All Stories

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

    Article • European Urology, March 2017, Elsevier

    Prof. Tero Aittokallio, Samuli Eldfors

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

    Article • Bioinformatics, September 2016, Oxford University Press (OUP)

    Prof. Tero Aittokallio

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

    Article • Preprints, August 2016, MDPI AG

    Prof. Tero Aittokallio

  4. Stronger pre-clinical statistics by optimal animal matching

    Article • Scientific Reports, August 2016, Nature

    Prof. Tero Aittokallio, Vidal Fey

  5. Transcriptional response networks for elucidating mechanisms of action of multitargeted agents

    Article • Drug Discovery Today, July 2016, Elsevier

    Professor Julio Saez-Rodriguez, Prof. Tero Aittokallio

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

    Article • European Urology, June 2016, Elsevier

    Prof. Tero Aittokallio

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

    Article • Molecular Cancer, May 2016, Springer Science + Business Media

    Prof. Tero Aittokallio

  8. Methods for High-Throughput Drug Combination Screening and Synergy Scoring

    Article • May 2016, Cold Spring Harbor Laboratory Press

    Prof. Tero Aittokallio

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

    Article • Molecular & Cellular Proteomics, October 2015, American Society for Biochemistry & Molecular Biology (ASBMB)

    Prof. Tero Aittokallio

  10. Identification of drug candidates and repurposing opportunities through compound–target interaction networks

    Article • Expert Opinion on Drug Discovery, October 2015, Informa Healthcare

    Prof. Tero Aittokallio

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

    Article • Disease Models & Mechanisms, October 2015, The Company of Biologists

    Prof. Tero Aittokallio

  12. What is synergy? The Saariselkä agreement revisited

    Article • Frontiers in Pharmacology, September 2015, Frontiers

    Prof. Tero Aittokallio

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

    Article • Scientific Reports, August 2015, Nature

    Prof. Tero Aittokallio

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

    Article • Bioinformatics, August 2015, Oxford University Press (OUP)

    Prof. Tero Aittokallio

  15. Abstract 1700: Dasatinib and everolimus show synergistic growth inhibition with paclitaxel in an ovarian granulosa cell tumor model

    Article • Cancer Research, August 2015, American Association for Cancer Research (AACR)

    Prof. Tero Aittokallio

  16. Abstract 5328: Protein phosphatase 2A activity is a major determinant of therapy response in cancer cells

    Article • Cancer Research, August 2015, American Association for Cancer Research (AACR)

    Prof. Tero Aittokallio

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

    Article • Chemistry & Biology, August 2015, Elsevier

    Prof. Tero Aittokallio

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

    Article • Natural Product Reports, January 2015, Royal Society of Chemistry

    Prof. Tero Aittokallio

  19. Searching for Drug Synergy in Complex Dose–Response Landscapes Using an Interaction Potency Model

    Article • Computational and Structural Biotechnology Journal, January 2015, Elsevier

    Prof. Tero Aittokallio

  20. Regularized Machine Learning in the Genetic Prediction of Complex Traits

    Article • PLoS Genetics, November 2014, PLOS

    Prof. Tero Aittokallio, Tapio Pahikkala

  21. Ovarian Endometriosis Signatures Established through Discovery and Directed Mass Spectrometry Analysis

    Article • Journal of Proteome Research, November 2014, American Chemical Society (ACS)

    Prof. Tero Aittokallio

  22. Castration Induces Up-Regulation of Intratumoral Androgen Biosynthesis and Androgen Receptor Expression in an Orthotopic VCaP Human Prostate Cancer Xenograft Model

    Article • American Journal Of Pathology, August 2014, Elsevier

    Prof. Tero Aittokallio

  23. Quantitative scoring of differential drug sensitivity for individually optimized anticancer therapies

    Article • Scientific Reports, June 2014, Springer Science + Business Media

    Prof. Tero Aittokallio

  24. Novel Lignan and Stilbenoid Mixture Shows Anticarcinogenic Efficacy in Preclinical PC-3M-luc2 Prostate Cancer Model

    Article • PLoS ONE, April 2014, PLOS

    Prof. Tero Aittokallio

  25. Making Sense of Large-Scale Kinase Inhibitor Bioactivity Data Sets: A Comparative and Integrative Analysis

    Article • Journal of Chemical Information and Computer Sciences, March 2014, American Chemical Society (ACS)

    Prof. Tero Aittokallio

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

    Article • Current Pharmaceutical Design, January 2014, Bentham Science Publishers

    Prof. Tero Aittokallio

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

    Article • January 2014, Springer Science + Business Media

    Prof. Tero Aittokallio

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

    Article • Proteome Science, January 2014, Springer Science + Business Media

    Prof. Tero Aittokallio

  29. Target Inhibition Networks: Predicting Selective Combinations of Druggable Targets to Block Cancer Survival Pathways

    Article • PLoS Computational Biology, September 2013, PLOS

    Prof. Tero Aittokallio

  30. Genetic variants and their interactions in disease risk prediction – machine learning and network perspectives

    Article • BioData Mining, March 2013, Springer Science + Business Media

    Prof. Tero Aittokallio, Tapio Pahikkala

  31. Predicting drug–target interactions through integrative analysis of chemogenetic assays in yeast

    Article • Molecular BioSystems, January 2013, Royal Society of Chemistry

    Tero Aittokallio, Prof. Tero Aittokallio

  32. Parallel Feature Selection for Regularized Least-Squares

    Article • January 2013, Springer Science + Business Media

    Prof. Tero Aittokallio

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

    Article • BioData Mining, March 2012, Springer Science + Business Media

    Prof. Tero Aittokallio

  34. The rocky road to personalized medicine: computational and statistical challenges

    Article • Personalized Medicine, March 2012, Future Medicine

    Prof. Tero Aittokallio

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

    Article • Frontiers in Physiology, January 2012, Frontiers

    Prof. Tero Aittokallio, Dr Tuomas O Kiviniemi

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

    Article • Algorithms for Molecular Biology, January 2012, Springer Science + Business Media

    Prof. Tero Aittokallio

  37. Fast and parallelized greedy forward selection of genetic variants in Genome-wide association studies

    Article • December 2011, Institute of Electrical & Electronics Engineers (IEEE)

    Prof. Tero Aittokallio

  38. Quantitative Subcellular Proteome and Secretome Profiling of Influenza A Virus-Infected Human Primary Macrophages

    Article • PLoS Pathogens, May 2011, PLOS

    Prof. Tero Aittokallio

  39. Quantitative maps of genetic interactions in yeast - Comparative evaluation and integrative analysis

    Article • BMC Systems Biology, January 2011, Springer Science + Business Media

    Prof. Tero Aittokallio

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

    Article • International Journal of Proteomics, January 2011, Hindawi Publishing Corporation

    Prof. Tero Aittokallio

  41. Mahalanobis distance screening of Arabidopsis mutants with chlorophyll fluorescence

    Article • Photosynthesis Research, August 2010, Springer Science + Business Media

    Dr Esa Tyystjärvi, Prof. Tero Aittokallio

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

    Article • Journal of Autoimmunity, August 2010, Elsevier

    Prof. Tero Aittokallio

  43. Genome-Wide Scoring of Positive and Negative Epistasis through Decomposition of Quantitative Genetic Interaction Fitness Matrices

    Article • PLoS ONE, July 2010, PLOS

    Prof. Tero Aittokallio

  44. An update on clinical proteomics in Alzheimer’s research

    Article • Journal of Neurochemistry, March 2010, Wiley

    Prof. Tero Aittokallio

  45. Understanding sleep-disordered breathing through mathematical modelling

    Article • Sleep Medicine Reviews, October 2009, Elsevier

    Prof. Tero Aittokallio

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

    Article • PROTEOMICS, February 2009, Wiley

    Prof. Tero Aittokallio

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

    Article • Genome Biology, January 2009, Springer Science + Business Media

    Prof. Tero Aittokallio

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

    Article • BMC Genomics, January 2009, Springer Science + Business Media

    Prof. Tero Aittokallio

  49. Predicting Quantitative Genetic Interactions by Means of Sequential Matrix Approximation

    Article • PLoS ONE, September 2008, PLOS

    Prof. Tero Aittokallio

  50. Overnight variability in transcutaneous carbon dioxide predicts vascular impairment in women

    Article • Experimental Physiology, June 2008, Wiley

    Prof. Tero Aittokallio

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

    Article • PROTEOMICS, February 2008, Wiley

    Prof. Tero Aittokallio

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

    Article • Artificial Intelligence in Medicine, January 2008, Elsevier

    Prof. Tero Aittokallio

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

    Article • BMC Bioinformatics, January 2008, Springer Science + Business Media

    Prof. Tero Aittokallio

  54. Can carotid body perfusion act as a respiratory controller?

    Article • Journal of Theoretical Biology, December 2007, Elsevier

    Prof. Tero Aittokallio

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

    Article • Electrophoresis, March 2007, Wiley

    Prof. Tero Aittokallio, Tapio Pahikkala

  56. Inspiratory flow shape clustering: An automated method to monitor upper airway performance during sleep

    Article • Computer Methods and Programs in Biomedicine, January 2007, Elsevier

    Prof. Tero Aittokallio

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

    Article • Respiratory Physiology & Neurobiology, January 2006, Elsevier

    Prof. Tero Aittokallio

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

    Article • Respiratory Medicine, July 2005, Elsevier

    Prof. Tero Aittokallio

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

    Article • April 2005, Springer Science + Business Media

    Prof. Tero Aittokallio

  60. Statistical Methods for Identifying Conserved Residues in Multiple Sequence Alignment

    Article • Statistical Applications in Genetics and Molecular Biology, January 2004, De Gruyter

    Prof. Tero Aittokallio

  61. Genetic Feature Learning Algorithm for Fluorescence Fingerprinting of Plants

    Article • January 2004, Springer Science + Business Media

    Dr Esa Tyystjärvi, Prof. Tero Aittokallio

  62. Computational Strategies for Analyzing Data in Gene Expression Microarray Experiments

    Article • Journal of Bioinformatics and Computational Biology, October 2003, World Scientific Pub Co Pte Lt

    Prof. Tero Aittokallio

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

    Article • Respiratory Physiology & Neurobiology, March 2003, Elsevier

    Prof. Tero Aittokallio

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

    Article • PROTEOMICS, November 2002, Wiley

    Prof. Tero Aittokallio

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

    Article • Maturitas, July 2001, Elsevier

    Prof. Tero Aittokallio

  66. Automated detection of differentially expressed fragments in mRNA differential display

    Article • Electrophoresis, June 2001, Wiley

    Prof. Tero Aittokallio

  67. A model of a snorer's upper airway

    Article • Mathematical Biosciences, March 2001, Elsevier

    Prof. Tero Aittokallio

  68. Analysis of Inspiratory Flow Shapes in Patients With Partial Upper-Airway Obstruction During Sleep

    Article • CHEST Journal, January 2001, Elsevier

    Prof. Tero Aittokallio

  69. Analysis of similarity of electrophoretic patterns in mRNA differential display

    Article • Electrophoresis, August 2000, Wiley

    Prof. Tero Aittokallio

  70. Module Finding Approaches for Protein Interaction Networks

    Article • IGI Global

    Prof. Tero Aittokallio

  71. Automated Pattern Ranking in Differential Display Data Analysis

    Article • Springer Science + Business Media

    Prof. Tero Aittokallio

  72. Predicting Gene Expression from Combined Expression and Promoter Profile Similarity with Application to Missing Value Imputation

    Article • Springer Science + Business Media

    Prof. Tero Aittokallio