Frank Emmert-Streib

Summary

Publications

  1. pmc Assessment method for a power analysis to identify differentially expressed pathways
    Shailesh Tripathi
    Computational Biology and Machine Learning Lab, Center for Cancer Research and Cell Biology, School of Medicine, Dentistry and Biomedical Sciences, Queen s University Belfast, Belfast, United Kingdom
    PLoS ONE 7:e37510. 2012
  2. pmc Bagging statistical network inference from large-scale gene expression data
    Ricardo de Matos Simoes
    Computational Biology and Machine Learning Lab, Center for Cancer Research and Cell Biology, School of Medicine, Dentistry and Biomedical Sciences, Queen s University Belfast, Belfast, United Kingdom
    PLoS ONE 7:e33624. 2012
  3. pmc Ensuring the statistical soundness of competitive gene set approaches: gene filtering and genome-scale coverage are essential
    Shailesh Tripathi
    Computational Biology and Machine Learning Laboratory, Center for Cancer Research and Cell Biology, School of Medicine, Dentistry and Biomedical Sciences, Queen s University Belfast, Belfast, 97 Lisburn Road, Belfast BT9 7BL, UK
    Nucleic Acids Res 41:e82. 2013
  4. pmc Statistical inference and reverse engineering of gene regulatory networks from observational expression data
    Frank Emmert-Streib
    Computational Biology and Machine Learning Lab, School of Medicine, Dentistry and Biomedical Sciences, Center for Cancer Research and Cell Biology, Queen s University Belfast Belfast, UK
    Front Genet 3:8. 2012
  5. pmc Influence of statistical estimators of mutual information and data heterogeneity on the inference of gene regulatory networks
    Ricardo de Matos Simoes
    Computational Biology and Machine Learning Lab, Center for Cancer Research and Cell Biology, School of Medicine, Dentistry and Biomedical Sciences, Queen s University Belfast, Belfast, United Kingdom
    PLoS ONE 6:e29279. 2011
  6. pmc Personalized medicine: Has it started yet? A reconstruction of the early history
    Frank Emmert-Streib
    Computational Biology and Machine Learning Laboratory, Center for Cancer Research and Cell Biology, School of Medicine, Dentistry and Biomedical Sciences, Faculty of Medicine, Health and Life Sciences, Queen s University Belfast Belfast, UK
    Front Genet 3:313. 2012
  7. doi request reprint Dry computational approaches for wet medical problems
    Frank Emmert-Streib
    Computational Biology and Machine Learning Laboratory, Center for Cancer Research and Cell Biology, School of Medicine, Dentistry and Biomedical Sciences, Queen s University Belfast, Lisburn Road 97, Belfast, UK
    J Transl Med 12:26. 2014
  8. pmc Influence of the experimental design of gene expression studies on the inference of gene regulatory networks: environmental factors
    Frank Emmert-Streib
    Computational Biology and Machine Learning Laboratory, Center for Cancer Research and Cell Biology, School of Medicine, Dentistry and Biomedical Sciences, Faculty of Medicine, Health and Life Sciences, Queen s University Belfast, Belfast, UK
    Peerj 1:e10. 2013
  9. pmc Detecting sequence dependent transcriptional pauses from RNA and protein number time series
    Frank Emmert-Streib
    Computational Biology and Machine Learning Lab, Center for CancerResearch and Cell Biology, School of Medicine, Dentistry and Biomedical Sciences, Queen s University Belfast, Belfast, UK
    BMC Bioinformatics 13:152. 2012
  10. pmc Structural properties and complexity of a new network class: Collatz step graphs
    Frank Emmert-Streib
    Computational Biology and Machine Learning Laboratory, Center for Cancer Research and Cell Biology, School of Medicine, Dentistry and Biomedical Sciences, Faculty of Medicine, Health and Life Sciences, Queen s University Belfast, Belfast, United Kingdom
    PLoS ONE 8:e56461. 2013

Collaborators

Detail Information

Publications37

  1. pmc Assessment method for a power analysis to identify differentially expressed pathways
    Shailesh Tripathi
    Computational Biology and Machine Learning Lab, Center for Cancer Research and Cell Biology, School of Medicine, Dentistry and Biomedical Sciences, Queen s University Belfast, Belfast, United Kingdom
    PLoS ONE 7:e37510. 2012
    ..Our study highlights the sensitivity of the studied methods on the parameters of the system...
  2. pmc Bagging statistical network inference from large-scale gene expression data
    Ricardo de Matos Simoes
    Computational Biology and Machine Learning Lab, Center for Cancer Research and Cell Biology, School of Medicine, Dentistry and Biomedical Sciences, Queen s University Belfast, Belfast, United Kingdom
    PLoS ONE 7:e33624. 2012
    ..An implementation of BC3NET is freely available as an R package from the CRAN repository...
  3. pmc Ensuring the statistical soundness of competitive gene set approaches: gene filtering and genome-scale coverage are essential
    Shailesh Tripathi
    Computational Biology and Machine Learning Laboratory, Center for Cancer Research and Cell Biology, School of Medicine, Dentistry and Biomedical Sciences, Queen s University Belfast, Belfast, 97 Lisburn Road, Belfast BT9 7BL, UK
    Nucleic Acids Res 41:e82. 2013
    ..For this reason, for biomedical and clinical studies, we strongly advice not to use GSEA, GSEArot and GAGE for such data sets...
  4. pmc Statistical inference and reverse engineering of gene regulatory networks from observational expression data
    Frank Emmert-Streib
    Computational Biology and Machine Learning Lab, School of Medicine, Dentistry and Biomedical Sciences, Center for Cancer Research and Cell Biology, Queen s University Belfast Belfast, UK
    Front Genet 3:8. 2012
    ..We complement the above by surveying global and local evaluation measures for assessing the performance of inference algorithms...
  5. pmc Influence of statistical estimators of mutual information and data heterogeneity on the inference of gene regulatory networks
    Ricardo de Matos Simoes
    Computational Biology and Machine Learning Lab, Center for Cancer Research and Cell Biology, School of Medicine, Dentistry and Biomedical Sciences, Queen s University Belfast, Belfast, United Kingdom
    PLoS ONE 6:e29279. 2011
    ..Hence, our study provides guidance for an efficient design of a simulation study in the context of network inference, supporting a systems approach...
  6. pmc Personalized medicine: Has it started yet? A reconstruction of the early history
    Frank Emmert-Streib
    Computational Biology and Machine Learning Laboratory, Center for Cancer Research and Cell Biology, School of Medicine, Dentistry and Biomedical Sciences, Faculty of Medicine, Health and Life Sciences, Queen s University Belfast Belfast, UK
    Front Genet 3:313. 2012
    ..That means we are providing a data-driven perspective of this field to estimate its current status and potential problems...
  7. doi request reprint Dry computational approaches for wet medical problems
    Frank Emmert-Streib
    Computational Biology and Machine Learning Laboratory, Center for Cancer Research and Cell Biology, School of Medicine, Dentistry and Biomedical Sciences, Queen s University Belfast, Lisburn Road 97, Belfast, UK
    J Transl Med 12:26. 2014
    ..The aim of the conference was to bring together leading experts from a variety of different areas that are key for Systems Medicine to exchange novel findings and promote interdisciplinary ideas and collaborations...
  8. pmc Influence of the experimental design of gene expression studies on the inference of gene regulatory networks: environmental factors
    Frank Emmert-Streib
    Computational Biology and Machine Learning Laboratory, Center for Cancer Research and Cell Biology, School of Medicine, Dentistry and Biomedical Sciences, Faculty of Medicine, Health and Life Sciences, Queen s University Belfast, Belfast, UK
    Peerj 1:e10. 2013
    ..Overall, we find that different statistical inference methods lead to comparable, but condition-specific results. Further, our results suggest that non-steady-state data enhance the inferability of regulatory networks...
  9. pmc Detecting sequence dependent transcriptional pauses from RNA and protein number time series
    Frank Emmert-Streib
    Computational Biology and Machine Learning Lab, Center for CancerResearch and Cell Biology, School of Medicine, Dentistry and Biomedical Sciences, Queen s University Belfast, Belfast, UK
    BMC Bioinformatics 13:152. 2012
    ..So far, a few pause-prone sequences have been identified from in vitro measurements of transcription elongation kinetics...
  10. pmc Structural properties and complexity of a new network class: Collatz step graphs
    Frank Emmert-Streib
    Computational Biology and Machine Learning Laboratory, Center for Cancer Research and Cell Biology, School of Medicine, Dentistry and Biomedical Sciences, Faculty of Medicine, Health and Life Sciences, Queen s University Belfast, Belfast, United Kingdom
    PLoS ONE 8:e56461. 2013
    ..Interestingly, in contrast to many other network models including the small-world network from Watts & Strogatz, we find that CS graphs become 'smaller' with an increasing size...
  11. pmc Harnessing the complexity of gene expression data from cancer: from single gene to structural pathway methods
    Frank Emmert-Streib
    Computational Biology and Machine Learning Laboratory, Queen s University Belfast, Belfast, UK
    Biol Direct 7:44. 2012
    ..Further, we provide recommendations for the selection of such analysis methods...
  12. pmc A Bayesian analysis of the chromosome architecture of human disorders by integrating reductionist data
    Frank Emmert-Streib
    Computational Biology and Machine Learning Lab, Center forCancer Research and Cell Biology, School of Medicine, Dentistry and Biomedical Sciences, Queen s University Belfast, 97 Lisburn Road, Belfast, UK
    Sci Rep 2:513. 2012
    ....
  13. pmc Structural measures for network biology using QuACN
    Laurin A J Mueller
    Institute for Bioinformatics and Translational Research, Department of Biomedical Sciences and Engineering, University for Health Sciences, Medical Informatics and Technology UMIT, EWZ 1, Hall in Tirol, Austria
    BMC Bioinformatics 12:492. 2011
    ..Hence, there is a strong need to provide freely available software packages to calculate and demonstrate the appropriate usage of structural graph measures in network biology...
  14. pmc Exploring statistical and population aspects of network complexity
    Frank Emmert-Streib
    Computational Biology and Machine Learning Lab, Center for Cancer Research and Cell Biology, School of Medicine, Dentistry and Biomedical Sciences, Queen s University Belfast, Belfast, United Kingdom
    PLoS ONE 7:e34523. 2012
    ..In order to apply our measure practically, we provide a statistical estimator for the diversity score, which is based on a finite number of samples...
  15. pmc Limitations of gene duplication models: evolution of modules in protein interaction networks
    Frank Emmert-Streib
    Computational Biology and Machine Learning Lab, Center for Cancer Research and Cell Biology, School of Medicine, Dentistry and Biomedical Sciences, Queen s University Belfast, Belfast, United Kingdom
    PLoS ONE 7:e35531. 2012
    ..This observation reveals our incomplete understanding of the structural evolution of protein networks on the module level...
  16. pmc Parametric construction of episode networks from pseudoperiodic time series based on mutual information
    Frank Emmert-Streib
    Computational Biology and Machine Learning Lab, Center for Cancer Research and Cell Biology, School of Medicine, Dentistry and Biomedical Sciences, Queen s University Belfast, Belfast, United Kingdom
    PLoS ONE 6:e27733. 2011
    ....
  17. pmc A topological algorithm for identification of structural domains of proteins
    Frank Emmert-Streib
    Stowers Institute for Medical Research, Kansas City, MO 64110, USA
    BMC Bioinformatics 8:237. 2007
    ....
  18. pmc Information processing in the transcriptional regulatory network of yeast: functional robustness
    Frank Emmert-Streib
    Computational Biology and Machine Learning, Center for Cancer Research and Cell Biology, School of Medicine, Dentistry and Biomedical Sciences, Queen s University Belfast, 97 Lisburn Road, Belfast, UK
    BMC Syst Biol 3:35. 2009
    ..In this respect, the functional understanding of the transcriptional regulatory network is considered as key to elucidate the functional organization of an organism...
  19. pmc Hierarchical coordination of periodic genes in the cell cycle of Saccharomyces cerevisiae
    Frank Emmert-Streib
    Center for Cancer Research and Cell Biology, Queen s University Belfast, UK
    BMC Syst Biol 3:76. 2009
    ..g., degree distributions. Their structural analysis to gain functional insights into organizational principles of, e.g., pathways remains so far under appreciated...
  20. doi request reprint Network biology: a direct approach to study biological function
    Frank Emmert-Streib
    Computational Biology and Machine Learning, Center for Cancer Research and Cell Biology, School of Biomedical Sciences, Queen s University Belfast, Belfast, UK
    Wiley Interdiscip Rev Syst Biol Med 3:379-91. 2011
    ..WIREs Syst Biol Med 2011 3 379-391 DOI: 10.1002/wsbm.134 For further resources related to this article, please visit the WIREs website...
  21. pmc Predicting cell cycle regulated genes by causal interactions
    Frank Emmert-Streib
    Computational Biology and Machine Learning, Center for Cancer Research and Cell Biology, School of Biomedical Sciences, Queen s University Belfast, Belfast, United Kingdom
    PLoS ONE 4:e6633. 2009
    ..This also shows that there is a wealth of information buried in the transcriptional regulatory network whose unraveling may require more elaborate concepts than it might seem at first...
  22. pmc Statistic complexity: combining kolmogorov complexity with an ensemble approach
    Frank Emmert-Streib
    Computational Biology and Machine Learning, Center for Cancer Research and Cell Biology, School of Medicine, Dentistry and Biomedical Sciences, Queen s University Belfast, Belfast, United Kingdom
    PLoS ONE 5:e12256. 2010
    ..The evaluation of the complexity of an observed object is an old but outstanding problem. In this paper we are tying on this problem introducing a measure called statistic complexity...
  23. ncbi request reprint Exploratory analysis of spatiotemporal patterns of cellular automata by clustering compressibility
    Frank Emmert-Streib
    Computational Biology and Machine Learning, Center for Cancer Research and Cell Biology, School of Medicine, Dentistry and Biomedical Sciences, Queen s University Belfast, 97 Lisburn Road, Belfast BT9 7BL, UK
    Phys Rev E Stat Nonlin Soft Matter Phys 81:026103. 2010
    ..Our numerical results are not only plausible confirming previous classification attempts but also shed light on the intricate influence of random initial conditions on the classification results...
  24. pmc Interfacing cellular networks of S. cerevisiae and E. coli: connecting dynamic and genetic information
    Ricardo de Matos Simoes
    Computational Biology and Machine Learning Laboratory Center for Cancer Research and Cell Biology, School of Medicine, Dentistry and Biomedical Sciences Faculty of Medicine, Health and Life Sciences, Queen s University, 97 Lisburn Road, Belfast, UK
    BMC Genomics 14:324. 2013
    ..g., between the protein interaction network and the gene regulatory network inferred from large-scale transcriptomic data, is largely unexplored...
  25. pmc Structural influence of gene networks on their inference: analysis of C3NET
    Gökmen Altay
    School of Medicine, Dentistry and Biomedical Sciences, Queen s University Belfast, Belfast, BT9 7BL, UK
    Biol Direct 6:31. 2011
    ..For this reason gene network inference methods gained considerable interest. However, our current knowledge, especially about the influence of the structure of a gene network on its inference, is limited...
  26. pmc Organizational structure and the periphery of the gene regulatory network in B-cell lymphoma
    Ricardo de Matos Simoes
    Computational Biology and Machine Learning Lab, Center for Cancer Research and Cell Biology, School of Medicine, Dentistry and Biomedical Sciences, Queen s University Belfast, Belfast, UK
    BMC Syst Biol 6:38. 2012
    ..However, our current knowledge about the gene regulatory mechanisms that are governed by extracellular signals is severely limited...
  27. pmc Inferring the conservative causal core of gene regulatory networks
    Gökmen Altay
    Computational Biology and Machine Learning, Center for Cancer Research and Cell Biology, School of Medicine, Dentistry and Biomedical Sciences, Queen s University Belfast, 97 Lisburn Road, Belfast, BT9 7BL, UK
    BMC Syst Biol 4:132. 2010
    ..Hence, from a methodological point of view, reliable estimation methods based on observational data are needed to approach this problem practically...
  28. ncbi request reprint Algorithmic computation of knot polynomials of secondary structure elements of proteins
    Frank Emmert-Streib
    Stowers Institute for Medical Research, Kansas City, Missouri 64110, USA
    J Comput Biol 13:1503-12. 2006
    ..This paves the way for an automatic classification of protein structures...
  29. doi request reprint Revealing differences in gene network inference algorithms on the network level by ensemble methods
    Gökmen Altay
    Computational Biology and Machine Learning, Center for Cancer Research and Cell Biology, School of Medicine, Dentistry and Biomedical Sciences, Queen s University Belfast, 97 Lisburn Road, Belfast BT9 7BL, UK
    Bioinformatics 26:1738-44. 2010
    ..However, due to the difficulty to establish reliable methods based on observational data there is so far only incomplete knowledge about possibilities and limitations of such inference methods in this context...
  30. doi request reprint Gene Sets Net Correlations Analysis (GSNCA): a multivariate differential coexpression test for gene sets
    Yasir Rahmatallah
    Division of Biomedical Informatics, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA and Computational Biology and Machine Learning Laboratory, Center for Cancer Research and Cell Biology, School of Medicine, Dentistry and Biomedical Sciences, Queen s University Belfast, Belfast BT9 7BL, UK
    Bioinformatics 30:360-8. 2014
    ..Instead, we propose Gene Sets Net Correlations Analysis (GSNCA), a multivariate differential coexpression test that accounts for the complete correlation structure between genes...
  31. ncbi request reprint The chronic fatigue syndrome: a comparative pathway analysis
    Frank Emmert-Streib
    Stowers Institute for Medical Research, Kansas City, Missouri 64110, USA
    J Comput Biol 14:961-72. 2007
    ..The structural comparison of UDGs of sick versus non-sick patients allows us to make predictions about the modification of pathways due to pathogenesis...
  32. pmc Collectives of diagnostic biomarkers identify high-risk subpopulations of hematuria patients: exploiting heterogeneity in large-scale biomarker data
    Frank Emmert-Streib
    Centre for Cancer Research and Cell Biology, Queens University Belfast, Belfast, Northern Ireland
    BMC Med 11:12. 2013
    ..We applied a systems biology approach to analyze clinical, demographic and biomarker measurements (n = 29) collected from 157 hematuric patients: 80 urothelial cancer (UC) and 77 controls with confounding pathologies...