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Biocomputing 2010 - Proceedings of the Pacific Symposium
| Biocomputing 2010 - Proceedings of the Pacific Symposium |
| Autore | Russ B Altman |
| Pubbl/distr/stampa | World Scientific Publishing Co, 2009 |
| Descrizione fisica | viii, 487 p. : ill. (some col.) |
| Disciplina | 572.8 |
| Altri autori (Persone) |
AltmanRuss
DunkerA. Keith <1943-> (Alan Keith) HunterLawrence <1961-> |
| Soggetto topico |
Bioinformatics
Genomics |
| Soggetto non controllato |
Protein Interactions
Metabolomics Biocomputing Computational Genetics Ontology Computational Proteomics Bioinformatics |
| ISBN |
1-282-76350-4
9786612763502 981-4295-29-9 |
| Formato | Materiale a stampa  |
| Livello bibliografico | Monografia |
| Lingua di pubblicazione | eng |
| Nota di contenuto | Computational challenges in comparative genomics. Session introduction / Bernard Moret ... [et al.]. Accurate taxonomic assignment of short pyrosequencing reads / José C. Clemente , Jesper Jansson, Gabriel Valiente. Benchmarking BLAST accuracy of genus/phyla classification of metagenomic reads / Steven D. Essinger, Gail L. Rosen. Guided genome halving : provably optimal solutions provide good insights into the preduplication ancestral genome of Saccharomyces cerevisiae / Haris Gavranovic, Eric Tannier. A practical algorithm for estimation of the maximum likelihood ancestral reconstruction error / Glenn Hickey, Mathieu Blanchette. Optimization methods for selecting founder populations for captive breeding of endangered species / Webb Miller ... [et al.] -- Computational studies of non-coding RNAs. Session introduction / Rolf Backofen ... [et al.]. RNA structural segmentation / Ivan Dotu ... [et al.]. RNAz 2.0 : improved noncoding RNA detection / Andreas R. Gruber ... [et al.]. Identification and classification of small RNAs in transcriptome sequence data / D. Langenberger ... [et al.]. Improvement of structure conservation index with centroid estimators / Yohei Okada, Kengo Sato, Yasubumi Sakakibara. Dynamic programming algorithms for RNA structure prediction with binding sites / Unyanee Poolsap, Yuki Kato, Tatsuya Akutsu. An algorithm for the energy barrier problem without pseudoknots and temporary arcs / Chris Thachuk ... [et al.] -- Dynamics of biological networks. Session introduction / Tanya Y. Berger-Wolf ... [et al.]. Local optimization for global alignment of protein interaction networks / Leonid Chindelevitch, Chung-Shou Liao, Bonnie Berger. Identification of coordinately dysregulated subnetworks in complex phenotypes / Salim A. Chowdhury, Mehmet Koyuturk. Subspace differential coexpression analysis : problem definition and a general approach / Gang Fang ... [et al.]. Estimation of protein and domain interactions in the switching motility system of Myxococcus xanthus ... [et al.]. Exploring biological network dynamics with ensembles of graph partitions / Saket Navlakha, Carl Kingsford. Geometric evolutionary dynamics of protein interaction networks / Natasa Przulj ... [et al.]. The steady states and dynamics of Urokinase-mediated plasmin activation / Lakshmi Venkatraman ... [et al.] -- Multi-resolution modeling of biological macromolecules. Session introduction / Samuel Flores ... [et al.]. Multi-resolution approach for interactively locating functionally linked ion binding sites by steering small molecules into electrostatic potential maps using a haptic device / Olivier Delalande ... [et al.]. Predicting RNA structure by multiple template homology modeling / Samuel C. Flores ... [et al.]. Constructing multi-resolution Markov State Models (MSMs) to elucidate RNA hairpin folding mechanisms / Xuhui Huang ... [et al.]. Multiscale dynamics of macromolecules using normal mode langevin / Jesus A. Izaguirre, Christopher R. Sweet, Vijay S. Pande. Insights into the intra-ring subunit order of TriC/CCT : structural and evolutionary analysis / Nir Kalisman, Michael Levitt. "Cross-graining :" Efficient multi-scale simulation via Markov state models / Peter Kasson, Vijay Pande. Toward understanding allosteric signaling mechanisms in the ATPase domain of molecular chaperones / Ying Liu, Ivet Bahar. 3D-blast : 3D protein structure alignment, comparison, and classification using spherical polar Fourier correlations / Lazaros Mavridis. David W. Ritchie. Structural prediction of protein-RNA interaction by computational docking with propensity-based statistical potentials / Laura Pérez-Cano ... [et al.] -- Personal genomics. Session introduction / Can Alkan ... [et al.]. Improving the prediction of pharmacogenes using text-derived gene-drug relationships / Yael Garten, Nicholas P. Tatonetti, Russ B. Altman. Finding unique filter sets in PLATO : a precursor to efficient interaction analysis in GWAS data / Benjamin J. Grady ... [et al.]. Enabling personal genomics with an explicit test of epistasis / Casey S. Greene ... [et al.]. Loss of post-translational modification sites in disease / Shuyan Li ... [et al.]. Detecting genome-wide haplotype polymorphism by combined use of mendelian constraints and local population structure / Xin Li, Yixuan Chen, Jing Li. Sequence Feature Variant Type (SFVT) analysis of the HLA genetic association in juvenile idiopathic arthritis / Glenys Thomson ... [et al.]. Cokgen : a software for the identification of rare copy number variation from SNP microarrays / Gökhan Yavas ... [et al.] -- Reverse engineering and synthesis of biomolecular systems. Session introduction / Gil Alterovitz ... [et al.]. Co-design in synthetic biology : a system-level analysis of the development of an environmental sensing device / David A. Ball ... [et al.]. Critical analysis of transcriptional and post-transcriptional regulatory networks in multiple myeloma / Marta Biasiolo ... [et al.]. A computational model of gene expression in an inducible synthetic circuit / Francesca Ceroni, Simone Furini, Silvio Cavalcanti. Retrovirus HTLV-1 gene circuit : a potential oscillator for eukaryotes / Alberto Corradin ... [et al.]. Emulsion based selection of T7 promoters of varying activity / Eric A. Davidson ... [et al.]. Clustering context-specific gene regulatory networks / Archana Ramesh ... [et al.]. Writing and compiling code into biochemistry / Adam Shea ... [et al.]. Synthesis of pharmacokinetic pathways through knowledge acquisition and automated reasoning / Luis Tari ... [et al.] -- Workshops. In silico biology / Richard Goldstein ... [et al.]. Genomic standards consortium workshop : Metagenomics, Metadata and Metaanalysis (M3) / Peter Sterk ... [et al.]. Extraction of genotype-phenotype-drug relationships from text : from entity recognition to bioinformatics application / Adrien Coulet ... [et al.]. |
| Record Nr. | UNINA-9910346696203321 |
Russ B Altman
|
||
| World Scientific Publishing Co, 2009 | ||
| Materiale a stampa | ||
| Lo trovi qui: Univ. Federico II | ||
| ||
Biocomputing 2013 - Proceedings of the Pacific Symposium [[electronic resource]]
| Biocomputing 2013 - Proceedings of the Pacific Symposium [[electronic resource]] |
| Autore | Altman Russ |
| Pubbl/distr/stampa | Singapore, : World Scientific Publishing Company, 2012 |
| Descrizione fisica | 1 online resource (471 p.) |
| Disciplina | 574.310724 |
| Soggetto topico |
Biology -- Computer simulation -- Congresses
Biology -- Mathematical models -- Congresses Biology -- Mathematical models Biology Health & Biological Sciences Biology - General |
| ISBN | 981-4447-97-8 |
| Formato | Materiale a stampa |
| Livello bibliografico | Monografia |
| Lingua di pubblicazione | eng |
| Nota di contenuto |
Modeling cell heterogeneity: from single-cell variations to mixed cells populations445; Computational Challenges of Mass Phenotyping454; The Future of Genome-Based Medicine456; 0session-intro-cdr.pdf; 1cheng; 1. Introduction; 2. Methods; 2.1. Data sources and data processing; 2.2. Pair-wise similarity scores; 2.3. Method nomenclature; 2.4. AUCs and p-values; 2.5. Expression signal strength; 3. Results; 4. Discussion; 5. Acknowledgments; 2felciano; 3phatak; 4shi; 5wang; 0intro-epigenomics.pdf; 1ahn; 2luo; 3sahu; 1gabr; 2gevaert; 3kim; 1. Introduction; 2. Methods
2.1. Introduction of the Module Cover Problem2.2. Integrated Module Cover; 2.3. Two-Step Module Cover; 3. Results; 3.1. Analysis of Glioblastoma Multiforme Data from GMDI; 3.1.1. Comparison of the Module Cover approaches. For an association to be specific in a given module, only a few regulatory associations should have highly significant p-values while the remaining loci are expected to have insignificant p-values. Thus, we defined the specificity of a module M as the area of a cumulative histogram of association significance values. Specifically, we partitioned the range from 0 to strength (M) into 10 bins of equal sizes and defined cj to be the cumulative percentage of j-th bin. Then the specificity is defi...3.1.2. Analysis of GBM data; 3.1.3. Analysis of Ovarian Cancer Data; 4. Discussion Uncovering modules that are associated with genomic alterations in a disease is a challenging task as well as an important step to understand complex diseases. To address this challenge we introduced a novel technique - module cover - that extends the concept of set cover to network modules. We provided a mathematical formalization of the problem and developed two heuristic solutions: the Integrated Module Cover approach, which greedily selects genes to cover disease cases while simultaneousl... In general, the module cover approach is especially helpful in analyzing and classifying heterogeneous disease cases by exploring the way different combinations of dys-regulated of modules relate to a particular disease subcategory. Indeed, our analysis indicated that the gene set selected by module cover approach may be used for classification. Equally important, the selected module covers may help to interpret classifications that were obtained with other methods.5. Materials; 5.1 Data Treatment for Glioblastoma Multiforme Data from GMDI Differentially Expressed Genes: Briefly, all samples were profiled using HG-U133 Plus 2.0 arrays that were normalized at the probe level with dChip (16, 19). Among probes representing each gene, we chose the probeset with the highest mean intensity in the tumor and control samples. We determined genes that are differentially expressed in each disease case compared to the non-tumor control cases with a Z-test. For a gene g and case c, we define cover(c, g) to be 1 if nominal p-value < 0.01 and... |
| Record Nr. | UNINA-9910346695703321 |
|
Altman Russ
|
||
| Singapore, : World Scientific Publishing Company, 2012 | ||
| Materiale a stampa | ||
| Lo trovi qui: Univ. Federico II | ||
| ||
Pacific Symposium on Biocomputing 2007 [[electronic resource] ] : Maui, Hawaii, 3-7 January 2007 / / edited by Russ B. Altman ... [et al.]
| Pacific Symposium on Biocomputing 2007 [[electronic resource] ] : Maui, Hawaii, 3-7 January 2007 / / edited by Russ B. Altman ... [et al.] |
| Pubbl/distr/stampa | Hackensack, N.J., : World Scientific, c2007 |
| Descrizione fisica | xvi, 507 p. : ill |
| Disciplina | 570.15 |
| Altri autori (Persone) | AltmanRuss |
| Soggetto topico |
Biology - Computer simulation
Biology - Mathematical models Molecular biology - Computer simulation Molecular biology - Mathematical models |
| Soggetto genere / forma | Electronic books. |
| ISBN |
1-281-91203-4
9786611912031 981-277-243-X |
| Formato | Materiale a stampa |
| Livello bibliografico | Monografia |
| Lingua di pubblicazione | eng |
| Nota di contenuto | Preface -- Protein interactions and diseases. Session introduction / Maricel Kann ... [et al.]. Graph kernels for disease outcome prediction from protein-protein interaction networks / Karsten M. Borgwardt ... [et al.]. Chalkboard: ontology-based pathway modeling and qualitative inference of disease mechanisms / Daniel L. Cook, Jesse C. Wiley, and John H. Gennari. Mining gene-disease relationships from biomedical literature weighting protein-protein interactions and connectivity measures / Graciela Gonzalez ... [et al.]. Predicting structure and dynamics of loosely-ordered protein complexes: influenza hemagglutinin fusion peptide / Peter M. Kasson and Vijay S. Pande. Protein interactions and disease phenotypes in the ABC transporter superfamily / Libusha Kelly, Rachel Karchin, and Andrej Sali. LTHREADER: prediction of Ligand-receptor interactions using localized threading / Vinay Pulim, Jadwiga Bienkowska, and Bonnie Berger. Discovery of protein interaction networks shared by diseases / Lee Sam ... [et al.]. An iterative algorithm for metabolic network-based drug target identification / Padmavati Sridhar, Tamer Kahveci, and Sanjay Ranka. Transcriptional interactions during smallpox infection and identification of early infection biomarkers / Willy A. Valdivia-Granda, Maricel G. Kann, and Jose Malaga -- Computational approaches to metabolomics. Session introduction / David S. Wishart and Russell Greiner. Leveraging latent information in NMR spectra for robust predictive models / David Chang, Aalim Weljie, and Jack Newton. Bioinformatics data profiling tools: a prelude to metabolic profiling / Natarajan Ganesan, Bala Kalyanasundaram, and Mahe Velauthapllai. Comparative QSAR analysis of bacterial, fungal, plant and human metabolites / Emre Karakoc, S. Cenk Sahinalp, and Artem Cherkasov. BioSpider: a web server for automating metabolome annotations / Craig Knox ... [et al.]. New bioinformatics resources for metabolomics / John L. Markley ... [et al.]. Setup X - a public study design database for metabolomic projects / Martin Scholz and Oliver Fiehn. Comparative metabolomics of breast cancer / Chen Yang ... [et al.]. Metabolic flux profiling of reaction modules in liver drug transformation / Jeongah Yoon and Kyongbum Lee -- New frontiers in biomedical text mining. Session introduction / Pierre Zweigenbaum ... [et al.]. Extracting semantic predications from medline citations for pharmacogenomics / Caroline B. Ahlers ... [et al.]. Annotating genes using textual patterns / Ali Cakmak and Gultekin Ozsoyoglu. A fault model for ontology mapping, alignment, and linking systems / Helen L. Johnson, K. Bretonnel Cohen, and Lawrence Hunter. Integrating natural language processing with flybase curation / Nikiforos Karamanis Y. ... [et al.]. A stacked graphical model for associating sub-images with sub-captions / Zhenzhen Kou, William W. Cohen, and Robert F. Murphy. GeneRIF quality assurance as summary revision / Zhiyong Lu, K. Bretonnel Cohen, and Lawrence Hunter. Evaluating the automatic mapping of human gene and protein mentions to unique identifiers / Alexander A. Morgan ... [et al.]. Multiple approaches to fine-grained indexing of the biomedical literature / Aurelie Neveol ... [et al.]. Mining patents using molecular similarity search / James Rhodes ... [et al.]. Discovering implicit associations between genes and hereditary diseases / Kazuhiro Seki and Javed Mostafa. A cognitive evaluation of four online search engines for answering definitional questions posed by physicians / Hong Yu and David Kaufman -- Biodiversity informatics: managing knowledge beyond humans and model organisms. Session introduction / Indra Neil Sarkar. Biomediator data integration and inference for functional annotation of anonymous sequences / Eithon Cadag ... [et al.]. Absent sequences: nullomers and primes / Greg Hampikian and Tim Andersen. An anatomical ontology for amphibians / Anne M. Maglia ... [et al.]. Recommending pathway genes using a compendium of clustering solutions / David M. Ng, Marcos H. Woehrmann, and Joshua M. Stuart. Semi-automated XML markup of biosystematic legacy literature with the Goldengate editor / Guido Sautter, Klemens B�ohm, and Donat Agosti -- Computational proteomics: high-throughput analysis for systems biology. Session introduction / William Cannon and Bobbie-Jo Webb-Robertson. Advancement in protein inference from shotgun proteomics using peptide detectability / Pedro Alves ... [et al.]. Mining tandem mass spectral data to develop a more accurate mass error model for peptide identification / Yan Fu ... [et al.]. Assessing and combining reliability of protein interaction sources / Sonia Leach ... [et al.]. Probabilistic modeling of systematic errors in two-hybrid experiments / David Sontag, Rohit Singh, and Bonnie Berger. Prospective exploration of biochemical tissue composition via imaging mass spectrometry guided by principal component analysis / Raf Van de Plas ... [et al.] -- DNA-protein interactions: integrating structure, sequence, and function. Session introduction / Martha L. Bulyk ... [et al.]. Discovering motifs with transcription factor domain knowledge / Henry C. M. Leung, Francis Y. L. Chin, and Bethany M. Y. Chan. Ab initio prediction of transcription factor binding sites / L. Angela Liu and Joel S. Bader. Comparative pathway annotation with protein-DNA interaction and operon information via graph tree decomposition / Jizhen Zhao, Dongsheng Che, and Liming Cai. |
| Record Nr. | UNINA-9910451938803321 |
| Hackensack, N.J., : World Scientific, c2007 | ||
| Materiale a stampa | ||
| Lo trovi qui: Univ. Federico II | ||
| ||
Pacific Symposium on Biocomputing 2007 [[electronic resource] ] : Maui, Hawaii, 3-7 January 2007 / / edited by Russ B. Altman ... [et al.]
| Pacific Symposium on Biocomputing 2007 [[electronic resource] ] : Maui, Hawaii, 3-7 January 2007 / / edited by Russ B. Altman ... [et al.] |
| Pubbl/distr/stampa | Hackensack, N.J., : World Scientific, c2007 |
| Descrizione fisica | xvi, 507 p. : ill |
| Disciplina | 570.15 |
| Altri autori (Persone) | AltmanRuss |
| Soggetto topico |
Biology - Computer simulation
Biology - Mathematical models Molecular biology - Computer simulation Molecular biology - Mathematical models |
| ISBN |
1-281-91203-4
9786611912031 981-277-243-X |
| Formato | Materiale a stampa |
| Livello bibliografico | Monografia |
| Lingua di pubblicazione | eng |
| Nota di contenuto | Preface -- Protein interactions and diseases. Session introduction / Maricel Kann ... [et al.]. Graph kernels for disease outcome prediction from protein-protein interaction networks / Karsten M. Borgwardt ... [et al.]. Chalkboard: ontology-based pathway modeling and qualitative inference of disease mechanisms / Daniel L. Cook, Jesse C. Wiley, and John H. Gennari. Mining gene-disease relationships from biomedical literature weighting protein-protein interactions and connectivity measures / Graciela Gonzalez ... [et al.]. Predicting structure and dynamics of loosely-ordered protein complexes: influenza hemagglutinin fusion peptide / Peter M. Kasson and Vijay S. Pande. Protein interactions and disease phenotypes in the ABC transporter superfamily / Libusha Kelly, Rachel Karchin, and Andrej Sali. LTHREADER: prediction of Ligand-receptor interactions using localized threading / Vinay Pulim, Jadwiga Bienkowska, and Bonnie Berger. Discovery of protein interaction networks shared by diseases / Lee Sam ... [et al.]. An iterative algorithm for metabolic network-based drug target identification / Padmavati Sridhar, Tamer Kahveci, and Sanjay Ranka. Transcriptional interactions during smallpox infection and identification of early infection biomarkers / Willy A. Valdivia-Granda, Maricel G. Kann, and Jose Malaga -- Computational approaches to metabolomics. Session introduction / David S. Wishart and Russell Greiner. Leveraging latent information in NMR spectra for robust predictive models / David Chang, Aalim Weljie, and Jack Newton. Bioinformatics data profiling tools: a prelude to metabolic profiling / Natarajan Ganesan, Bala Kalyanasundaram, and Mahe Velauthapllai. Comparative QSAR analysis of bacterial, fungal, plant and human metabolites / Emre Karakoc, S. Cenk Sahinalp, and Artem Cherkasov. BioSpider: a web server for automating metabolome annotations / Craig Knox ... [et al.]. New bioinformatics resources for metabolomics / John L. Markley ... [et al.]. Setup X - a public study design database for metabolomic projects / Martin Scholz and Oliver Fiehn. Comparative metabolomics of breast cancer / Chen Yang ... [et al.]. Metabolic flux profiling of reaction modules in liver drug transformation / Jeongah Yoon and Kyongbum Lee -- New frontiers in biomedical text mining. Session introduction / Pierre Zweigenbaum ... [et al.]. Extracting semantic predications from medline citations for pharmacogenomics / Caroline B. Ahlers ... [et al.]. Annotating genes using textual patterns / Ali Cakmak and Gultekin Ozsoyoglu. A fault model for ontology mapping, alignment, and linking systems / Helen L. Johnson, K. Bretonnel Cohen, and Lawrence Hunter. Integrating natural language processing with flybase curation / Nikiforos Karamanis Y. ... [et al.]. A stacked graphical model for associating sub-images with sub-captions / Zhenzhen Kou, William W. Cohen, and Robert F. Murphy. GeneRIF quality assurance as summary revision / Zhiyong Lu, K. Bretonnel Cohen, and Lawrence Hunter. Evaluating the automatic mapping of human gene and protein mentions to unique identifiers / Alexander A. Morgan ... [et al.]. Multiple approaches to fine-grained indexing of the biomedical literature / Aurelie Neveol ... [et al.]. Mining patents using molecular similarity search / James Rhodes ... [et al.]. Discovering implicit associations between genes and hereditary diseases / Kazuhiro Seki and Javed Mostafa. A cognitive evaluation of four online search engines for answering definitional questions posed by physicians / Hong Yu and David Kaufman -- Biodiversity informatics: managing knowledge beyond humans and model organisms. Session introduction / Indra Neil Sarkar. Biomediator data integration and inference for functional annotation of anonymous sequences / Eithon Cadag ... [et al.]. Absent sequences: nullomers and primes / Greg Hampikian and Tim Andersen. An anatomical ontology for amphibians / Anne M. Maglia ... [et al.]. Recommending pathway genes using a compendium of clustering solutions / David M. Ng, Marcos H. Woehrmann, and Joshua M. Stuart. Semi-automated XML markup of biosystematic legacy literature with the Goldengate editor / Guido Sautter, Klemens B�ohm, and Donat Agosti -- Computational proteomics: high-throughput analysis for systems biology. Session introduction / William Cannon and Bobbie-Jo Webb-Robertson. Advancement in protein inference from shotgun proteomics using peptide detectability / Pedro Alves ... [et al.]. Mining tandem mass spectral data to develop a more accurate mass error model for peptide identification / Yan Fu ... [et al.]. Assessing and combining reliability of protein interaction sources / Sonia Leach ... [et al.]. Probabilistic modeling of systematic errors in two-hybrid experiments / David Sontag, Rohit Singh, and Bonnie Berger. Prospective exploration of biochemical tissue composition via imaging mass spectrometry guided by principal component analysis / Raf Van de Plas ... [et al.] -- DNA-protein interactions: integrating structure, sequence, and function. Session introduction / Martha L. Bulyk ... [et al.]. Discovering motifs with transcription factor domain knowledge / Henry C. M. Leung, Francis Y. L. Chin, and Bethany M. Y. Chan. Ab initio prediction of transcription factor binding sites / L. Angela Liu and Joel S. Bader. Comparative pathway annotation with protein-DNA interaction and operon information via graph tree decomposition / Jizhen Zhao, Dongsheng Che, and Liming Cai. |
| Record Nr. | UNINA-9910778260903321 |
| Hackensack, N.J., : World Scientific, c2007 | ||
| Materiale a stampa | ||
| Lo trovi qui: Univ. Federico II | ||
| ||
Pacific Symposium on Biocomputing 2007 [[electronic resource] ] : Maui, Hawaii, 3-7 January 2007 / / edited by Russ B. Altman ... [et al.]
| Pacific Symposium on Biocomputing 2007 [[electronic resource] ] : Maui, Hawaii, 3-7 January 2007 / / edited by Russ B. Altman ... [et al.] |
| Pubbl/distr/stampa | Hackensack, N.J., : World Scientific, c2007 |
| Descrizione fisica | xvi, 507 p. : ill |
| Disciplina | 570.15 |
| Altri autori (Persone) | AltmanRuss |
| Soggetto topico |
Biology - Computer simulation
Biology - Mathematical models Molecular biology - Computer simulation Molecular biology - Mathematical models |
| ISBN |
1-281-91203-4
9786611912031 981-277-243-X |
| Formato | Materiale a stampa |
| Livello bibliografico | Monografia |
| Lingua di pubblicazione | eng |
| Nota di contenuto | Preface -- Protein interactions and diseases. Session introduction / Maricel Kann ... [et al.]. Graph kernels for disease outcome prediction from protein-protein interaction networks / Karsten M. Borgwardt ... [et al.]. Chalkboard: ontology-based pathway modeling and qualitative inference of disease mechanisms / Daniel L. Cook, Jesse C. Wiley, and John H. Gennari. Mining gene-disease relationships from biomedical literature weighting protein-protein interactions and connectivity measures / Graciela Gonzalez ... [et al.]. Predicting structure and dynamics of loosely-ordered protein complexes: influenza hemagglutinin fusion peptide / Peter M. Kasson and Vijay S. Pande. Protein interactions and disease phenotypes in the ABC transporter superfamily / Libusha Kelly, Rachel Karchin, and Andrej Sali. LTHREADER: prediction of Ligand-receptor interactions using localized threading / Vinay Pulim, Jadwiga Bienkowska, and Bonnie Berger. Discovery of protein interaction networks shared by diseases / Lee Sam ... [et al.]. An iterative algorithm for metabolic network-based drug target identification / Padmavati Sridhar, Tamer Kahveci, and Sanjay Ranka. Transcriptional interactions during smallpox infection and identification of early infection biomarkers / Willy A. Valdivia-Granda, Maricel G. Kann, and Jose Malaga -- Computational approaches to metabolomics. Session introduction / David S. Wishart and Russell Greiner. Leveraging latent information in NMR spectra for robust predictive models / David Chang, Aalim Weljie, and Jack Newton. Bioinformatics data profiling tools: a prelude to metabolic profiling / Natarajan Ganesan, Bala Kalyanasundaram, and Mahe Velauthapllai. Comparative QSAR analysis of bacterial, fungal, plant and human metabolites / Emre Karakoc, S. Cenk Sahinalp, and Artem Cherkasov. BioSpider: a web server for automating metabolome annotations / Craig Knox ... [et al.]. New bioinformatics resources for metabolomics / John L. Markley ... [et al.]. Setup X - a public study design database for metabolomic projects / Martin Scholz and Oliver Fiehn. Comparative metabolomics of breast cancer / Chen Yang ... [et al.]. Metabolic flux profiling of reaction modules in liver drug transformation / Jeongah Yoon and Kyongbum Lee -- New frontiers in biomedical text mining. Session introduction / Pierre Zweigenbaum ... [et al.]. Extracting semantic predications from medline citations for pharmacogenomics / Caroline B. Ahlers ... [et al.]. Annotating genes using textual patterns / Ali Cakmak and Gultekin Ozsoyoglu. A fault model for ontology mapping, alignment, and linking systems / Helen L. Johnson, K. Bretonnel Cohen, and Lawrence Hunter. Integrating natural language processing with flybase curation / Nikiforos Karamanis Y. ... [et al.]. A stacked graphical model for associating sub-images with sub-captions / Zhenzhen Kou, William W. Cohen, and Robert F. Murphy. GeneRIF quality assurance as summary revision / Zhiyong Lu, K. Bretonnel Cohen, and Lawrence Hunter. Evaluating the automatic mapping of human gene and protein mentions to unique identifiers / Alexander A. Morgan ... [et al.]. Multiple approaches to fine-grained indexing of the biomedical literature / Aurelie Neveol ... [et al.]. Mining patents using molecular similarity search / James Rhodes ... [et al.]. Discovering implicit associations between genes and hereditary diseases / Kazuhiro Seki and Javed Mostafa. A cognitive evaluation of four online search engines for answering definitional questions posed by physicians / Hong Yu and David Kaufman -- Biodiversity informatics: managing knowledge beyond humans and model organisms. Session introduction / Indra Neil Sarkar. Biomediator data integration and inference for functional annotation of anonymous sequences / Eithon Cadag ... [et al.]. Absent sequences: nullomers and primes / Greg Hampikian and Tim Andersen. An anatomical ontology for amphibians / Anne M. Maglia ... [et al.]. Recommending pathway genes using a compendium of clustering solutions / David M. Ng, Marcos H. Woehrmann, and Joshua M. Stuart. Semi-automated XML markup of biosystematic legacy literature with the Goldengate editor / Guido Sautter, Klemens B�ohm, and Donat Agosti -- Computational proteomics: high-throughput analysis for systems biology. Session introduction / William Cannon and Bobbie-Jo Webb-Robertson. Advancement in protein inference from shotgun proteomics using peptide detectability / Pedro Alves ... [et al.]. Mining tandem mass spectral data to develop a more accurate mass error model for peptide identification / Yan Fu ... [et al.]. Assessing and combining reliability of protein interaction sources / Sonia Leach ... [et al.]. Probabilistic modeling of systematic errors in two-hybrid experiments / David Sontag, Rohit Singh, and Bonnie Berger. Prospective exploration of biochemical tissue composition via imaging mass spectrometry guided by principal component analysis / Raf Van de Plas ... [et al.] -- DNA-protein interactions: integrating structure, sequence, and function. Session introduction / Martha L. Bulyk ... [et al.]. Discovering motifs with transcription factor domain knowledge / Henry C. M. Leung, Francis Y. L. Chin, and Bethany M. Y. Chan. Ab initio prediction of transcription factor binding sites / L. Angela Liu and Joel S. Bader. Comparative pathway annotation with protein-DNA interaction and operon information via graph tree decomposition / Jizhen Zhao, Dongsheng Che, and Liming Cai. |
| Record Nr. | UNINA-9910819119103321 |
| Hackensack, N.J., : World Scientific, c2007 | ||
| Materiale a stampa | ||
| Lo trovi qui: Univ. Federico II | ||
| ||
Pacific Symposium on Biocomputing 2012 Kohala Coast, Hawaii, USA, 3-7 January 2012
| Pacific Symposium on Biocomputing 2012 Kohala Coast, Hawaii, USA, 3-7 January 2012 |
| Pubbl/distr/stampa | [Place of publication not identified], : World Scientific Pub Co, 2012 |
| Descrizione fisica | 1 online resource (442 p.) : ill. (some col.) |
| Disciplina | 572.8 |
| Soggetto topico |
Engineering & Applied Sciences
Computer Science |
| Formato | Materiale a stampa |
| Livello bibliografico | Monografia |
| Lingua di pubblicazione | eng |
| Nota di contenuto |
Identification of aberrant pathway and network activity from high-throughput data. Session introduction / Rachel Karchin ... [et al.]. SSLPred : predicting synthetic sickness lethality / Nirmalya Bandyopadhyayy, Sanjay Ranka, and Tamer Kahveci. Predicting the effects of copy-number variation in double and triple mutant combinations / Gregory W. Carter ... [et al.]. Integrative network analysis to identify aberrant pathway networks in ovarian cancer / Li Chen ... [et al.] -- Role of synthetic genetic interactions in understanding functional interactions among pathways / Shahin Mohammadi, Giorgos Kollias, and Ananth Grama -- Discovery of mutated subnetworks associated with clinical data in cancer / Fabio Vandin ... [et al.] -- Intrinsically disordered proteins : analysis, prediction, simulation, and biology. Session introduction / Jianhan Chen, Jianlin Cheng, and A. Keith Dunker. Quasi-anharmonic analysis reveals intermediate states in the nuclear co-activator receptor binding domain ensemble / Virginia M. Burger ... [et al.]. Efficient construction of disordered protein ensembles in a Bayesian framework with optimal selection of conformations / Charles K. Fisher, Orly Ullman, and Collin M. Stultz. Correlation between posttranslational modification and intrinsic disorder in protein / Jianjiong Gao and Dong Xu. Intrinsic disorder within and flanking the DNA-binding domains of human transcription factors / Xin Guo, Martha L. Bulyk, and Alexander J. Hartemink. Intrinsic protein disorder and protein-protein interactions / Wei-Lun Hsu ... [et al.]. Subclassifying disordered proteins by the CH-CDF plot method / Fei Huang ... [et al.]. Coevolved residues and the functional association for intrinsically disordered proteins / Chan-Seok Jeong and Dongsup Kim. Cryptic disorder: an order-disorder transformation regulates the function of nucleophosmin / Diana M. Mitrea and Richard W. Kriwacki. Functional annotation of intrinsically disordered domains by their amino acid content using IDD navigator / Ashwini Patil ... [et al.]. On the complementarity of the consensus-based disorder prediction / Zhenling Peng and Lukasz Kurgan. Modulating protein-DNA interactions by post-translational modifications at disordered regions / Dana Vuzman, Yonit Hoffman, and Yaakov Levy -- Microbiome studies: analytical tools and techniques. Session introduction / James A. Foster ... [et al.]. Estimating population diversity with unreliable low frequency counts / John Bunge ... [et al.]. Comparisons of distance methods for combining covariates and abundances in microbiome studies / Julia Fukuyama ... [et al.]. Proteotyping of microbial communities by optimization of tandem mass spectrometry data interpretation / Alys Hugo ... [et al.]. phyloseq: a bioconductor package for handling and analysis of high-throughput phylogenetic sequence data / Paul J. McMurdie and Susan Holmes. SEPP: SATe-enabled phylogenetic placement / Siavash Mirarab, Nam Nguyen, and Tandy Warnow. Artificial functional difference between microbial communities caused by length difference of sequencing reads / Quan Zhang, Thomas G. Doak, and Yuzhen Ye. MetaDomain: a profile HMM-based protein domain classification tool for short sequences / Yuan Zhang and Yanni Sun.
Modeling host-pathogen interactions: computational biology and bioinformatics for infectious disease research. Session introduction / Jason E. Mcdermott ... [et al.]. Structural models for host-pathogen protein-protein interactions: assessing coverage and bias / Eric A. Franzosa and Yu Xia. Identification of cell cycle-regulated, putative hyphal genes in Candida Albicans / Raluca Gordan, Saumyadipta Pyne, and Martha L. Bulyk. Determining confidence of predicted interactions between HIV-1 and human proteins using conformal method / Ilia Nouretdinov ... [et al.] -- Personalized medicine: from genotypes and molecular phenotypes towards computed therapy. Session introduction / Oliver Stegle ... [et al.]. Finding genome-transcriptome-phenome associations with structured association mapping and visualization in GenAMap / Ross E. Curtis ... [et al.]. Interpretome: a freely available, modular, and secure personal genome interpretation engine / Konrad J. Karczewski ... [et al.]. A kinase inhibition map approach for tumor sensitivity prediction and combination therapy design for targeted drugs / Ranadip Pal and Noah Berlow. Mixture model for sub-phenotyping in GWAS / David Warde-Farley ... [et al.] -- Text and knowledge mining for pharmacogenomics: genotypephenotype-drug relationships. Session introduction / Kevin Bretonnel Cohen ... [et al.]. The extraction of pharmacogenetic and pharmacogenomic relations - A case study using PharmGKB / Ekaterina Buyko, Elena Beisswanger, and Udo Hahn. Linking PharmGKB to phenotype studies and animal models of disease for drug repurposing / Robert Hoehndorf ... [et al.]. Integrating VA's NDF-RT drug terminology with PharmGKB: preliminary results / Jyotishman Pathak ... [et al.]. Discovery and explanation of drug-drug interactions via text mining / Bethany Percha, Yael Garten, and Russ B. Altman. Ranking gene-drug relationships in biomedical literature using latent Dirichlet allocation / Yonghui Wu ... [et al.] -- Workshops. The structure and function of chromatin and chromosomes / William Stafford Noble ... [et al.]. Law, bioethics and the current status of ownership, privacy, informed consent in the genomic age / Greg Hampikian and Eric M. Meslin. Systems pharmacogenomics-bridging the gap / Marylyn Ritchie ... [et al.]. |
| Record Nr. | UNINA-9910346695903321 |
| [Place of publication not identified], : World Scientific Pub Co, 2012 | ||
| Materiale a stampa | ||
| Lo trovi qui: Univ. Federico II | ||
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Pacific Symposium on Biocomputing 2015 : Kohala Coast, Hawaii, USA, 4-8 January 2015 / / edited by Russ B. Altman and five others
| Pacific Symposium on Biocomputing 2015 : Kohala Coast, Hawaii, USA, 4-8 January 2015 / / edited by Russ B. Altman and five others |
| Autore | Russ B Altman |
| Pubbl/distr/stampa | World Scientific Publishing Co, 2014 |
| Descrizione fisica | 1 online resource (viii, 505 pages) : illustrations |
| Disciplina | 570.151 |
| Soggetto topico |
Biology - Computer simulation - Congresses
Biology - Mathematical models - Congresses Molecular biology - Mathematical models - Congresses |
| Soggetto non controllato |
Protein Interactions
Metabolomics Biocomputing Computational Genetics Ontology Computational Proteomics Bioinformatics |
| ISBN | 981-4644-73-0 |
| Formato | Materiale a stampa |
| Livello bibliografico | Monografia |
| Lingua di pubblicazione | eng |
| Record Nr. | UNINA-9910141778503321 |
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Russ B Altman
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| World Scientific Publishing Co, 2014 | ||
| Materiale a stampa | ||
| Lo trovi qui: Univ. Federico II | ||
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Pacific Symposium on Biocomputing 2016 : Kohala Coast, Hawaii, USA, 4-8 January 2016 / / edited by Russ B. Altman and five others
| Pacific Symposium on Biocomputing 2016 : Kohala Coast, Hawaii, USA, 4-8 January 2016 / / edited by Russ B. Altman and five others |
| Autore | Russ B Altman |
| Pubbl/distr/stampa | World Scientific Publishing Co, 2015 |
| Descrizione fisica | 1 online resource (592 pages) : illustrations |
| Disciplina | 570.113 |
| Soggetto topico |
Biology - Computer simulation - Congresses
Biology - Mathematical models - Congresses Molecular biology - Computer simulation - Congresses |
| Soggetto non controllato |
Protein Interactions
Metabolomics Biocomputing Computational Genetics Ontology Computational Proteomics Bioinformatics |
| ISBN | 981-4749-41-9 |
| Formato | Materiale a stampa |
| Livello bibliografico | Monografia |
| Lingua di pubblicazione | eng |
| Record Nr. | UNINA-9910137229403321 |
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Russ B Altman
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| World Scientific Publishing Co, 2015 | ||
| Materiale a stampa | ||
| Lo trovi qui: Univ. Federico II | ||
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Pacific Symposium on Biocomputing 2020 : Kohala Coast, Hawaii, USA, 3-7 January 2020 / / edited by Russ B. Altman ... [et al.]
| Pacific Symposium on Biocomputing 2020 : Kohala Coast, Hawaii, USA, 3-7 January 2020 / / edited by Russ B. Altman ... [et al.] |
| Pubbl/distr/stampa | Singapore, : World Scientific, [2019] |
| Descrizione fisica | 1 online resource (500 p.) : ill |
| Disciplina | 570.151 |
| Altri autori (Persone) | AltmanRuss |
| Soggetto topico |
Biology - Mathematical models
Biology - Computer simulation |
| Soggetto genere / forma | Conference papers and proceedings. |
| ISBN | 981-12-1563-4 |
| Formato | Materiale a stampa |
| Livello bibliografico | Monografia |
| Lingua di pubblicazione | eng |
| Nota di contenuto | Session introduction: Artificial intelligence for enhancing clinical medicine / Roxana Daneshjou ... [et al.] -- Predicting longitudinal outcomes of Alzheimer's disease via a tensor-based joint classification and regression model / Lodewijk Brand ... [et al.] -- Robustly extracting medical knowledge from EHRs: a case study of learning a health knowledge graph / Irene Y. Chen ... [et al.] -- Increasing clinical trial accrual via automated matching of biomarker criteria / Jessica W. Chen ... [et al.] -- Addressing the credit assignment problem in treatment outcome prediction using temporal difference learning / Sahar Harati ... [et al.] -- Multiclass disease classification from microbial whole-community metagenomes / Saad Khan and Libusha Kelly -- LitGen: genetic literature recommendation guided by human explanations / Allen Nie ... [et al.] -- From genome to phenome: predicting multiple cancer phenotypes based on somatic genomic alterations via the genomic impact transformer / Yifeng Tao ... [et al.] -- Automated phenotyping of patients wsith non-alcolholic fatty liver disease reveals clinically relevant disease subtypes / Maxence Vandromme [et al.] -- Monitoring ICU mortality risk with a long short-term memory recurrent neural network / Ke Yu ... [et al.] -- Multilevel self-attention model and its use on medical risk prediction / Xianlong Zeng ... [et al.] -- Identifying transitional high cost users from unstructured patient profiles written by primary care physicians / Haoran Zhang ... [et al.] --Obtaining dual-energy computed tomography (CT) information from a single-energy CT image for quantitative imaging analysis of living subjects by using deep learning / Wei Zhao ... [et al.] -- On the importance of computational biology and bioinformatics to the origins and rapid progression of the intrinsically disordered proteins field / Lukasz Kurgan ... [et al.] -- Many-to-one binding by intrinsically disordered problem regions / Wei-Lun Alterovitz ... [et al.] -- Disordered function conjunction: on the in-silico function annotation of intrinsically disordered regions / Sina Ghadermarzi ... [et al.] -- De novo ensemble modeling suggests that AP2-binding to disordered regions can increase steric volume of Epsin but not Eps15 / N. Suhas Jagannathan ... [et al.] -- Modulation of p53 transactivation domain conformations by ligand binding and cancer-associated mutations / Xiaorong Liu and Jianhan Chen -- Exploring relationship between the density of charged tracts within disordered regions and phase separation / Ramiz Somjee, Diana M. Mitrea and Richard W. Kriwacki -- Session introduction: Mutational signatures: etiology, properties, and role in cancer / Mark D.M. Leiserson, Teresa M. Przytycka and Roded Sharan -- PhySigs: phylogenetic inference of mutational signature dynamics / Sarah Chistensen, Mark D.M. Leiserson and Mohammed El-Kebir -- TrackSigFreq: subclonal reconstructions based on mutation signatures and allele frequencies / Caitlin F. Harrigan ... [et al.] -- Impact of mutational signatures on microRNA and their response elements / Eirini Stamoulakatou ... [et al.] -- DNA repair footprint uncovers contribution of DNA repair mechanism to mutational signatures / Damian Wojtowicz ... [et al.] -- Genome gerrymandering: optimal division of the genome into regions with cancer type specific differences in mutation rates / Adamo Young ... [et al.] -- Ongoing challenges and innovative approaches for recognizing pattern across large-scale, integrative biomedical datasets / Shilpa Nadimpalli ... [et al.] -- Clinical concept embeddings learned from massive sources of multimodal medical data / Andrew L. Beam ... [et al.] -- Assessment of imputation methods for missing gene expression data in meta-analysis of distinct cohorts of tuberculosis patients / Carly A. Bobak ... [et al.] -- Towards identifying drug side effects from social media using active learning and crowd sourcing / Sophie Burkhardt ... [et al.] -- Microvascular dynamics from 4D microscopy using temporal segmentation / Shir Gur ... [et al.] -- Using transcriptional signatures to find cancer drivers with LURE / David Haan ... [et al.] -- and other papers. |
| Record Nr. | UNINA-9910367718703321 |
| Singapore, : World Scientific, [2019] | ||
| Materiale a stampa | ||
| Lo trovi qui: Univ. Federico II | ||
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