neck Carcinoma Cell Lines for Novel Biomarkers of Drug Efficacy

scientific article published on 03 July 2018

Early metabolic markers identify potential targets for the prevention of type 2 diabetes

scientific article published on 08 June 2017

Early suppression of immune response pathways characterizes children with prediabetes in genome-wide gene expression profiling

article

Effect of medroxyprogesterone on inspiratory flow shapes during sleep in postmenopausal women

scientific article published in March 2003

Efficient estimation of emission probabilities in profile hidden Markov models

scientific article published in December 2003

Enhanced sensitivity to glucocorticoids in cytarabine-resistant AML

scientific article published on 11 November 2016

Erratum: Crowdsourced assessment of common genetic contribution to predicting anti-TNF treatment response in rheumatoid arthritis

scientific article published on 10 October 2016

Evaluation of statistical approaches for association testing in noisy drug screening data

scientific article published on 18 May 2022

Feature learning with a genetic algorithm for fluorescence fingerprinting of plant species

article

Filtering strategies for improving protein identification in high-throughput MS/MS studies

scientific article published on February 2009

From drug response profiling to target addiction scoring in cancer cell models

scientific article published on October 2015

GOlorize: a Cytoscape plug-in for network visualization with Gene Ontology-based layout and coloring

scientific article

Genetic and functional implications of an exonic TRIM55 variant in heart failure

scientific article published on 19 December 2019

Genetic variants and their interactions in disease risk prediction - machine learning and network perspectives

scientific article published on March 2013

Genetic variants and their interactions in the prediction of increased pre-clinical carotid atherosclerosis: the cardiovascular risk in young Finns study

scientific article

Genome-wide off-targets of drugs: risks and opportunities

scientific article published on 20 August 2019

Genome-wide profiling of interleukin-4 and STAT6 transcription factor regulation of human Th2 cell programming

scientific article

Genome-wide scoring of positive and negative epistasis through decomposition of quantitative genetic interaction fitness matrices

scientific article

Genoscape: a Cytoscape plug-in to automate the retrieval and integration of gene expression data and molecular networks

scientific article

Geometrical distortions in two-dimensional gels: applicable correction methods.

scientific article

Global proteomics profiling improves drug sensitivity prediction: results from a multi-omics, pan-cancer modeling approach.

scientific article published on 27 November 2017

Graph-based methods for analysing networks in cell biology

scientific article published on 30 July 2006

Hierarchical grid transformation for image warping in the analysis of two-dimensional electrophoresis gels

scientific article published on 01 November 2002

Identification of drug candidates and repurposing opportunities through compound-target interaction networks

scientific article published on October 2015

Identification of novel IL-4/Stat6-regulated genes in T lymphocytes.

scientific article

Identification of novel genes regulated by IL-12, IL-4, or TGF-beta during the early polarization of CD4+ lymphocytes

scientific article published on 01 November 2003

Identification of selective cytotoxic and synthetic lethal drug responses in triple negative breast cancer cells.

scientific article published on 10 May 2016

Immune cell contexture in the bone marrow tumor microenvironment impacts therapy response in CML

scholarly article by Oscar Brück et al published 20 June 2018 in Leukemia

Impact of normalization methods on high-throughput screening data with high hit rates and drug testing with dose-response data

scientific article

Improved detection of differentially represented DNA barcodes for high-throughput clonal phenomics

scientific article published on 01 March 2020

Improved statistical modeling of tumor growth and treatment effect in preclinical animal studies with highly heterogeneous responses in vivo

scientific article

Improving identification of differentially expressed genes by integrative analysis of Affymetrix and Illumina arrays

scientific article published in January 2006

Improving missing value estimation in microarray data with gene ontology

scientific article

Improving the efficacy-safety balance of polypharmacology in multi-target drug discovery

scientific article published on 12 December 2017

In Search of System-Wide Productivity Gains - The Role of Global Collaborations in Preclinical Translation.

scientific article

Individualized systems medicine strategy to tailor treatments for patients with chemorefractory acute myeloid leukemia.

scientific article published on 20 September 2013

Inspiratory flow shape clustering: an automated method to monitor upper airway performance during sleep

scientific article published on 3 November 2006

Integrated Analysis of Drug Sensitivity and Selectivity to Predict Synergistic Drug Combinations and Target Coaddictions in Cancer

scientific article published on 01 January 2019

Integrating probe-level expression changes across generations of Affymetrix arrays

scientific article

Interactive visual analysis of drug-target interaction networks using Drug Target Profiler, with applications to precision medicine and drug repurposing

scientific article published on 18 December 2018

Intra-tissue steroid profiling indicates differential progesterone and testosterone metabolism in the endometrium and endometriosis lesions

scientific article published on 19 August 2014

JAK/STAT-Activating Genomic Alterations Are a Hallmark of T-PLL

scientific article published on 21 November 2019

JAK1/2 and BCL2 inhibitors synergize to counteract bone marrow stromal cell-induced protection of AML.

scientific article

Kinetics and STAT4- or STAT6-mediated regulation of genes involved in lymphocyte polarization to Th1 and Th2 cells.

scientific article

Label-free quantitative phosphoproteomics with novel pairwise abundance normalization reveals synergistic RAS and CIP2A signaling.

scientific article

Learning with multiple pairwise kernels for drug bioactivity prediction.

scientific article published in July 2018

Leveraging multi-way interactions for systematic prediction of pre-clinical drug combination effects

scientific article published on 01 December 2020

Liver lipid metabolism is altered by increased circulating estrogen to androgen ratio in male mouse

scientific article published on 9 December 2015

Machine Learning of Bone Marrow Histopathology Identifies Genetic and Clinical Determinants in Patients with MDS

scientific article published on 22 March 2021

Machine learning and feature selection for drug response prediction in precision oncology applications

scientific article published on 10 August 2018

Mahalanobis distance screening of Arabidopsis mutants with chlorophyll fluorescence

scientific article published on 21 August 2010

Making sense of large-scale kinase inhibitor bioactivity data sets: a comparative and integrative analysis

scientific article

Matched preclinical designs for improved translatability

scientific article published in May 2017

MediSyn: uncertainty-aware visualization of multiple biomedical datasets to support drug treatment selection

scientific article published on 13 September 2017

Medroxyprogesterone improves nocturnal breathing in postmenopausal women with chronic obstructive pulmonary disease

scientific article

Methods for High-throughput Drug Combination Screening and Synergy Scoring.

scientific article published in January 2018

MicroRNA-135b regulates ERα, AR and HIF1AN and affects breast and prostate cancer cell growth

scientific article published on 21 March 2015

Mining high-throughput screens for cancer drug targets-lessons from yeast chemical-genomic profiling and synthetic lethality

Missing value imputation improves clustering and interpretation of gene expression microarray data

scientific article published on 18 April 2008

Model-based analysis of mechanisms responsible for sleep-induced carbon dioxide differences.

scientific article published on February 2006

Model-based prediction of sequence alignment quality

scientific article published on 4 August 2008

Modelling of killer T-cell and cancer cell subpopulation dynamics under immuno- and chemotherapies

scientific article published on 27 December 2019

Module Finding Approaches for Protein Interaction Networks

Module Finding Approaches for Protein Interaction Networks

Multi-Omics Studies towards Novel Modulators of Influenza A Virus-Host Interaction

scientific article

Multi-modal meta-analysis of cancer cell line omics profiles identifies ECHDC1 as a novel breast tumor suppressor

scientific article published on 01 March 2021

Multiobjective optimization identifies cancer-selective combination therapies

scientific article published on 28 December 2020

Network Pharmacology Strategies Toward Multi-Target Anticancer Therapies: From Computational Models to Experimental Design Principles ⬇️

scientific article published on January 1, 2014

Network pharmacology applications to map the unexplored target space and therapeutic potential of natural products

scientific article published on July 2015

Network pharmacology modeling identifies synergistic Aurora B and ZAK interaction in triple-negative breast cancer

scientific article published on 08 July 2019

Nocturnal transcutaneous carbon dioxide tension in postmenopausal estrogen users and non-users

scientific article published in September 2009

Non-invasive respiratory monitoring during wakefulness and sleep in pre- and postmenopausal women

scientific article published on 31 May 2005

Novel Lignan and stilbenoid mixture shows anticarcinogenic efficacy in preclinical PC-3M-luc2 prostate cancer model

scientific article

Novel Screening Method Identifies PI3Kα, mTOR, and IGF1R as Key Kinases Regulating Cardiomyocyte Survival

scientific article published on 16 October 2019

Novel activities of safe-in-human broad-spectrum antiviral agents

scientific article published on 23 April 2018

Obatoclax, saliphenylhalamide, and gemcitabine inhibit influenza a virus infection

scientific article

Optimized design and analysis of preclinical intervention studies in vivo

scientific article

Optimized detection of differential expression in global profiling experiments: case studies in clinical transcriptomic and quantitative proteomic datasets

scientific article published on 23 June 2009

Optimized detection of transcription factor-binding sites in ChIP-seq experiments

scientific article

Orphan G protein-coupled receptor GPRC5A modulates integrin β1-mediated epithelial cell adhesion.

scientific article published on 7 October 2016

Ovarian endometriosis signatures established through discovery and directed mass spectrometry analysis

scientific article published on 20 August 2014

Overnight features of transcutaneous carbon dioxide measurement as predictors of metabolic status

scientific article published on 5 November 2007

Overnight variability in transcutaneous carbon dioxide predicts vascular impairment in women

scientific article published on 22 February 2008

PP2A inhibition is a druggable MEK inhibitor resistance mechanism in KRAS-mutant lung cancer cells

scientific article published on 01 July 2018

Parallel Feature Selection for Regularized Least-Squares

article by Sebastian Okser et al published 2013 in Lecture Notes in Computer Science

Parameter estimation of a respiratory control model from noninvasive carbon dioxide measurements during sleep

scientific article published on 12 December 2006

Patient-customized Drug Combination Prediction and Testing for T-cell Prolymphocytic Leukemia Patients.

scientific article published on 26 February 2018

Pharmacological reactivation of MYC-dependent apoptosis induces susceptibility to anti-PD-1 immunotherapy

scientific article published in Nature Communications

Phenotypic Screening Combined with Machine Learning for Efficient Identification of Breast Cancer-Selective Therapeutic Targets

scientific article published on 02 May 2019

PhosFox: a bioinformatics tool for peptide-level processing of LC-MS/MS-based phosphoproteomic data

scientific article

Phosphoproteomics combined with quantitative 14-3-3-affinity capture identifies SIRT1 and RAI as novel regulators of cytosolic double-stranded RNA recognition pathway.

scientific article

Phosphoproteomics to Characterize Host Response During Influenza A Virus Infection of Human Macrophages

scientific article published on 2 August 2016

PolyAlign: A Versatile LC-MS Data Alignment Tool for Landmark-Selected and -Automated Use.

scientific article

Pravastatin-induced improvement in coronary reactivity and circulating ATP and ADP levels in young adults with type 1 diabetes

scientific article

Predicting drug-target interactions through integrative analysis of chemogenetic assays in yeast

scientific article

Predicting quantitative genetic interactions by means of sequential matrix approximation

scientific article

Prediction of drug combination effects with a minimal set of experiments

scientific article published on 09 December 2019

Prediction of overall survival for patients with metastatic castration-resistant prostate cancer: development of a prognostic model through a crowdsourced challenge with open clinical trial data

scientific article

Probabilistic analysis of probe reliability in differential gene expression studies with short oligonucleotide arrays

scientific article published in January 2011

Probe-level estimation improves the detection of differential splicing in Affymetrix exon array studies

scientific article published on 16 July 2009

Publisher Correction: Pharmacological reactivation of MYC-dependent apoptosis induces susceptibility to anti-PD-1 immunotherapy

scientific article published on 20 February 2019

Quality classification of tandem mass spectrometry data

scientific article

Quantitative maps of genetic interactions in yeast - comparative evaluation and integrative analysis

scientific article

Quantitative proteomics analysis of the nuclear fraction of human CD4+ cells in the early phases of IL-4-induced Th2 differentiation

scientific article

Quantitative scoring of differential drug sensitivity for individually optimized anticancer therapies

scientific article

Quantitative subcellular proteome and secretome profiling of influenza A virus-infected human primary macrophages

scientific article

RUNX1 mutations in blast-phase chronic myeloid leukemia associate with distinct phenotypes, transcriptional profiles, and drug responses

scientific article published on 11 August 2020

Rapalogs can promote cancer cell stemness in vitro in a Galectin-1 and H-ras-dependent manner.

scientific article

Re: Fatemeh Seyednasrollah, Mehrad Mahmoudian, Liisa Rautakorpi, et al. How Reliable are Trial-based Prognostic Models in Real-world Patients with Metastatic Castration-resistant Prostate Cancer? Eur Urol. 2017;71:838-40.

scientific article

Regularized Machine Learning in the Genetic Prediction of Complex Traits

scientific article (publication date: 13 November 2014)

Reinstated p53 response and high anti-T-cell leukemia activity by the novel alkylating deacetylase inhibitor tinostamustine

scientific article published on 25 February 2020

Relevance Rank Platform (RRP) for Functional Filtering of High Content Protein-Protein Interaction Data.

scientific article

Reproducibility-optimized test statistic for ranking genes in microarray studies

scientific article published in July 2008

Resampling reveals sample-level differential expression in clinical genome-wide studies

scientific article published in October 2009

Searching for Drug Synergy in Complex Dose-Response Landscapes Using an Interaction Potency Model

scientific article published on 25 September 2015

Secreted frizzled-related protein 2 (SFRP2) expression promotes lesion proliferation via canonical WNT signaling and indicates lesion borders in extraovarian endometriosis.

scientific article published on 15 February 2018

Seed-effect modeling improves the consistency of genome-wide loss-of-function screens and identifies synthetic lethal vulnerabilities in cancer cells

scientific article published on June 2017

Sleep quality, daytime sleepiness and fasting insulin levels in women with chronic obstructive pulmonary disease

scientific article published on 23 January 2005

Specific cancer-associated mutations in the switch III region of Ras increase tumorigenicity by nanocluster augmentation.

scientific article

Statistical detection of quantitative protein biomarkers provides insights into signaling networks deregulated in acute myeloid leukemia.

scientific article published on 15 October 2014

Susceptibility of low-density lipoprotein particles to aggregate depends on particle lipidome, is modifiable, and associates with future cardiovascular deaths

SynToxProfiler: An interactive analysis of drug combination synergy, toxicity and efficacy

scientific article published on 03 February 2020

SynergyFinder 2.0: visual analytics of multi-drug combination synergies

scientific article published on 04 April 2020

SynergyFinder: a web application for analyzing drug combination dose-response matrix data

scientific article

Systematic Identification of MicroRNAs That Impact on Proliferation of Prostate Cancer Cells and Display Changed Expression in Tumor Tissue

scientific article published on 19 October 2015

Systematic Mapping of Kinase Addiction Combinations in Breast Cancer Cells by Integrating Drug Sensitivity and Selectivity Profiles.

scientific article published on 22 July 2015

Systematic construction of gene coexpression networks with applications to human T helper cell differentiation process

scientific article

Systematic drug screening reveals specific vulnerabilities and co-resistance patterns in endocrine-resistant breast cancer

scientific article

Systematic drug sensitivity testing reveals synergistic growth inhibition by dasatinib or mTOR inhibitors with paclitaxel in ovarian granulosa cell tumor cells

scientific article published on 16 January 2017

Systematic identification of feature combinations for predicting drug response with Bayesian multi-view multi-task linear regression

scientific article published on July 2017

TIMMA-R: an R package for predicting synergistic multi-targeted drug combinations in cancer cell lines or patient-derived samples

scientific article

Target inhibition networks: predicting selective combinations of druggable targets to block cancer survival pathways

scientific article

Th1 response and cytotoxicity genes are down-regulated in cutaneous T-cell lymphoma

scientific article published on August 2006

The Hydroxysteroid (17β) Dehydrogenase Family Gene HSD17B12 Is Involved in the Prostaglandin Synthesis Pathway, the Ovarian Function, and Regulation of Fertility.

scientific article published on 4 August 2016

The inconvenience of data of convenience: computational research beyond post-mortem analyses

scientific article

The rocky road to personalized medicine: computational and statistical challenges

Toward more realistic drug-target interaction predictions

scientific article published on 9 April 2014

Transcriptional response networks for elucidating mechanisms of action of multitargeted agents

scientific article published on 11 March 2016

Transcutaneous carbon dioxide profile during sleep reveals metabolic risk factors in post-menopausal females.

scientific article published on 2 July 2009

UBR5 Is Coamplified with MYC in Breast Tumors and Encodes an Ubiquitin Ligase That Limits MYC-Dependent Apoptosis

scientific article published on 06 February 2020

Understanding sleep-disordered breathing through mathematical modelling

scientific article published on 14 March 2009

What is synergy? The Saariselkä agreement revisited

scientific article

Whole-genome view of the consequences of a population bottleneck using 2926 genome sequences from Finland and United Kingdom

scientific article published on February 2017

Wrapper-based selection of genetic features in genome-wide association studies through fast matrix operations

scientific article

ePCR: an R-package for survival and time-to-event prediction in advanced prostate cancer, applied to real-world patient cohorts

scientific article published in 2018

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