Computational biology / bioinformatics Books
University of Chicago Press Truth Machine The Contentious History of DNA
Book SynopsisDNA profiling is often heralded as unassailable criminal evidence, a veritable "truth machine" that can overturn convictions based on eyewitness testimony, confessions, and other forms of forensic evidence. This book traces the controversial history of DNA fingerprinting by looking at court cases in the US and UK from the mid-1980s onwards.Trade Review"I could not put it down. This is a must-read for anyone interested in the history of science." (Times Higher Education) "An interesting read.... It illustrates that the controversy of DNA profiling is rooted not in the science, but mainly in the restrictions of the adversarial system." (Nature)"
£80.00
Springer Cytochrome P450 Structure Mechanism and Biochemistry
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£999.99
National Academies Press Achievements of the National Plant Genome
Book SynopsisLife on Earth would be impossible without plants. Humans rely on plants for most clothing, furniture, food, as well as for many pharmaceuticals and other products. This title discusses how the plant immune system controls pathogen defense, demonstrate that the plant genome science community is capable of driving technological advancement.Table of Contents1 Front Matter; 2 Summary; 3 1 Introduction; 4 2 Assessment; 5 3 Recommendations and Goals: New Horizons in Plant Genomics; 6 Glossary; 7 References; 8 Appendixes; 9 A: Committee Biographies; 10 B: Publications in Genomics of the Top 40 Most-Cultivated Crops; 11 C: Questionnaire to Lead Principal Investigators of NPGI Grants; 12 D: Workshop on the National Plant Genome Initiative (Agenda); 13 E: Summary of Grants Given by the National Plant Genome Initiative; 14 F: List of Websites That Lead Principal Investigators of NPGI Grants Reported as the Top Five Websites Used for NPGI Research; 15 G: Impact Factor of Journals in Which Awardees of NPGI Grants Published Their Articles; 16 H: NPGI-Funded K-12 Outreach Activities with Broad Potential Impact; 17 I: Examples of Joint Call for Proposals and Co-funded Programs by IWG Members; 18 J: Examples of Interactions with Industry and Plant Breeders Reported by Principal Investigators of NPGI; 19 K: Tree Genomics or Molecular Genetics Support Provided by the U.S. Department of Agriculture Forest Service; 20 L: Number and Type of Mutants Distributed by the National Plant Germplasm System
£41.80
Elsevier Science Health Information Exchange
Book SynopsisTable of ContentsSection 1: Health Information Exchange Fundamentals1. What is Health Information Exchange?2. Health Information Exchange as a Profession3. Policies and Incentives for Adoption: Towards Broader Use Section 2: Organizational Aspects of Managing Health Information Exchange 4. Engaging and Sustaining Stakeholders: Towards Governance5. Managing the Business of Health Information Exchange: Towards Sustainability6. Managing Privacy, Confidentiality, and Risk: Towards Trust7. Managing Threats to Health Data and Information: Towards Security Section 3: Technical Architecture and Building Blocks 8. Architectures and Approaches to Manage the Evolving Health Information Infrastructure9. Syntactic Interoperability and the Role of Syntactic Standards in Health Information Exchange10. Standardizing Health Care Data across an Enterprise11. Shared, Longitudinal Health Records for Clinical and Population Health12. Client Registries: Identifying and Linking Patients13. Facility Registries: Metadata for Where Care Is Delivered14. Health Worker Registries: Managing the Health Care Workforce15. Finance and Insurance Services: Supporting Achievement of Universal Healthcare Section 4: Impacting Health Care Delivery and Outcomes16. The Evidence Base for HIE17. Measuring the Value of HIE18. Leveraging HIE to Facilitate Large Scale Data Analytics19. Incorporating Social, Genomic, and Environmental Determinants into HIE20. Cross-border HIE to Achieve World Health Outcomes21. Future Directions for Health Information Exchange Section 5: Case Studies in Health Information Exchange22. The Indiana Health Information Exchange23. Using Health Information Exchange to Support Public Health Activities in Western New York: A Case Study24. Creating a 21st Century Health Information Technology Infrastructure: New York’s Health Care Efficiency and Affordability Law for New Yorkers Capital Grant Program25. Use of HIEs for Value-Based Care Delivery: A Case Study of Maryland’s HIE26. Return on Investment: The Case of the Social Security Administration27. HIE-Enhanced Care Coordination: Implementation and Evaluation of Event Notification Services in the Veterans Health Administration28. A Resilient Infrastructure to Facilitate Digital Health: The Case of HIE in Denmark29. National Health Information Systems: Exchange in Multiple African Nations30. Health Information Exchange in Taiwan: Multiple Layers to Facilitate Broad Access and Use of Data for Clinical and Population Health31. Israel’s National HIE Network Ofek: A Robust Infrastructure for Clinical and Population Health32. Bringing HIE to the Middle East and North Africa: The Case of Malaffi in Abu Dhabi
£82.76
Elsevier Science & Technology Practical Data Analytics for Innovation in
Book SynopsisTable of ContentsPart I: Historical Perspective and the Issues of Concern for Health Care Delivery in the 21st Century 1. History of Medical Health Care Delivery & Basic Medical Research 2. "Things That Matter !!!" - Why This Book? 3. Biomedical Informatics 4. Access to Data for Analytics – the ‘Biggest Issue’ in Medical and Healthcare Predictive Analytics 5. Regulatory Measures – Agencies, and Data Issues in Medicine and Healthcare 6. Personalized Medicine 7. Patient-Directed Healthcare 8. OMICS or MULTIOMICS 9. Challenges and Considerations of AI and Genomics Part II: Practical Step-by-Step Tutorials and Case Studies TUTORIAL A Case Study: Imputing Medical Specialty Using Data Mining Models TUTORIAL AA: VOC for Cancer Detection / Prediction TUTORIAL B Case Study: Using Association Rules of Investigate Characteristics of Hospital Readmissions TUTORIAL BB Case Study: COVID-19 Descriptive Analysis Around the World TUTORIAL C Constructing Decision Trees for Medicare Claims Using R and Rattle TUTORIAL D Predictive and Prescriptive Analytics for Optimal Decisioning: Hospital Readmission Risk Mitigation TUTORIAL E Obesity Group: Predicting Medicine and Conditions That Achieved the Greatest Weight Loss in a Group of Obese/Morbidly Obese Patients TUTORIAL F1 Obesity Individual: Predicting Best Treatment or an Individual from Portal Data at a Clinic TUTORIAL F2 Obesity Individual: Automatic Binning of Continuous Variables and WoE to Produce a Better Model than the "Hand Binned" Stepwise Regression Model TUTORIAL G Resiliency Study for First- and Second-Year Medical Residents TUTORIAL H Medicare Enrollment Analysis Using Visual Data Mining TUTORIAL I Case Study: Detection of Stress-Induced Ischemia in Patients with Chest Pain "Rule-Out ACS" Protocol TUTORIAL J1 Predicting Survival or Mortality for Patients with Disseminated Intravascular Coagulation and/or Critical illnesses TUTORIAL J2 Decisioning for DIC TUTORIAL K Predicting Allergy Symptoms TUTORIAL L Exploring Discrete Database Networks of TriCare Health Data Using R and Shiny TUTORIAL M Schistosomiasis Data from WHO TUTORIAL N The Poland Medical Bundle TUTORIAL O Medical Advice Acceptance Prediction TUTORIAL P Using Neural Network Analysis to Assist in Classifying Neuropsychological Data TUTORIAL Q Developing Interactive Decision Trees using Inpatient Claims (with SAS Enterprise Miner) TUTORIAL R Divining Healthcare Charges for Optimal Health Benefits Under the Affordable Care Act TUTORIAL S Availability of Hospital Beds for Newly Admitted Patients: The Impact of Environmental Services on Hospital Throughput TUTORIAL T Predicting Vascular Thrombosis: Comparing Predictive Analytic Models and Building an Ensemble Model for "Best Prediction" TUTORIAL U Predicting Breast Cancer Diagnosis Using Support Vector Machines TUTORIAL V Heart Disease: Evaluating Variables That Might Have an Effect on Cholesterol Level (Using Recode of Variables Function) TUTORIAL W Blood Pressure Predictive Factors TUTORIAL X Gene Search and the Related Risk Estimates: A Statistical Analysis of Prostate Cancer Data TUTORIAL Y Ovarian Cancer Prediction via Proteomic Mass Spectrometry TUTORIAL Z Influence of Stent Vendor Representatives in the Catheterization Lab Part III: Practical Solutions and Advanced Topics in Administration and Delivery of Health Care Including Practical Predictive Analytics for Medicine 1. Challenges for Healthcare Administration and Delivery: Integrating Predictive and Prescriptive Modeling into Personalized Health Care 2. Challenges of Medical Research for the Remainder of the 21st Century 3. Introduction to the Cornerstone Chapters of this Book, Chapters 12 -15: The "Three Processes": Quality Control, Predictive Analytics, and Decisioning 4. The Nature of Insight from Data and Implications for Automated Decisioning: Predictive and Prescriptive Models, Decisions, and Actions 5. Decisioning Systems (Platforms) Coupled with Predictive Analytics in a Real Hospital Setting - A Model for the World 6. The Latest in Predictive and Prescriptive Analytics 7. The Coming Standard for a Data Model – OMOP (Observational Medical Outcomes Partnership) as per Observational Health Data Sciences and Informatics (OHDS) at University of California-Irvine 8. A Real Case Study of GLAUCOMA (eye disease) and suggested PREDICTIVE MODELING for identifying individual patient predictions of best treatment with high accuracy 9. Analytics Architectures for the 21st Century 10. Causation and How This ‘Cutting Edge Concept’ Works with Predictive Analytics and Prescriptive Analytics (Decisioning) 11. 21st Century Healthcare and Wellness: Getting the Health Care Delivery System That Meets Global Needs
£999.99
Elsevier Science Digital Transformation in Healthcare in
Book SynopsisTable of Contents1. The Challenges in the HealthCare in the post-COVID-19 era2. The enabling technologies for the Digital Transformation3. A value driven approach to the delivery of patient centric top-quality health services4. Analytics and Enhanced Decision Making in Health5. Best Practices for Training towards Digital Transformation and Sustainable health
£103.50
Elsevier Science Cognitive Intelligence with Neutrosophic
Book SynopsisTable of Contents1. Introduction to Neutrosophic Probability 2. Introduction to Neutrosophic Statistics 3. Applications Applications of Neutrosophic Statistics to Medicine Applications of Neutrosophic Statistics to Cognitive Data Applications of Neutrosophic Statistics to Bioinformatics
£999.99
Taylor & Francis Ltd DNA Methylation Microarrays Experimental Design and Statistical Analysis
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£61.99
Springer Neural Cell Behavior and Fuzzy Logic
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£999.99
Springer In Silico Immunology
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£999.99
Springer Semantic Web Revolutionizing Knowledge Discovery in the Life Sciences
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£999.99
Springer Mathematical Biology
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£999.99
Springer Biomechanics
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£999.99
Springer Understanding Nonlinear Dynamics
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£999.99
Springer Mathematical Approaches to Biomolecular Structure and Dynamics
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£999.99
Springer Diffusion and Ecological Problems Modern Perspectives
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£999.99
Springer Analysis and Simulation of Chaotic Systems
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£999.99
WW Norton & Co DNA Is Not Destiny The Remarkable Completely
Book SynopsisOne of the world’s leading cultural psychologists debunks the hype surrounding DNA testing and puts to rest our mistaken anxieties about our genes.Trade Review"Steven Heine is one of the leading cultural psychologists in the world. In DNA Is Not Destiny, Heine serves as a trustworthy guide through the moral minefield of genetic differences and lays out a new way to think rationally about our genes." -- Jonathan Haidt, Thomas Cooley Professor of Ethical Leadership at New York University's Stern School of Business and author of The Righteous Mind "Steven Heine is one of the leading cultural psychologists in the world. In DNA Is Not Destiny, Heine serves as a trustworthy guide through the moral minefield of genetic differences and lays out a new way to think rationally about our genes." -- Jonathan Haidt, Thomas Cooley Professor of Ethical Leadership at New York University's Stern School of Business and author of The Righteous Mind "At some point everyone wonders: 'Who am I and where did I come from?' Is there any question more fascinating? In this important book, Steve Heine tells us what our DNA can and cannot reveal about our nature, our origins, and our futures. The material is fascinating, and Heine's vibrant writing makes it come alive with personal significance for every reader." -- Carol Dweck, Lewis and Virginia Eaton Professor of Psychology at Stanford University and author of Mindset "At some point everyone wonders: 'Who am I and where did I come from?' Is there any question more fascinating? In this important book, Steve Heine tells us what our DNA can and cannot reveal about our nature, our origins, and our futures. The material is fascinating, and Heine's vibrant writing makes it come alive with personal significance for every reader." -- Carol Dweck, Lewis and Virginia Eaton Professor of Psychology at Stanford University and author of Mindset "Your genes contribute to your beliefs, behaviors, and life outcomes. Only in rare cases are they determinative. This brilliant, invaluable book sets straight crucial matters of heredity and environment and their interaction-and does so in lively and lucid prose." -- Richard Nisbett, Theodore M. Newcomb Distinguished Professor of Social Psychology at the University of Michigan and author of Mindware "Your genes contribute to your beliefs, behaviors, and life outcomes. Only in rare cases are they determinative. This brilliant, invaluable book sets straight crucial matters of heredity and environment and their interaction-and does so in lively and lucid prose." -- Richard Nisbett, Theodore M. Newcomb Distinguished Professor of Social Psychology at the University of Michigan and author of Mindware "A highly accessible and entertaining guide to genes: what they are, how they work, and most important, what they can and cannot explain. For all the dinner table or classroom conversations on the genetic bases of gender, race, or intelligence; the morality of genetic engineering; or the hardest question of all, 'Who am I?,' DNA Is Not Destiny is the new must-read." -- Hazel Markus, Davis-Brack Professor in the Behavioral Sciences at Stanford University and author of Clash!: How to Thrive in a Multicultural World "A highly accessible and entertaining guide to genes: what they are, how they work, and most important, what they can and cannot explain. For all the dinner table or classroom conversations on the genetic bases of gender, race, or intelligence; the morality of genetic engineering; or the hardest question of all, "Who am I?," DNA Is Not Destiny is the new must-read." -- Hazel Markus, Davis-Brack Professor in the Behavioral Sciences at Stanford University and author of Clash!: How to Thrive in a Multicultural World "Heine ranges broadly, discussing both historical and ethical concerns, and draws heavily on social science research to investigate how people's beliefs about the power of genes influence their behavior. Heine also makes a strident critique of the direct-to-consumer genetic testing industry and a robust defense of most genetically modified organisms... Enjoyable and informative." -- Publishers Weekly "An accessible contribution to what the author calls 'genetic literacy' and a satisfyingly hard-edged work of popular science." -- Kirkus Reviews
£999.99
WW Norton & Co The Seven Daughters of Eve The Science that
Book SynopsisThe national bestseller that reveals how we are descended from seven prehistoric women.Trade Review"A lovely, rollicking book, direct and clear.... [A] fascinating glimpse into anthropology in the era of the genome." -- Wall Street Journal"Sykes recounts his tale of discovery with the drama it warrants...gripping." -- New York Times Book Review"Scientifically accurate and understandable to the layperson.... [The Seven Daughters of Eve] will be recognized as an important work, bringing molecular anthropology to a mass audience." -- Nature"A natural storyteller, [Sykes] relates the history of developing genetics up to contemporary times as the DNA of genes is decoded.... A riveting account showing how archeological evidence and molecular biology findings complement one another in the challenge to unearth our past and our beginnings." -- Choice"Sykes has solved some of the hottest debates about human origins." -- Publishers Weekly
£13.99
Springer Chaos in Real Data The Analysis of NonLinear Dynamics from Short Ecological Time Series 27 Population and Community Biology Series
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£999.99
Elsevier Science Emerging Practices in Telehealth
Book SynopsisTable of Contents1. Telehealth basics - what’s known, how it works 2. Technology and workflow implementation for telehealth 3. Integration into EMRs and clinical workflows 4. Billing basics / Fundamentals 5. Optimizing the patient experience 6. Using RPM with Telehealth 7. Creating the perfect telehealth product 8. Increasing access and decreasing disparity with telehealth 9. International telehealth implementation - The Russian experience 10. International telehealth implementation – The Gujarat experience 11. Global telehealth and digital health – how to support programs and infrastructure 12. The rise of artificial intelligence in telehealth
£999.99
Wiley DNA Interactions with Polymers and Surfactants
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£167.36
John Wiley and Sons Ltd Plant Transposons and Genome Dynamics in
Book SynopsisThe transposable genetic elements, or transposons, as they are now known, have had a tumultuous history. Discovered in the mid-20th century by Barbara McClintock, they were initially received with puzzlement. When their genomic abundance began to be apparent, they were categorized as junk DNA and acquired the label of parasites.Trade Review“I do love books where the text points toward the future as well as distilling the past and present. This volume does both.” (The Quarterly Review of Biology, 1 December 2014) Table of ContentsContributors ix Foreword xiDavid Botstein Introduction xiiiNina V. Fedoroff Chapter 1 The Discovery of Transposition 3Nina V. Fedoroff Introduction 3 Studies on Variegation 3 Mutable Genes 5 McClintock’s Studies on Chromosome Breakage 6 Recognition that Ds Transposes 8 Explaining Mutable Genes 9 Molecular Endnote 12 References 12 Chapter 2 A Field Guide to Transposable Elements 15Alan H. Schulman and Thomas Wicker The C-value Paradox 15 The Quantity of Transposable Elements Determines Genome Size 16 General Classification Scheme for Transposable Elements 17 Class II Elements 19 Class I: The Non-LTR and LTR Retrotransposons 20 Evolutionary Origins of Transposable Elements 25 Non-autonomous Transposable Elements 28 Transposable Element Demography and Genome Ecology 30 Conclusions: Rehabilitation of Transposable Elements 32 Acknowledgments 34 References 34 Chapter 3 The Mechanism of Ac/Ds Transposition 41Thomas Peterson and Jianbo Zhang Transposition of Ac/Ds Elements 41 The Enigmatic Ac Dosage Effect 42 cis and trans Effects on Ac/Ds Transposition 43 Molecular Characterization of Transposable Elements 44 The Excision and Insertion Reactions 45 Formation of Ds from Ac 48 Standard versus Alternative Transposition 48 Sister Chromatid Transposition 48 Reversed-ends Transposition 51 How Does Ds Break Chromosomes? 53 Alternative Transposition, DNA Methylation, and the Sequence of Transposition Reactions 54 Potential Applications of Alternative Transposition 55 Perspective 56 References 56 Chapter 4 McClintock and Epigenetics 61Nina V. Fedoroff Introduction 61 Spm-suppressible Alleles 61 Spm-dependent Alleles 64 Cryptic Spm 66 Presetting 66 Molecular Machinery of Epigenetic Regulation 67 Summary 68 References 69 Chapter 5 Molecular Mechanisms of Transposon Epigenetic Regulation 71Robert A. Martienssen and Vicki L. Chandler Introduction 71 Chromatin Remodeling, DNA and Histone Modification 73 RNA Interference (RNAi) and RNA-Directed DNA Methylation (RdDM) 75 Heterochromatin Reprogramming and Germ Cell Fate 79 Transgenerational Inheritance of Transposon Silencing 82 Paramutation 83 Conclusions 85 References 85 Chapter 6 Transposons in Plant Gene Regulation 93Damon R. Lisch Introduction 93 New Regulatory Functions 94 TE-Induced Down-Regulation 97 Deletions and Rearrangements 98 Suppressible Alleles 100 TEs and Plant Domestication 103 The Dynamic Genome 108 References 110 Chapter 7 Imprinted Gene Expression and the Contribution of Transposable Elements 117Mary A. Gehring Why are Genes Imprinted? 118 The Developmental Origin of Endosperm 118 Selection for Imprinted Expression 121 Principles Derived from the First Imprinted Gene 122 Gene Imprinting and Parent-of-Origin Effects on Seed Development 124 What Genes are Imprinted? 124 Epigenome Dynamics during Seed Development 127 Epigenetic Landscape in Vegetative Tissues 127 Cytological Observations of Chromatin in Seeds 129 Epigenomic Profiling in Seeds 130 Mechanisms of Gene Imprinting and the Relation to TEs 132 TEs and Allele-Specific Imprinting 136 Insights from Whole Genome Studies 137 Outstanding Questions 138 References 138 Chapter 8 Transposons and Gene Creation 143Hugo K. Dooner and Clifford F. Weil Introduction 143 Capture of Gene Fragments by TEs and Formation of Chimeric Genes 144 Co-Option of a TE Gene by the Host 148 Fusion of TE and Host Genes 150 Alterations of Host Gene Sequences by TE Excisions 151 Alterations of Host Coding Sequences by TE Insertions 152 Acquisition by Host Genes of New Regulatory Sequences from TEs 153 Interaction of TEs with Target Gene mRNA Splicing and Structure 155 Reshuffling of Host Sequences by Alternative Transpositions 156 Conclusion 158 References 158 Chapter 9 Transposons in Plant Speciation 165Avraham A. Levy Introduction 165 Genetic Models of Speciation 165 Speciation – a Gradual or a Rapid Process? 166 Speciation Through Accumulation of Mutations 166 DNA Cut-and-Paste TEs and Speciation 167 Copy-and-Paste TEs and Speciation 168 TE-Mediated Speciation – a Likely Scenario? 169 Plant Speciation Through Hybridization and Allopolyploidization 169 Induction of Transposition upon Hybridization and Polyploidization 170 Epigenetic Alteration of TEs upon Hybridization and Polyploidization 170 Transcriptional Activation of TEs upon Hybridization and Polyploidization 171 Alterations in Small RNAs upon Hybridization and Polyploidization 171 A Mechanistic Model for Responses to Genome Shock 172 Dysregulation of Gene Expression by Novel Interactions Between Regulatory Factors 173 Altered Protein Complexes 174 Why TEs Become Activated when Cellular Processes are Dysregulated 174 Conclusions 175 Acknowledgments 176 References 176 Chapter 10 Transposons, Genomic Shock, and Genome Evolution 181Nina V. Fedoroff and Jeffrey L. Bennetzen How Transposons Came to be Called “Selfish” DNA 181 The “Selfish DNA” Label Stuck to Transposons 182 Transposons Coevolved with Eukarotic Genomes 182 Sequence Duplication: The Real Innovation 183 The Facilitator: Epigenetic Control of Homologous Recombination 183 Epigenetic Mechanisms, Duplication and Genome Evolution 185 Plant Genome Organization: Gene Islands in a Sea of Repetitive DNA 186 Transposon Neighborhoods and Insertion Site Selection 187 Genome Evolution: Colinearity and Its Erosion 189 Genome Contraction and Divergence of Intergenic Sequences 191 Transposases Sculpt Genomes 192 Small Regulatory RNAs from Transposons 193 Genome Shocks 194 Genome Evolvability 195 References 196 Index 203
£175.70
John Wiley and Sons Ltd Polyploid and Hybrid Genomics
Book SynopsisPolyploidy plays an important role in biological diversity, trait improvement, and plant species survival. Understanding the evolutionary phenomenon of polyploidy is a key challenge for plant and crop scientists.Table of ContentsContributors xi Preface xvii Section I Genomics of Hybrids 1 1 Yeast Hybrids and Polyploids as Models in Evolutionary Studies 3 Avraham A. Levy, Itay Tirosh, Sharon Reikhav, Yasmin Bloch, and Naama Barkai 2 Transcriptome Profiling of Drosophila Interspecific Hybrids: Insights into Mechanisms of Regulatory Divergence and Hybrid Dysfunction 15 Jos´e M. Ranz, Shu-Dan Yeh, Kevin G. Nyberg, and Carlos A. Machado 3 cis- and trans-Regulation in Drosophila Interspecific Hybrids 37 Joseph D. Coolon and Patricia J. Wittkopp 4 Gene Expression and Heterosis in Maize Hybrids 59 Mei Guo and J. Antoni Rafalski 5 Integrating “Omics” Data and Expression QTL to Understand Maize Heterosis 85 Camille Rustenholz and Patrick S. Schnable 6 Genomics and Heterosis in Hexaploid Wheat 105 Zhongfu Ni, Yingyin Yao, Huiru Peng, Zhaorong Hu, and Qixin Sun 7 Progress of Genomics and Heterosis Studies in Hybrid Rice 117 Lei Zhang, Yonggang Peng, Yang Dong, Hongtao Li, Wen Wang, and Zhen Zhu 8 Heterosis: The Case for Single-Gene Overdominance 137 Katie L. Liberatore, Ke Jiang, Dani Zamir, and Zachary B. Lippman Section II Genomics of Polyploids 153 9 Genomics and Transcriptomics of Photosynthesis in Polyploids 155 Jeremy E. Coate and Jeff J. Doyle 10 Chromosomal and Gene Expression Changes in Brassica Allopolyploids 171 Eric Jenczewski, A.M. Ch`evre, and K. Alix 11 Dynamics of Duplicated Gene Expression in Polyploid Cotton 187 Keith L. Adams and Jonathan F. Wendel 12 Reprogramming of Gene Expression in the Genetically Stable Bread Allohexaploid Wheat 195 Dominique Arnaud, Houda Chelaifa, Joseph Jahier, and Boulos Chalhoub 13 Nucleocytoplasmic Interaction Hypothesis of Genome Evolution and Speciation in Polyploid Plants Revisited: Polyploid Species-Specific Chromosomal Polymorphisms inWheat 213 Bikram S. Gill and B. Friebe Section III Mechanisms for Novelty in Hybrids and Polyploids 223 14 Genes Causing Postzygotic Hybrid Incompatibility in Plants: A Window into Co-Evolution 225 Kirsten Bomblies 15 Meiosis in Polyploids 241 Graham Moore 16 Genomic Imprinting: Parental Control of Gene Expression in Higher Plants 257 Peter C. McKeown, Antoine Fort, and Charles Spillane 17 Seed Development in Interploidy Hybrids 271 Roderick J. Scott, Julia L. Tratt, and Ahmed Bolbol 18 Chromatin and Small RNA Regulation of Nucleolar Dominance 291 Pedro Costa-Nunes and Olga Pontes 19 Genetic Rules of Heterosis in Plants 313 James A. Birchler 20 Chromatin and Gene Expression Mechanisms in Hybrids 323 Guangming He and Xing-Wang Deng 21 Genetic and Epigenetic Mechanisms for Polyploidy and Hybridity 335 Z. Jeffrey Chen and Helen H. Yu Index 355 A color plate is located between pages 174 and 175.
£175.70
John Wiley & Sons Inc Guide to Analysis of DNA Microarray Data
Book SynopsisWritten for biologists and medical researchers who don''t have any special training in data analysis and statistics, Guide to Analysis of DNA Microarray Data, Second Edition begins where DNA array equipment leaves off: the image produced by the microarray. The text deals with the questions that arise starting at this point, providing an introduction to microarray technology, then moving on to image analysis, data analysis, cluster analysis, and beyond. With all chapters rewritten, updated, and expanded to include the latest generation of technology and methods, Guide to Analysis of DNA Microarray Data, Second Edition offers practitioners reliable information using concrete examples and a clear, comprehensible style. This Second Edition features entirely new chapters on: * Image analysis * Experiment design * Automated analysis, integrated analysis, and systems biology * Interpretation of results Intended for readers seeking practical applications, thTrade Review"Bioinformaticians, statisticians, computer scientists, biologists, and medical researchers will find this well written book extremely useful." (Journal of Statistical Computation and Simulation, September 2005) "...useful for anybody who wants to catch up with the marvels of modern laboratory technology..." (Chemistry & Industry, 17th January 2005) "This book would be useful for anyone working with the DNA microarray technology." (Annals of Biomedical Engineering, November 2004) "...concisely written with clear illustrations and tables [with]...a good deal of new material." (E-STREAMS, November 2004)Table of ContentsPreface. Acknowledgments. 1. Introduction to DNA Microarray Technology. 1.1 Hybridization. 1.2 Gold Rush? 1.3 The Technology behind DNA Microarrays. 1.3.1 Affymetrix GeneChip Technology. 1.3.2 Spotted Arrays. 1.3.3 Digital Micromirror Arrays. 1.3.4 Inkjet Arrays. 1.3.5 Bead Arrays. 1.3.6 Serial Analysis of Gene Expression (SAGE). 1.4 Parallel Sequencing on Microbead Arrays. 1.4.1 Emerging Technologies 1.5 Example: Affymetrix vs. Spotted Arrays. 1.6 Summary. 1.7 Further Reading. 2. Overview of Data Analysis. 3. Image Analysis. 3.1 Gridding. 3.2 Segmentation. 3.3 Intensity Extraction. 3.4 Background Correction. 3.5 Software. 3.5.1 Free Software for Array Image Analysis. 3.5.2 Commercial Software for Array Image Analysis. 3.6 Summary. 3.7 Further Reading. 4. Basic Data Analysis. 4.1 Normalization. 4.1.1 One or More Genes are Assumed Expressed at Constant Rate. 4.1.2 Sum of Genes is Assumed Constant. 4.1.3 Subset of Genes is Assumed Constant. 4.1.4 Majority of Genes Assumed Constant. 4.1.5 Spike Controls. 4.2 Dye Bias, Spatial Bias, Print Tip Bias. 4.3 Expression Indices. 4.3.1 Average Difference. 4.3.2 Signal. 4.3.3 Model-Based Expression Index. 4.3.4 Robust Multiarray Average. 4.3.5 Position Dependent Nearest Neighbor Model. 4.4 Detection of Outliers. 4.5 Fold Change. 4.6 Significance. 4.6.1 Multiple Conditions. 4.6.2 Nonparametric Tests. 4.6.3 Correction for Multiple Testing. 4.6.4 Example I: t-Test and ANOVA. 4.6.5 Example II: Number of Replicates. 4.7 Mixed Cell Populations. 4.8 Summary. 4.9 Further Reading. 5. Visualization by Reduction of Dimensionality. 5.1 Principal Component Analysis. 5.2 Example 1: PCA on Small Data Matrix. 5.3 Example 2: PCA on Real Data. 5.4 Summary. 5.5 Further Reading. 6. Cluster Analysis. 6.1 Hierarchical Clustering. 6.2 K-means Clustering. 6.3 Self-Organizing Maps. 6.4 Distance Measures. 6.4.1 Example: Comparison of Distance Measures. 6.5 Gene Normalization. 6.6 Visualization of Clusters. 6.6.1 Example: Visualization of Gene Clusters in Bladder Cancer. 6.7 Summary. 6.8 Further Reading. 7. Beyond Cluster Analysis. 7.1 Function Prediction. 7.2 Discovery of Regulatory Elements in Promoter Regions. 7.2.1 Example 1: Discovery of Proteasomal Element. 7.2.2 Example 2: Rediscovery of Mlu Cell Cycle Box (MCB). 7.3 Summary. 7.4 Further Reading. 8. Automated Analysis, Integrated Analysis and Systems Biology. 8.1 Integrated Analysis. 8.2 Systems Biology. 8.3 Further Reading. 9. Reverse Engineering of Regulatory Networks. 9.1 The Time-Series Approach. 9.2 The Steady-State Approach. 9.3 Limitations of Network Modeling. 9.4 Example 1: Steady-State Model. 9.5 Example 2: Steady-State Model on Bacillus Data. 9.6 Example 3: Linear Time-Series Model. 9.7 Further Reading. 10. Molecular Classifiers. 10.1 Feature Selection. 10.2 Validation. 10.3.1 Nearest Neighbor. 10.3.2 Nearest Centroid. 10.3.3 Neural Networks. 10.3.4 Support Vector Machine. 10.4 Performance Evaluation. 10.5 Example I: Classification of Bladder Cancer Subtypes. 10.6 Example II: Classification of SRBCT Cancer Subtypes. 10.7 Summary. 10.8 Further Reading. 11. The Design of Probes for Arrays. 11.1 Selection of Genes for an Array. 11.2 Gene Finding. 11.3 Selection of Regions Within Genes. 11.4 Selection of Primers for PCR. 11.4.1 Example: Finding PCR Primers for Gene AF105374. 11.5 Selection of Unique Oligomer Probes. 11.6 Remapping of Probes. 11.7 Further Reading. 12. Genotyping and Resequencing Chips. 12.1 Example: Neural Networks for GeneChip Prediction. 12.2 Further Reading. 13. Experiment Design and Interpretation of Results. 13.1 Factorial Designs. 13.2 Designs for Two-Channel Arrays. 13.3 Hypothesis Driven Experiments. 13.4 Independent Verification. 13.5 Interpretation of Results. 13.6 Limitations of Expression Analysis. 13.6.1 Relative Versus Absolute RNA Quantification. 13.7 Further Reading. 14. Software Issues and Data Formats. 14.1 Standardization Efforts. 14.2 Databases. 14.3 Standard File Format. 14.4 Software for Clustering. 14.4.1 Example: Clustering with ClustArray. 14.5 Software for Statistical Analysis. 14.5.1 Example: Statistical Analysis with R. 14.5.2 The Affy Package of Bioconductor. 14.5.3 Commercial Statistics Packages. 14.6 Summary. 14.7 Further Reading. Appendix A: Web Resources: Commercial Software Packages. References. Index.
£73.76
John Wiley & Sons Inc DrugDNA Interactions
Book SynopsisLearn vital information about drug-DNA interactions from Drug-DNA Interactions: Structures and Spectra, the only comprehensive book written about this topic. Understand the types of structural and bonding information that can be obtained using specific physico-chemical methods and discover how to design new drugs that are more effective than current treatments and have fewer side effects. Find detailed information about X-ray crystallography, NMR spectroscopy, molecular modeling, and optical spectroscopy such as UV-Visible absorption, fluorescence, circular dichroism (CD), flow linear dichroism (FLD), infrared (IR) and Raman spectroscopy.Table of ContentsPreface. Introduction. 1. DNA Structures and Spectra. 1.1. DNA Structures. 1.2. Electronic Spectra. 1.3. Vibrational Spectra. 1.4. NMR Spectra. 1.5. Electron Spin Resonance Spectra. 1.6. X-Ray Crystallography. 1.7. Molecular Modeling an molecular Mechanics. 2. Intercalating Drugs. 2.1. Acridine Dyes. 2.2. Ethidium Bromide. 2.3. Aclacinomycin. 2.4. Sequence Preference. 2.5. Bis- and Tris- Intercalators. 3. Groove- Binding Drugs. 3.1. Netropsin and Distamycin. 3.2. Derivatives of Netropsin and Distamycin. 3.3. Hoechst 33258, SN6999, and their Derivatives. 3.4. Chromomycin, Mithramycin, and Other GC Binders. 3.5. Groove Binding and Intercalation. 4. Covalent Bonding Drugs. 4.1. (+) CC1065 and Related Drugs. 4.2. Anthramycin and Tomaymycin. 4.3. Ecteinascidins. 4.4. Mitomycins. 4.5. Intercalating Alkylators. 5. Strand-Breaking Drugs. 5.1. Bleomycins. 5.2. Enediyne Antibiotics. 6. Metal-Containing Drugs. 6.1. Cisplatin. 6.2. Cisplatin Derivatives. 6.3. Transplatin and Derivatives. 6.4. Monofunctional Platinum Complexes. 6.5. Polynuclear and High-valent Platinum Complexes. 6.6. Complexes Containing Other Metals. Appendixes. Index.
£143.40
Cambridge University Press Systems Biology of Cancer
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£999.99
Cambridge University Press Methods for Computational Gene Prediction
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£999.99
Cambridge University Press Signals Switches Regulons and Cascades Control of Bacterial Gene Expression 61 Society for General Microbiology Symposia Series Number 61
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£999.99
Cambridge University Press Gene Expression Profiling by Microarrays
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£999.99
Cambridge University Press Methods for Computational Gene Prediction
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£999.99
Prentice Hall (a Pearson Education company) The Double Helix A Personal Account of the
Book SynopsisThe classic personal account of Watson and Crick’s groundbreaking discovery of the structure of DNA, now with an introduction by Sylvia Nasar, author of A Beautiful Mind.By identifying the structure of DNA, the molecule of life, Francis Crick and James Watson revolutionized biochemistry and won themselves a Nobel Prize. At the time, Watson was only twenty-four, a young scientist hungry to make his mark. His uncompromisingly honest account of the heady days of their thrilling sprint against other world-class researchers to solve one of science’s greatest mysteries gives a dazzlingly clear picture of a world of brilliant scientists with great gifts, very human ambitions, and bitter rivalries. With humility unspoiled by false modesty, Watson relates his and Crick’s desperate efforts to beat Linus Pauling to the Holy Grail of life sciences, the identification of the basic building block of life. Never has a scientist been so truthful in cap
£23.40
John Wiley and Sons Ltd Equine Genomics
Book SynopsisThe complete mapping of the horse genome sequence makes a significant contribution to understanding equine biology. This book provides a timely comprehensive overview of equine genomic research.Trade Review“Equine Genomicsis an excellent text that compiles historical accomplishments in equine genetics and molecular biology, describes state-of-theart approaches to understanding the equine genome, and provides glimpses of where the field may go in the future . . . It is our responsibility to try to keep up, and I believe this book will help us do that.” (Journal of the American Veterinary Medical Association, 15 June 2014)Table of ContentsContributors ix Preface xi Chapter 1 Defining the equine genome: The nuclear genome and the mitochondrial genome 1Bhanu P. Chowdhary Chapter 2 Genetic linkage maps 11June Swinburne and Gabriella Lindgren Chapter 3 Physical and comparative maps 49Terje Raudsepp and Bhanu P. Chowdhary Chapter 4 The Y-chromosome 73Terje Raudsepp, Nandina Paria, and Bhanu P. Chowdhary Chapter 5 Unexpected structural features of the equine major histocompatibility complex 93Loren C. Skow and Candice L. Brinkmeyer-Langford Chapter 6 Assembly and analysis of the equine genome sequence 103Claire M. Wade Chapter 7 Genomic tools and resources: Development and applications of an equine SNP genotyping array 113Molly McCue and Jim Mickelson Chapter 8 Functional genomics 125Stephen J. Coleman, Michael J. Mienaltowski, and James N. MacLeod Chapter 9 Coat color genomics 143Samantha A. Brooks and Rebecca R. Bellone Chapter 10 Genomics of skin disorders 155Amy E. Young, Stephen D. White, and Danika L. Bannasvch Chapter 11 Genomics of muscle disorders 171James R. Mickelson, Stephanie J. Valberg, Carrie J. Finno, and Molly E. McCue Chapter 12 Genomics of skeletal disorders 187Ottmar Distl Chapter 13 Genomics of reproduction and fertility 199Terje Raudsepp, Pranab J. Das and Bhanu P. Chowdhary Chapter 14 Genetics of equine neurologic disease 217Carrie J. Finno and Monica Aleman Chapter 15 Molecular genetic testing and karyotyping in the horse 241M. C. T. Penedo and Terje Raudsepp Chapter 16 Genomics of laminitis 255Jim K. Belknap Chapter 17 Genomics of performance 265Emmeline W. Hill, Lisa M. Katz, and David E. MacHugh Chapter 18 Genomics of the circadian clock 285Barbara A. Murphy Chapter 19 Mitochondrial genome: Clues about the evolution of extant equids and genomic diversity of horse breeds 311Cynthia C. Steiner, Kateryna D. Makova, and Oliver A. Ryder Index 323
£145.30
University of Pittsburgh Press Above the Gene Beyond Biology
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£59.15
Taylor & Francis Inc DNA Methylation
Book SynopsisDNA Methylation: Approaches, Methods and Applications describes the relation DNA methylation has to gene silencing in disease, and explores its promising role in treating cancer. Written by leaders in the field, this exceptional compilation of articles outlines the best techniques to use when addressing questions concerning the cytosine methylation status of genomic DNA. It includes concepts, experimental models, and clinical uses of demethylating agents. The book provides a balance between articles clarifying methodological details and more general review chapters that offer broad biological perspectives on DNA methylation. This is an invaluable handbook for researchers and clinicians interested in genetics and molecular biology, particularly epigenetic therapies and gene silencing.Trade Review"… written by leaders in the field. … interesting for both researchers and clinicians. It is an excellent summary of the subject for scientists starting in the field of epigenetics and it is also a reference book for professionals already familiar with the subject." – Assam El-Osta, Baker Heart Research Institute, Australia in CHEMMEDCHEM, 3, 2008Table of ContentsDescribing the relation DNA methylation has to gene silencing in disease, this book explores its promising role in treating cancer. Written by leaders in the field, it outlines the best techniques to use when addressing questions concerning the cytosine methylation status of genomic DNA. Including concepts, experimental models, and clinical uses of demethylating agents, the book provides articles clarifying methodological details and more general review chapters that offer broad biological perspectives on DNA methylation. This is an invaluable handbook for researchers and clinicians interested in genetics and molecular biology, particularly epigenetic therapies and gene silencing.
£292.96
Taylor & Francis Inc Comparative Genomics
Book Synopsis When genomic research first came on the scene, much of the biomedical research community viewed it as a limited venture with limited potential. We now know that such an assessment was both highly premature and wonderfully inaccurate. In the last ten years, we've witnessed such remarkable acceleration in the merger of basic and applied genomic research that, among other things, genomic research is now thought of as being intrinsic to current drug research. Through rigorous comparative analysis, the genomes of cold-blooded vertebrate, avian, and other mammalian species are providing a deeper understanding of the human genome. Moreover, genomic sequences, which are becoming available for several species have proven to be highly relevant to drug research with regard to a number of otherwise intractable conditions. Rather than offering a comprehensive volume covering every aspect of comparative genomics, Comparative Genomics: Basic and Applied Research embodies the diverse Table of ContentsIntroduction. Basic Research. Applied Research
£190.00
Cold Spring Harbor Laboratory Press,U.S. An A to Z of DNA Science
Book Synopsis
£12.53
Cold Spring Harbor Laboratory Press,U.S. Gene Machines
£9.08
Cold Spring Harbor Laboratory Press,U.S. Untangling the Double Helix
Book Synopsis
£999.99
Cambridge University Press Understanding Forensic DNA
a huge range and FREE tracked UK delivery on ALL orders.
£999.99
Springer-Verlag New York Inc. Computer Simulations of Aggregation of Proteins and Peptides
Book SynopsisThis volume provides computational methods and reviews various aspects of computational studies of protein aggregation. Chapters discuss the relationship between protein misfolding and protein aggregation, methods of prediction of aggregation propensities of protein, peptides, protein structure, results of computer simulations of aggregation, and computational simulations focused on specific diseases such as Alzheimer''s, Parkinson''s, and preeclampsia. Written in the highly successful Methods in Molecular Biology series format, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and tips on troubleshooting and avoiding known pitfalls. Authoritative and cutting-edge, Computer Simulations of Aggregation of Proteins and Peptides aims to ensure successful results in the further study of this vital field.Table of Contents1. Bioinformatics Methods in Predicting Amyloid Propensity of Peptides and Proteins Małgorzata Kotulska and Jakub W. Wojciechowski 2. Protocols for Rational Design of Protein Solubility and Aggregation Properties using Aggrescan3D Standalone Aleksander Kuriata, Aleksandra E. Badaczewska-Dawid, Jordi Pujols, Salvador Ventura, and Sebastian Kmiecik 3. Using Surface Hydrophobicity Together with Empirical Potentials to Identify Protein-Protein Binding Sites. Application to the Interactions of E-cadherins Robert L. Jernigan, Pranav Khade, Ambuj Kumar, and Andrzej Kloczkowski 4. Computational Models for Study of Protein Aggregation Nguyen Truong Co, Mai Suan Li, and Pawel Krupa 5. Probing Protein Aggregation Using the Coarse-Grained UNRES Force Field Ana V. Rojas, Gia G. Maisuradze, Harold A. Scheraga, and Adam Liwo 6. Contact-based Analysis of Aggregation of Intrinsically Disordered Proteins Marek Cieplak, Łukasz Mioduszewski, and Mateusz Chwastyk 7. Molecular Insights into the Effect of Metals on Amyloid Aggregation Yifat Miller 8. From Quantum Mechanics, Classical Mechanics and Bioinformatics to Artificial Intelligence Studies in Neurodegenerative Diseases Orkid Coskuner-Weber, M. Gokhan Habiboglu, David Teplow, and Vladimir N. Uversky 9. Computer Simulations Aimed at Exploring Protein Aggregation and Dissociation Phuong H. Nguyen and Philippe Derreumaux 10. All-atom Molecular Dynamics Simulation Methods for Aggregation of Protein and Peptides: Replica-exchange/permutation and Nonequilibrium Simulations Satoru G. Itoh and Hisashi Okumura 11. Key Factors Controlling Fibril Formation of Proteins Tran Thi Minh Thu, Andrzej Kloczkowski, Mai Suan Li, and Maksim Kouza 12. Determination of the Most Stable Packing Of Peptides From Ribosomal S1 Protein, Protein Bgl2p and Aβ peptide in β-layers during Molecular Dynamics Simulations Glyakina A.V., Balabaev N.K., and Galzitskaya O.V 13. Molecular Dynamics Simulations Of Protein Aggregation: Protocols For Simulation Setup and Analysis with Markov State Models And Transition Networks Suman Samantray, Wibke Schumann, Alexander-Maurice Illig, Arghadwip Paul, Bogdan Barz, and Birgit Strodel 14. Challenges in Experimental Methods Marlena E. Gąsior-Głogowska, Natalia Szulc, and Monika Szefczyk 15. Aggregates Sealed By Ions Giovanni La Penna and Silvia Morante 16. Modifying Amyloid Motif Aggregation through Local Structure Sofia Bali and Lukasz A. Joachimiak 17. Assessing the Stability Of Biological Fibrils By Molecular-Scale Simulations Rodrigo A. Moreira 18. Predictive Modeling of Neurotoxic α-Synuclein Polymorphs Liang Xu, Shayon Bhattacharya, and Damien Thompson 19. Characterization of Amyloidogenic Peptide Aggregability in Helical Subspace Shayon Bhattacharya, Liang Xu, and Damien Thompson 20. Exploration of Protein Aggregations in Parkinson’s Disease through Computational Approaches and Big Data Analytics Saba Shahzadi, Muhammad Yasir, Bisma Jawad, Sumbal Baber, Mubashir Hassan 21. Computational Studies of Protein Aggregation In Preeclampsia Maksim Kouza, Andrzej Kolinski, Irina Buhimschi, and Andrzej Kloczkowski 22. Final remarks Mai Suan Li, Andrzej Kloczkowski, Marek Cieplak, and Maksim Kouza
£143.99
Springer-Verlag New York Inc. Proteomics in Systems Biology
Book SynopsisThis detailed book highlights the diverse techniques and applications of proteomics in an accessible, informative, and concise manner.Table of Contents1. Review of the Real and Sometimes Hidden Costs in Proteomics Experimental Workflows Aicha Asma Houfani and Leonard James Foster 2. High-Throughput Mass Spectrometry-Based Proteomics with dia-PASEF Patricia Skowronek and Florian Meier 3. Isolation of Detergent Insoluble Proteins from Mouse Brain Tissue for Quantitative Analysis Using Data Independent Acquisition (DIA) Cristen Molzahn, Lorenz Nierves, Philipp F. Lange, and Thibault Mayor 4. Rodent Lung Tissue Sample Preparation and Processing for Shotgun Proteomics Hadeesha Piyadasa, Ying Lao, Oleg Krokhin, and Neeloffer Mookherjee 5. Protein Purification and Digestion Methods for Bacterial Proteomic Analyses Nicole Hansmeier, Samrachana Sharma, and Tzu-Chiao Chao 6. Mapping Cell Surface Proteolysis with Plasma Membrane-Targeted Subtiligase Aspasia A. Amiridis and Amy M. Weeks 7. N-Terminomics/TAILS of Tissue and Liquid Biopsies Anthonia Anowai, Sameeksha Chopra, Barbara Mainoli, Daniel Young, and Antoine Dufour 8. HUNTER: Sensitive Automated Characterization of Proteolytic Systems by N Termini Enrichment from Microscale Specimen Anuli C. Uzozie, Janice Tsui, and Philipp F. Lange 9. Phosphoproteomics and Organelle Proteomics in Pancreatic Islets Özum Sehnaz Caliskan, Giorgia Massacci, Natalie Krahmer, and Francesca Sacco 10. Phosphoproteomic Sample Preparation for Global Phosphorylation Profiling of a Fungal Pathogen Brianna Ball, Jonathan Krieger, and Jennifer Geddes-McAlister 11. Glycopeptide-Centric Approaches for the Characterization of Microbial Glycoproteomes Nichollas E. Scott 12. Integrated Network Discovery Using Multi-Proteomic Data Rafe Helwer and Vincent C. Chen 13. Targeted Cross-Linking Mass Spectrometry on Single-Step Affinity Purified Molecular Complexes in the Yeast Saccharomyces cerevisiae Christian Trahan and Marlene Oeffinger 14. A Crosslinking – Mass Spectrometry Protocol for the Structural Analysis of Microtubule-Associated Proteins Atefeh Rafiei and David C. Schriemer 15. Comprehensive Interactome Mapping of Nuclear Receptors Using Proximity Biotinylation Lynda Agbo, Sophie Anne Blanchet, Pata-Eting Kougnassoukou Tchara, Amélie Fradet-Turcotte, and Jean-Philippe Lambert 16. Mining Proteomics Datasets to Uncover Functional Pseudogenes Anna Meller and François-Michel Boisvert 17. Proteomic Profiling of the Interplay between a Bacterial Pathogen and Host Uncovers Novel Anti-Virulence Strategies Arjun Sukumaran and Jennifer Geddes-McAlister 18. Affinity-Enrichment of Salmonella-Modified Membranes from Murine Macrophages for Proteomic Analyses Tzu-Chiao Chao, Samina Thapa, and Nicole Hansmeier 19. Proteomic Profiling of Interplay between Agrobacterium tumefaciens and Nicotiana benthamiana for Improved Molecular Pharming Outcomes Nicholas Prudhomme, Jonathan R. Krieger, Michael D. McLean, Doug Cossar, and Jennifer Geddes-McAlister 20. Label-Free Quantitative Proteomic Profiling of Fusarium Head Blight in Wheat Boyan Liu, Danisha Johal, Mitra Serajazari, and Jennifer Geddes-McAlister 21. DIA Proteomics and Machine Learning for the Fast Identification of Bacterial Species in Biological Samples Florence Roux-Dalvai, Mickaël Leclercq, Clarisse Gotti, and Arnaud Droit 22. Novel Bioinformatics Strategies Driving Dynamic Metaproteomic Studies Caitlin M.A. Simopoulos, Daniel Figeys, and Mathieu Lavallée-Adam 23. MaxQuant Module for the Identification of Genomic Variants Propagated into Peptides Pavel Sinitcyn, Maximilian Gerwien, and Jürgen Cox 24. Untargeted Metabolomic Profiling of Fungal Species Populations Thomas E. Witte and David P. Overy
£999.99
Springer-Verlag New York Inc. Systems Medicine
Book SynopsisThis volume explores the latest technological advances and covers all facets of systems medicine with respect to precision medicine. The chapters in this book are organized into four parts. Part One highlights the recent achievements in proteomics for biomarkers identification, integration of omics and phenotypic data for precision medicine, and medicine-guided treatment of drug-induced Stevens-Johnson syndrome. Part Two covers systems-based computational approaches for pharmaceutical research and drug development, the principle of optimizing systemic exposure of drugs, and Animal Rule for drug repurposing. Part Three looks at computational tools and methodologies of network biology, quantitative systems toxicology, and modeling and stimulating patient response variabilities. Part Four talks about how systems medicine can address unmet medical and health needs, and identify educational needs. Written in the highly successful Methods in Molecular Biology series format, chapters include Table of ContentsAcknowledgements…Preface…Table of Contents…Contributing Authors…Part I Scientific and Medical Advances1. Mass Spectrometry-Based Proteomics for Biomarker DiscoveryZhijun Cao and Li-Rong Yu2. Integration of Omics and Phenotypic Data for Precision MedicineJuan Zhao, QiPing Feng, and Wei-Qi Wei3. Stevens-Johnson Syndrome and Toxic Epidermal Necrolysis in the Era of Systems MedicineChun-Bing Chen, Chuang-Wei Wang, and Wen-Hung ChungPart II Acceleration of Pharmaceutical Research and Development4. Integration of Engineered Delivery with the Pharmacokinetics of Medical Candidates via Physiology-Based PharmacokineticsYuching Yang and Xinyuan Zhang5. Applications of Quantitative System Pharmacology Modeling to Model Informed Drug DevelopmentAndy Z.X. Zhu and Mark Rogge6. Combating Viral Diseases in the Era of Systems MedicineJane P.F. Bai and Ellen Y. Guo7. Toxicity Analysis of Pentachlorophenol Data with a Bioinformatics Tool SetNatalia Polouliakh, Takeshi Hase, Samik Ghosh, and Hiroaki KitanoPart III Tools and Methodologies8. Virtual Populations for Quantitative Systems Pharmacology ModelsYougan Cheng, Ronny Straube, Abed E. Alnaif, Lu Huang, Tarek A. Leil, and Brian J. Schmidt9. Quantitative Systems Toxicology and Drug Development: The DILIsym ExperiencePaul B. Watkins10. Introduction to Genomic Network Reconstruction for Cancer ResearchGuillermo de Anda Jáuregui, Hugo Tovar, Segio Alcalá-Corona, Enrique Hernández-Lemus11. Learning in Medicine: The Importance of Statistical ThinkingMassimiliano Russo and Bruno Scarpa12. Development and Applications of Interoperable Biomedical Ontologies for Integrative Data and Knowledge Representation and Multiscale Modeling in Systems MedicineYongqun HePart IV Systems Medicine to Address Unmet Medical Needs13. Systems Biology to Address Unmet Medical Needs in Neurological DisordersMasha G. Savelieff, Mohamed H. Noureldein, and Eva L. Feldman14. Informatics in Medical Product Regulation: The Right Drug at the Right Dose for the Right PatientEileen Navarro Almario, Anna Kettermann, and Vaishali Popat15. Personal Dense Dynamic Data Clouds Connect Systems Bio-Medicine to Scientific WellnessGilbert S. Omenn, Andrew T. Magis, Nathan D. Price, and Leroy Hood16. Educational Needs for Quantitative Systems Pharmacology ScientistsJames M. GalloSubject Index List…
£143.99
Springer-Verlag New York Inc. PhaseSeparated Biomolecular Condensates
Book SynopsisThis volume provides readers with a broad collection of theoretical, computational, and experimental methods to quantitatively study the properties of phase-separate biomolecular condensates in diverse systems. The chapters in this book cover topics such as theoretical and computational methods; methods for in vitro characterization of biomolecular condensates; and techniques that enable in-cell characterization of biomolecular condensates. Written in the highly successful Methods in Molecular Biology series format, chapters include introduction to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and expert tips on troubleshooting and avoiding known pitfalls.Comprehensive and thorough, Phase-Separated Biomolecular Condensates: Methods and Protocols is a valuable resource that helps researchers learn and use established methods to study both biophysical properties and biological funcTable of ContentsPreface…Table of Contents…Contributing Authors…1. Calculating Binodals and Interfacial Tension of Phase-Separated Condensates from Molecular Simulations, with Finite-Size CorrectionsKonstantinos Mazarakos, Sanbo Qin, and Huan-Xiang Zhou2. Field-Theoretic Simulation Method to Study the Liquid-Liquid Phase Separation of PolymersSaeed Najafi, James McCarty, Kris T. Delaney, Glenn H. Fredrickson, and Joan-Emma Shea3. Numerical Techniques for Applications of Analytical Theories to Sequence-Dependent Phase Separations of Intrinsically Disordered ProteinsYi-Hsuan Lin, Jonas Wessén, Tanmoy Pal, Suman Das, and Hue Sun Chan4. An Introduction to the Stickers-and-Spacers Framework as Applied to Biomolecular CondensatesGarrett M. Ginell and Alex S. Holehouse5. Multi-Scale Modeling of Protein-RNA Condensation In and Out of EquilibriumRabia Laghmach, Isha Malhotra, and Davit A. Potoyan6. Fluorescence Lifetime Imaging Microscopy of Biomolecular CondensatesMy Diem Quan. Shih-Chu Leff Liao, Josephine C. Ferreon, and Allan Chris M. Ferreon7. Single-Molecule Fluorescence Methods to Study Protein-RNA Interactions Underlying Biomolecular CondensatesLaura R. Ganser, Yingda Ge, and Sua Myong8. Fluorescence Correlation Spectroscopy and Phase SeparationJuan Jeremías Incicco, Debjit Roy, Melissa D. Stuchell-Brereton, and Andrea Soranno9. Measurement of Protein and Nucleic Acid Diffusion Coefficients within Biomolecular Condensates Using In-Droplet Fluorescence Correlation SpectroscopyIbraheem Alshareedah and Priya R. Banerjee10. Single-Molecule Imaging of the Phase Separation-Modulated DNA Compaction to Study Transcriptional RepressionLinyu Zuo, Luhua Lai, and Zhi Qi11. Phase Separation-Based Biochemical Assays for Biomolecular InteractionsGaofeng Pei, Min Zhou, Weifan Xu, Jing Wang, and Pilong Li12. Determining Thermodynamic and Material Properties of Biomolecular Condensates by Confocal Microscopy and Optical TweezersArchishman Ghosh, Divya Kota, and Huan-Xiang Zhou13. A High-Throughput Method to Profile Protein Liquid-Liquid Phase SeparationYichen Li, Jinge Gu, Cong Liu, and Dan Li14. Phase Separation of Rubisco by the Folded SSUL Domains of CcmM in Beta-Carboxysome BiogenesisHuping Wang and Manajit Hayer-Hartl15. Cryo-Electron Tomography of Reconstituted Biomolecular CondensateFergus Tollervey, Xiaojie Zhang, Mainak Bose, Jenny Sachweh, Jeffrey B. Woodruff, Titus M. Franzmann, and Julia Mahamid16. Sedimentation Assays to Assess the Impact of Post-Translational Modifications on Phase Separation of RNA-Binding Proteins In Vitro and In CellsLara A. Gruijs da Silva and Dorothee Dormann17. Synthetic Organelles for Multiple mRNA Selective Genetic Code Expansion in EukaryotesChristopher D. Reinkemeier and Edward A. Lemke18. Single Molecule Tracking of RNA Polymerase In and Out of Condensates in Live Bacterial Cells Baljyot Singh Parmar and Stephanie C. Weber19. An Optogenetic Toolkit for the Control of Phase Separation in Living CellsChaelim Kim and Yongdae Shin20. Assessing the Phase Separation Propensity of Proteins in Living Cells Through Optodroplet Formation Anne Rademacher, Fabian Erdel, Robin Weinmann, and Karsten Rippe21. Mass Balance Imaging: A Phase Portrait Analysis for Characterizing Growth Kinetics of Biomolecular Condensates Jan Giesler, Victoria Tianjing Yan, Stephan Grill, and Arjun Narayanan22. Characterizing Properties of Biomolecular Condensates Below the Diffraction Limit In VivoGanesh Pandey, Alisha Budhathoki, and Jan-Hendrik SpilleSubject Index List…
£116.99
Springer-Verlag New York Inc. Transposable Elements
Book SynopsisThe volume presents a small selection of state-of-the-art approaches for studying transposable elements(TE). Chapters guide readers through HTS-based approaches, bioinformatic tools, methods to studyTE protein complexes, and the functional impact on the host. Written in the successful Methods in Molecular Biology series format, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible protocols, and notes on troubleshooting and avoiding known pitfalls. Authoritative and cutting-edge, Transposable Elements: Methods and Protocols aims to be a useful practical guide to researches to help further their study in this field. Table of Contents1. An overview of best practices for transposable element identification, classification and annotation in eukaryotic genomes Fernando Rodriguez and Irina R. Arkhipova 2. Assembly-free annotation and quantification of transposable elements with dnaPipeTE Clément Goubert 3. Best practice for the identification of horizontally transferred transposons James D Galbraith, Zhipeng Qu, Atma M Ivancevic, David L Adelson 4. Genotyping of transposable elements insertions segregating in the human populations using short-read re-alignments Xun Chen, Guillaume Bourque, and Clément Goubert 5. A Pangenome approach to detect and genotype TE insertion polymorphisms Cristian Groza, Guillaume Bourque, and Clément Goubert 6. Experimental validation of transposable element insertions using the Polymerase Chain Reaction (PCR) Miriam Merenciano, Marta Coronado-Zamora, and Josefa González 7. Quantification of LINE-1 RNA expression from bulk RNA-seq using L1EM Wilson McKerrow 8. Genome-wide profiling of L1 DNA methylation by bs-ATLAS-seq Claude Philippe and Gael Cristofari 9. Nanopore epigenomic analysis of transposable element DNA modifications Nathan Smits and Geoffrey Faulkner 10. Targeted resequencing and methylation analysis of L1 elements by nanopore sequencing Arpita Sarkar, Sophie Lanciano, and Gael Cristofari 11. Inferring protein-DNA binding profiles at interspersed repeats using HiChIP and PatChER Darren Taylor and Miguel R Branco 12. Affinity-based Interactome Analysis of Endogenous LINE-1 Macromolecules Luciano H. Di Stefano, Leila Saba, Mehrnoosh Oghbaie, Hua Jiang, Wilson McKerrow, Maria Benitez-Guijarro, Martin S. Taylor, and John LaCava 13. LINE-1 retrotransposition assays in embryonic stem cells Marta Garcia-Canadas, Francisco Sanchez-Luque, Laura Sanchez, Johana Rojas, and Jose Garcia Perez 14. Detecting somatic transposable element insertions in Drosophila tissues Katarzyna Siudeja 15. Precise and scarless insertion of transposable elements by Cas9-mediated genome engineering” Vivien M Weber, Aurelien J Doucet, and Gael Cristofari 16. Epigenetic editing of transposable and repetitive elements Joanna M Jachowicz 17. Using CRISPR to investigate the regulatory activity of transposable elements David M Simpson, Conor R Kelly, and Edward B Chuong
£999.99
Cambridge University Press Bayesian Evolutionary Analysis with BEAST
Book SynopsisA comprehensive overview of Bayesian approaches to phylogenetics using Markov chain Monte Carlo (MCMC) methods, offering theoretical insight, pragmatic advice and tools to develop further models. This title is a one-stop reference to applying the latest phylogenetic models in BEAST 2, interpreting the analyses and extending these models further.Trade Review'Want to construct a phylogeny, add in calibrated time points or work out the past history of an epidemic? The open source package BEAST has established itself as the industry standard for all this and more. This definitive book, explaining what is under the hood, how the user can customize extensions and, most critically, a simple 'how to' users guide, is necessary reading for beginners and specialists alike.' Laurence D. Hurst, University of Bath'In concert with the dramatic improvements to DNA sequencing technology, Bayesian inference has revolutionized population genetics, phylogenetics, and divergence time estimation. A similar impact on epidemiology appears imminent via a suite of new Bayesian methods that incorporate host and pathogen DNA sequence data into established mathematical frameworks. This book is an accessible and thorough introduction to these Bayesian procedures. However, the book does far more than explain the theory. It also includes clear guides on how to use the BEAST 2 software for performing Bayesian analyses, and how to visualize the results. Because the software is designed to be extensible, the book instructs users to write their own code to supplement the diverse methods that are already implemented in BEAST 2. This book is timely and is written by two of the leaders of the field. I highly recommend it.' Jeff Thorne, North Carolina State UniversityTable of ContentsPreface; Acknowledgements; Part I. Theory: 1. Introduction; 2. Evolutionary trees; 3. Substitution and site models; 4. The molecular clock; 5. Structured trees and phylogeography; Part II. Practice: 6. Bayesian evolutionary analysis by sampling trees; 7. Setting up and running a phylogenetic analysis; 8. Estimating species trees from multilocus data; 9. Advanced analysis; 10. Posterior analysis and post-processing; 11. Exploring phylogenetic tree space; Part III. Programming: 12. Getting started with BEAST; 13. BEAST XML; 14. Coding and design patterns; 15. Putting it all together; Bibliography; List of authors; List of subjects.
£999.99
Cambridge University Press Biophysics of DNA
Book SynopsisSurveying the last sixty years of research, this book describes the physical properties of DNA in the context of its biological functioning. It is designed to enable both students and researchers of molecular biology, biochemistry and physics to better understand the biophysics of DNA, addressing key questions and facilitating further research. The chapters integrate theoretical and experimental approaches, emphasising throughout the importance of a quantitative knowledge of physical properties in building and analysing models of DNA functioning. For example, the book shows how the relationship between DNA mechanical properties and the sequence specificity of DNA-protein binding can be analyzed quantitatively by using our current knowledge of the physical and structural properties of DNA. Theoretical models and experimental methods in the field are critically considered to enable the reader to engage effectively with the current scientific literature on the physical properties of DNA.Table of ContentsPreface; 1. DNA structures; 2. Conformational transitions; 3. Equilibrium large-scale conformational properties of DNA; 4. DNA dynamics; 5. DNA-protein interaction; 6. Circular DNA; Index.
£999.99
Cambridge University Press GenomeWide Association Studies
Book SynopsisOver the last twenty years, genome-wide association studies (GWAS) have revealed a great deal about the genetic basis of a wide range of complex diseases and they will undoubtedly continue to have a broad impact as we move to an era of personalised medicine. This authoritative text, written by leaders and innovators from both academia and industry, covers the basic science as well as the clinical, biotechnological and pharmaceutical potential of these methods. With special emphasis given to highlighting pharmacogenomics and population genomics studies using next-generation technology approaches, this is the first book devoted to combining association studies with single nucleotide polymorphisms, copy number variants, haplotypes and expressed quantitative trait loci. A reliable guide for newcomers to the field as well as for experienced scientists, this is a unique resource for anyone interested in how the revolutionary power of genomics can be applied to solve problems in complex disease.Trade Review'Genome-Wide Association Studies: From Polymorphism to Personalized Medicine, edited by Krishnarao Appasani, summarizes most elegantly the contributions of GWAS as a major discovery tool linking complex disease phenotypes to genetic variants and associated biological pathways and gene networks that were previously unknown. GWAS has transformed the genetic landscape in complex disease and has informed us more about the genetic underpinnings of common diseases and pharmacogenomics traits than any other tool to date. The present book captures this development elegantly and is a pleasure to read.' Hakon Hakonarson, University of Pennsylvania'From genotype to phenotype: this biological paradigm is now elucidated and extended to the vision of genomic medicine. This highly informative book combines the current knowledge of genome wide association studies with the pathophysiology, epidemiology of human disease, and health condition, especially, implicating in the development of personalized and precision medicine. The combination of technical, scientific, medical, and pharmaco-economic aspects supports the high value of this book for scientists and medical specialists working in the field.' Christine Günther, Chief Executive Officer, apceth GmbH and Co. KG, Munich, Germany'Through my 30 years' experience in genetics of diabetes, I realize that now is an exciting time in the history of medical genetics thanks to successful genome-wide association studies and challenging whole-genome studies using next-generation sequencing technologies. This excellent book, covering a wide-range of topics and their practical examples in this field, is undoubtedly recommended for readers who are interested in or engaged in genomic medicine.' Takuya Awata, International University of Health and Welfare Hospital, Tochigi, Japan'Genome-Wide Association Studies: From Polymorphism to Personalized Medicine has an impressive and diverse list of contributors and will become a highly valuable resource for both experts and researchers entering the field.' Jeanette Schmidt, Vice President of Informatics, Affymetrix, Inc., Santa Clara, USA'This book details how the huge experimental efforts of GWAS can be put into both a biological and medically relevant context, indeed an excellent read for any researcher trying to understand the functional effect of genetic disease association with complex disease.' Tara Caffrey, University of Oxford'This volume provides a great resource for beginners to learn about the recent advances in GWAS and for domain experts to identity the gaps in the area. … The provided software and case studies can guide readers through the procedures and will easily allow a researcher to finish a project on their own. I think this book will be a reliable guide for anyone who wants to learn and understand GWAS. I hope other readers will enjoy the book as much as I did.' Jinliang Yang, The Quarterly Review of BiologyTable of ContentsList of contributors; Foreword Stephen W. Scherer; Foreword Peter M. Visscher; Preface; Part I. Genome-Wide Association Studies: 1. Introduction to genome-wide association Krishnarao Appasani and Raghu K. Appasani; 2. GWAS: a milestone in the road from genotypes to phenotypes Urko Martinez-Marigorta, Juan Antonio Rodriguez and Arcadi Navarro; 3. Introduction to statistical methods in genome-wide association studies Can Yang, Cong Li, Dongjun Chung, Mengjie Chen, Joel Gelernter and Hongyu Zhao; 4. GWAS replicability across time and space Urko Martinez-Marigorta, Juan Antonio Rodriguez and Arcadi Navarro; Part II. Genome-Wide Studies in Disease Biology: 5. Genome-wide association studies of body mass index Tuomas O. Kilpelainen; 6. Identification of myocardial infarction susceptible genes and their functional analyses Kouichi Ozaki and Toshihiro Tanaka; 7. Admixture mapping for disease gene discovery Randall C. Johnson, Cheryl A. Winkler and Meredith Yeager; 8. Genome-wide association analysis in schizophrenia Sven Stringer, Dorien H. Nieman, René S. Kahn and Eske M. Derks; 9. Epigenome-wide association studies in neurodevelopmental disorders Takeo Kubota, Kunio Miyake and Takae Hirasawa; Part III. Single Nucleotide Polymorphisms, Copy Number Variants, Haplotypes and eQTLs: 10. Finding SNPs that affect microRNA regulation in disease-associated genomic regions Laurent F. Thomas and Pal Saetrom; 11. From linkage to complex associations: the role of GABRA2 as a risk factor for alcohol use Sandra Villafuerte, Elisa M. Trucco and Margit Burmeister; 12. Copy number variation in monozygous twins Erwin Brosens, K. G. Snoek, D. Veenma, H. Eussen, D. Tibboel and A. de Klein; 13. Haplotypes of CpG-related SNPs and association with DNA methylation patterns Yiyi Ma, Caren E. Smith, Yu-Chi Lee, Laurence D. Parnell, Chao-Qiang Lai and José M. Ordovás; 14. eQTL mapping Mengjie Chen, Can Yang, Cong Li and Hongyu Zhao; Part IV. Next-Generation Sequencing Technology and Pharmacogenomics: 15. Next-generation sequencing for rare diseases Elena Bosch and Ferran Casals; 16. Next-generation sequencing for complex disorders Ferran Casals and Elena Bosch; 17. Chromosomal breakpoints in breast cancer co-localize with differentially methylated regions Man-Hung Eric Tang, Vinay Varadan, Sitharthan Kamalakaran, Michael Q. Zhang, James Hicks and Nevenka Dimitrova; 18. Signaling network analysis of genomic alterations predict breast cancer drug targets Naif Zaman and Edwin Wang; 19. Pharmacogenetic studies in pediatric acute myeloid leukemia Neha S. Bhise, Lata Chauhan and Jatinder K. Lamba; 20. Pharmacogenomics of antiretroviral drugs Chonlaphat Sukasem, Apichaya Puangpetch and Sadeep Medhasi; Part V. Population Genetics and Personalized Medicine: 21. Population stratification and its implications: lessons from genome-wide studies Sheikh Nizamuddin, Rakesh Tamang and Kumarasamy Thangaraj; 22. How to solve genetic disease on a population scale Barry Merriman; 23. Economics of personalized medicine Katherine Payne and Martin Eden; Index.
£999.99
