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ISBN: 9789048542727

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DOI: 10.1515/9789048542727b

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URL: De Gruyter

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ISBN: 9781783745548 , 1783745541 , 9781783745562 , 1783745568 , 1783745541 , 1783745568 , 9781783745548 , 9781783745562

Content: 6. Remembering Hermynia Zur Mühlen: A Tribute7. Works by Hermynia Zur Mühlen in English Translation; 8. Image Portfolio; List of Illustrations

Content: Translator's Introductory Note; Acknowledgements; 1. The End and the Beginning: The Book of My Life by Hermynia Zur Mühlen; 2. Supplement to The End and the Beginning* by Hermynia Zur Mühlen; 3. Notes on Persons and Events Mentioned in the Memoir by Lionel Gossman; 4. Feuilletons and Fairy Tales: A Sampling; The Red Redeemer; Confession; High Treason; Death of a Shade; A Secondary Happiness; The Señora; Miss Brington; We Have to Tell Them; Painted on Ivory; The Sparrow; The Spectacles; 5. Our Daughters the Nazi Girls. A Synopsis in English

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Additional Edition: ISBN 9781783745555

Additional Edition: ISBN 9781783745555

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Keywords: Electronic books ; Electronic books ; Electronic books. ; Criticism, interpretation, etc.

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Author information: Zur Mühlen, Hermynia 1883-1951

Author information: Gossman, Lionel 1929-2021

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Format: 1 online resource (325 pages)

ISBN: 9781786390615

Content: This book investigates the experiences and issues involved with rebuilding extension systems n post-conflict settings. It evaluates the impact of different extension policy approaches and practice in such settings, and identifes the key elements needed to effectively rebuild agricultural extension systems and programs in post-conflict contexts.

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Additional Edition: ISBN 9781786390592

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Format: 1 online resource (150 pages)

Edition: 1st ed.

ISBN: 9783031447310

Content: Intro -- Acknowledgements -- Contents -- Contributors -- List of Figures -- Situating Women's Private Practices of Knowledge Production in the Early Modern Context -- References -- Primary Sources -- Bibliography -- Lady Jane Lumley's Private Education and Its Political Resonances -- Introduction: Education at a Noble Household -- The Private, the Public, and the Political in Lady Lumley's Writings -- Lady Lumley's The Tragedie of Euripides Called Iphigeneia -- Comparing Translations of Iphigenia at Aulis -- In Conclusion -- References -- Primary Sources -- Secondary Sources -- Camilla Herculiana (Erculiani): Private Practices of Knowledge Production -- Herculiana's Private Life and Connections: Biographical and Contextual Framework -- Camilla Herculiana é Gregetta, Lettere di philosophia naturale (1584) -- Paratextual Analysis -- Letters' Analysis -- Inquisitional Trial -- Conclusion -- References -- Primary Sources -- Bibliography -- From Behind the Folding Screen to the Collège de France: Victorine de Chastenay's Privacy Dynamics for Knowledge in the Making -- Note-Taking and Knowledge Acquisition as Private Practices -- Adapting the Household's Privacy to Reconcile Writing and Social Obligations -- Privacy in Institutional Spaces -- Conclusion -- References -- Primary Sources -- Archival -- Printed Sources -- Bibliography -- "Fait à mes heures de loisir": Women's Private Libraries as Spaces of Learning and Knowledge Production -- The Ducal Libraries: Private Collections? -- Elisabeth Sophie Marie and Philippine Charlotte of Brunswick-Wolfenbüttel -- The Duchesses' Book Use and Knowledge Production -- Private Knowledge Spaces: Concluding Remarks -- References -- Primary Sources -- Archival Material -- Printed Sources -- Bibliography -- Contingent Privacies: Knowledge Production and Gender Expectations from 1500 to 1800.

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Additional Edition: ISBN 9783031447303

Additional Edition: Erscheint auch als Druck-Ausgabe ISBN 9783031447303

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Format: 1 online resource (572 pages)

Edition: 1st ed.

ISBN: 9789811270611

Additional Edition: Print version: Altman, Russ B Biocomputing 2023 - Proceedings Of The Pacific Symposium Singapore : World Scientific Publishing Company,c2022 ISBN 9789811270604

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Format: 1 online resource (502 pages)

ISBN: 9789814295291

Note: Intro -- CONTENTS -- PREFACE -- COMPUTATIONAL CHALLENGES IN COMPARATIVE GENOMICS -- SESSION INTRODUCTION -- ACCURATE TAXONOMIC ASSIGNMENT OF SHORT PYROSEQUENCING READS -- BENCHMARKING BLAST ACCURACY OF GENUS/PHYLA CLASSIFICATION OF METAGENOMIC READS -- GUIDED GENOME HALVING: PROVABLY OPTIMAL SOLUTIONS PROVIDE GOOD INSIGHTS INTO THE PREDUPLICATION ANCESTRAL GENOME OF SACCHAROMYCES CEREVISIAE -- A PRACTICAL ALGORITHM FOR ESTIMATION OF THE MAXIMUM LIKELIHOOD ANCESTRAL RECONSTRUCTION ERROR -- OPTIMIZATION METHODS FOR SELECTING FOUNDER INDIVIDUALS FOR CAPTIVE BREEDING OR REINTRODUCTION OF ENDANGERED SPECIES -- COMPUTATIONAL STUDIES OF NON-CODING RNAS -- SESSION INTRODUCTION -- RNA STRUCTURAL SEGMENTATION -- RNAZ 2.0: IMPROVED NONCODING RNA DETECTION -- IDENTIFICATION AND CLASSIFICATION OF SMALL RNAS IN TRANSCRIPTOME SEQUENCE DATA -- IMPROVEMENT OF STRUCTURE CONSERVATION INDEX WITH CENTROID ESTIMATORS -- DYNAMIC PROGRAMMING ALGORITHMS FOR RNA STRUCTURE PREDICTION WITH BINDING SITES -- AN ALGORITHM FOR THE ENERGY BARRIER PROBLEM WITHOUT PSEUDOKNOTS AND TEMPORARY ARCS -- DYNAMICS OF BIOLOGICAL NETWORKS -- SESSION INTRODUCTION -- LOCAL OPTIMIZATION FOR GLOBAL ALIGNMENT OF PROTEIN INTERACTION NETWORKS -- IDENTIFICATION OF COORDINATELY DYSREGULATED SUBNETWORKS IN COMPLEX PHENOTYPES -- SUBSPACE DIFFERENTIAL COEXPRESSION ANALYSIS: PROBLEM DEFINITION AND A GENERAL APPROACH -- ESTIMATION OF PROTEIN AND DOMAIN INTERACTIONS IN THE SWITCHING MOTILITY SYSTEM OF MYXOCOCCUS XANTHUS -- EXPLORING BIOLOGICAL NETWORK DYNAMICS WITH ENSEMBLES OF GRAPH PARTITIONS -- GEOMETRIC EVOLUTIONARY DYNAMICS OF PROTEIN INTERACTION NETWORKS -- THE STEADY STATES AND DYNAMICS OF UROKINASE-MEDIATED PLASMIN ACTIVATION -- MULTI-RESOLUTION MODELING OF BIOLOGICAL MACROMOLECULES -- SESSION INTRODUCTION. , MULTI-RESOLUTION APPROACH FOR INTERACTIVELY LOCATING FUNCTIONALLY LINKED ION BINDING SITES BY STEERING SMALL MOLECULES INTO ELECTROSTATIC POTENTIAL MAPS USING A HAPTIC DEVICE -- PREDICTING RNA STRUCTURE BY MULTIPLE TEMPLATE HOMOLOGY MODELING -- CONSTRUCTING MULTI-RESOLUTION MARKOV STATE MODELS (MSMS) TO ELUCIDATE RNA HAIRPIN FOLDING MECHANISMS -- MULTISCALE DYNAMICS OF MACROMOLECULES USING NORMAL MODE LANGEVIN -- INSIGHTS INTO THE INTRA-RING SUBUNIT ORDER OF TRIC/CCT: A STRUCTURAL AND EVOLUTIONARY ANALYSIS -- "CROSS-GRAINING:" EFFICIENT MULTI-SCALE SIMULATION VIA MARKOV STATE MODELS -- TOWARD UNDERSTANDING ALLOSTERIC SIGNALING MECHANISMS IN THE ATPASE DOMAIN OF MOLECULAR CHAPERONES -- 3D-BLAST: 3D PROTEIN STRUCTURE ALIGNMENT, COMPARISON, AND CLASSIFICATION USING SPHERICAL POLAR FOURIER CORRELATIONS -- STRUCTURAL PREDICTION OF PROTEIN-RNA INTERACTION BY COMPUTATIONAL DOCKING WITH PROPENSITY-BASED STATISTICAL POTENTIALS -- PERSONAL GENOMICS -- SESSION INTRODUCTION -- IMPROVING THE PREDICTION OF PHARMACOGENES USING TEXT-DERIVED DRUG-GENE RELATIONSHIPS -- FINDING UNIQUE FILTER SETS IN PLATO: A PRECURSOR TO EFFICIENT INTERACTION ANALYSIS IN GWAS DATA -- ENABLING PERSONAL GENOMICS WITH AN EXPLICIT TEST OF EPISTASIS -- LOSS OF POST-TRANSLATIONAL MODIFICATION SITES IN DISEASE -- DETECTING GENOME-WIDE HAPLOTYPE POLYMORPHISM BY COMBINED USE OF MENDELIAN CONSTRAINTS AND LOCAL POPULATION STRUCTURE -- SEQUENCE FEATURE VARIANT TYPE (SFVT) ANALYSIS OF THE HLA GENETIC ASSOCIATION IN JUVENILE IDIOPATHIC ARTHRITIS -- ÇOKGEN: A SOFTWARE FOR THE IDENTIFICATION OF RARE COPY NUMBER VARIATION FROM SNP MICROARRAYS -- REVERSE ENGINEERING AND SYNTHESIS OF BIOMOLECULAR SYSTEMS -- SESSION INTRODUCTION -- CO-DESIGN IN SYNTHETIC BIOLOGY: A SYSTEM-LEVEL ANALYSIS OF THE DEVELOPMENT OF AN ENVIRONMENTAL SENSING DEVICE. , CRITICAL ANALYSIS OF TRANSCRIPTIONAL AND POST-TRANSCRIPTIONAL REGULATORY NETWORKS IN MULTIPLE MYELOMA -- A COMPUTATIONAL MODEL OF GENE EXPRESSION IN AN INDUCIBLE SYNTHETIC CIRCUIT -- RETROVIRUS HTLV-1 GENE CIRCUIT: A POTENTIAL OSCILLATOR FOR EUKARYOTES -- EMULSION BASED SELECTION OF T7 PROMOTERS OF VARYING ACTIVITY -- CLUSTERING CONTEXT-SPECIFIC GENE REGULATORY NETWORKS -- WRITING AND COMPILING CODE INTO BIOCHEMISTRY -- SYNTHESIS OF PHARMACOKINETIC PATHWAYS THROUGH KNOWLEDGE ACQUISITION AND AUTOMATED REASONING -- WORKSHOPS -- INSILICO BIOLOGY -- GENOMIC STANDARDS CONSORTIUM WORKSHOP: METAGENOMICS, METADATA AND METAANALYSIS (M3) -- EXTRACTION OF GENOTYPE-PHENOTYPE-DRUG RELATIONSHIPS FROM TEXT: FROM ENTITY RECOGNITION TO BIOINFORMATICS APPLICATION.

Additional Edition: Print version: Altman, Russ B Biocomputing 2010 - Proceedings Of The Pacific Symposium Singapore : World Scientific Publishing Company,c2009 ISBN 9789814299473

Language: English

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Format: 1 online resource (517 pages)

ISBN: 9789814644730

Note: 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.

Additional Edition: Print version: Altman, Russ B Pacific Symposium On Biocomputing 2015 Singapore : World Scientific Publishing Company,c2014 ISBN 9789814644723

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UID:

Format: 1 online resource (762 pages)

ISBN: 9789811215636

Note: Intro -- Content -- Preface -- ARTIFICIAL INTELLIGENCE FOR ENHANCING CLINICAL MEDICINE -- Session Introduction: Artificial Intelligence for Enhancing Clinical Medicine -- 1. Introduction -- 2. Novel Research Applying Artificial Intelligence to Clinical Medicine -- 2.1. Artificial intelligence for predicting patient outcomes -- 2.2. Artificial intelligence for improved insight into disease pathogenesis and features -- 3. Artificial intelligence for advancing medical workflows -- 4. Artificial intelligence for improving imaging -- 5. Conclusion -- References -- Predicting Longitudinal Outcomes of Alzheimer's Disease via a Tensor-Based Joint Classification and Regression Model -- 1. Introduction -- 2. Methods -- 2.1. The Longitudinal Joint Learning Model -- 2.2. The Solution Algorithm Using the Multi-Block ADMM -- 3. Experiments -- 3.1. Performance -- 3.2. Empirical Convergence -- 3.3. Biomarker Identification -- 4. Conclusion -- Acknowledgements -- References -- Robustly Extracting Medical Knowledge from EHRs: A Case Study of Learning a Health Knowledge Graph -- 1. Introduction -- 2. Related Work -- 3. Methods -- 3.1. Data collection and preparation -- 3.2. Evaluation with GHKG -- 3.3. Disease predictability analysis -- 3.4. Demographic analysis -- 3.5. Non-linear methods -- 4. Results -- 5. Discussion -- 5.1. Data size does not always matter. -- 5.2. Confounders may explain errors -- 5.3. Increased model complexity does not necessarily help -- 5.4. Limitations remain as an opportunity for future work -- 6. Conclusion -- Acknowledgements -- References -- Increasing Clinical Trial Accrual via Automated Matching of Biomarker Criteria -- 1. INTRODUCTION -- 2. MATERIALS AND METHODS -- 2.1. Specimens and Retrospective Analysis -- 2.2. Real-time Analysis -- 2.3. Source of Biomarker-based Clinical Trial Data -- 3. RESULTS. , 3.1. STAMP assay identifies somatic mutations -- 3.2. Algorithmic pipeline flags eligible patients for precision medicine clinical trials -- 3.2.1. Automation of Feature Matching -- 3.2.2. Manual Review of Matching Output -- 3.3. Validation of algorithmic pipeline -- 3.4. Match rate analysis of STAMP-identified mutations -- 4. DISCUSSION -- 4.1. Incorporation of informatics into clinical workflows -- 4.2. Limitations of algorithmic pipelines -- 5. CONCLUSION -- 6. AUTHOR CONTRIBUTIONS -- 7. ACKNOWLEDGEMENTS -- 8. REFERENCES -- 9. FIGURES -- 10. SUPPLEMENTARY TABLES AND FIGURES -- Addressing the Credit Assignment Problem in Treatment Outcome Prediction Using Temporal Difference Learning -- 1. Introduction -- 2. Dataset -- 3. Methods -- 3.1. Feature Extraction -- 3.2. Temporal Difference Learning -- 3.2.1. State-Estimation -- 3.2.2. Value Iteration -- 3.2.3. Optimization -- 3.3. Baselines and Performance Measure -- 4. Results -- 5. Discussion and Conclusion -- References -- Multiclass Disease Classification from Microbial Whole-Community Metagenomes -- 1. Introduction -- 2. Previous Work -- 3. Problem Setup -- 3.1. Dataset Construction -- 3.2. Graph Convolutional Neural Networks -- 3.3. Models -- 3.4. Training -- 4. Results -- 5. Conclusion -- 6. Acknowledgments -- 7. External Links -- References -- LitGen: Genetic Literature Recommendation Guided by Human Explanations -- 1. Introduction -- 2. Clinical Variant Curation Data -- 2.1. ClinGen's Variant Curation Interface (VCI) -- 2.2. Labeled papers -- 2.3. Unlabeled papers -- 3. Method -- 3.1. BiLSTM baseline -- 3.2. Leveraging unlabeled data -- 3.3. Explanations in multitask learning -- 3.4. Explanations as feature selection for proxy labeling -- 4. Experimental results -- 4.1. Evaluation metrics -- 4.2. Performance comparison -- 4.3. Performance of Proxy Labeling Model. , 4.4. Performance by Evidence Types -- 5. Discussion -- References -- From Genome to Phenome: Predicting Multiple Cancer Phenotypes Based on Somatic Genomic Alterations via the Genomic Impact Transformer -- 1. Introduction -- 2. Materials and methods -- 2.1. SGAs and DEGs pre-processing -- 2.2. The GIT neural network -- 2.2.1. GIT network structure: encoder-decoder architecture -- 2.2.2. Pre-training gene embeddings using Gene2Vec algorithm -- 2.2.3. Encoder: multi-head self-attention mechanism -- 2.2.4. Decoder: multi-layer perceptron (MLP) -- 2.3. Training and evaluation -- 3. Results -- 3.1. GIT statistically detects real biological signals -- 3.2. Gene embeddings compactly represent the functional impact of SGAs -- 3.4. Personalized tumor embeddings reveal distinct survival profiles -- 3.5. Tumor embeddings are predictive of drug responses of cancer cell lines -- 4. Conclusion and Future Work -- Acknowledgments -- Funding -- References -- Automated Phenotyping of Patients with Non-Alcoholic Fatty Liver Disease Reveals Clinically Relevant Disease Subtypes -- 1. Introduction -- 2. Methods -- 2.1. NAFLD definition -- 2.2. Natural language processing -- 2.3. Data collection -- 2.4. Clinical feature standardization and quality control -- 2.4.1. Demographic data -- 2.4.2. Diagnoses, procedures, medications -- 2.4.3. Laboratory tests -- 2.4.4. Vital signs -- 2.5. Patient pairwise distance and clustering -- 2.6. Statistical analysis -- 2.6.1. Descriptive statistics -- 2.6.2. Survival analysis -- 3. Results -- 3.1. Descriptive statistics for the cohort -- 3.2. Identification of NAFLD subtypes -- 3.3. Identification of distinct outcomes by NAFLD subtype -- 3.4. Internal cross-validation of the subtypes discovered -- 4. Conclusion -- 5. References -- References -- Monitoring ICU Mortality Risk with a Long Short-Term Memory Recurrent Neural Network. , 1. Introduction -- 2. Background and Related Work -- 3. Data and Preprocessing -- 3.1. Data Source and Cohort Selection -- 3.2. Data Extraction and Preprocessing -- 4. Methodology -- 4.1. Mortality Monitoring Task -- 4.2. Average Pooling and Attention Mechanism -- 4.3. Recurrent Neural Network (RNN) -- 5. Experimental Design -- 5.1. Sampling Strategy -- 5.2. Baseline Model -- 5.3. Experimental Settings -- 6. Results and Analysis -- 6.1. Dimensionality Analysis -- 6.2. Prediction with Different Feature Representations -- 6.3. Interpreting Mortality of Learned Representation -- 7. Discussion and Conclusions -- References -- Multilevel Self-Attention Model and Its Use on Medical Risk Prediction -- 1. Introduction -- 2. Related Work -- 2.1. Future disease prediction -- 3. Methods -- 3.1. Terminology and Notation -- 3.2. Model Architecture -- 3.3. Self-attention Encoder Unit -- 3.4. Loss Function -- 4. Experiments -- 4.1. Source of Data -- 4.2. Dataset preprocessing -- 4.3. Implementation details -- 5. Results -- 5.1. Future disease prediction -- 5.2. Future cost prediction -- 5.3. Case study for the self-attention mechanism -- 6. Conclusion -- 7. Bibliography -- Identifying Transitional High Cost Users from Unstructured Patient Profiles Written by Primary Care Physicians -- 1. Introduction -- 2. Data -- 2.1. EMRPC -- 2.2. Total Healthcare Costs -- 2.3. Encoding of Ordinal Variables -- 2.4. Word Embeddings -- 3. Methods -- 3.1. Bag of Words -- 3.2. EmbEncode -- 3.3. Historical Baseline -- 3.4. Varying the Training Set -- 3.5. Varying the Evaluation Set -- 4. Results -- 5. Discussion -- Acknowledgments -- References -- Obtaining Dual-Energy Computed Tomography (CT) Information from a Single-Energy CT Image for Quantitative Imaging Analysis of Living Subjects by Using Deep Learning -- 1. Introduction -- 2. Methods -- 3. Results. , 4. Discussion and Conclusion -- 5. Acknowledge -- References -- INTRINSICALLY DISORDERED PROTEINS (IDPS) AND THEIR FUNCTIONS -- Session Introduction: On the Importance of Computational Biology and Bioinformatics to the Origins and Rapid Progression of the Intrinsically Disordered Proteins Field -- 1. Introduction -- 2. Computational prediction of IDPs and IDRs and their functions -- 3. Popularization of research on IDPs and IDRs -- 4. A Collection of Recent Papers on IDPs and IDRs -- References -- Many-to-One Binding by Intrinsically Disordered Protein Regions -- 1. Introduction -- 2. Results -- 2.1. Many-to-one binding datasets -- 2.2. Many-to-one binding profiles: independent and overlapping -- 2.3 Comparing VOR (with backbone only) and RMSΔASA Values -- 2.4. Selected many-to-one case studies -- 3. Discussion -- 4. Materials and Methods -- 4.1. Dataset preparation -- 4.2. MoRF sequence similarity -- 4.3. MoRF interface similarity -- References -- Disordered Function Conjunction: On the In-Silico Function Annotation of Intrinsically Disordered Regions -- 1. Introduction -- 2. Materials and Methods -- 2.1. Data collection -- 2.2. Computational workflow -- 2.2.1. Feature-based representation of protein regions -- 2.2.2. Prediction of protein region functions -- 2.2.3. Assessment of the function prediction and clustering -- 3. Results and Discussion -- 3.1. Prediction of individual functions of IDRs -- 3.2. IDRs described in multidimensional space form function-related clusters -- 3.3. Case studies -- 4. Conclusions -- Acknowledgments -- References -- De novo Ensemble Modeling Suggests that AP2-Binding to Disordered Regions Can Increase Steric Volume of Epsin but Not Eps15 -- 1. Introduction -- 2. Methods -- 2.1. Generation of structural ensembles -- 2.2. Filtering Epsin conformers to mimic the effect of Plasma membrane. , 2.3. Docking AP2α to the IDRs by superposition.

Additional Edition: Print version: Altman, Russ B Biocomputing 2020 - Proceedings Of The Pacific Symposium Singapore : World Scientific Publishing Company,c2019 ISBN 9789811215629

Language: English

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URL: https://www.worldscientific.com/worldscibooks/10.1142/11698#t=toc

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Format: 1 online resource (386 pages)

ISBN: 9789814335058

Note: Intro -- CONTENTS -- PREFACE -- INTEGRATIVE -OMICS FOR TRANSLATIONAL SCIENCE -- 1. Introduction -- 2. Session Summary -- 3. Acknowledgments -- TOWARDS INTEGRATIVE GENE PRIORITIZATION IN ALZHEIMER'S DISEASE -- 1. Introduction -- 2. Material and methods -- 3. Results -- 4. Discussion and conclusion -- 5. Acknowledgement -- References -- SYSTEMS BIOLOGY ANALYSES OF GENE EXPRESSION AND GENOME WIDEASSOCIATION STUDY DATA IN OBSTRUCTIVE SLEEP APNEA -- 1. Introduction -- 2. Material and Methods -- 3. Results and Discussion -- 4. Conclusion -- 5. Acknowledgments -- References -- FINDING MOST LIKELY HAPLOTYPES IN GENERAL PEDIGREESTHROUGH PARALLEL SEARCH WITH DYNAMIC LOAD BALANCING -- 1. Introduction -- 2. Background -- 3. Setup and Parallel Scheme -- 4. Predicting Subproblem Size Using the Cost Function -- 5. Experiments -- 6. Conclusion & -- FutureWork -- Acknowledgements -- References -- DYNAMIC, MULTI-LEVEL NETWORK MODELS OF CLINICAL TRIALS -- 1. Background -- 2. The scope and construction of a clinical trials network -- 3. Annotation of multiple network levels -- 4. Assessment of network dynamics -- 5. Network characteristics of "influential" trials -- 6. Discussion -- Acknowledgments -- References -- MINING FUNCTIONALLY RELEVANT GENE SETS FOR ANALYZINGPHYSIOLOGICALLY NOVEL CLINICAL EXPRESSION DATA -- 1. Introduction -- 2. Methods -- 3. Results -- 4. Discussion -- References -- GENOTYPE PHENOTYPE MAPPING IN RNA VIRUSES - DISJUNCTIVENORMAL FORM LEARNING -- 1. INTRODUCTION -- 2. Related computational work -- 3. Disjunctive Normal Form (DNF) learning algorithms -- 4. RESULTS -- 5. CONCLUSIONS -- 6. ACKNOWLEDGEMENTS -- References -- GENOME-WIDE ASSOCIATION MAPPING AND RARE ALLELES: FROMPOPULATION GENOMICS TO PERSONALIZED MEDICINE -- References. , AN APPLICATION AND EMPIRICAL COMPARISON OF STATISTICAL ANALYSISMETHODS FOR ASSOCIATING RARE VARIANTS TO A COMPLEX PHENOTYPE -- 1. Introduction -- 2. Sequencing the MGLL and FAAH genes in obese and control individuals -- 3. Statistical methods for rare variant associations -- 4. Results -- 5. Conclusions and Future Directions -- Acknowledgments -- References -- 2. Sequencing the MGLL and FAAH genes in obese and control individuals -- 3. Statistical methods for rare variant associations -- 4. Results -- 5. Conclusions and Future Directions -- Acknowledgments -- References -- HAPLOTYPE PHASING BY MULTI-ASSEMBLY OF SHAREDHAPLOTYPES: PHASE-DEPENDENT INTERACTIONS BETWEEN RARE VARIANTS -- 1. Introduction -- 2. Multi-Assembly of Shared Haplotypes -- 3. Algorithmic Strategies -- 4. Results on Simulated Data -- 5. Acknowledgments -- References -- AN EVALUATION OF POWER TO DETECT LOW-FREQUENCY VARIANTASSOCIATIONS USING ALLELE-MATCHING TESTS THAT ACCOUNTFOR UNCERTAINTY -- 1. Introduction -- 2. Allele-Matching Tests -- 3. Simulation Study -- 4. Discussion -- References -- PENALIZED REGRESSION FOR GENOME-WIDE ASSOCIATIONSCREENING OF SEQUENCE DATA -- 1. Introduction -- 2. Methods -- 3. Analysis of Simulated Data -- 4. Software Implementation and Illustration of Real Data -- 5. Discussion -- Acknowledgments -- References -- MICROBIOME STUDIES: PSB 2011 SPECIAL SESSION INTRODUCTION -- 1. Introduction to Microbiome Studies -- 2. Papers in this session -- ESTIMATING THE NUMBER OF SPECIES WITH CATCHALL -- 1. Introduction -- 2. Analysis of a microbial diversity dataset -- 3. Conclusions and future directions -- Acknowledgments -- References -- A FRAMEWORK FOR ANALYSIS OF METAGENOMIC SEQUENCING DATA -- 1. Background -- 2. Framework -- 3. Workflow -- 4. Discussion and Future Work -- 5. Conclusion -- Acknowledgements -- References. , VISUALIZATION AND STATISTICAL COMPARISONS OF MICROBIALCOMMUNITIES USING R PACKAGES ON PHYLOCHIP DATA -- 1. Introduction -- 2. Details of the Data Analysis Procedures -- 3. Batch E ect Detection using projections on Principal Planes -- 4. Incorporating and adjusting the phylogenetic information -- 5. Summary -- Acknowledgments -- References -- HUMAN MICROBIOME VISUALIZATION USING 3D TECHNOLOGY -- 1. Introduction -- 2. Methods -- 3. Results -- 4. Discussion -- 5. Acknowledgments -- References -- COMPARING BACTERIAL COMMUNITIES INFERRED FROM 16S rRNA GENE SEQUENCING AND SHOTGUN METAGENOMICS -- 1. Introduction -- 2. Methods -- 3. Results -- 4. Discussion -- 5. Availability -- 6. Acknowledgments -- References -- MULTI-SCALE MODELLING OF BIOSYSTEMS: FROM MOLECULAR TOMESOCALE -- 1. Background -- 2. Session Summary -- 3. Acknowledgements -- COMPUTATIONAL GENERATION INHIBITOR-BOUND CONFORMERS OF P38 MAPKINASE AND COMPARISON WITH EXPERIMENTS -- 1. Introduction -- 2. Materials and Methods -- 3. Results and Discussion -- 4. Conclusion -- Acknowledgements -- References -- MOLECULAR DYNAMICS SIMULATIONS OF THE FULL TRIPLE HELICALREGION OF COLLAGEN TYPE I PROVIDE AN ATOMIC SCALE VIEW OF THEPROTEIN'S REGIONAL HETEROGENEITY -- 1. Introduction -- 2. Materials and Methods -- 3. Results -- 4. Discussion -- 5. Acknowledgments -- References -- STRUCTURAL INSIGHTS INTO PRE-TRANSLOCATION RIBOSOME MOTIONS -- 1. Introduction -- 2. Background -- 3. Method -- 4. Results -- 5. Discussion -- Acknowledgements and availability -- References -- NEW CONFORMATIONAL SEARCH METHOD USING GENETICALGORITHM AND KNOT THEORY FOR PROTEINS -- 1. Introduction -- 2. Method -- 3. Results and Discussion -- 4. Conclusions -- Acknowledgments -- References -- PERSONAL GENOMICS -- 1. Introduction -- 2. Session Summary -- 3. Acknowledgments. , THE REFERENCE HUMAN GENOME DEMONSTRATES HIGH RISK OF TYPE 1DIABETES AND OTHER DISORDERS -- 1. Introduction -- 2. Methods -- 3. Results: -- 4. Discussion -- 5. Acknowledgements -- References -- MATCHING CANCER GENOMES TO ESTABLISHED CELL LINESFOR PERSONALIZED ONCOLOGY -- 1. Introduction -- 2. Methods -- 3. Results -- 4. Discussion -- Acknowledgements -- References -- USE OF BIOLOGICAL KNOWLEDGE TO INFORM THE ANALYSIS OF GENE-GENEINTERACTIONS INVOLVED IN MODULATING VIROLOGIC FAILURE WITHEFAVIRENZ-CONTAINING TREATMENT REGIMENS IN ART-NAÏVE ACTG CLINICALTRIALS PARTICIPANTS -- 1. Introduction -- 2. Methods -- 3. Results -- 4. Discussion -- 5. Acknowledgements -- References -- VISUAL INTEGRATION OF RESULTS FROM A LARGE DNA BIOBANK (BIOVU)USING SYNTHESIS-VIEW -- 1. Introduction -- 2. Methods -- 3. Visualization of Results -- 4. Conclusions -- 5. Acknowledgments -- 6. References -- MULTIVARIATE ANALYSIS OF REGULATORY SNPS: EMPOWERING PERSONALGENOMICS BY CONSIDERING CIS-EPISTASIS AND HETEROGENEITY -- 1. Introduction -- 2. Methods -- 3. Results -- 4. Discussion -- References -- HAPLOTYPE INFERENCE FROM SHORT SEQUENCE READS USING APOPULATION GENEALOGICAL HISTORY MODEL -- 1. Introduction -- 2. Background -- 3. Haplotyping with Short Reads -- 4. Results -- Funding and Acknowledgment -- References -- REVERSE ENGINEERING AND SYNTHESIS OF BIOMOLECULAR SYSTEMS -- 1. Introduction -- 2. Session Papers -- Acknowledgments -- References -- BINARY COUNTING WITH CHEMICAL REACTIONS -- 1. Introduction -- 2. Counting in Binary -- 3. Synchronization -- 4. Simulation results -- 5. Discussion -- References -- DEFINING THE PLAYERS IN HIGHER-ORDER NETWORKS: PREDICTIVE MODELINGFOR REVERSE ENGINEERING FUNCTIONAL INFLUENCE NETWORKS -- 1. Introduction -- 2. Methods -- 3. Results and Discussion -- 4. Conclusions -- 5. Acknowledgements -- 6. References. , RATE-INDEPENDENT CONSTRUCTS FOR CHEMICAL COMPUTATION -- 1. Introduction -- 2. Chemical Model -- 3. Computational Constructs -- 4. A Multiplier -- 5. Simulation Results -- 6. Discussion -- References -- TOWARDS REAL-TIME CONTROL OF GENE EXPRESSION:CONTROLLING THE HOG SIGNALING CASCADE -- 1. Introduction -- 2. A platform for real-time control of gene expression -- 3. Controlling transcription factor nuclear localization using a simplecontrol approach -- 4. Design of an improved control approach -- 5. Discussion -- References -- IDENTIFYING TARGETS FOR INTERVENTION BY ANALYZING BASINSOF ATTRACTION -- 1. Introduction -- 2. Background -- 3. Methods -- 4. Results -- 5. Conclusion and Future Work -- Supplementary Material -- Acknowledgement -- References -- MINING THE PHARMACOGENOMICS LITERATURE -- Abstract: -- Goals of the workshop: -- IDENTIFICATION OF ABERRANT PATHWAY AND NETWORKACTIVITY FROM HIGH-THROUGHPUT DATA -- 1. Introduction -- 2. Pathways in Human Disease -- 3. High-Throughput Data -- 4. Analysis Approaches and Tools -- 5. Conclusion -- References -- WORKSHOP ON THE VALIDATION AND MODELING OF ELECTRON CRYOMICROSCOPYSTRUCTURES OF BIOLOGICAL NANOMACHINES -- 1. Electron Cryo-microscopy -- 2. Challenges of CryoEM Map Interpretation -- 3. The CryoEM Modeling Challenge 2010 -- 4. Available Modeling Techniques -- 5. Conclusions -- 6. Acknowledgements -- References.

Additional Edition: Print version: Altman, Russ B Biocomputing 2011 - Proceedings Of The Pacific Symposium Singapore : World Scientific Publishing Company,c2010 ISBN 9789814335041

Language: English

Keywords: Electronic books. ; Electronic books.

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Format: 1 online resource (436 pages)

ISBN: 9789814583220

Note: Intro -- 0psb-preface-14-rba.pdf -- 1cp-all -- 0cp-intro-rev.pdf -- aguiar-rev -- badea -- 1.   Introduction and motivation -- 2.   Data and preprocessing -- 2.1.   The TCGA AML dataset -- 2.2.   Generalized mutations -- 2.3.   Protein-to-protein interaction data -- 3.   Proteins mutated in AML form pp interaction cliques -- 4.   Joint analysis of gene expression data and mutations using pp interaction data -- 4.1.   The joint clustering of expression and mutation interactor data -- 4.2.   The dimensionality of the factorization -- 4.3.   Significant sample-specific mutations -- 5.   Conclusions -- 6.   Acknowledgments -- chaibubneto (1) -- gitter-rev -- hu -- mayba -- min-rev -- morgan -- 2cad-all -- 0intro-cdr-rev -- blucher -- brubaker -- ng -- yang -- yera-rev -- zhu -- 3pleiotropy-all -- 0Pleiotropy_Proceedings_Introduction.pdf -- darabos-rev -- hall -- philip -- 4pm-all -- 0pm-intro-rev -- daneshjou -- martin -- parikh -- patwardhan-rev -- 1. Introduction -- 2. Methods -- 2.1. Subject Samples -- 2.2. Genomic Library Construction, Exome Sequencing, Alignment and Variant Calling -- 2.3. Problematic Regions of the Genome -- 2.4. Case Control Analysis -- 3. Results -- 4. Discussion -- 5text-all -- 0intro-text -- clark -- funk -- han -- komandurelayavilli -- liu (1) -- malinowski (2) -- vembu-rev -- zitnik (1) -- 1NoncodingRNA_workshop_PSB2014.pdf -- 2training -- Untitled.

Additional Edition: Print version: Altman, Russ B Pacific Symposium On Biocomputing 2014 Singapore : World Scientific Publishing Company,c2013 ISBN 9789814596343

Language: English

Keywords: Electronic books. ; Electronic books.

URL: Click to View

URL: Click here to view book