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Prostate Cancer Research Center

Predictive Society and Data Analytics Lab <!--Emmert-Streib-->

2020

  1. Emmert-Streib, F, Yli-Harja, O, Dehmer, M. Artificial Intelligence: A Clarification of Misconceptions, Myths and Desired Status. Front Artif Intell. 2020;3 :524339. doi: 10.3389/frai.2020.524339. PubMed PMID:33733197 PubMed Central PMC7944138.
  2. Emmert-Streib, F, Yang, Z, Feng, H, Tripathi, S, Dehmer, M. An Introductory Review of Deep Learning for Prediction Models With Big Data. Front Artif Intell. 2020;3 :4. doi: 10.3389/frai.2020.00004. PubMed PMID:33733124 PubMed Central PMC7861305.
  3. Manjang, K, Tripathi, S, Yli-Harja, O, Dehmer, M, Emmert-Streib, F. Graph-based exploitation of gene ontology using GOxploreR for scrutinizing biological significance. Sci Rep. 2020;10 (1):16672. doi: 10.1038/s41598-020-73326-3. PubMed PMID:33028846 PubMed Central PMC7542435.
  4. Perera, N, Dehmer, M, Emmert-Streib, F. Named Entity Recognition and Relation Detection for Biomedical Information Extraction. Front Cell Dev Biol. 2020;8 :673. doi: 10.3389/fcell.2020.00673. PubMed PMID:32984300 PubMed Central PMC7485218.
  5. Doan, P, Musa, A, Murugesan, A, Sipilä, V, Candeias, NR, Emmert-Streib, F et al.. Glioblastoma Multiforme Stem Cell Cycle Arrest by Alkylaminophenol Through the Modulation of EGFR and CSC Signaling Pathways. Cells. 2020;9 (3):. doi: 10.3390/cells9030681. PubMed PMID:32164385 PubMed Central PMC7140667.
  6. Yang, Z, Dehmer, M, Yli-Harja, O, Emmert-Streib, F. Combining deep learning with token selection for patient phenotyping from electronic health records. Sci Rep. 2020;10 (1):1432. doi: 10.1038/s41598-020-58178-1. PubMed PMID:31996705 PubMed Central PMC6989657.

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2019

  1. Emmert-Streib, F, Dehmer, M, Yli-Harja, O. Ensuring Quality Standards and Reproducible Research for Data Analysis Services in Oncology: A Cooperative Service Model. Front Cell Dev Biol. 2019;7 :349. doi: 10.3389/fcell.2019.00349. PubMed PMID:31921859 PubMed Central PMC6929679.
  2. Emmert-Streib, F, Yli-Harja, O, Dehmer, M. Utilizing Social Media Data for Psychoanalysis to Study Human Personality. Front Psychol. 2019;10 :2596. doi: 10.3389/fpsyg.2019.02596. PubMed PMID:31803123 PubMed Central PMC6873989.
  3. Smolander, J, Stupnikov, A, Glazko, G, Dehmer, M, Emmert-Streib, F. Comparing biological information contained in mRNA and non-coding RNAs for classification of lung cancer patients. BMC Cancer. 2019;19 (1):1176. doi: 10.1186/s12885-019-6338-1. PubMed PMID:31796020 PubMed Central PMC6892207.
  4. Dehmer, M, Chen, Z, Emmert-Streib, F, Tripathi, S, Mowshowitz, A, Levitchi, A et al.. Measuring the complexity of directed graphs: A polynomial-based approach. PLoS One. 2019;14 (11):e0223745. doi: 10.1371/journal.pone.0223745. PubMed PMID:31725742 PubMed Central PMC6855486.
  5. Emmert-Streib, F, Moutari, S, Dehmer, M. A comprehensive survey of error measures for evaluating binary decision making in data science. Wiley Interdiscip Rev Data Min Knowl Discov. 2019;9 (5):e1303. doi: 10.1002/widm.1303. PubMed PMID:31656552 PubMed Central PMC6777486.
  6. Glazko, G, Zybailov, B, Emmert-Streib, F, Baranova, A, Rahmatallah, Y. Proteome-transcriptome alignment of molecular portraits achieved by self-contained gene set analysis: Consensus colon cancer subtypes case study. PLoS One. 2019;14 (8):e0221444. doi: 10.1371/journal.pone.0221444. PubMed PMID:31437237 PubMed Central PMC6705791.
  7. Musa, A, Tripathi, S, Dehmer, M, Emmert-Streib, F. L1000 Viewer: A Search Engine and Web Interface for the LINCS Data Repository. Front Genet. 2019;10 :557. doi: 10.3389/fgene.2019.00557. PubMed PMID:31258549 PubMed Central PMC6588157.
  8. Musa, A, Tripathi, S, Dehmer, M, Yli-Harja, O, Kauffman, SA, Emmert-Streib, F et al.. Systems Pharmacogenomic Landscape of Drug Similarities from LINCS data: Drug Association Networks. Sci Rep. 2019;9 (1):7849. doi: 10.1038/s41598-019-44291-3. PubMed PMID:31127155 PubMed Central PMC6534546.
  9. Smolander, J, Dehmer, M, Emmert-Streib, F. Comparing deep belief networks with support vector machines for classifying gene expression data from complex disorders. FEBS Open Bio. 2019;9 (7):1232-1248. doi: 10.1002/2211-5463.12652. PubMed PMID:31074948 PubMed Central PMC6609581.
  10. Ghorbani, M, Dehmer, M, Rajabi-Parsa, M, Mowshowitz, A, Emmert-Streib, F. On Properties of Distance-Based Entropies on Fullerene Graphs. Entropy (Basel). 2019;21 (5):. doi: 10.3390/e21050482. PubMed PMID:33267196 PubMed Central PMC7514971.
  11. Moore, D, Simoes, RM, Dehmer, M, Emmert-Streib, F. Prostate Cancer Gene Regulatory Network Inferred from RNA-Seq Data. Curr Genomics. 2019;20 (1):38-48. doi: 10.2174/1389202919666181107122005. PubMed PMID:31015790 PubMed Central PMC6446481.
  12. Doan, P, Musa, A, Candeias, NR, Emmert-Streib, F, Yli-Harja, O, Kandhavelu, M et al.. Alkylaminophenol Induces G1/S Phase Cell Cycle Arrest in Glioblastoma Cells Through p53 and Cyclin-Dependent Kinase Signaling Pathway. Front Pharmacol. 2019;10 :330. doi: 10.3389/fphar.2019.00330. PubMed PMID:31001122 PubMed Central PMC6454069.
  13. Azam, MF, Musa, A, Dehmer, M, Yli-Harja, OP, Emmert-Streib, F. Global Genetics Research in Prostate Cancer: A Text Mining and Computational Network Theory Approach. Front Genet. 2019;10 :70. doi: 10.3389/fgene.2019.00070. PubMed PMID:30838019 PubMed Central PMC6383410.
  14. Viswanathan, A, Kute, D, Musa, A, Konda Mani, S, Sipilä, V, Emmert-Streib, F et al.. 2-(2-(2,4-dioxopentan-3-ylidene)hydrazineyl)benzonitrile as novel inhibitor of receptor tyrosine kinase and PI3K/AKT/mTOR signaling pathway in glioblastoma. Eur J Med Chem. 2019;166 :291-303. doi: 10.1016/j.ejmech.2019.01.021. PubMed PMID:30731398 .

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2018

  1. Stupnikov, A, O’Reilly, PG, McInerney, CE, Roddy, AC, Dunne, PD, Gilmore, A et al.. Impact of Variable RNA-Sequencing Depth on Gene Expression Signatures and Target Compound Robustness: Case Study Examining Brain Tumor (Glioma) Disease Progression. JCO Precis Oncol. 2018;2 :. doi: 10.1200/PO.18.00014. PubMed PMID:30324181 PubMed Central PMC6186166.
  2. Emmert-Streib, F, Yli-Harja, OP, Dehmer, M. Data Analytics Applications for Streaming Data From Social Media: What to Predict?. Front Big Data. 2018;1 :2. doi: 10.3389/fdata.2018.00002. PubMed PMID:33693318 PubMed Central PMC7931880.
  3. Musa, A, Tripathi, S, Kandhavelu, M, Dehmer, M, Emmert-Streib, F. Harnessing the biological complexity of Big Data from LINCS gene expression signatures. PLoS One. 2018;13 (8):e0201937. doi: 10.1371/journal.pone.0201937. PubMed PMID:30157183 PubMed Central PMC6114505.
  4. Baltakys, K, Kanniainen, J, Emmert-Streib, F. Multilayer Aggregation with Statistical Validation: Application to Investor Networks. Sci Rep. 2018;8 (1):8198. doi: 10.1038/s41598-018-26575-2. PubMed PMID:29844512 PubMed Central PMC5974194.
  5. Musa, A, Ghoraie, LS, Zhang, SD, Glazko, G, Yli-Harja, O, Dehmer, M et al.. A review of connectivity map and computational approaches in pharmacogenomics. Brief Bioinform. 2018;19 (3):506-523. doi: 10.1093/bib/bbw112. PubMed PMID:28069634 PubMed Central PMC5952941.

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2017

  1. Emmert-Streib, F, Dehmer, M, Yli-Harja, O. Lessons from the Human Genome Project: Modesty, Honesty, and Realism. Front Genet. 2017;8 :184. doi: 10.3389/fgene.2017.00184. PubMed PMID:29218057 PubMed Central PMC5703740.
  2. Glazko, G, Rahmatallah, Y, Zybailov, B, Emmert-Streib, F. Extracting the Strongest Signals from Omics Data: Differentially Expressed Pathways and Beyond. Methods Mol Biol. 2017;1613 :125-159. doi: 10.1007/978-1-4939-7027-8_7. PubMed PMID:28849561 PubMed Central PMC5846121.
  3. Tripathi, S, Lloyd-Price, J, Ribeiro, A, Yli-Harja, O, Dehmer, M, Emmert-Streib, F et al.. sgnesR: An R package for simulating gene expression data from an underlying real gene network structure considering delay parameters. BMC Bioinformatics. 2017;18 (1):325. doi: 10.1186/s12859-017-1731-8. PubMed PMID:28676075 PubMed Central PMC5496254.
  4. Musa, A, Ghoraie, LS, Zhang, SD, Glazko, G, Yli-Harja, O, Dehmer, M et al.. A review of connectivity map and computational approaches in pharmacogenomics. Brief Bioinform. 2017;18 (5):903. doi: 10.1093/bib/bbx023. PubMed PMID:28334173 PubMed Central PMC6113891.
  5. Rahmatallah, Y, Zybailov, B, Emmert-Streib, F, Glazko, G. GSAR: Bioconductor package for Gene Set analysis in R. BMC Bioinformatics. 2017;18 (1):61. doi: 10.1186/s12859-017-1482-6. PubMed PMID:28118818 PubMed Central PMC5259853.

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2016

  1. Stupnikov, A, Tripathi, S, de Matos Simoes, R, McArt, D, Salto-Tellez, M, Glazko, G et al.. samExploreR: exploring reproducibility and robustness of RNA-seq results based on SAM files. Bioinformatics. 2016;32 (21):3345-3347. doi: 10.1093/bioinformatics/btw475. PubMed PMID:27402900 .
  2. Emmert-Streib, F, Dehmer, M, Yli-Harja, O. Against Dataism and for Data Sharing of Big Biomedical and Clinical Data with Research Parasites. Front Genet. 2016;7 :154. doi: 10.3389/fgene.2016.00154. PubMed PMID:27630666 PubMed Central PMC5005320.
  3. Emmert-Streib, F, Tuomisto, L, Yli-Harja, O. The Need for Formally Defining “Modern Medicine” by Means of Experimental Design. Front Genet. 2016;7 :60. doi: 10.3389/fgene.2016.00060. PubMed PMID:27148357 PubMed Central PMC4837140.
  4. Tripathi, S, Moutari, S, Dehmer, M, Emmert-Streib, F. Comparison of module detection algorithms in protein networks and investigation of the biological meaning of predicted modules. BMC Bioinformatics. 2016;17 :129. doi: 10.1186/s12859-016-0979-8. PubMed PMID:26987731 PubMed Central PMC4797184.
  5. Buckley, NE, Haddock, P, De Matos Simoes, R, Parkes, E, Irwin, G, Emmert-Streib, F et al.. A BRCA1 deficient, NFκB driven immune signal predicts good outcome in triple negative breast cancer. Oncotarget. 2016;7 (15):19884-96. doi: 10.18632/oncotarget.7865. PubMed PMID:26943587 PubMed Central PMC4991425.
  6. Emmert-Streib, F, Moutari, S, Dehmer, M. The Process of Analyzing Data is the Emergent Feature of Data Science. Front Genet. 2016;7 :12. doi: 10.3389/fgene.2016.00012. PubMed PMID:26904100 PubMed Central PMC4746257.
  7. Rahmatallah, Y, Emmert-Streib, F, Glazko, G. Gene set analysis approaches for RNA-seq data: performance evaluation and application guideline. Brief Bioinform. 2016;17 (3):393-407. doi: 10.1093/bib/bbv069. PubMed PMID:26342128 PubMed Central PMC4870397.

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2015

  1. Emmert-Streib, F, Dehmer, M. Biological networks: the microscope of the twenty-first century?. Front Genet. 2015;6 :307. doi: 10.3389/fgene.2015.00307. PubMed PMID:26528327 PubMed Central PMC4602153.
  2. Olsen, C, Fleming, K, Prendergast, N, Rubio, R, Emmert-Streib, F, Bontempi, G et al.. Using shRNA experiments to validate gene regulatory networks. Genom Data. 2015;4 :123-6. doi: 10.1016/j.gdata.2015.03.011. PubMed PMID:26484195 PubMed Central PMC4535466.
  3. Dehmer, M, Emmert-Streib, F, Shi, Y, Stefu, M, Tripathi, S. Discrimination Power of Polynomial-Based Descriptors for Graphs by Using Functional Matrices. PLoS One. 2015;10 (10):e0139265. doi: 10.1371/journal.pone.0139265. PubMed PMID:26479495 PubMed Central PMC4610680.
  4. Rahmatallah, Y, Emmert-Streib, F, Glazko, G. Gene set analysis approaches for RNA-seq data: performance evaluation and application guideline. Brief Bioinform. 2016;17 (3):393-407. doi: 10.1093/bib/bbv069. PubMed PMID:26342128 PubMed Central PMC4870397.
  5. Alvi, MA, McArt, DG, Kelly, P, Fuchs, MA, Alderdice, M, McCabe, CM et al.. Comprehensive molecular pathology analysis of small bowel adenocarcinoma reveals novel targets with potential for clinical utility. Oncotarget. 2015;6 (25):20863-74. doi: 10.18632/oncotarget.4576. PubMed PMID:26315110 PubMed Central PMC4673235.
  6. Stupnikov, A, Glazko, GV, Emmert-Streib, F. Effects of subsampling on characteristics of RNA-seq data from triple-negative breast cancer patients. Chin J Cancer. 2015;34 (10):427-38. doi: 10.1186/s40880-015-0040-8. PubMed PMID:26253000 PubMed Central PMC4593382.
  7. Dehmer, M, Kurt, Z, Emmert-Streib, F, Them, C, Schulc, E, Hofer, S et al.. Structural Analysis of Treatment Cycles Representing Transitions between Nursing Organizational Units Inferred from Diabetes. PLoS One. 2015;10 (6):e0127152. doi: 10.1371/journal.pone.0127152. PubMed PMID:26030296 PubMed Central PMC4452654.
  8. de Matos Simoes, R, Dalleau, S, Williamson, KE, Emmert-Streib, F. Urothelial cancer gene regulatory networks inferred from large-scale RNAseq, Bead and Oligo gene expression data. BMC Syst Biol. 2015;9 :21. doi: 10.1186/s12918-015-0165-z. PubMed PMID:25971253 PubMed Central PMC4460634.
  9. Emmert-Streib, F, Zhang, SD, Hamilton, P. Computational cancer biology: education is a natural key to many locks. BMC Cancer. 2015;15 :7. doi: 10.1186/s12885-014-1002-2. PubMed PMID:25588624 PubMed Central PMC4298945.

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