Encyclopedia of Genetics, Genomics, Proteomics and Bioinformatics [1 ed.] 9780470849743, 0470849746

Table of contents :
Cover......Page 1
Population genomics- patterns of genetic variation within populations......Page 2
Modeling human genetic history......Page 10
Homeobox gene repertoires- implications for the evolution of diversity......Page 31
Geographic structure of human genetic variation- medical and evolutionary implications......Page 52
Studies of human genetic history using the Y chromosome......Page 65
Studies of human genetic history using mtDNA variation......Page 69
The genetic structure of human pathogens......Page 74
Genetic signatures of n atural selection......Page 78
The role of gene regulation in evolution......Page 85
Modeling p rotein evolution......Page 89
Measuring variation in natural populations- a primer......Page 93
Human cytogenetics and human chromosome abnormalities......Page 101
The visualization of chromosomes......Page 109
Meiosis and meiotic errors......Page 114
Acquired chromosome abnormalities- the cytogenetics of cancer......Page 134
Human X chromosome inactivation......Page 148
Nondisjunction......Page 165
Microdeletions......Page 170
Mosaicism......Page 176
Uniparental disomy......Page 182
Cytogenetics of infertility......Page 187
Preimplantation genetic d iagnosis for chromosome abnormalities......Page 193
FISH......Page 202
Comparative genomic hybridization......Page 209
Cytogenetic analysis of lymphomas......Page 219
Human sperm – FISH f or identifying potential paternal risk factors for chromosomally abnormal reproductive outcomes......Page 229
Imprinting and epigenetic inheritance in human disease......Page 236
Regulation of DNA methylation by Dnmt3L......Page 243
The histone code and epigenetic inheritance......Page 249
Imprinting and epigenetics in mouse models and embryogenesis- understanding the requirement for both parental genomes......Page 259
Imprinting in Prader–Willi and Angelman syndromes......Page 269
Beckwith – Wiedemann syndrome......Page 283
Imprinting at the GNAS locus and endocrine disease......Page 300
Developmental regulation of DNA methyltransferases......Page 310
Epigenetic variation- amount, causes, and consequences......Page 323
How to get extra performance from a chromosome- recognition and modification of the X chromosome in male Drosophila melanogaster......Page 339
DNA methylation in epigenetics, development, and imprinting......Page 354
Epigenetic reprogramming in germ cells and preimplantation embryos......Page 361
Epigenetics and imprint resetting in cloned animals......Page 366
Imprinted QTL in farm animals- a fortuity or a common phenomenon......Page 374
Variable expressivity and epigenetics......Page 378
Evolution of genomic imprinting in mammals......Page 385
Rapidly evolving imprinted loci......Page 390
Imprinting and behavior......Page 395
Spreading of X-chromosome inactivation......Page 400
Initiation of X-chromosome inactivation......Page 407
Mechanisms of epigenetic loss of chromosomes in insects......Page 412
Epigenetic inheritance and RNAi at the centromere and heterochromatin......Page 420
Techniques in genomic imprinting research......Page 426
Bioinformatics and t he identification of imprinted genes in mammals......Page 431
UPD in human and mouse and role in identification of imprinted loci......Page 436
Introduction to gene mapping- linkage at a crossroads......Page 440
Parametric versus nonparametric and two-point versus multipoint- controversies in gene mapping......Page 444
Gene mapping, imprinting, and epigenetics......Page 450
Gene mapping and t he transition from STRPs to SNPs......Page 460
Consequences of error......Page 470
Choices in gene mapping- populations and family structures......Page 485
Algorithmic improvements in gene mapping......Page 490
Information content in gene mapping......Page 496
Sex-specific maps and consequences for linkage mapping......Page 501
Polymorphic inversions, deletions, and duplications in gene mapping......Page 509
Impact of linkage disequilibrium on multipoint linkage analysis......Page 513
Computation of L OD scores......Page 517
Genetics of complex diseases- lessons from type 2 diabetes......Page 523
Importance of complex traits......Page 532
Concept of complex trait genetics......Page 539
The common disease common variant concept......Page 551
Population selection in complex disease gene mapping......Page 561
Allergy and asthma......Page 575
Inflammation and inflammatory bowel disease......Page 581
Hypertension genetics- under pressure......Page 588
Genetics of cognitive disorders......Page 594
Complexity of cancer as a genetic disease......Page 606
The mitochondrial genome......Page 611
Approach t o rare monogenic and chromosomal disorders......Page 621
Approach to common chronic disorders of adulthood......Page 631
Current approaches t o prenatal screening and diagnosis......Page 647
Advances in newborn screening for biochemical genetic disorders......Page 655
Advances in cytogenetic d iagnosis......Page 675
Current approaches to molecular diagnosis......Page 691
The clinical and economic implications of pharmacogenomics......Page 723
Molecular dysmorphology......Page 744
Changing paradigms of genetic counseling......Page 748
Ethical and legal issues in medical genetics......Page 754
Mechanisms of inheritance......Page 759
Genetic f amily history, pedigree analysis, and risk assessment......Page 768
The physical examination in clinical genetics......Page 777
Genetic t esting and genotype–phenotype correlations......Page 782
Genetic counseling p rocess......Page 787
Treatment of m onogenic disorders......Page 791
Carrier screening- a t utorial......Page 797
Prenatal aneuploidy screening......Page 800
Gene identification in common disorders- a tutorial......Page 806
Uses of databases......Page 810
The m icrodeletion syndromes......Page 814
Cancer genetics......Page 818
Familial adenomatous polyposis......Page 826
Gene therapy I- principles and clinical applications......Page 836
Gene therapy II- viral vectors and treatment modalities......Page 845
Hematopoietic stem cell gene therapy......Page 857
Gene therapy in the central nervous system......Page 870
Cardiovascular gene t herapy......Page 879
Artificial self-assembling systems for gene therapy......Page 892
Adenovirus vectors......Page 898
Adeno-associated viral vectors- depend(o)ble stability......Page 906
Retro-lentiviral vectors......Page 912
Immunity and t olerance induction in gene therapy......Page 918
Gene transfer vectors as medicinal products- risks and benefits......Page 927
Gene transfer to skeletal muscle......Page 932
Gene transfer to the liver......Page 938
Gene transfer to the skin......Page 941
Control of t ransgene expression in mammalian cells......Page 946
Eukaryotic genomics......Page 951
Genome sequencing of m icrobial species......Page 960
Hierarchical, ordered mapped large insert clone shotgun sequencing......Page 969
Sequencing templates – shotgun clone isolation versus amplification approaches......Page 974
Robotics and automation......Page 984
Microelectrophoresis d evices for DNA sequencing......Page 989
Single molecule array-based sequencing......Page 995
Real-time DNA sequencing......Page 1001
Genome mapping overview......Page 1005
Linking DNA to production- the mapping of quantitative trait loci in livestock......Page 1011
Mapping complex disease phenotypes......Page 1016
Haplotype mapping......Page 1036
YAC-STS content mapping......Page 1048
The construction and use of radiation hybrid maps in genomic research......Page 1059
Linkage mapping......Page 1073
Microarray comparative genome hybridization......Page 1091
Linkage disequilibrium and whole-genome association studies......Page 1100
Fingerprint mapping......Page 1106
Restriction f ragment fingerprinting software......Page 1117
Synteny mapping......Page 1122
Hitchhiking mapping......Page 1126
The Happy mapping approach......Page 1130
Digital karyotyping- a powerful tool for cancer gene discovery......Page 1135
The technology tour de force of the Human Genome Project......Page 1140
The Human Genome Project......Page 1145
Genome assembly......Page 1154
Segmental duplications and the human genome......Page 1166
Noncoding RNAs in mammals......Page 1184
The d istribution of genes in human genome......Page 1196
Pseudogenes......Page 1205
Alternative splicing- conservation and function......Page 1210
Overlapping genes in t he human genome......Page 1215
Comparisons with primate genomes......Page 1219
Transcriptional p romoters......Page 1225
Human microRNAs......Page 1230
Endogenous retroviruses......Page 1237
Genome archaeology......Page 1241
Functional analysis of genes......Page 1245
Mouse models......Page 1252
The rat as a m odel physiological system......Page 1264
Farm animals......Page 1282
Mouse mutagenesis and gene function......Page 1295
Systematic mutagenesis of nonmammalian model species......Page 1313
Functional genomics in Saccharomyces cerevisiae......Page 1329
The C. elegans genome......Page 1336
The Drosophila genome(s)......Page 1339
The Fugu and Zebrafish genomes......Page 1343
The mouse genome sequence......Page 1349
Comparative sequencing of vertebrate genomes......Page 1353
The chimpanzee genome......Page 1362
Functional annotation of the mouse genome- the challenge of phenotyping......Page 1367
Bacterial pathogens of man......Page 1372
Eukaryotic parasite genome projects......Page 1378
Genomics of enterobacteriaceae......Page 1383
Genomics of the Mycobacterium tuberculosis complex and Mycobacterium leprae......Page 1396
The Mycoplasmas – a congruent path toward minimal life functions......Page 1412
The nuclear genome of apicomplexan parasites......Page 1426
Reverse vaccinology- a critical analysis......Page 1444
The staphylococci......Page 1455
Genome-wide analysis of group A Streptococcus......Page 1460
Yersinia......Page 1467
Chlamydiae......Page 1476
Spirochete genomes......Page 1481
Comparative genomics of the ε-proteobacterial human pathogens Helicobacter pylori and Campylobacter jejuni......Page 1484
The n eisserial genomes- what they reveal about the diversity and behavior of these species......Page 1489
Kinetoplastid genomics......Page 1495
The organelles of apicomplexan parasites......Page 1503
Environmental shotgun sequencing......Page 1512
Methods f or detecting h orizontal transfer of genes......Page 1518
Genomics of Rickettsia......Page 1523
Listeriae......Page 1530
History of genetic mapping......Page 1537
Normal DNA sequence variations in humans......Page 1544
Reliability and utility of single nucleotide polymorphisms for genetic association studies......Page 1555
Pharmacogenetics and t he future of medicine......Page 1571
SNPs and human history......Page 1589
Evolutionary modeling in haplotype analysis......Page 1597
Creating LD maps of the genome......Page 1602
Finding and using haplotype blocks in candidate gene association studies......Page 1609
Avoiding stratification in association studies......Page 1620
Mapping by admixture linkage disequilibrium (MALD)......Page 1629
Genotyping technology- the present and the future......Page 1636
What is an EST......Page 1641
Technologies for systematic analysis of eukaryotic transcriptomes......Page 1645
EST resources, clone sets, and databases......Page 1655
Using E STs f or genome annotation – predicting the transcriptome......Page 1665
Using ORESTES ESTs to mine gene cancer expression data......Page 1675
Proteome knowledge bases in the context of cancer......Page 1683
Disease gene candidacy and E STs......Page 1708
The role of n onsense-mediated decay in physiological and pathological processes......Page 1712
Pilot gene d iscovery in plasmodial pathogens......Page 1720
Manufacturing EST libraries......Page 1725
EST clustering- a short t utorial......Page 1731
Using UniGene, S TACK, and TIGR indices......Page 1735
Microarrays- an overview......Page 1741
Creating and hybridizing spotted DNA arrays......Page 1746
Using oligonucleotide arrays......Page 1755
Microarray CGH......Page 1770
Expression and localization of proteins in mammalian cells......Page 1782
Integrating genotypic, m olecular profiling, and clinical data to elucidate common human diseases......Page 1799
The promise of gene signatures in cancer diagnosis and prognosis......Page 1818
Seven years of yeast m icroarray analysis......Page 1827
Bacterial genome organization- comparative expression profiling, operons, regulons, and beyond......Page 1836
Genomic analysis of host pathogen interactions......Page 1847
Protein m icroarrays as an emerging tool for proteomics......Page 1854
Tissue m icroarrays......Page 1865
The u se of external controls in microarray experiments......Page 1871
SAGE......Page 1878
Core methodologies......Page 1883
Advances of LC-MS and CZE-MS in proteome analysis......Page 1887
Sample preparation for proteomics......Page 1893
Tandem m ass spectrometry database searching......Page 1901
Interpreting tandem mass spectra of peptides......Page 1910
FT-ICR......Page 1923
Laser-based m icrodissection approaches and applications......Page 1932
Orbitrap mass analyzer......Page 1944
Time-of-flight mass spectrometry......Page 1954
Quadrupole mass analyzers- theoretical and practical considerations......Page 1965
Quadrupole ion t raps and a new era of evolution......Page 1974
Hybrid MS......Page 1982
Nano-MALDI and Nano-ESI MS......Page 1987
Protein fingerprinting......Page 1992
Multidimensional liquid chromatography tandem mass spectrometry for biological discovery......Page 2000
Sample preparation for MALDI and electrospray......Page 2006
Handling m embrane p roteins......Page 2013
Improvement of sequence coverage in peptide mass fingerprinting......Page 2018
Tutorial on tandem mass spectrometry database searching......Page 2024
Techniques f or ion d issociation (fragmentation) and scanning in MS-MS......Page 2031
Making nanocolumns and tips......Page 2038
Tutorial on protein fingerprinting......Page 2042
Separation-dependent approaches for protein expression profiling......Page 2048
Separation-independent approaches for protein expression profiling......Page 2052
Two-dimensional gel electrophoresis......Page 2062
ICAT and other labeling strategies for semiquantitative LC-based expression profiling......Page 2075
Protein arrays......Page 2085
2D DIGE......Page 2097
Image analysis......Page 2105
Detecting p rotein posttranslational modifications using small molecule probes and multiwavelength imaging devices......Page 2112
Real-time measurements of protein dynamics......Page 2116
Two-dimensional gel electrophoresis (2-DE)......Page 2120
2-D Difference Gel Electrophoresis – an accurate quantitative method for protein analysis......Page 2126
MS-based methods for identification of 2-DE-resolved proteins......Page 2131
Arraying proteins and antibodies......Page 2136
Basic techniques for the use of reverse phase protein microarrays for signal pathway profiling......Page 2141
Protein interactions in cellular signaling......Page 2149
Structural biology of protein complexes......Page 2155
Biochemistry of protein complexes......Page 2160
Inferring gene function and biochemical networks from protein interactions......Page 2170
The C . elegans interactome project......Page 2182
The yeast interactome......Page 2196
Human signaling pathways analyzed by protein interaction mapping......Page 2214
Investigating protein–protein interactions in multisubunit proteins- the case of eukaryotic RNA polymerases......Page 2220
Membrane-anchored protein complexes......Page 2226
Energy t ransfer – based approaches to study G protein–coupled receptor dimerization and activation......Page 2237
Protein interaction d atabases......Page 2242
Computational methods for the prediction of protein interaction partners......Page 2253
Functional classification of proteins based on protein interaction data......Page 2259
Analyzing proteomic, genomic and transcriptomic elemental compositions to uncover the intimate evolution of biopolymers......Page 2266
Topology of protein interaction networks and cell physiology......Page 2272
Bioluminescence resonance energy transfer......Page 2277
Probing cellular f unction with bioluminescence imaging......Page 2284
Small molecule fluorescent probes for protein labeling and their application to cell-based imaging (including FlAsH etc.)......Page 2295
Using photoactivatable GFPs to study protein dynamics and function......Page 2302
FRET-based reporters for intracellular enzyme activity......Page 2311
Quantitative EM techniques......Page 2320
High content screening......Page 2336
Photobleaching (FRAP-FLIP) and dynamic imaging......Page 2340
Probing p rotein function in cells using CALI......Page 2345
Imaging protein f unction using fluorescence lifetime imaging microscopy (FLIM)......Page 2352
Elucidating p rotein dynamics and function using fluorescence correlation spectroscopy (FCS)......Page 2360
Quantum dots for multiparameter measurements......Page 2365
Immunofluorescent labeling and fluorescent dyes......Page 2371
Quantitative image analysis and the Open Microscopy Environment......Page 2378
siRNA approaches in cell b iology......Page 2386
Posttranslational m odification of proteins......Page 2392
Glycosylation......Page 2401
Protein phosphorylation analysis by mass spectrometry......Page 2413
Structure-function of N -glycans......Page 2432
Structure-function of O -glycans......Page 2443
GPI anchors......Page 2456
Glycosylation and hepatacellular carcinoma......Page 2466
Protein glycosylation and renal cancer......Page 2478
Posttranslational cleavage of cell-surface receptors......Page 2490
S-nitrosylation and thiolation......Page 2497
Glycosylation in b acteria- that, what, how, why, now what......Page 2504
O -glycan p rocessing......Page 2509
O -Mannosylation......Page 2515
O-linked N -acetylglucosamine (O-GlcNAc)......Page 2521
Posttranslational modifications to plants – glycosylation......Page 2526
Protein phosphorylation analysis – a primer......Page 2533
Glycoproteomics......Page 2543
Mass spectrometry......Page 2548
Analysis of N- and O-linked glycans of glycoproteins......Page 2558
Glycosylphosphatidylinositol anchors – a structural perspective......Page 2571
Classification of p roteins into families......Page 2576
Metalloproteins......Page 2584
Peptidases, f amilies, and clans......Page 2613
Transporter p rotein families......Page 2626
Structure comparison and protein structure classifications......Page 2639
InterPro......Page 2661
Functionally and structurally relevant residues in PROSITE motif descriptors......Page 2667
The PRINTS protein fingerprint database- functional and evolutionary applications......Page 2673
Pfam- the protein families database......Page 2680
The PIR SuperFamily (PIRSF) classification system......Page 2686
Equivalog protein f amilies in the TIGRFAMs database......Page 2692
The CAT H domain structure database......Page 2696
COGs- an evolutionary classification of genes and proteins from sequenced genomes......Page 2705
PANTHER- Protein families and subfamilies modeled on the divergence of function......Page 2710
Functional prediction through phylogenetic inference and structural classification of proteins......Page 2715
Classification of p roteins by sequence signatures......Page 2724
Classification of p roteins by clustering techniques......Page 2730
Getting the most out of protein family classification resources......Page 2737
What use is a protein structure......Page 2745
History and future of X-ray structure determination......Page 2752
Fundamentals of protein structure and function......Page 2757
Structural genomics – expanding protein structural universe......Page 2772
Target selection f or structural genomics......Page 2795
Protein–ligand docking and structure-based drug design......Page 2808
Large complexes by X-ray methods......Page 2825
Large complexes and m olecular machines by electron microscopy......Page 2832
The importance of protein structural dynamics and the contribution of NMR spectroscopy......Page 2839
New approaches to bridging the timescale gap in the computer simulation of biomolecular processes......Page 2844
Modeling m embrane p rotein structures......Page 2849
X-ray crystallography......Page 2854
NMR......Page 2862
Electron m icroscopy as a tool for 3D structure determination in molecular structural biology......Page 2869
Integrative approaches to biology in the twenty-first century......Page 2874
Functional networks in mammalian cells......Page 2880
Analyzing and reconstructing gene regulatory networks......Page 2892
Reverse engineering gene regulatory networks......Page 2903
Functional inference from probabilistic protein interaction networks......Page 2921
Constraint-based modeling of metabolomic systems......Page 2933
Metabolic dynamics in cells viewed as multilayered, distributed, mass-energy-information networks......Page 2944
A complex systems approach to understand how cells control their shape and make cell fate decisions......Page 2960
Systems b iology of the h eart......Page 2974
Integrative m odeling of the pancreatic β-cell......Page 2983
EGFR network......Page 2994
Data collection and analysis in systems biology......Page 2997
Contig mapping and analysis......Page 3006
Algorithmic challenges in mammalian whole-genome assembly......Page 3015
Genome signals and assembly......Page 3025
Microbial sequence assembly......Page 3035
Comparative analysis for mapping and sequence assembly......Page 3037
Statistical signals......Page 3043
Errors in sequence assembly and corrections......Page 3049
Genome maps and t heir use in sequence assembly......Page 3054
Repeatfinding......Page 3061
Graphs and m etrics......Page 3067
Algorithms for sequence errors......Page 3071
Polymorphism and sequence assembly......Page 3078
Prokaryotic gene identification in silico......Page 3087
Eukaryotic gene finding......Page 3093
Spliced alignment......Page 3101
Searching f or genes and biologically related signals in DNA sequences......Page 3109
Pair hidden Markov m odels......Page 3119
Information t heory as a model of genomic sequences......Page 3130
Promoter prediction......Page 3142
Operon finding in bacteria......Page 3148
Gene structure prediction in plant genomes......Page 3154
Eukaryotic regulatory sequences......Page 3159
Alternative splicing in humans......Page 3163
Exonic splicing enhancers and exonic splicing silencers......Page 3168
Gene finding using multiple related species- a classification approach......Page 3173
Dynamic programming for gene finders......Page 3181
Gene structure prediction by genomic sequence alignment......Page 3185
Computational m otif discovery......Page 3190
In silico approaches t o f unctional analysis of proteins......Page 3193
Contextual inference of protein function......Page 3205
Protein d omains in eukaryotic signal transduction systems......Page 3221
Sequence complexity of p roteins and its significance in annotation......Page 3232
Protein repeats......Page 3238
Large-scale p rotein annotation......Page 3242
Measuring evolutionary constraints as protein properties reflecting underlying mechanisms......Page 3248
Large-scale, classification-driven, rule-based functional annotation of proteins......Page 3258
Signal peptides and p rotein localization prediction......Page 3269
Transmembrane topology prediction......Page 3276
IMPALA-RPS-BLAST-PSIBLAST in protein sequence analysis......Page 3282
The domains of life and their evolutionary implications......Page 3288
Phylogenetic p rofiling......Page 3299
Reconstructing vertebrate phylogenetic trees......Page 3309
Evolution of regulatory n etworks......Page 3319
Phylogenomic approaches to bacterial phylogeny......Page 3336
Phylogenomics for studies of microbial evolution......Page 3343
Mapping mutations on phylogenies......Page 3348
Phylogenetic analysis of BLAST results......Page 3358
Connecting genes by comparative genomics......Page 3362
Chromosome phylogeny......Page 3367
Integrating statistical approaches in experimental design and data analysis......Page 3374
Mass spectrometry and computational proteomics......Page 3381
Experimental design......Page 3390
Statistical methods for gene expression analysis......Page 3399
Algorithms for gene expression analysis......Page 3412
Differential expression with the Bioconductor Project......Page 3423
Mass spectrometric data mining for protein sequences......Page 3438
Low-level analysis of oligonucleotide expression arrays......Page 3452
CGH d ata analysis......Page 3459
A comparison of existing tools for ontological analysis of gene expression data......Page 3467
Extracting networks from expression data......Page 3490
Data standardization and the HUPO proteomics standards initiative......Page 3496
Large error models for microarray intensities......Page 3501
Relevance networks......Page 3507
Protein structure analysis and prediction......Page 3511
Analysis and p rediction of membrane protein structure......Page 3518
Ab initio structure prediction......Page 3531
Score f unctions for structure prediction......Page 3539
Protein domains......Page 3551
Complexity in biological structures and systems......Page 3566
Modeling b y h omology......Page 3589
The Protein Data Bank (PDB) and the Worldwide PDB http...www.wwpdb.org......Page 3603
Threading for protein-fold recognition......Page 3608
CASP......Page 3612
Molecular simulations in structure prediction......Page 3616
Protein structure comparison......Page 3623
Secondary structure p rediction......Page 3628
DNA-protein m odeling......Page 3634
Modeling tertiary structure of RNA......Page 3639
Introduction to ontologies in biomedicine- from powertools to assistants......Page 3644
BioPAX – biological pathway data exchange format......Page 3649
Ontologies for t he life sciences......Page 3656
Unified Medical L anguage System and associated vocabularies......Page 3677
The Gene Ontology project......Page 3686
Ontologies for information retrieval......Page 3697
Ontologies for n atural language processing......Page 3706
TAMBIS- transparent access to multiple bioinformatics services......Page 3723
Automatic concept identification in biomedical literature......Page 3732
Merging and comparing ontologies......Page 3737
Bioinformatics pathway representations, databases, and algorithms......Page 3742
Proteomics data representation and management......Page 3750
Ontologies for t hree-dimensional molecular structure.......Page 3755
MAGE-OM- An object model for the communication of microarray data......Page 3762
Frame-based systems- Protege......Page 3768
Description logics- OWL and DAML + OIL......Page 3772
Detecting p rotein homology using NCBI tools......Page 3776
Integrated bioinformatics software at NCBI......Page 3785
Bioconductor- software and development strategies for statistical genomics......Page 3795
RNA secondary structure prediction......Page 3809
Ensembl and UniProt (Swiss-Prot)......Page 3822
Hidden Markov m odels and neural networks......Page 3833
Threading algorithms......Page 3842
Acedb genome database......Page 3856
Design of KEGG and GO......Page 3860
Simulation of b iochemical networks......Page 3865
Using the Python programming language for bioinformatics......Page 3874
Perl in bioinformatics......Page 3883
The MATLAB bioinformatics toolbox......Page 3893
Gibbs sampling and bioinformatics......Page 3903
Applications of RNA minimum free energy computations......Page 3907
Cluster architecture......Page 3913
Relational databases in bioinformatics......Page 3918
Support vector machine software......Page 3922
Brief Python t utorial for bioinformatics......Page 3929
A brief Perl tutorial for bioinformatics......Page 3939
Grid technologies......Page 3946
Attacking performance bottlenecks......Page 3951
Glossary Terms......Page 3961