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Hidden Treasures in Contemporary RNA Sequencing / / by Serghei Mangul, Harry Taegyun Yang, Eleazar Eskin, Noah Zaitlen
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
Opac: Controlla la disponibilità qui
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
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
Opac: Controlla la disponibilità qui
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
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
Opac: Controlla la disponibilità qui
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
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
Opac: Controlla la disponibilità qui
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
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
Opac: Controlla la disponibilità qui
Regulatory genomics : RECOMB 2004 international workshop, RRG 2004, San Diego, CA, USA, March 26-27, 2004 : revised selected papers / / Eleazar Eskin, Chris Workman (eds.)
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
Opac: Controlla la disponibilità qui
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]
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
Opac: Controlla la disponibilità qui
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]
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
Opac: Controlla la disponibilità qui