Hidden Treasures in Contemporary RNA Sequencing / / by Serghei Mangul, Harry Taegyun Yang, Eleazar Eskin, Noah Zaitlen |
Autore | Mangul Serghei |
Edizione | [1st ed. 2019.] |
Pubbl/distr/stampa | Cham : , : Springer International Publishing : , : Imprint : Springer, , 2019 |
Descrizione fisica | 1 online resource (99 pages) |
Disciplina |
547.79
572.8633 |
Collana | SpringerBriefs in Computer Science |
Soggetto topico |
Bioinformatics
Genetics Computational Biology/Bioinformatics Genetics and Genomics |
ISBN | 3-030-13973-5 |
Formato | Materiale a stampa |
Livello bibliografico | Monografia |
Lingua di pubblicazione | eng |
Nota di contenuto | Abstract -- Main Text -- Acknowledgement -- Disclosure -- References. |
Record Nr. | UNINA-9910337570903321 |
Mangul Serghei | ||
Cham : , : Springer International Publishing : , : Imprint : Springer, , 2019 | ||
Materiale a stampa | ||
Lo trovi qui: Univ. Federico II | ||
|
Regulatory genomics [[electronic resource] ] : proceedings of the 3rd annual RECOMB workshop : National University of Singapore, Singapore 17-18 July 2006 / / editors, Leong Hon Wai, Sung Wing-Kin, Eleazar Eskin |
Pubbl/distr/stampa | London, : Imperial College Press, c2008 |
Descrizione fisica | 1 online resource (144 p.) |
Disciplina | 572.865 |
Altri autori (Persone) |
EskinEleazar
LeongHon Wai <1955-> SungWing-Kin |
Collana | Series on advances in bioinformatics and computational biology |
Soggetto topico |
Genetic regulation
Genomics |
Soggetto genere / forma | Electronic books. |
ISBN | 1-84816-252-9 |
Formato | Materiale a stampa |
Livello bibliografico | Monografia |
Lingua di pubblicazione | eng |
Nota di contenuto |
Foreword; RECOMB Regulatory Genomics 2006 Organization; CONTENTS; Keynote Papers; Computational Prediction of Regulatory Elements by Comparative Sequence Analysis M. Tompa; A Tale of Two Topics - Motif Significance and Sensitivity of Spaced Seeds M. Li; Computational Challenges for Top-Down Modeling and Simulation of Biological Pathways S. Miyano; An Improved Gibbs Sampling Method for Motif Discovery via Sequence Weighting T. Jiang; Discovering Motifs with Transcription Factor Domain Knowledge F. Chin; Applications of ILP in Computational Biology A . Dress
On the Evolution of Transcription Regulation Networks R. Shamir Systems Pharmacology in Cancer Therapeutics: Iterative Informatics-Experimental Interface E. Liu; Computational Structural Proteomics and Inhibitor Discovery R. Abagyan; Characterization of Transcriptional Responses to Environmental Stress by Differential Location Analysis H. Tang; A Knowledge-based Hybrid Algorithm for Protein Secondary Structure Prediction W. L. Hsu; Monotony and Surprise (Conservative Approaches to Pattern Discovery) A . Apostolic0; Evolution of Bacterial Regulatory Systems M. S. Gelfand; Contributed Papers TScan: A Two-step De NOVO Motif Discovery Method 0. Abul, G. K. Sandve, and F. Drabbs1. Introduction; 2. Method; 2.1. Step 1; 2.2. Step 2; 2.2.1, Over-representation Conservation Scoring; 2.2.2. Frith et al. Scoring; 3. Experiments; 4. Conclusion; References; Redundancy Elimination in Motif Discovery Algorithms H. Leung and F. Chin; 1. Introduction; 2. Maximizing Likelihood; 3. The Motif Redundancy Problem; 3.1. The motif redundancy problem; 3.2. Formal definition; 4. Algorithm; 5. Experimental Results; 6. Concluding Remarks; Appendix; References GAMOT: An Efficient Genetic Algorithm for Finding Challenging Motifs in DNA Sequences N. Karaoglu, S. Maurer-Stroh, and B. Manderick1. Introduction; 2. GA for Motif Finding; 3. An Efficient Algorithm (GAMOT); 3.1. Fast motif discovery; 3.2. The genetic algorithm; 4. Experimental Results; 4.1. Comparison with exhaustive search; 4.2. Comparison with GAI and GA2; 4.3. Comparison with other algorithms; 4.3.1. Quality of the solutions; 4.4. GAMOTparameters; 5. Conclusions and Future Work; References; Identification of Spaced Regulatory Sites via Submotif Modeling E. Wijaya and R. Kanagasabai 1. Introduction 2. Related Work; 3. Our Approach; 4. Problem Definition; 5. Algorithm SPACE; 5.1. Generation of candidate motifs; 5.2. Constrained frequent pattern mining; 5.2.1. Generalized gap; 5.2.2. Mining of constrained frequent patterns; 5.3. Significance testing and scoring; 6. Experimental Results; 6.1. Results on Tompa's benchmark data set; 6.2. Results on synthetic data set; 7. Discussion and Conclusions; References; Refining Motif Finders with E-value Calculations N. Nagarajan, P. Ng, and U. Keich; 1. Introduction; 2. Efficiently Computing E-values 3. Optimizing for E-values - Conspv |
Record Nr. | UNINA-9910455059103321 |
London, : Imperial College Press, c2008 | ||
Materiale a stampa | ||
Lo trovi qui: Univ. Federico II | ||
|
Regulatory genomics [[electronic resource] ] : proceedings of the 3rd annual RECOMB workshop : National University of Singapore, Singapore 17-18 July 2006 / / editors, Leong Hon Wai, Sung Wing-Kin, Eleazar Eskin |
Pubbl/distr/stampa | London, : Imperial College Press, c2008 |
Descrizione fisica | 1 online resource (144 p.) |
Disciplina | 572.865 |
Altri autori (Persone) |
EskinEleazar
LeongHon Wai <1955-> SungWing-Kin |
Collana | Series on advances in bioinformatics and computational biology |
Soggetto topico |
Genetic regulation
Genomics |
ISBN | 1-84816-252-9 |
Formato | Materiale a stampa |
Livello bibliografico | Monografia |
Lingua di pubblicazione | eng |
Nota di contenuto |
Foreword; RECOMB Regulatory Genomics 2006 Organization; CONTENTS; Keynote Papers; Computational Prediction of Regulatory Elements by Comparative Sequence Analysis M. Tompa; A Tale of Two Topics - Motif Significance and Sensitivity of Spaced Seeds M. Li; Computational Challenges for Top-Down Modeling and Simulation of Biological Pathways S. Miyano; An Improved Gibbs Sampling Method for Motif Discovery via Sequence Weighting T. Jiang; Discovering Motifs with Transcription Factor Domain Knowledge F. Chin; Applications of ILP in Computational Biology A . Dress
On the Evolution of Transcription Regulation Networks R. Shamir Systems Pharmacology in Cancer Therapeutics: Iterative Informatics-Experimental Interface E. Liu; Computational Structural Proteomics and Inhibitor Discovery R. Abagyan; Characterization of Transcriptional Responses to Environmental Stress by Differential Location Analysis H. Tang; A Knowledge-based Hybrid Algorithm for Protein Secondary Structure Prediction W. L. Hsu; Monotony and Surprise (Conservative Approaches to Pattern Discovery) A . Apostolic0; Evolution of Bacterial Regulatory Systems M. S. Gelfand; Contributed Papers TScan: A Two-step De NOVO Motif Discovery Method 0. Abul, G. K. Sandve, and F. Drabbs1. Introduction; 2. Method; 2.1. Step 1; 2.2. Step 2; 2.2.1, Over-representation Conservation Scoring; 2.2.2. Frith et al. Scoring; 3. Experiments; 4. Conclusion; References; Redundancy Elimination in Motif Discovery Algorithms H. Leung and F. Chin; 1. Introduction; 2. Maximizing Likelihood; 3. The Motif Redundancy Problem; 3.1. The motif redundancy problem; 3.2. Formal definition; 4. Algorithm; 5. Experimental Results; 6. Concluding Remarks; Appendix; References GAMOT: An Efficient Genetic Algorithm for Finding Challenging Motifs in DNA Sequences N. Karaoglu, S. Maurer-Stroh, and B. Manderick1. Introduction; 2. GA for Motif Finding; 3. An Efficient Algorithm (GAMOT); 3.1. Fast motif discovery; 3.2. The genetic algorithm; 4. Experimental Results; 4.1. Comparison with exhaustive search; 4.2. Comparison with GAI and GA2; 4.3. Comparison with other algorithms; 4.3.1. Quality of the solutions; 4.4. GAMOTparameters; 5. Conclusions and Future Work; References; Identification of Spaced Regulatory Sites via Submotif Modeling E. Wijaya and R. Kanagasabai 1. Introduction 2. Related Work; 3. Our Approach; 4. Problem Definition; 5. Algorithm SPACE; 5.1. Generation of candidate motifs; 5.2. Constrained frequent pattern mining; 5.2.1. Generalized gap; 5.2.2. Mining of constrained frequent patterns; 5.3. Significance testing and scoring; 6. Experimental Results; 6.1. Results on Tompa's benchmark data set; 6.2. Results on synthetic data set; 7. Discussion and Conclusions; References; Refining Motif Finders with E-value Calculations N. Nagarajan, P. Ng, and U. Keich; 1. Introduction; 2. Efficiently Computing E-values 3. Optimizing for E-values - Conspv |
Record Nr. | UNINA-9910777933003321 |
London, : Imperial College Press, c2008 | ||
Materiale a stampa | ||
Lo trovi qui: Univ. Federico II | ||
|
Regulatory genomics : proceedings of the 3rd annual RECOMB workshop : National University of Singapore, Singapore 17-18 July 2006 / / editors, Leong Hon Wai, Sung Wing-Kin, Eleazar Eskin |
Edizione | [1st ed.] |
Pubbl/distr/stampa | London, : Imperial College Press, c2008 |
Descrizione fisica | 1 online resource (144 p.) |
Disciplina | 572.865 |
Altri autori (Persone) |
EskinEleazar
LeongHon Wai <1955-> SungWing-Kin |
Collana | Series on advances in bioinformatics and computational biology |
Soggetto topico |
Genetic regulation
Genomics |
ISBN | 1-84816-252-9 |
Formato | Materiale a stampa |
Livello bibliografico | Monografia |
Lingua di pubblicazione | eng |
Nota di contenuto |
Foreword; RECOMB Regulatory Genomics 2006 Organization; CONTENTS; Keynote Papers; Computational Prediction of Regulatory Elements by Comparative Sequence Analysis M. Tompa; A Tale of Two Topics - Motif Significance and Sensitivity of Spaced Seeds M. Li; Computational Challenges for Top-Down Modeling and Simulation of Biological Pathways S. Miyano; An Improved Gibbs Sampling Method for Motif Discovery via Sequence Weighting T. Jiang; Discovering Motifs with Transcription Factor Domain Knowledge F. Chin; Applications of ILP in Computational Biology A . Dress
On the Evolution of Transcription Regulation Networks R. Shamir Systems Pharmacology in Cancer Therapeutics: Iterative Informatics-Experimental Interface E. Liu; Computational Structural Proteomics and Inhibitor Discovery R. Abagyan; Characterization of Transcriptional Responses to Environmental Stress by Differential Location Analysis H. Tang; A Knowledge-based Hybrid Algorithm for Protein Secondary Structure Prediction W. L. Hsu; Monotony and Surprise (Conservative Approaches to Pattern Discovery) A . Apostolic0; Evolution of Bacterial Regulatory Systems M. S. Gelfand; Contributed Papers TScan: A Two-step De NOVO Motif Discovery Method 0. Abul, G. K. Sandve, and F. Drabbs1. Introduction; 2. Method; 2.1. Step 1; 2.2. Step 2; 2.2.1, Over-representation Conservation Scoring; 2.2.2. Frith et al. Scoring; 3. Experiments; 4. Conclusion; References; Redundancy Elimination in Motif Discovery Algorithms H. Leung and F. Chin; 1. Introduction; 2. Maximizing Likelihood; 3. The Motif Redundancy Problem; 3.1. The motif redundancy problem; 3.2. Formal definition; 4. Algorithm; 5. Experimental Results; 6. Concluding Remarks; Appendix; References GAMOT: An Efficient Genetic Algorithm for Finding Challenging Motifs in DNA Sequences N. Karaoglu, S. Maurer-Stroh, and B. Manderick1. Introduction; 2. GA for Motif Finding; 3. An Efficient Algorithm (GAMOT); 3.1. Fast motif discovery; 3.2. The genetic algorithm; 4. Experimental Results; 4.1. Comparison with exhaustive search; 4.2. Comparison with GAI and GA2; 4.3. Comparison with other algorithms; 4.3.1. Quality of the solutions; 4.4. GAMOTparameters; 5. Conclusions and Future Work; References; Identification of Spaced Regulatory Sites via Submotif Modeling E. Wijaya and R. Kanagasabai 1. Introduction 2. Related Work; 3. Our Approach; 4. Problem Definition; 5. Algorithm SPACE; 5.1. Generation of candidate motifs; 5.2. Constrained frequent pattern mining; 5.2.1. Generalized gap; 5.2.2. Mining of constrained frequent patterns; 5.3. Significance testing and scoring; 6. Experimental Results; 6.1. Results on Tompa's benchmark data set; 6.2. Results on synthetic data set; 7. Discussion and Conclusions; References; Refining Motif Finders with E-value Calculations N. Nagarajan, P. Ng, and U. Keich; 1. Introduction; 2. Efficiently Computing E-values 3. Optimizing for E-values - Conspv |
Record Nr. | UNINA-9910822091103321 |
London, : Imperial College Press, c2008 | ||
Materiale a stampa | ||
Lo trovi qui: Univ. Federico II | ||
|
Regulatory Genomics [[electronic resource] ] : RECOMB 2004 International Workshop, RRG 2004, San Diego, CA, USA, March 26-27, 2004, Revised Selected Papers / / edited by Eleazar Eskin, Chris Workman |
Edizione | [1st ed. 2005.] |
Pubbl/distr/stampa | Berlin, Heidelberg : , : Springer Berlin Heidelberg : , : Imprint : Springer, , 2005 |
Descrizione fisica | 1 online resource (VIII, 116 p.) |
Disciplina | 572 |
Collana | Lecture Notes in Bioinformatics |
Soggetto topico |
Biochemistry
Algorithms Computer science—Mathematics Data structures (Computer science) Database management Bioinformatics Biochemistry, general Algorithm Analysis and Problem Complexity Discrete Mathematics in Computer Science Data Structures Database Management |
Formato | Materiale a stampa |
Livello bibliografico | Monografia |
Lingua di pubblicazione | eng |
Nota di contenuto | Predicting Genetic Regulatory Response Using Classification: Yeast Stress Response -- Detecting Functional Modules of Transcription Factor Binding Sites in the Human Genome -- Fishing for Proteins in the Pacific Northwest -- PhyloGibbs: A Gibbs Sampler Incorporating Phylogenetic Information -- Application of Kernel Method to Reveal Subtypes of TF Binding Motifs -- Learning Regulatory Network Models that Represent Regulator States and Roles -- Using Expression Data to Discover RNA and DNA Regulatory Sequence Motifs -- Parameter Landscape Analysis for Common Motif Discovery Programs -- Inferring Cis-region Hierarchies from Patterns in Time-Course Gene Expression Data -- Modeling and Analysis of Heterogeneous Regulation in Biological Networks. |
Record Nr. | UNISA-996466014403316 |
Berlin, Heidelberg : , : Springer Berlin Heidelberg : , : Imprint : Springer, , 2005 | ||
Materiale a stampa | ||
Lo trovi qui: Univ. di Salerno | ||
|
Regulatory genomics : RECOMB 2004 international workshop, RRG 2004, San Diego, CA, USA, March 26-27, 2004 : revised selected papers / / Eleazar Eskin, Chris Workman (eds.) |
Edizione | [1st ed. 2005.] |
Pubbl/distr/stampa | Berlin ; ; New York, : Springer, c2005 |
Descrizione fisica | 1 online resource (VIII, 116 p.) |
Disciplina | 572 |
Altri autori (Persone) |
EskinEleazar
WorkmanChris |
Collana | Lecture notes in computer science. Lecture notes in bioinformatics |
Soggetto topico | Genetic regulation |
Formato | Materiale a stampa |
Livello bibliografico | Monografia |
Lingua di pubblicazione | eng |
Nota di contenuto | Predicting Genetic Regulatory Response Using Classification: Yeast Stress Response -- Detecting Functional Modules of Transcription Factor Binding Sites in the Human Genome -- Fishing for Proteins in the Pacific Northwest -- PhyloGibbs: A Gibbs Sampler Incorporating Phylogenetic Information -- Application of Kernel Method to Reveal Subtypes of TF Binding Motifs -- Learning Regulatory Network Models that Represent Regulator States and Roles -- Using Expression Data to Discover RNA and DNA Regulatory Sequence Motifs -- Parameter Landscape Analysis for Common Motif Discovery Programs -- Inferring Cis-region Hierarchies from Patterns in Time-Course Gene Expression Data -- Modeling and Analysis of Heterogeneous Regulation in Biological Networks. |
Altri titoli varianti |
RECOMB 2004
RRG 2004 |
Record Nr. | UNINA-9910483148503321 |
Berlin ; ; New York, : Springer, c2005 | ||
Materiale a stampa | ||
Lo trovi qui: Univ. Federico II | ||
|
Systems biology and regulatory genomics : Joint Annual RECOMB 2005 Satellite Workshops on Systems Biology and on Regulatory Genomics, San Diego, CA, USA, December 2-4, 2005 : revised selected papers / / edited by Eleazar Eskin [and three others] |
Edizione | [1st ed. 2006.] |
Pubbl/distr/stampa | Berlin, Germany ; ; New York, New York : , : Springer, , [2007] |
Descrizione fisica | 1 online resource (X, 261 p.) |
Disciplina | 572.865 |
Collana | Lecture Notes in Bioinformatics |
Soggetto topico |
Genetic regulation - Data processing
Bioinformatics Systems biology |
ISBN |
1-280-90212-4
9786610902125 3-540-48540-6 |
Formato | Materiale a stampa |
Livello bibliografico | Monografia |
Lingua di pubblicazione | eng |
Nota di contenuto | An Interactive Map of Regulatory Networks of Pseudomonas aeruginosa Genome -- The Pathalyzer: A Tool for Analysis of Signal Transduction Pathways -- Decomposition of Overlapping Protein Complexes: A Graph Theoretical Method for Analyzing Static and Dynamic Protein Associations -- Comparison of Protein-Protein Interaction Confidence Assignment Schemes -- Characterization of the Effects of TF Binding Site Variations on Gene Expression Towards Predicting the Functional Outcomes of Regulatory SNPs -- Comparative Systems Biology of the Sporulation Initiation Network in Prokaryotes -- Improvement of Computing Times in Boolean Networks Using Chi-square Tests -- Build a Dictionary, Learn a Grammar, Decipher Stegoscripts, and Discover Genomic Regulatory Elements -- Causal Inference of Regulator-Target Pairs by Gene Mapping of Expression Phenotypes -- Examination of the tRNA Adaptation Index as a Predictor of Protein Expression Levels -- Improved Duplication Models for Proteome Network Evolution -- Application of Expectation Maximization Clustering to Transcription Factor Binding Positions for cDNA Microarray Analysis -- Combinatorial Genetic Regulatory Network Analysis Tools for High Throughput Transcriptomic Data -- Topological Robustness of the Protein-Protein Interaction Networks -- A Bayesian Approach for Integrating Transcription Regulation and Gene Expression: Application to Saccharomyces Cerevisiae Cell Cycle Data -- Probabilistic in Silico Prediction of Protein-Peptide Interactions -- Improved Pattern-Driven Algorithms for Motif Finding in DNA Sequences -- Annotation of Promoter Regions in Microbial Genomes Based on DNA Structural and Sequence Properties -- An Interaction-Dependent Model for Transcription Factor Binding -- Computational Characterization and Identification of Core Promoters of MicroRNA Genes in C. elegans, H. sapiens and A. thaliana -- A Comprehensive Kinetic Model of the Exocytotic Process: Evaluation of the Reaction Mechanism. |
Record Nr. | UNINA-9910484907103321 |
Berlin, Germany ; ; New York, New York : , : Springer, , [2007] | ||
Materiale a stampa | ||
Lo trovi qui: Univ. Federico II | ||
|
Systems biology and regulatory genomics : Joint Annual RECOMB 2005 Satellite Workshops on Systems Biology and on Regulatory Genomics, San Diego, CA, USA, December 2-4, 2005 : revised selected papers / / edited by Eleazar Eskin [and three others] |
Edizione | [1st ed. 2006.] |
Pubbl/distr/stampa | Berlin, Germany ; ; New York, New York : , : Springer, , [2007] |
Descrizione fisica | 1 online resource (X, 261 p.) |
Disciplina | 572.865 |
Collana | Lecture Notes in Bioinformatics |
Soggetto topico |
Genetic regulation - Data processing
Bioinformatics Systems biology |
ISBN |
1-280-90212-4
9786610902125 3-540-48540-6 |
Formato | Materiale a stampa |
Livello bibliografico | Monografia |
Lingua di pubblicazione | eng |
Nota di contenuto | An Interactive Map of Regulatory Networks of Pseudomonas aeruginosa Genome -- The Pathalyzer: A Tool for Analysis of Signal Transduction Pathways -- Decomposition of Overlapping Protein Complexes: A Graph Theoretical Method for Analyzing Static and Dynamic Protein Associations -- Comparison of Protein-Protein Interaction Confidence Assignment Schemes -- Characterization of the Effects of TF Binding Site Variations on Gene Expression Towards Predicting the Functional Outcomes of Regulatory SNPs -- Comparative Systems Biology of the Sporulation Initiation Network in Prokaryotes -- Improvement of Computing Times in Boolean Networks Using Chi-square Tests -- Build a Dictionary, Learn a Grammar, Decipher Stegoscripts, and Discover Genomic Regulatory Elements -- Causal Inference of Regulator-Target Pairs by Gene Mapping of Expression Phenotypes -- Examination of the tRNA Adaptation Index as a Predictor of Protein Expression Levels -- Improved Duplication Models for Proteome Network Evolution -- Application of Expectation Maximization Clustering to Transcription Factor Binding Positions for cDNA Microarray Analysis -- Combinatorial Genetic Regulatory Network Analysis Tools for High Throughput Transcriptomic Data -- Topological Robustness of the Protein-Protein Interaction Networks -- A Bayesian Approach for Integrating Transcription Regulation and Gene Expression: Application to Saccharomyces Cerevisiae Cell Cycle Data -- Probabilistic in Silico Prediction of Protein-Peptide Interactions -- Improved Pattern-Driven Algorithms for Motif Finding in DNA Sequences -- Annotation of Promoter Regions in Microbial Genomes Based on DNA Structural and Sequence Properties -- An Interaction-Dependent Model for Transcription Factor Binding -- Computational Characterization and Identification of Core Promoters of MicroRNA Genes in C. elegans, H. sapiens and A. thaliana -- A Comprehensive Kinetic Model of the Exocytotic Process: Evaluation of the Reaction Mechanism. |
Record Nr. | UNISA-996466146103316 |
Berlin, Germany ; ; New York, New York : , : Springer, , [2007] | ||
Materiale a stampa | ||
Lo trovi qui: Univ. di Salerno | ||
|