EPEPT: a web service for enhanced P-value estimation in permutation testsTheo A Knijnenburg
Institute for Systems Biology, Seattle, WA, USA
BMC Bioinformatics 12:411. 2011
..This is computationally expensive and often infeasible. Recently, we proposed an alternative estimator, which requires far fewer permutations compared to the standard empirical approach while still reliably estimating small P-values...
- Insulin-like growth factor binding protein 2 promotes ovarian cancer cell invasion
Eun Ju Lee
Department of Pathology, The University of Texas M D Anderson Cancer Center, 1515 Holcombe Blvd, Houston, Texas, 77030, USA
Mol Cancer 4:7. 2005
..The purpose of this study was to assess the role of increased IGFBP2 in ovarian cancer cells...
- Using cell fate attractors to uncover transcriptional regulation of HL60 neutrophil differentiation
Albert C Huang
University of Washington, Seattle, USA
BMC Syst Biol 3:20. 2009
..The temporal behavior of the network states progressing toward different cell fate attractors has the potential to elucidate the underlying molecular mechanisms governing differentiation...
An inhibition-based stochastic countable-time decision modelIlya Shmulevich
Tampere International Center for Signal Processing, Tampere University of Technology, Finland
Br J Math Stat Psychol 55:17-25. 2002
..This model is compared to an existing inhibition-based continuous-time decision model and the probability distribution functions for work and distraction periods are derived...
- Eukaryotic cells are dynamically ordered or critical but not chaotic
Ilya Shmulevich
Institute for Systems Biology, Seattle, WA 98103, USA
Proc Natl Acad Sci U S A 102:13439-44. 2005
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- The role of certain Post classes in Boolean network models of genetic networks
Ilya Shmulevich
Cancer Genomics Laboratory, University of Texas M D Anderson Cancer Center, Houston, TX 77030, USA
Proc Natl Acad Sci U S A 100:10734-9. 2003
..Finally, functions from this class have a natural way of ensuring robustness against noise and perturbations, thus representing plausible evolutionarily selected candidates for regulatory rules in genetic networks...
- Binary analysis and optimization-based normalization of gene expression data
Ilya Shmulevich
Cancer Genomics Laboratory, Department of Pathology, University of Texas MD Anderson Cancer Center, 1515 Holcombe Blvd, Box 85, Houston, TX 77030, USA
Bioinformatics 18:555-65. 2002
..The binary approach offers several advantages, such as noise resilience and computational efficiency, making it a viable approach to extracting meaningful biological information from gene expression data...
- Data extraction from composite oligonucleotide microarrays
Ilya Shmulevich
Cancer Genomics Laboratory, University of Texas M D Anderson Cancer Center, 1515 Holcombe Boulevard, Unit 85, Houston, TX 77030, USA
Nucleic Acids Res 31:e36. 2003
..We propose a novel approach to design so-called composite microarrays, which allow more replicates to be obtained without increasing the number of printed spots...
- Probabilistic Boolean Networks: a rule-based uncertainty model for gene regulatory networks
Ilya Shmulevich
Cancer Genomics Laboratory, University of Texas M D Anderson Cancer Center, 1515 Holcombe Blvd, Box 85, Houston, TX 77030, USA
Bioinformatics 18:261-74. 2002
..Finally, we present methods for quantifying the influence of genes on other genes, within the context of PBNs. Examples illustrating the above concepts are presented throughout the paper...
- Gene perturbation and intervention in probabilistic Boolean networks
Ilya Shmulevich
Cancer Genomics Laboratory, University of Texas M D Anderson Cancer Center, 1515 Holcombe Blvd, Box 85, Houston, TX 77030, USA
Bioinformatics 18:1319-31. 2002
..We consider the general question of the potential effect of individual genes on the global dynamical network behavior, both from the view of random gene perturbation as well as intervention in order to elicit desired network behavior...
- Genome-wide histone acetylation data improve prediction of mammalian transcription factor binding sites
Stephen A Ramsey
Institute for Systems Biology, 1441 North 34th Street, Seattle, WA 98103, USA
Bioinformatics 26:2071-5. 2010
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- Highly accurate two-gene classifier for differentiating gastrointestinal stromal tumors and leiomyosarcomas
Nathan D Price
Institute for Systems Biology, Seattle, WA 98103, USA
Proc Natl Acad Sci U S A 104:3414-9. 2007
..We expect that the use of simple marker pairs that exhibit these traits will be of significant clinical use in a variety of contexts...
- A K-means segmentation method for finding 2-D object areas based on 3-D image stacks obtained by confocal microscopy
Antti Niemistö
Institute for Systems Biology, Seattle, Washington, USA
Conf Proc IEEE Eng Med Biol Soc 2007:5559-62. 2007
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- An integrated study of aberrant gene copy number and gene expression in GIST and LMS
Da Yang
Department of Pathology, Sarcoma Medical Oncology The University of Texas M D Anderson Cancer Center, Houston Texas, USA
Technol Cancer Res Treat 9:171-8. 2010
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- A data integration framework for prediction of transcription factor targets
Matti Nykter
Institute for Systems Biology, Seattle, Washington, USA
Ann N Y Acad Sci 1158:205-14. 2009
..This analysis shows that with assessment of the quality and biological relevance of the data, reliable predictions can be obtained with this computational framework...
- In silico microdissection of microarray data from heterogeneous cell populations
Harri Lähdesmäki
Institute of Signal Processing, Tampere University of Technology, P O Box 553, 33101 Tampere, Finland
BMC Bioinformatics 6:54. 2005
..Similarly, irrelevant gene combinations can be discovered in the case of gene expression based classification...
- Function of C/EBPdelta in a regulatory circuit that discriminates between transient and persistent TLR4-induced signals
Vladimir Litvak
Institute for Systems Biology, Seattle, Washington, USA
Nat Immunol 10:437-43. 2009
..Our results suggest a mechanism that enables the innate immune system to detect the duration of infection and to respond appropriately...
- Pathway alterations during glioma progression revealed by reverse phase protein lysate arrays
Rongcai Jiang
Department of Pathology, The University of Texas M. D. Anderson Cancer Center, 1515 Holcombe Boulevard, Houston, TX 77030, USA
Proteomics 6:2964-71. 2006
..The marked association of phosphorylation of AKT at Thr308, but not Ser473, with glioblastoma suggests a specific event of PI3K pathway activation in glioma progression...
- Molecular voting for glioma classification reflecting heterogeneity in the continuum of cancer progression
Gregory N Fuller
Department of Pathology, University of Texas M.D. Anderson Cancer Center, Houston, TX 77030, USA
Oncol Rep 14:651-6. 2005
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- Robust estimation of protein expression ratios with lysate microarray technology
Cristian Mircean
Department of Pathology, University of Texas M.D. Anderson Cancer Center, Houston, USA
Bioinformatics 21:1935-42. 2005
..AVAILABILITY: http://www.cs.tut.fi/~mirceanc/lysate_array_bioinformatics.htm..
NGAL decreases E-cadherin-mediated cell-cell adhesion and increases cell motility and invasion through Rac1 in colon carcinoma cellsLimei Hu
Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
Lab Invest 89:531-48. 2009
..NGAL may therefore be a new target for therapeutic intervention in colorectal carcinoma...
- Bright field microscopy as an alternative to whole cell fluorescence in automated analysis of macrophage images
Jyrki Selinummi
Institute for Systems Biology, Seattle, Washington, United States of America
PLoS ONE 4:e7497. 2009
..This technique, however, has a number of drawbacks such as the limited number of available fluorescent channels in microscopes, overlapping excitation and emission spectra of the stains, and phototoxicity...
- SEQADAPT: an adaptable system for the tracking, storage and analysis of high throughput sequencing experiments
David B Burdick
Institute for Systems Biology, 1441 North 34th Street, Seattle, WA 98103, USA
BMC Bioinformatics 11:377. 2010
..However, the existing software systems for managing and processing these data have not provided the flexible infrastructure that research requires...
- Uncovering a macrophage transcriptional program by integrating evidence from motif scanning and expression dynamics
Stephen A Ramsey
Institute for Systems Biology, Seattle, Washington, United States of America
PLoS Comput Biol 4:e1000021. 2008
..The network incorporates known regulators and gives insight into the transcriptional control of macrophage activation. Our analysis identified a novel regulator (TGIF1) that may have a role in macrophage activation...
- Genome-wide analysis of effectors of peroxisome biogenesis
Ramsey A Saleem
Institute for Systems Biology, Seattle, Washington, USA
PLoS ONE 5:e11953. 2010
..By integration with extant data sets, we present a total of 211 genes linked to peroxisome biogenesis and highlight the complex networks through which information flows during peroxisome biogenesis and function...
- Robust regression for periodicity detection in non-uniformly sampled time-course gene expression data
Miika Ahdesmäki
Institute of Signal Processing, Tampere University of Technology, Tampere, Finland
BMC Bioinformatics 8:233. 2007
..In many circumstances we are interested in finding targets that are expressed periodically. To tackle the problems of uneven sampling and unknown type of noise in periodicity detection, we propose to use robust regression...
- Critical networks exhibit maximal information diversity in structure-dynamics relationships
Matti Nykter
Institute of Signal Processing, Tampere University of Technology, Tampere, Finland
Phys Rev Lett 100:058702. 2008
..Here we use an information theoretic approach to study structure-dynamics relationships within a unified framework and show that these relationships are most diverse in the critical regime...
- Trade-off between responsiveness and noise suppression in biomolecular system responses to environmental cues
Alexander V Ratushny
Institute for Systems Biology, Seattle, Washington, United States of America
PLoS Comput Biol 7:e1002091. 2011
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- Unsupervised analysis uncovers changes in histopathologic diagnosis in supervised genomic studies
Matti Nykter
Department of Pathology, The University of Texas M. D. Anderson Cancer Center, Houston, Texas, USA
Technol Cancer Res Treat 5:177-82. 2006
..Further, unsupervised analysis often proves to be a critical quality control step in identifying structural problems that may exist. Finally, MDS analysis further supports that GIST is a distinct type of sarcoma...
- A regression model approach to enable cell morphology correction in high-throughput flow cytometry
Theo A Knijnenburg
Institute for Systems Biology, 401 Terry Avenue North, 1441 North 34th Street, Seattle, WA 98109 5234, USA
Mol Syst Biol 7:531. 2011
..We identify a group of epigenetic regulators and nucleoporins that, by maintaining an 'unresponsive population,' may provide the population with the advantage of diversified bet hedging...
- Adaptable data management for systems biology investigations
John Boyle
Institute for Systems Biology, 1441 N 34th Street, Seattle, WA 98103, USA
BMC Bioinformatics 10:79. 2009
..To support these requirements data management systems are needed that can be rapidly built and readily adapted for new usage...
- Pathway analysis of informative genes from microarray data reveals that metabolism and signal transduction genes distinguish different subtypes of lymphomas
Cristian Mircean
Institute of Signal Processing, Tampere University of Technology, FIN-33101 Tampere, Finland
Int J Oncol 24:497-504. 2004
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- Gene expression dynamics in the macrophage exhibit criticality
Matti Nykter
Institute of Signal Processing, Tampere University of Technology, 33101 Tampere, Finland
Proc Natl Acad Sci U S A 105:1897-900. 2008
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- Deterministic and stochastic models of genetic regulatory networks
Ilya Shmulevich
Institute for Systems Biology, Seattle, Washington, USA
Methods Enzymol 467:335-56. 2009
..For each combination of these categories, a model is presented and discussed in the context of the yeast cell cycle, illustrating how different types of questions can be addressed by different model classes...
- Simcluster: clustering enumeration gene expression data on the simplex space
Ricardo Z N Vencio
Institute for Systems Biology, 1441 North 34th Street, Seattle, WA 98103 8904, USA
BMC Bioinformatics 8:246. 2007
..Therefore, pattern recognition methods commonly used for microarray data analysis may be non-informative for the data generated by transcript enumeration techniques since they ignore certain fundamental properties of this space...
- Distinguishing key biological pathways between primary breast cancers and their lymph node metastases by gene function-based clustering analysis
Harri Lähdesmäki
Cancer Genomics Laboratory, Department of Pathology, The University of Texas M D Anderson Cancer Center, Houston, TX 77030, USA
Int J Oncol 24:1589-96. 2004
..The results also suggest that the altered cell adhesion and migration potentials that are required for tumors to metastasize already exist in the primary tumors as a whole...
- ProbCD: enrichment analysis accounting for categorization uncertainty
Ricardo Z N Vencio
Institute for Systems Biology, 1441 North 34th Street, Seattle, WA 98103 8904, USA
BMC Bioinformatics 8:383. 2007
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- Extraction of the number of peroxisomes in yeast cells by automated image analysis
Antti Niemistö
Institute of Signal Processing, Tampere University of Technology, Finland
Conf Proc IEEE Eng Med Biol Soc 1:2353-6. 2006
..The peroxisomes are detected by thresholding the fluorescent image. The method is tested with several images of a budding yeast Saccharomyces cerevisiae population, and the results are compared with manually obtained results...
- Entropy of complex relevant components of Boolean networks
Peter Krawitz
Institute for Systems Biology, Seattle, Washington 98103, USA
Phys Rev E Stat Nonlin Soft Matter Phys 76:036115. 2007
..We also demonstrate that basin entropy can be estimated from time-series data and is therefore also applicable to nondeterministic networks models...
- Probabilistic analysis of gene expression measurements from heterogeneous tissues
Timo Erkkilä
Department of Signal Processing, Tampere University of Technology, Finland
Bioinformatics 26:2571-7. 2010
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- Association of BRCA1 and BRCA2 mutations with survival, chemotherapy sensitivity, and gene mutator phenotype in patients with ovarian cancer
Da Yang
Department of Pathology, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
JAMA 306:1557-65. 2011
..Attempts to determine the clinical significance of BRCA1/2 mutations in ovarian cancer have produced conflicting results...
- Fewer permutations, more accurate P-values
Theo A Knijnenburg
Institute for Systems Biology, Seattle, WA, USA
Bioinformatics 25:i161-8. 2009
..Thereby, it imposes upon itself the need for a very large number of permutations when small P-values are to be accurately estimated. This is computationally expensive and often infeasible...
- Tumor specific gene expression profiles in human leiomyosarcoma: an evaluation of intratumor heterogeneity
Ilya Shmulevich
Department of Pathology, The University of Texas M. D. Anderson Cancer Center, 1515 Holcombe Boulevard, Houston, TX 77030, USA
Cancer 94:2069-75. 2002
..The authors also identified genes that are expressed differentially in tumor and normal tissue...
- Biochemical and statistical network models for systems biology
Nathan D Price
Institute for Systems Biology, 1441 N 34th Street, Seattle, WA 98103, USA
Curr Opin Biotechnol 18:365-70. 2007
..In particular, we discuss a number of modeling approaches in the context of the assumptions that they entail, the types of data required for their inference, and the range of their applicability...
- Analysis of angiogenesis using in vitro experiments and stochastic growth models
Antti Niemistö
Institute of Signal Processing, Tampere University of Technology, P O Box 553, 33101 Tampere, Finland
Phys Rev E Stat Nonlin Soft Matter Phys 72:062902. 2005
..It is found that invasion percolation is better than diffusion limited aggregation at matching experimental data. We also present evidence that the distribution of the lengths of real tubule complexes follows a power law...
- The Innate Immune Database (IIDB)
Martin Korb
Institute for Systems Biology, 1441 North 34thStreet, Seattle, Washington 98103 8904, USA
BMC Immunol 9:7. 2008
..It provides a broad resource to the research community, and a stepping stone towards the delineation of the network of transcriptional regulatory interactions underlying the integrated response of macrophages to pathogens...
- Systems biology driven software design for the research enterprise
John Boyle
Institute for Systems Biology, 1441 N 34th Street, Seattle, WA 98103, USA
BMC Bioinformatics 9:295. 2008
..As scientists work in isolated groups, integration with other groups is rarely a consideration when building the required software tools...
- Probabilistic inference of transcription factor binding from multiple data sources
Harri Lähdesmäki
Institute for Systems Biology, Seattle, Washington, United States of America
PLoS ONE 3:e1820. 2008
..Test data set, a web tool, source codes and supplementary data are available at: http://www.probtf.org...
- Basin entropy in Boolean network ensembles
Peter Krawitz
Institute for Systems Biology, Seattle, Washington 98103, USA
Phys Rev Lett 98:158701. 2007
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- Activities and sensitivities in boolean network models
Ilya Shmulevich
Cancer Genomics Laboratory, University of Texas M. D. Anderson Cancer Center, Houston, Texas 77030, USA
Phys Rev Lett 93:048701. 2004
..Finally, we demonstrate the important role of the average sensitivity in determining the dynamical behavior of a Boolean network...
- Taming data
Alan Aderem
Institute for Systems Biology, 1441 North 34th Street, Seattle, WA 98103, USA
Cell Host Microbe 4:312-3. 2008
..innatedb.ca), a publicly available, manually curated database of experimentally verified molecular interactions and pathways involved in innate immunity, is a powerful new resource that facilitates such integrative systems-level analyses...
- Microarray reveals differences in both tumors and vascular specific gene expression in de novo CD5+ and CD5- diffuse large B-cell lymphomas
Tohru Kobayashi
The Second Department of Internal Medicine, Mie University School of Medicine, Tsu, 514-8507, Japan
Cancer Res 63:60-6. 2003
..Those results suggest that CD5(+) and CD5(-) DLBCLs have different gene expression signatures in both tumor cells and their vascular systems...
- Differential gene and protein expression in primary breast malignancies and their lymph node metastases as revealed by combined cDNA microarray and tissue microarray analysis
Xishan Hao
Tianjin Medical University Cancer Hospital, Tianjin, China
Cancer 100:1110-22. 2004
..Therefore, gene expression profiling and tissue array validation should be combined to elucidate molecular events associated with the metastatic process...
- Critical dynamics in genetic regulatory networks: examples from four kingdoms
Enrique Balleza
Instituto de Ciencias Fisicas, Universidad Nacional Autonoma de Mexico, Cuernavaca, Morelos, Mexico
PLoS ONE 3:e2456. 2008
..The generality of this result suggests that criticality at the genetic level might constitute a fundamental evolutionary mechanism that generates the great diversity of dynamically robust living forms that we observe around us...
- Identification of combination gene sets for glioma classification
Seungchan Kim
Department of Electrical Engineering, Texas A and M University, College Station, Texas 77840, USA
Mol Cancer Ther 1:1229-36. 2002
..Two-gene and three-gene combinations thus provide robust classifiers possessing the potential to translate expression microarray results into diagnostic histopathological assays for clinical utilization...
- Identification of signature genes by microarray for acute myeloid leukemia without maturation and acute promyelocytic leukemia with t(15;17)(q22;q12)(PML/RARalpha)
Jun Morikawa
The Second Department of Internal Medicine, Mie University School of Medicine, 2-174 Edobashi, Tsu 514-8507, Japan
Int J Oncol 23:617-25. 2003
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- Growing genetic regulatory networks from seed genes
Ronaldo F Hashimoto
Department of Electrical Engineering, Texas A and M University, College Station, TX, USA 77843, USA
Bioinformatics 20:1241-7. 2004
..AVAILABILITY: Software for the seed-growing algorithm will be available at the website for Probabilistic Boolean Networks: http://www2.mdanderson.org/app/ilya/PBN/PBN.htm..
- Robust quantification of in vitro angiogenesis through image analysis
Antti Niemistö
IEEE Trans Med Imaging 24:549-53. 2005
..We have implemented a software package that utilizes the methods. The software as well as a set of test images are available at http://www.cs.tut.fi/sgn/csb/angioquant/...
- Model selection in genomics
Ilya Shmulevich
Environ Health Perspect 111:A328-9. 2003
