Holdings: Introduction to computational genomics

Introduction to computational genomics: a case studies approach

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Bibliographic Details
Main Authors:	Cristianini, Nello 1968- (Author), Hahn, Matthew W. (Author)
Format:	Book
Language:	English
Published:	Cambridge Cambridge Univ. Press 2007
Edition:	1. publ.
Subjects:	Computermethoden Genomica Datenverarbeitung Genomics > Statistical methods Computational biology Genomics > Data processing Genomics > methods Computational Biology > methods Genanalyse Bioinformatik Einführung
Online Access:	Table of contents only Publisher description Contributor biographical information Inhaltsverzeichnis Inhaltsverzeichnis
Item Description:	Includes bibliographical references (p. [173]-178) and index
Physical Description:	XVII, 182 S. graph. Darst. 26 cm
ISBN:	9780521856034 0521856035 0521671914

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adam_text	INTRODUCTION TO COMPUTATIONAL GENOMICS NELLO CRISTIANINI AND MATTHEW W. HAHN SUB GOTTINGEN 7 220 002 533 2007 A 20 UNIVERSITY PRESS CONTENTS PREFACE PAGE IX PROLOGUE: IN PRAISE OF CELLS XI CHAPTER I THE FIRST LOOK AT A GENOME: SEQUENCE STATISTICS 1 1.1 GENOMIC ERA, YEAR ZERO 1 1.2 THE ANATOMY OF A GENOME 3 1.3 PROBABILISTIC MODELS OF GENOME SEQUENCES 5 1.4 ANNOTATING A GENOME: STATISTICAL SEQUENCE ANALYSIS 10 1.5 FINDING DATA: GENBANK, EMBL, AND DDBJ 18 1.6 EXERCISES 20 1.7 READING LIST 21 CHAPTER 2 ALL THE SEQUENCE S MEN: GENE FINDING 22 2.1 THE HUMAN GENOME SWEEPSTAKES 22 2.2 AN INTRODUCTION TO GENES AND PROTEINS 23 2.3 GENOME ANNOTATION: GENE FINDING 29 2.4 DETECTING SPURIOUS SIGNALS: HYPOTHESIS TESTING 31 2.5 EXERCISES 37 2.6 READING LIST 37 CHAPTER 3 ALL IN THE FAMILY: SEQUENCE ALIGNMENT 38 3.1 EYE OF THE TIGER 38 3.2 ON SEQUENCE ALIGNMENT 39 3.3 ON SEQUENCE SIMILARITY 40 3.4 SEQUENCE ALIGNMENT: GLOBAL AND LOCAL 42 3.5 STATISTICAL ANALYSIS OF ALIGNMENTS 47 3.6 BLAST: FAST APPROXIMATE LOCAL ALIGNMENT 50 3.7 MULTIPLE SEQUENCE ALIGNMENT 53 3.8* COMPUTING THE ALIGNMENTS 55 3.9 EXERCISES 60 3.10 READING LIST 60 CHAPTER 4 THE BOULEVARD OF BROKEN GENES: HIDDEN MARKOV MODELS 61 4.1 THE NOSE KNOWS 61 4.2 HIDDEN MARKOV MODELS 63 4.3 PROFILE HMMS 67 4.4 FINDING GENES WITH HIDDEN MARKOV MODELS 69 4.5 CASE STUDY: ODORANT RECEPTORS 70 4.6* ALGORITHMS FOR HMM COMPUTATIONS 75 4.7 EXERCISES 77 4.8 READING LIST 77 CONTENTS CHAPTER 5 ARE NEANDERTHALS AMONG US?: VARIATION WITHIN AND BETWEEN SPECIES 78 5.1 VARIATION IN DNA SEQUENCES 79 5.2 MITOCHONDRIAL DNA: A MODEL FOR THE ANALYSIS OF VARIATION . . 83 5.3 VARIATION BETWEEN SPECIES 85 5.4 ESTIMATING GENETIC DISTANCE 87 5.5 CASE STUDY: ARE NEANDERTHALS STILL AMONG US? 92 5.6 EXERCISES 94 5.7 READING LIST 95 CHAPTER 6 FIGHTING HIV: NATURAL SELECTION AT THE MOLECULAR LEVEL 96 6.1 A MYSTERIOUS DISEASE 96 6.2 EVOLUTION AND NATURAL SELECTION 97 6.3 HIV AND THE HUMAN IMMUNE SYSTEM 98 6.4 QUANTIFYING NATURAL SELECTION ON DNA SEQUENCES 99 6.5 ESTIMATING K A /K S 102 6.6 CASE STUDY: NATURAL SELECTION AND THE HIV GENOME 105 6.7 EXERCISES 108 6.8 READING LIST 109 CHAPTER 7 SARS - A POST-GENOMIC EPIDEMIC: PHYLOGENETIC ANALYSIS HO 7.1 OUTBREAK 110 7.2 ON TREES AND EVOLUTION 112 7.3 INFERRING TREES 115 7.4 CASE STUDY: PHYLOGENETIC ANALYSIS OF THE SARS EPIDEMIC 120 7.5 THE NEWICK FORMAT 126 7.6 EXERCISES 127 7.7 READING LIST *: 127 CHAPTER 8 WELCOME TO THE HOTEL CHLAMYDIA: WHOLE GENOME COMPARISONS 128 8.1 UNINVITED GUESTS 128 8.2 BY LEAPS AND BOUNDS: PATTERNS OF GENOME EVOLUTION 129 8.3 BEANBAG GENOMICS 130 8.4 SYNTENY 135 8.5 EXERCISES 138 8.6 READING LIST 139 CHAPTER 9 THE GENOMICS OF WINE-MAKING: ANALYSIS OF GENE EXPRESSION 141 9.1 CHATEAU HAJJI FERUZ TEPE 141 9.2 MONITORING CELLULAR COMMUNICATION 143 9.3 MICROARRAY TECHNOLOGIES 145 9.4 CASE STUDY: THE DIAUXIC SHIFT AND YEAST GENE EXPRESSION 147 9.5 BONUS CASE STUDY: CELL-CYCLE REGULATED GENES 155 CONTENTS 9.6 EXERCISES 158 9.7 READING LIST 158 CHAPTER 10 A BED-TIME STORY: IDENTIFICATION OF REGULATORY SEQUENCES 159 10.1 THE CIRCADIAN CLOCK 159 10.2 BASIC MECHANISMS OF GENE EXPRESSION 161 10.3 MOTIF-FINDING STRATEGIES 162 10.4 CASE STUDY: THE CLOCK AGAIN 167 10.5 EXERCISES 172 10.6 READING LIST 172 BIBLIOGRAPHY 173 INDEX 179
adam_txt	INTRODUCTION TO COMPUTATIONAL GENOMICS NELLO CRISTIANINI AND MATTHEW W. HAHN SUB GOTTINGEN 7 220 002 533 2007 A 20 UNIVERSITY PRESS CONTENTS PREFACE PAGE IX PROLOGUE: IN PRAISE OF CELLS XI CHAPTER I THE FIRST LOOK AT A GENOME: SEQUENCE STATISTICS 1 1.1 GENOMIC ERA, YEAR ZERO 1 1.2 THE ANATOMY OF A GENOME 3 1.3 PROBABILISTIC MODELS OF GENOME SEQUENCES 5 1.4 ANNOTATING A GENOME: STATISTICAL SEQUENCE ANALYSIS 10 1.5 FINDING DATA: GENBANK, EMBL, AND DDBJ 18 1.6 EXERCISES 20 1.7 READING LIST 21 CHAPTER 2 ALL THE SEQUENCE'S MEN: GENE FINDING 22 2.1 THE HUMAN GENOME SWEEPSTAKES 22 2.2 AN INTRODUCTION TO GENES AND PROTEINS 23 2.3 GENOME ANNOTATION: GENE FINDING 29 2.4 DETECTING SPURIOUS SIGNALS: HYPOTHESIS TESTING 31 2.5 EXERCISES 37 2.6 READING LIST 37 CHAPTER 3 ALL IN THE FAMILY: SEQUENCE ALIGNMENT 38 3.1 EYE OF THE TIGER 38 3.2 ON SEQUENCE ALIGNMENT 39 3.3 ON SEQUENCE SIMILARITY 40 3.4 SEQUENCE ALIGNMENT: GLOBAL AND LOCAL 42 3.5 STATISTICAL ANALYSIS OF ALIGNMENTS 47 3.6 BLAST: FAST APPROXIMATE LOCAL ALIGNMENT 50 3.7 MULTIPLE SEQUENCE ALIGNMENT 53 3.8* COMPUTING THE ALIGNMENTS 55 3.9 EXERCISES 60 3.10 READING LIST 60 CHAPTER 4 THE BOULEVARD OF BROKEN GENES: HIDDEN MARKOV MODELS 61 4.1 THE NOSE KNOWS 61 4.2 HIDDEN MARKOV MODELS 63 4.3 PROFILE HMMS 67 4.4 FINDING GENES WITH HIDDEN MARKOV MODELS 69 4.5 CASE STUDY: ODORANT RECEPTORS 70 4.6* ALGORITHMS FOR HMM COMPUTATIONS 75 4.7 EXERCISES 77 4.8 READING LIST 77 CONTENTS CHAPTER 5 ARE NEANDERTHALS AMONG US?: VARIATION WITHIN AND BETWEEN SPECIES 78 5.1 VARIATION IN DNA SEQUENCES 79 5.2 MITOCHONDRIAL DNA: A MODEL FOR THE ANALYSIS OF VARIATION . . 83 5.3 VARIATION BETWEEN SPECIES 85 5.4 ESTIMATING GENETIC DISTANCE 87 5.5 CASE STUDY: ARE NEANDERTHALS STILL AMONG US? 92 5.6 EXERCISES 94 5.7 READING LIST 95 CHAPTER 6 FIGHTING HIV: NATURAL SELECTION AT THE MOLECULAR LEVEL 96 6.1 A MYSTERIOUS DISEASE 96 6.2 EVOLUTION AND NATURAL SELECTION 97 6.3 HIV AND THE HUMAN IMMUNE SYSTEM 98 6.4 QUANTIFYING NATURAL SELECTION ON DNA SEQUENCES 99 6.5 ESTIMATING K A /K S 102 6.6 CASE STUDY: NATURAL SELECTION AND THE HIV GENOME 105 6.7 EXERCISES 108 6.8 READING LIST 109 CHAPTER 7 SARS - A POST-GENOMIC EPIDEMIC: PHYLOGENETIC ANALYSIS HO 7.1 OUTBREAK 110 7.2 ON TREES AND EVOLUTION 112 7.3 INFERRING TREES 115 7.4 CASE STUDY: PHYLOGENETIC ANALYSIS OF THE SARS EPIDEMIC 120 7.5 THE NEWICK FORMAT 126 7.6 EXERCISES 127 7.7 READING LIST *: 127 CHAPTER 8 WELCOME TO THE HOTEL CHLAMYDIA: WHOLE GENOME COMPARISONS 128 8.1 UNINVITED GUESTS 128 8.2 BY LEAPS AND BOUNDS: PATTERNS OF GENOME EVOLUTION 129 8.3 BEANBAG GENOMICS 130 8.4 SYNTENY 135 8.5 EXERCISES 138 8.6 READING LIST 139 CHAPTER 9 THE GENOMICS OF WINE-MAKING: ANALYSIS OF GENE EXPRESSION 141 9.1 CHATEAU HAJJI FERUZ TEPE 141 9.2 MONITORING CELLULAR COMMUNICATION 143 9.3 MICROARRAY TECHNOLOGIES 145 9.4 CASE STUDY: THE DIAUXIC SHIFT AND YEAST GENE EXPRESSION 147 9.5 BONUS CASE STUDY: CELL-CYCLE REGULATED GENES 155 CONTENTS 9.6 EXERCISES 158 9.7 READING LIST 158 CHAPTER 10 A BED-TIME STORY: IDENTIFICATION OF REGULATORY SEQUENCES 159 10.1 THE CIRCADIAN CLOCK 159 10.2 BASIC MECHANISMS OF GENE EXPRESSION 161 10.3 MOTIF-FINDING STRATEGIES 162 10.4 CASE STUDY: THE CLOCK AGAIN 167 10.5 EXERCISES 172 10.6 READING LIST 172 BIBLIOGRAPHY 173 INDEX 179
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spelling	Cristianini, Nello 1968- Verfasser (DE-588)133181499 aut Introduction to computational genomics a case studies approach Nello Cristianini and Matthew W. Hahn 1. publ. Cambridge Cambridge Univ. Press 2007 XVII, 182 S. graph. Darst. 26 cm txt rdacontent n rdamedia nc rdacarrier Includes bibliographical references (p. [173]-178) and index Computermethoden gtt Genomica gtt Datenverarbeitung Genomics Statistical methods Computational biology Genomics Data processing Genomics methods Computational Biology methods Genanalyse (DE-588)4200230-8 gnd rswk-swf Bioinformatik (DE-588)4611085-9 gnd rswk-swf (DE-588)4151278-9 Einführung gnd-content Genanalyse (DE-588)4200230-8 s Bioinformatik (DE-588)4611085-9 s DE-604 Hahn, Matthew W. Verfasser aut http://www.loc.gov/catdir/enhancements/fy0702/2007273397-t.html Table of contents only http://www.loc.gov/catdir/enhancements/fy0702/2007273397-d.html Publisher description http://www.loc.gov/catdir/enhancements/fy0733/2007273397-b.html Contributor biographical information http://www3.ub.tu-berlin.de/ihv/001734609.pdf Inhaltsverzeichnis GBV Datenaustausch application/pdf http://bvbr.bib-bvb.de:8991/F?func=service&doc_library=BVB01&local_base=BVB01&doc_number=016272958&sequence=000001&line_number=0001&func_code=DB_RECORDS&service_type=MEDIA Inhaltsverzeichnis
spellingShingle	Cristianini, Nello 1968- Hahn, Matthew W. Introduction to computational genomics a case studies approach Computermethoden gtt Genomica gtt Datenverarbeitung Genomics Statistical methods Computational biology Genomics Data processing Genomics methods Computational Biology methods Genanalyse (DE-588)4200230-8 gnd Bioinformatik (DE-588)4611085-9 gnd
subject_GND	(DE-588)4200230-8 (DE-588)4611085-9 (DE-588)4151278-9
title	Introduction to computational genomics a case studies approach
title_auth	Introduction to computational genomics a case studies approach
title_exact_search	Introduction to computational genomics a case studies approach
title_exact_search_txtP	Introduction to computational genomics a case studies approach
title_full	Introduction to computational genomics a case studies approach Nello Cristianini and Matthew W. Hahn
title_fullStr	Introduction to computational genomics a case studies approach Nello Cristianini and Matthew W. Hahn
title_full_unstemmed	Introduction to computational genomics a case studies approach Nello Cristianini and Matthew W. Hahn
title_short	Introduction to computational genomics
title_sort	introduction to computational genomics a case studies approach
title_sub	a case studies approach
topic	Computermethoden gtt Genomica gtt Datenverarbeitung Genomics Statistical methods Computational biology Genomics Data processing Genomics methods Computational Biology methods Genanalyse (DE-588)4200230-8 gnd Bioinformatik (DE-588)4611085-9 gnd
topic_facet	Computermethoden Genomica Datenverarbeitung Genomics Statistical methods Computational biology Genomics Data processing Genomics methods Computational Biology methods Genanalyse Bioinformatik Einführung
url	http://www.loc.gov/catdir/enhancements/fy0702/2007273397-t.html http://www.loc.gov/catdir/enhancements/fy0702/2007273397-d.html http://www.loc.gov/catdir/enhancements/fy0733/2007273397-b.html http://www3.ub.tu-berlin.de/ihv/001734609.pdf http://bvbr.bib-bvb.de:8991/F?func=service&doc_library=BVB01&local_base=BVB01&doc_number=016272958&sequence=000001&line_number=0001&func_code=DB_RECORDS&service_type=MEDIA
work_keys_str_mv	AT cristianininello introductiontocomputationalgenomicsacasestudiesapproach AT hahnmattheww introductiontocomputationalgenomicsacasestudiesapproach

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