Altman, Russ B.
Pacific Symposium On Biocomputing 2015. - 1 online resource (517 pages)
Intro -- 2PSB20AnniversaryFinalv2 -- all-cp -- 0intro-cancerpanomics -- ching -- deshwar -- jang -- lehman -- nasser -- wu -- all-cp -- 0intro-cancerpathways -- engin -- kim -- 1. Introduction -- 2. Methods -- 2.1. Data -- 2.2. BioBin -- 2.3. ATHENA -- 2.4. Grammatical Evolution Neural Networks (GENN) -- 2.5. Survival fitness function -- 2.6. Experiment setup -- 3. Results and Discussion -- 3.1. Binning somatic mutations using BioBin -- 3.2. GENN modeling for somatic mutation burden -- 3.3. Biological interpretation -- 4. Conclusions -- Acknowledgments -- lockwood -- poon -- tan -- yang -- all-interactions -- 1intro-interactions -- crawford -- darabos -- frost -- holzinger -- Holzinger_PSB2015_r2VIM_1Oct2014 -- 1. Introduction -- 1.1. Variable selection that allows for interactions -- 2. Methods -- 2.1. r2VIM -- 2.2. Data Simulation -- 3. Results -- 3.1. Simulated Data -- 4. Discussion -- hu -- jeff -- patel -- restrepo -- wang -- all-crowd -- 1intro-crowdsourcing -- binder -- good -- irshad -- odgers -- waldispuhl -- all-pm -- 0intro-pm -- birol -- chang -- diggans -- fan-minogue -- glicksberg -- hinterberg -- huang -- makashir -- 2. Methods -- 2.1. Statistical framework for meta-analysis of differential co-expression -- 2.1.1. s score definition -- 2.1.2. Probability distribution of s scores -- 2.2. SLE dataset selection for meta-analysis -- 2.3. Data pre-processing -- 2.4. Meta-analysis of differential gene co-expression in SLE -- 2.5. Comparison of Type I error rates and statistical power -- 2.6. Differential expression analysis -- 2.7. Identification and annotation of gene modules -- 3. Results -- 3.1. A network of genes specifically co-expressed in SLE -- 3.2. Gene co-expression modules specific to SLE -- 3.2.1. Type I interferon response. 3.2.2. Cell movement and response to wounding -- 3.2.3. Immune defense against extracellular organisms -- 4. Discussion -- 5. Conclusions -- nie -- sengupta -- all-wkshop -- 1wkshop-human -- 2wkshop-discovery -- 3wkshp-public -- 4wkshop-bioinfo -- 5psb15-erratum.
9789814644730
Electronic books.
Pacific Symposium On Biocomputing 2015. - 1 online resource (517 pages)
Intro -- 2PSB20AnniversaryFinalv2 -- all-cp -- 0intro-cancerpanomics -- ching -- deshwar -- jang -- lehman -- nasser -- wu -- all-cp -- 0intro-cancerpathways -- engin -- kim -- 1. Introduction -- 2. Methods -- 2.1. Data -- 2.2. BioBin -- 2.3. ATHENA -- 2.4. Grammatical Evolution Neural Networks (GENN) -- 2.5. Survival fitness function -- 2.6. Experiment setup -- 3. Results and Discussion -- 3.1. Binning somatic mutations using BioBin -- 3.2. GENN modeling for somatic mutation burden -- 3.3. Biological interpretation -- 4. Conclusions -- Acknowledgments -- lockwood -- poon -- tan -- yang -- all-interactions -- 1intro-interactions -- crawford -- darabos -- frost -- holzinger -- Holzinger_PSB2015_r2VIM_1Oct2014 -- 1. Introduction -- 1.1. Variable selection that allows for interactions -- 2. Methods -- 2.1. r2VIM -- 2.2. Data Simulation -- 3. Results -- 3.1. Simulated Data -- 4. Discussion -- hu -- jeff -- patel -- restrepo -- wang -- all-crowd -- 1intro-crowdsourcing -- binder -- good -- irshad -- odgers -- waldispuhl -- all-pm -- 0intro-pm -- birol -- chang -- diggans -- fan-minogue -- glicksberg -- hinterberg -- huang -- makashir -- 2. Methods -- 2.1. Statistical framework for meta-analysis of differential co-expression -- 2.1.1. s score definition -- 2.1.2. Probability distribution of s scores -- 2.2. SLE dataset selection for meta-analysis -- 2.3. Data pre-processing -- 2.4. Meta-analysis of differential gene co-expression in SLE -- 2.5. Comparison of Type I error rates and statistical power -- 2.6. Differential expression analysis -- 2.7. Identification and annotation of gene modules -- 3. Results -- 3.1. A network of genes specifically co-expressed in SLE -- 3.2. Gene co-expression modules specific to SLE -- 3.2.1. Type I interferon response. 3.2.2. Cell movement and response to wounding -- 3.2.3. Immune defense against extracellular organisms -- 4. Discussion -- 5. Conclusions -- nie -- sengupta -- all-wkshop -- 1wkshop-human -- 2wkshop-discovery -- 3wkshp-public -- 4wkshop-bioinfo -- 5psb15-erratum.
9789814644730
Electronic books.
