585

Subject Index

A A. fulgidus see Archaeoglobus fulgidus ALOX5 373 A. thaliana see Arabidopsis thaliana – activity 374 abandoned samples 518 alternative splicing 240 Abbe’s Diffraction Limit, DNA sequencing 160 aMAZE 442 ABC see ATP-binding cassette permeases AmiGO GOst server 337 ABI1 gene 111 amino-modified oligonucleotide sequences 228 ABI3 gene 111 Aminoactyl-tRNA Synthetase Database 442 ABI4 gene 111 amplicon, DNA microarrays 229, 232–234 academic secrecy, commercialization of biobank amplified fragment length polymorphism 107 resources 542 analysis of intact proteins 203 acceptable uses of genetic technologies 541 analytic models 472 access by third parties, genetic information 514 anion-exchange prefractionation, Mass accountability 551 Spectrometry 202 ACeDB 31 anion transporters 372 acetyl-CoA synthase 19 anion-transporting polypeptides 372 Acidobacter, model organisms 51 AnnAt1, plants 69 acute lymphoblastic leukemia 255 anomalous dispersion, multiple wavelength 274 acute myeloid leukemia 255 anonymization process, samples 520 acute promyelocytic leukemia 373 anonymized samples, DNA 510, 517 adaptive automation, DNA sequencing 153 ANTHEPROT 334 additives, protein crystallography 278–279 anti-cancer drug screen study, Bioinformatics 359 adenomatous polyposis coli 93 antiapopotic gene 94 Adh1 locus 116 antimicrobials 53 adiponectin receptor 366 antisense RNA expression 76 adverse drug effects 366, 368 Apache affinity tagging 262, 277 – Batik 406 Affymetrix 223, 357, 417, 421 – software, JAVA-based 406 AFLP see amplified fragment length – Xalan-Java 409 polymorphism – Xerces 406 agarose gel simulation, MAGPIE 403 APC AGAVE XML 412 – gene 93 age of enlightment 566 – protein 93 Agilent Technologies 417, 421 Apium graveolens, model organisms 64 AHEC 523 apo-calmodulin 289 Albers-Schonberg disease, type II 364 Aquifex aeolicus, model organisms 17 albuterol 357 Arabidopsis thaliana 4 alignment, Bioinformatics 301–302 – comprehensive genetic map 26 Alkaloid biosynthesis 471 – duplicated segments 29 allelic heterogeneity, human genome 87 – favorable feature 26

Handbook of Genome Research. Genomics, Proteomics, Metabolomics, Bioinformatics, Ethical and Legal Issues. Edited by Christoph W. Sensen Copyright © 2005 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim ISBN: 3-527-31348-6 586 Subject Index

– functional genomics 30 ASD 356 – Genome Initiative 27 ASEdb 442 – model organisms 25, 59, 110, 239, 411 Asilomar conference 6 – plant-specific functions 29 ASN.1 466 – potential functional assignments 29 – tools 438 – repeats of transposeable elements 28 Asparagales, model organisms 64 – repetitive elements 28 assembly lines, genome research 576 – sequencing strategy 27 Assistance Publique-Hopitaux de Paris 546 – stock centers 27 association studies 88 – tandem repeats 29 Asterand 542 archaea 16 at-risk information, automatic communication – halophilic 49 526 Archaeoglobales 16 ATH1 GeneChip 121 Archaeoglobus fulgidus, model organisms 3 ATNOS 287 – carbon source 19 ATP-binding cassette permeases 11 – characterization of the genome 18 attrition, protein crystallography 275 – electron-micrograph 16 Australian Health Ethics Committee 523 – gene density 19 Australian Law Reform Commission 522–523 – genes for RNA 18 AutoAssign 286 – genome size 17 automated microscopes 279 – iron sulfide 16 automated sequencers, DNA sequencing 138 – IS elements 18 automatic communication of at-risk information – isoelectric point 19 526 – long coding repeats 18 autonomic neuropathy 85 – minimum sequence coverage 17 autosomes 84 – non-coding repeats 18 – Caenorhabditis elegans 31 – paralogous gene families 19 average difference 422 – putative functions 19 award, 21st Century Achievement Award 359 – regions with low G+C content 18 AXR1 gene 111 – regulatory networks 20 – research articles 20 B – sensory networks 20 B-cell lymphoma – sequencing strategy 18 – diffuse large 255 – sulfate reduction 19 –large diffuse 245 archived human biological material 528 B-statistics 253 Ardais 542 B. subtilis see Bacillus subtilis argon ion laser 144 BAC see bacterial artificial chromosomes ARIA 287 BAC fingerprint database 120 Aristotle 537 Bacillus subtilis, model organisms 3, 10, 448 array printing methodology, DNA microarrays – cold shock response 14 241 – collection of mutants 14 array scanners, DNA microarrays 250 – Electron micrograph 10 ArrayAnalyzer 423 – enzyme production 15 arrayers, DNA microarrays 243 – food products, humanization 15 ArrayExpress 420 – foodsupply fermentation 15 ArrayIt SuperFilter plates 232 – functional genomics 13–15 ArrayViewer 420 – gene classes 13 arrhythmias, familial 96 – gene families 11 arrhythmogenic right ventricular cardiomyopathy – genes of completely unknown function 16 96 – genome 11 artifcicial neural nets 339 – hay bacterium 10 artificial intelligence 323 – humanization of the content of food products Asc gene 110 15 ASCII text 466 – iron metabolism 15 Subject Index 587

– leading replication strands 14 Biobank UK 551 – macriarray studies 14 Biobanks 516, 537–559 – natural selection 12 – ethical concerns 538 – normal habitat 10 – for Research 529 – order of the genes 15 – governance 551, 553–554 – osmotic stress 11 – initiatives, viability 551 – proteome 14 – legal concerns 538 – replication 12 – linkage to health information 539 – saltstress response 15 – risk and benefits 537 – strain 168 12 – social concerns 538 – traditional techniques 15 BioCarta 339, 443 – transcription 14 Biocatalysis/Biodegredation Database 443 – transformation 12 biochemical essay simulation, Bioinformatics – truncated tagged protein, Bacillus subtilis 13 384 backcrosses 106 biochemical systems, hierarchical 482 bacterial artificial chromosomes 62, 114 BioChipNet 243 bacteriophage f1 DNA 129 bioconductor project 254, 420 bacteriophage RNA 129 BioCYC 359, 445 bait and prey proteins 203, 496 bioethical discussion 564 band tilt, DNA sequencing 155 biofilm 50 BandCheck 232 – acid mine drainage 50 banking 509 – drinking water 50 barley, model organisms 110, 122 Bioinformatics 299–322 BASE 254, 420 – 2D gel analysis software 324 base calling, DNA sequencing 155–156 – 2D threading 343 bases – 3D threading 343 – individual, DNA sequencing 156 – alignment methods 299–305 – mispairing 249 – alternative splicing variants 356 Bayesian probabilistic approaches 331, 342, 424 – anti-cancer drug screen study 359 BBID 442 – applied 353–381 BDGP see Drosophila Genome Project – assembly engine 387 beamlines 279 – bending in a DNA double helix 312 Belgian Society of Human Genetics 547 – Berkeley Database Manager 385 benefit-sharing 512 – biochemical essay simulation 384 – genetic material 527 – Caenorhabditis elegans 31 – genetic resources 549 – cheminformatics 359 benefits, non-monetary 550 – codon preference statsistics 318 bermuda agreement 583 – codon usage analysis 315 beta-blockers 373 – coiled-coil domains 341 bi-directional sequencing, simultaneous, DNA – coloration of analysis data 386 sequencing 144 – consensus methods 309 Bias 429 – CpG islands 313 BIBAC vector 114 – data mining software 361 biclustering algorithms 426 – database alignment algorithms 333 bifurcation analyzer 482 – databases 353–362 BIND 338, 435 – detection of patterns 311 – data model 435 – disease-oriented target identification 364–365 – database standards 439–440 – display idioms 386 – domains 440 – DNA comparison matrix 301 – see also Biomolecular Interaction Network – domain identification 341 Database – dot plots 300 binding protein, FK506 265 – drug-target discovery 362 BindingdB 442 – dynamic programming 305 bio-ethical questions 567 – EST sequence database 355–356 588 Subject Index

– evidence 384 – substitution matrices 333 – exact substring matches 332 – threading 334, 342 – expression database 357–358 – tilting technique 391 – fuzzy matching 332 – transmembrane helices 339 – gaps 301 – transmembrane helics prediction 340 – General Feature Format 385 – two dimensional canvas 385 – genome features 384 – user preferences 385 – global alignment 301 – XML data 384 – globularity 340 – XML documents 384 – graphical display systems 383 BioJava 420 – helical wheels 345 biological material, ownership 538 –hidden Markov model 305, 334 biological samples, forseeable uses 553 – k-tuples 305 Biology, in silicio 579 – local alignment 301–303 biomarker discovery 372–373 – local sequence similarity 332 – projects 188 – localized ungapped alignments 305 biomaterials, commodification 543 – MAGPIE hierarchy 386 BioML 412 – manual user annotations 385 BIOMOBY 405 – Mass Spectrometry 193–195 Biomolecular Interaction Network Database – metabonomic database 354 437–439 – microarray databases 369 BioPAX 440 – modular computer code 385 BioPerl 420 – Needleman-Wunsch 301 BioPNML 478 – neural network analysis 334 biopsies 185 – nucleotide sequence pattern 314 biosynthesis, natural-product 53 – one-letter-code 309 biotech industry, currency 544 – open reading frame 317–318 biotechnology programs, EU 21 – open source effort 321 BioTools 345 – pairwise alignment 300 bladder cancer 256 –panes 391 blanket conset, DNA banking 524 – pathway databases 358 blanket conset 521 – pattern display 386 BLAST 331, 333, 345, 384 – pharmacoepidemology database 376 – database search program 301 – polymorphism databases 356–357 – search 195 – precomputed results 384 Blattner, F. 7 – profile-based similarity searching 363 BLOCKS 336, 384 – Proteomics database 360 blood clotting 95 – reading frame statistics 320–321 blotting, Western 326 – repeat identification 310 Bluejay 384, 404–405 – representation of the responses 386 – applet 412 – restriction mapping 315 – application 412 – scoring methods 300 – architecture 405–407 – sequence based homology searching 363 – context tree 408 – sequence databases 354 – core 405 – sequence variations 356–357 – data exploration 407 – shape 340 – document object model 406 – similarity 299 – eurokariotic genomes 411 – simple-sequence masking 309–309 – individual elements 410–411 – Smith-Waterman alignment 303 – information flow 406 – splice site consenus sequences 305 – interactive legend 409 – spliced cDNA sequences 300 – interface 407–408 – stability 340 – operations on the sequences 408 –standard key identifiers 362 – semantic zoom 408 – static graphical mode 385 – usable features 411 Subject Index 589

– XLink standard 411 Canada’s Tri-Council Policy Statement 551 Blueprint 583 Canadian Bioinformatics Resource 398, 577 bodily existence 563 Canadian Biotechnology Advisory Committee Bonferroni 423 548 Bonn Guidelines 549 Canadian DPG 35 Boolean models 500 Canadian Lifelong Initiative 538 Boolean nets 462 Canadian National Birth Cohort 538 bootom-up approach 469 cancer 90–94, 255–256, 567 bootstrap clustering, parametric 427 cancer genes 37 Br gene 111 Cancer Genome Anatomy Project 355, 358 brain cancer 185 Cancer Research UK 547 Brassica CANDID 287 – genome project 27 Candida albicans, model organisms 228 – model organisms 26, 61 capillary electrophoresis 70, 183, 211–222, 232 BRCA families 92 – capillaries 212 BRCA1 91, 546 – capillary sieving electrophoresis 215–216 BRCA1/2 545 – cell-to-cell variation 221 BRCA2 91, 546 – critical micelle concentration 217 breast biopsies 185 – detection 214 breast cancer 91–93 – detection limits 218 Breast Cancer Linkage consortium 92 – dextran 216 BRENDA 443, 462 – electrokinetic injection 212 Bristol-Myers Squibb 359 – electroosmosis 212–213, 215 BRITE 443 – electrophoresis 213 bronchoconstrictor leukotrienes 374 – fluorescence detection 214 brugada syndrome 96 – fluorogenetic reagents 214 budding yeast, model organisms 440 – free solution electrophoresis 217–218 bulk segregant analysis 112 – high fields 213 – high-molecular-weight proteins 215 C – high-performance liquid chromatography 220 C. elegans see Caenorhabditis elegans – hydrodynamic injection 212 CAE tool, Petri net tools 477 – injection 212 Caenorhabditis briggsae, model organisms 32 – instrumentation 212 Caenorhabditis elegans 4 – isoelectric focusing 215 – autosomes 31 – labeling chemistry 214 – Bioinformatics 31 – mass spectrometry 214 – cell lineage 30 – micellar separation 217 – conserved genes 32 – non-crosslinked polymers 216 – GC content 33 – poly(ethylene oxide) 216 – gene prediction 32 – pressurized 215 – genome project 31 – pullulan 216 –model organisms 29–30, 37, 218, 262, 354, – separation 213–214 447, 581 – separation buffer 214 – nervous systems 30 – separation time 213 – physical map 30 – sheath-flow cuvette detector 219 – postgenome era 33 – single-cell analysis 218–219 – predicted genes 32 – spiking of the sample 221 – predicted protein products 32 – surfactant 214 – repeat families 33 – tandem 328 – RNA genes 32 – two-dimensional separations 219–220 – tandem repeat regions 32–33 – UV absorbance 214 calmodulin 282 capillary gels, DNA sequencing 146, 151 Calvin cycle enzymes, plants 71 capillary sieving electrophoresis, capillary Campbell-like integration of foreign DNA 12 electrophoresis 215 590 Subject Index

carbon source, Archaeoglobus fulgidus 19 chromatographic gradients, ultra-long, mass carcinogens 91 spectrometry 200 cardiac troponin T 95 chromatography 187 cardiomyopathy – microscale 183 – arrhythmogenic right ventricular 96 chromosomal instability 93 – familial dilated 96 chromosome cardiovascular disease 94–97 – mitochondrial 61 – multifactorial 96 – plastid 60 carrier screening, human genome 86 chromosome landing 112 CAS chemical compound numbers 442 CID see collisionally induced dissociation catalase genes 11 CIHR 538 cation transporters 372 CIN see chromosomal instability CAVE automated virtual reality environments – tumors 93 578 CIOMS 518, 538 CBAC 548 – guidelines 512 CCD cameras, DNA microarrays 235 class discovery, microarrays 418 CDD 341 class prediction, microarrays 418, 425–426 cDNA, microarrays 416 client-server models 575 cDNA sequences clinical care, sample collection 519 – full-length 353 clinical trial 368 – spliced 300 clinical validation 542 CE see capillary electrophoresis cloned children 562 cell behavior 472 cloned DNA, DNA microarrays 224 cell-cycle regulator 94 cloning, genes, structural genomics 277 cell-free in-vitro expression 284 cloning vectors, DNA sequencing 141 cell lineage, Caenorhabditis elegans 30 clotting factor V 95 cellular CAD system 437 clustering algorithms 252 Cenarchaeum symbiosum, model organisms 48 – microarrays 426 centi-Morgan 62, 109 cM see centi-Morgan central bio-ethical questions 567 co-suppression with sense RNA 76 CGI 385 codcmp 321 chain-terminating nucleotide, DNA sequencing Code Link surface, DNA microarrays 242 130 coded, DNA banking 517 chaos game representation 311 coding repeats, Archaeoglobus fulgidus 18 chaotropic action 246 codomiant markers 106 chaperone-mediated folding 282 codon preference statsistics, Bioinformatics 318 chaperones, molecular 11 codon statistics 320 CHEK2 91 codon usage analysis, Bioinformatics 315 chemical cleavage, DNA sequencing 130 coeluting peptides, mass spectrometry 200 chemical compound numbers 442 cold shock response, Bacillus subtilis 14 chemical graph description 436 Cold Spring Harbor Phage course 6 chemical noise, mass spectrometry 199 colinearity 116 chemical shifts 286, 288 collaboratory 573 – peak-assignment process 286 collisionally induced dissociation 192 childhood eye cancer retinoblastoma 91 colon cancer 91, 93–94 children, cloned 562 colorectal cancer 91 chimera 562 columns, mass spectrometry 200 chimerism 114 COMET 360 ChIP on Chip 429 commercial gain, biobank resources 543 ChipWriterPro 234 commercial process 541 cholesterol ester transfer protein 357 commercial structural genomics 275 Christian point of view 566 commercialization 537 chromatin immunoprecipitation 241 – of biobank resources 541–543 chromatin remodeling 92 – of research 531 Subject Index 591

– of biomaterials 543 COX-1 374 common heritage concept, genetic material 527 CpG islands 115 common heritage of humanity, genetic material CPGISLE database 313 526 cpgplot 313 common heritage resource 549 CPL 465 community consent 512 CPN 478 comparative genome research 365–366, 584 crenarchaeota 46 comparative mapping 115 – mesophilic 53 comparison, DNA microarrays 245 criminal investigations 541 COMPEL 444 CRITICA 18 complementation 72 critical micelle concentration, capillary complementation test 118 electrophoresis 217 complete genome sequences 3 crop improvement 63 – sequence gaps 17 cryogenic data collection 274 – shotgun approach 8 cryogenically cooled probes, high-resolution – whole-genome random sequencing 17 solution NMR 285 complex dynamic networks 462 crystallization conditions 278 Compugen 363 crystallography, protein 273–274 compund toxicity 369–372 CSNDB 444, 462 Computer World Magazine 359 cSNP 88 confidence values, DNA sequencing 157 CTR1 gene 111 confidentiality, Biobanks 553 cultivation techniques 46 confocal scanning devices, DNA microarrays 235 cultured cell lines 186 connexin gene 37, 96 Curagen Pathcalling 444 consensus methods, Bioinformatics 309 cures for genetic diseases 541 consent 517 currency of the biotech industry 544 – for new collections 521 cuvette detector 219 – forms 530 CYANA 287 consequences of genetic activities 563 cyanobacteria 28, 50 conserved gene orders, positional mapping 116 Cyber-T-package 424 Consortium on Pharmacogenetics 519 cycle-sequencing, DNA sequencing 142 contact printing 234 cyclooxygenase isozyme COX-3 374 – DNA microarrays 224 cyclotron mass spectrometer 332 contaminating proteins, Proteomics 330 CYP see cytochrome P450 isoenzymes contigs 48, 62 CYP genes, regulation of the expression 371 continuous infusion mode 198 CYP2C9 371 controlled humidity cabinets, DNA microarrays CYP2C9*3 mutations 374 243 CYP2D6 371 Convention on Biological Diversity 549 CYP3A4 371 coordination office 582 cystic fibrosis 86 COPE 444 cytochrome P450 isoenzymes 371 CORBA 442 Cytophagales 51 corn, model organisms 64 Cytoscape 428, 440 Corona virus, model organisms 354 correlation analysis 323 D correlation spectroscopy, 2D 288 Darwinian selection, human genome 83 cosmid libraries, Saccharomyces cerevisiae 21 data collection system 573 cosmid vector 54 data fusion 462 Coulombic forces 223 data integration 483 Council for International Organizations of Data normalization 252 Medical Sciences 511–512, 518–519 data-protection safeguards, biobanks 553 Council of Europe 521 Data Protection Working Party 514 Council of Regional Networks for Genetic data reduction, intelligent, DNA sequencing 153 Services 523 data warehouse 465 592 Subject Index

database alignment algorithms, Bioinformatics disorders, mental 512 333 dispersion, anomalous 274 database extension 470 dissociation, collisionally induced 192 database scheme 470 Distributed computational infrastructure 578 databases DMSO, DNA microarrays 234 – Bioinformatics 353–362 DNA – genome research 577 – arrays 54 dbEST 118 – banking 509, 516 Dbsolve 479, 482 – based diagnosis 86 DDBJ 462 – based patents 545 dead-on-arrival fluorophores, DNA sequencing – breaks, double-strand 92 160 – comparison matrix, Bioinformatics 301 deceased individuals 512 – Data Bank of Japan 354 Declaration on Genetic Data 515 – degradation strategy, single molecule detection deCODE Genetics 543 161–162 deconvolution, DNA sequencing 156 – double helix, bending 312 Decypher TimeLogic 384 – high-molecular-weight, purifying 51 degradation strategy 161–162 – horizontal transfer 321 Deinococcus radiodurans, model organisms 17, – hybridization strategy, single molecule 220 detection 163–164 Delbrück, M. 6 – re-sequencing, human genome 90 deletion method, nested, DNA sequencing 139 – replication machinery, basic, Drosophila Delta2D 324 melanogaster 36 Denhardt’s regent 249 – sciences 542 density lipoprotein receptor 366 – seperation technology 574 deoxyviolacein 53 – sequence analysis 153–158 Design/CPN, Petri net tools 478 – sequencers 575 Desulfotalea psychrophilia, model organisms 19 DNA microarrays 223, 261 detection limits, capillary electrophoresis 218 – amplicon 229 deuteration, high-resolution solution NMR 284 – amplicon generation 232–234 dextran, capillary electrophoresis 216 – application 239–260 dextrometorphan 357 – array content 242 diabetes 87 – array printing methodology 241 diagnostics, pre-implantation 567 – array scanners 250 dideoxy method, DNA sequencing 130 – arrayers 243 differential equations 482 – background 247, 249 differentially expressed proteins 186 – CCD cameras 235 diffuse large B-cell lymphoma 245, 255 – cloned DNA 224 DIGE, multicolored multiplexed 324 – Code Link surface 242 digestion, reactor-based, Proteomics 198 – commercial array industry 242 dihedral angle restraints 286 – confocal scanning devices 235 DIP 338, 440, 444 – contact printing 224 direct cDNA selection 115 – controlled humidity cabinets 243 direct labeling procedure, DNA microarrays 247 – data analysis 251 disabled 512 – data aquisition 250–251 Discovery Link 465 – data extraction 251 discovery research 223 – data handling 228 Discovery Studio Gene 344 – database 228–230 discrete-event approach 473 – definition 240 discrete models 472 – design of the oligonucleotides 242 discrimination 513 – direct comparison 245 disease-oriented target identification, – direct labeling procedure 247 Bioinformatics 364 – DMSO 234 disease-related proteins 182 – documentation 254 Subject Index 593

– dye bias 244 – acrylamide gel 131 – experimental design 244–246 – adaptive automation 153 – fabrication 224 – AmpliTaq 142 – fabrication strategy 223–238 – applications 138–140 – flagging of amibigious spots 252 – automated 131 – fluorescent tags 244 – automated sequencers 138 –forward primers 229 – automation 130 – genome-wide arrays 240 – background level 143 – glass microscope slides 224 – band tilt 155 – high variability within expression values 253 – base calling 155–156 – hybridization 235, 244 – biochemistry 138–144 – hybridization kinetics 250 – by hybridization 152 – hybridization step 249 – capillary gels 146, 151 – indirect comparison 245 – cDNA see cDNA sequences – indirect labeling method 248 – chain-terminating nucleotide 130 – ink-jet spotting 224 – chemical cleavage 130 – inkjet technology 241 – cloning vectors 141 – instrumentation 228 – compressions 143 – labeling 247 – confidence values 157 – long oligonucleotide 250 – Cy5 133 – main application 224 – Cy5.5 133 – melting temperature 249 – cycle-sequencing 142 – microarraying robots 234 – daily production 159 – mismatched hybrids 250 – de novo sequencing 138 – mispairing of bases 249 – dead-on-arrival fluorophores 160 – multi-color fluorescent labels 235 – deconvolution 156 – obtaining pure intact RNA 246 – detectors 146 – oligonucleotide arrays 229 – dideoxy method 130 – PCR failures 230 – double-stranded DNA template 140–141 – photolithography 223, 241 – dR110 133 – post-synthesis arraying 224 – dR6G 133 –pre-made arrays 243 – dROX 133 – probe 240 – dTAMRA 133 – probing 234 – dye-labeled primer sequencing 142 – production 241–243 – dye-labeled terminator sequencing 142 – quantitation software 235 – electroosmotic pumping 151 – reagent costs 231 – energy transfer 138 – reverse primers 230 – excitation energy sources 144 – sample preparation 246 – FAM 133 – scanning 234 – fluorescein dye 133 –slide substrates 242–243 – fluorescence detection 145 – spatially ordered synthesis 223 – fluorescence dye chemistry 131–138 – specifity 242 – fluorescence lifetime 137–138 – spot saturation 251 – fluorescence lifetime discrimination 138 – spotting concentration 230 – fluorescence samples 145 – spotting pins 243 – fluorescent detection 131 – target 240 – fluorophore blinking 160 – TIFF images 250 – fluorophore characteristics 132 – unmodified or amino-modified oligonucleotide – forms of electrophoresis 149 sequences 228 – four dye/one-lane approach 138 – user of the technology 244 – four-color discrimination 136 – variation 244 – gel matrix 146 DNA sequencing 574 – Heisenberg’s Uncertainity Principle 160 – Abbe’s Diffraction Limit 160 – identification of the individual bases 156 594 Subject Index

– information independence 148 – Stokes Shift 132 – information per channel 147–148 – strategies 138–140 – information througput 147–148 – TAMRA 133 – instrument design 148–149 – Taq DNA polymerase 142 – instrumentation 144–153 – template 143 – intelligent data reduction 153 – template preparation 140–141 – internal labeling 142 – template-primer-polymerase complex 143 – IRDye40 132 – tethered donor and aceptor dye 137 – IRDye41 132 – thermal diffusion 160 – IRDye700 133 – Thermo Sequenase 142 – IRDye800 132 – time per sample 148 – JOE 133 – trace generation 155–156 – labeled terminators 137 – tracking 153 – labeling strategy 142–143 – transposon insertion 139 – lane detection 153 – universal sequencing primer 140 – lane trace profiles 155 – whole-genome shotgun assembly 139 – lane tracker 154 DNA sequencing technology 129 – large insert clones 141 DNA synthesis, high-throughput 230–232, 575 – microfluidic channel gels 146 DNA synthesis strategy, single molecule detection – micro-grooved channel gel electrophoresis 151 162–163 – mobility correction 156 DNA template – modified nucleoside triphosphates 130 – DNA sequencing 143 – multiplex DNA sequencing 147 – double-stranded, DNA sequencing 140–141 – nanopore filtering 161 – preparation, DNA sequencing 140–141 – nested deletion method 139 – single stranded, DNA sequencing 140 – non-electrophoresis methods 152 DNase 247 – non-fluorescence methods 152–156 – activity 246 – oligonucleotide primer 143 DNAstar 344 – one-dye/four-lane approach 138 Dolly 561 – PCR products 141 domain identification, Bioinformatics 341 – PCR purification kit 141 domains, SH33 433 – photobleaching 160 dopamine D3 receptor 375 – PHRED values 158 dot plots, Bioinformatics 300 – plasmid purification kit 141 dot-tup 306 – plus/minus method 129 dotmatcher 300 – polymerases 141–142 double-coded, DNA banking 517 – potential gradient 146 double recombinants 109 – primer walking 139 double-strand DNA breaks 92 – quality predictor 157 double-stranded DNA template, DNA sequencing – R110 133 140–141 – R6G 133 doubled haploids 106 – random shotgun sequencing 139 Down’s syndrome 564 – removal bases 152 DPG see Drosophila Genome Project – resequencing 138, 140 DPInteract 445 – ROX 133 Draft Guidellines on Bioethics 515 – sample channels 147 DRC 445 – Sequenase v2.0 141 Drosophila melanogaster 4 – simultaneous bi-directional sequencing 144 – basic DNA replication machinery 36 – single stranded DNA template 140 – gene regulation 36 – single-base extension 152 – genetic analysis 37 – single-molecule detector 160 – Genome Project 35 – slab gels 146, 149–151 – genomic organization 35 – spectral wavelength of fuorescent emission – genomic resources 36 132 – heterochromatin 35 Subject Index 595

– HOX genes 35 – capillary sieving 215 –model organisms 29, 34, 37, 262, 354, 446 – DNA sequencing 149 – mutant phenotypes 34 – free solution 217 – number of genes 36 – gel 187 – protein-protein interaction studies 37 – gel, DNA sequencing 151 – sequencing 35 – two-phase 51 – transcription factors 36 electrophoretic karyotypes, Saccharomyces – transferrins 36 cerevisiae 21 drug design, structure based 289 electrospray ionization 68, 214 drug effects, adverse 366, 368 – mass spectrometry 189 drug efficacy 373 Embden-Meyerhof-Parnas pathway genes 13 drug life-cycle management 376 EMBL 397, 462 drug resistance 372 – see also European Molecular Biology drug target 368 Laboratory drug-target discovery 372 EMBL Data Library 354 DS Gene 344 EMBOSS 299 DTD 478 embryo, planed 562 dual-labeled, microarrays 417 embryo research 512 dust 309 embryonic stem cells 565 duty to warn 525 EMP 445 dye bias, DNA microarrays 244 EMSY 92 DynaFit 480 endosymbiont hypothesis 61 dynamic light scattering 278 ENSEMBL 355, 361 dynamic models – database 240 – mathematical formalism 499 EnsMArt 361 – systems biology 499 Entrez 345, 398, 465, 578 dynamic Petri nets 473 environmental genomics 45–57, 584 dynamic programming 323 environmental surveys 46 dynamic representation 481–481 enzymatic processing, Proteomics 197 ENZYME 446, 476 E Enzyme Comission 398 E-cadherin 256 enzymes 461 E-Cell 480, 482 – metabolic 433 E. coli see Escherichia coli – production, Bacillus subtilis 15 EASED 356 – with novel properties 53 EBarrays 425 EPD 462 Eberwine method 235 epidemology studies 510 EC see Enzyme Comission EPO Opposition Division 547 EcoCyc 10, 440, 445 eQTL 121 EcoCyc/MetaCyc 464 equicktandem 310 EcoCYG 359 Escherich, T. 5 ecosystem 49 Escherichia coli, model organisms 3, 284, 307, – marine 48 448, 476, 492 Edman degradation 332 – K12 6, 359, 407–408 effective number of codons statistics 320 – minimum set of genes 10 EIN2 gene 111 – nontoxic strains 9 einverted 310 – O157 7 electrokinetic injection, capillary electrophoresis – physical genetic map 7 212 – restriction map 7 electroosmosis, capillary electrophoresis – systematic sequencing 7 212–213, 215 – toxic strains 9 electroosmotic pumping, DNA sequencing 151 ESHG 515, 520 electrophoresis 213 ESI see electrospray ionization – capillary 183, 211–222, 328 EST, plants see expressed sequence tag 596 Subject Index

EST databases 329 extensible markup language 405 est2genome 304, 306 – see also XML Estonia 524 extreme thermophiles 49 – biobanks 538 etandem 310 F eternal life 562 F plasmid 114 ethical aspects, genome research 509 F2 population 106 ethical fallout, biobanks 540 factor V Leiden 95 ethical framework , tissue or genetic research factories, large scale 582 511 faktor X 278 ethical guidelines 510 false positives, microarrays 423 ethical issues 544 familial adenomatous polyposis 93 ethical norms 509 familial arrhythmias 96 ethical obligation of international collaboration familial dilated cardiomyopathy 96 518 FAP see familial adenomatous polyposis ethical principles, general 510 FASTA 333, 384 Ethics and Governance Framework 528 federated database systems 437, 465 ethics committee 510, 520 fenfluramines 376 ethics review 524 fermentation, foodsupply, Bacillus subtilis 15 ETR gene 111 fetuses 512 EU biotechnology programs 21 filtering strategy, nanopore 164 eubacterium 4 FIMM 446 eukaryotic genomes, counterparts, plants 63 First Genetic Trust 542 eukaryotic organisms, evolution 38 Fisher volume ratio 341 European Parliament 547 Fisher’s LSD adjustments 423 EUROFAN 25 FK506 binding protein 265 eurokariotic genomes, Bluejay 411 flagging of amibigious spots, DNA microarrays European Bioinformatics Institute 321 252 European Convention on Biomedicine and flap endonucleases 20 Human Rights 512 Flicker 326 European DGP 35 flow cytometry 581 European Directive 527 fluorescein dye, DNA sequencing 133 European Directive on the Legal Protection of fluorescence detection, capillary electrophoresis Biotechnological Inventions 514 214 European Molecular Biology Laboratory 64 fluorescence dye chemistry, DNA sequencing – see also EMBL 131 European Patent Convention 514 fluorescence energy transfer, single molecule European Patent Office 546 detection 163 European Society of Human Genetics 520 fluorescent biochemistries 573 European yeast genome project 580 fluorescent labels, multi-color 235 European Convention on Human Rights and fluorescent tags, DNA microarrays 244 Biomedicine 520 fluorogenetic reagents, capillary electrophoresis exception for professional disclosure 515 214 exon trapping 115 fluorophore blinking, DNA sequencing 160 ExPASy 386 fluorophore characteristics, DNA sequencing experimental design 132 – DNA microarrays 244 fly, model organisms 492 – microarrays 417–419 FlyNets 446 expressed sequence tag 64 flyview 36 expression, cell-free 284 fold-space 283 expression levels 500 – protein 273 expression profiles 418 Food and Drug Administration 511 expression systems 277 foreign DNA, Campbell-like integration 12 – insect cells 277 formamide 249 Subject Index 597 forseeable uses, biological samples 553 – 2D 187 forward genetics, plants 72 – DNA sequencing 151 forward primers, DNA microarrays 229 Gellab II+ 324 founder effect 87 gels four-color discrimination, DNA sequencing 136 – DNA sequencing 146 Fourier-transform cyclotron mass spectrometer – Proteomics 324, 326 332 GelScape 326 fractionation procedures, Proteomics 186 Genaissance Pharmaceuticals 542 frameshift mutation 11 GenBank 332, 354, 397, 462 Frankenfoods 583 – XML 412 free solution electrophoresis, capillary gene classes, Bacillus subtilis 13 electrophoresis 217–218 gene clusters, polyketide synthase 54 Freedom of Research 565 gene deletions, genome-wide 261 French Conseil Consultatif National d’Éthique gene density, Archaeoglobus fulgidus 19 pour les Sciences de la Vie et de la Santé 529 gene duplication 11 French Hospital Federation 547 – Saccharomyces cerevisiae 24 French Ministries of Public Health an Research Gene Expresseion Database 358 547 gene expression 415 French National Consultative Ethics Committee – body map 369 523 – plants 64, 66 French National Consultative Ethics Committee gene families for Health and Life Sciences 525 – Bacillus subtilis 11 frequency doubled solid-state – paralogous, Archaeoglobus fulgidus 19 neodymium:yttrium-aluminum-garnet laser gene knockout, tandem 434 144 Gene Logic 369 FT-ICR 198 Gene Ontology 361, 428, 481 full-length cDNA sequences 353 Gene Ontology Consortium 254 functional assignment 580 Gene Ontology database 336 functional genomics gene orders, conserved, positional mapping 116 – Bacillus subtilis 13 gene orthologs 366 – consortium 13 gene prediction, Caenorhabditis elegans 32 – plants 72 gene profiling 417 future, life science research 573–584 gene regulation 461 fuzznuc 315 – Drosophila melanogaster 36 fuzzy analyzer 482 gene regulatory networs 499 gene silencing, virus-induced 76 G gene therapy 87 G-protein coupled receptors 362 gene therapy research 510 G-protein fusion system 266–267 gene transfers, horizontal 49 GA1 gene 111 gene variation 373 GAI gene 111 GeneChip 120 gain-of-function 90 – Affymetrix 9 Gal4p 262 – microarrays 9 b-galactosidase complementation assay 269 GeneMark 118, 384 gamete 564 GeneNet 446, 462 gas chromatography 70 general ethical principles 510 gas phase, mass spectrometry 189 genes 111 GC see gas chromatography – catalase 11 GC content – cloning 277 – Caenorhabditis elegans 33 – human 433 – periodicity, Saccharomyces cerevisiae 24 – minimum set 10 GCC Wisconsin package 344 – multifunctional 8 GD.pm 385 – sh2-al 116 gel electrophoresis – stress-induced, plants 66 598 Subject Index

genes controlling flowering time 117 – Brassica 27 genes of completely unknown function, Bacillus – Caenorhabditis elegans 31 subtilis 16 – human see human GeneScan 118, 384 genome research 573 GeneSmith 18 – comparative 584 GeNet 447 – ethical aspects 509 genethics 513–516 genome research-related hardware 575 Genethon 115 genome sequences, complete 3 genetic activities, consequences 563 Genome Sequencing Center 580 genetic algorithm 370 genome size, Archaeoglobus fulgidus 17 genetic analysis, Drosophila melanogaster 37 genome structure, mosaic 50 genetic basis of human health and disease 540 genome synteny study 366 genetic discrimination and stigmazation 538 genome-wide arrays, DNA microarrays 240 genetic diseases, cures 541 genome-wide gene deletions 261 genetic heterogeneity 86 genomic microheterogeneity 48 genetic information 540 genomic resources, Drosophila melanogaster 36 – implications for family members 541 Genomics –misuse 551 – comparative 365–366 – predictive quality 541 – environmental 584 genetic initiatives, large scale population 552 Genomics Collaborative 542 genetic linkage map 61 GEO 420 genetic map Gepasi 479 – comprehensive, Arabidopsis thaliana 26 germ-line interventions 513 – Saccharomyces cerevisiae 21 German Catholic Conference of Bishops 561 genetic map unit 61 German Hygiene Museum 568 genetic mapping 120–122 German National Ethics Advisory Board 561 genetic material, special status 526 German National Ethics Council 516 genetic predisposition 357 German Nationaler Ethikrat 529 Genetic Privacy Act 530 German Research Foundation 529 genetic redundancy, internal, Saccharomyces German Senate Commission on Genetic cerevisiae 24 Research 523 genetic research 509, 540 GFT-NMR 285 – ethical framework 511 gift relationship, genetic material 527 – participation 550 Gilbert 129 genetic risk factors 509 GLIM 110 genetic screening 365–366 Glimmer 118, 384 genetic technologies, acceptable use 541 global public good, genetic resources 549 genetic testing, human genome 86 glucose, plants 67 genetically directed representational difference glycosylation 182 analysis 112 Gmendel 110 genetically modified foods 71 GNU Public License 439 GeneTrust 543 GO see Gene Ontology database GENIE 36 GO annotations 336 genome – biological processes 337 – $1000 159–164 – cellular component 337 – Bacillus subtilis 11 – molecular function 337 – partly-recovered 54 gobalization 511 genome annotation, plants 63 God 564 Genome Browser 355 Golub’s weighted voting method 425 genome characterization, Archaeoglobus fulgidus GoMiner 428 18 GON Cell Illustrator, Petri net tools 478 genome features, Bioinformatics 384 governance of biobanks 551 genome-mapping approaches 105 government funding 542 genome project GPCR 373 Subject Index 599 graph abstraction 434–435 HGP 537 – edges 435 HGVbase 357 – nodes 435 hidden Markov models 323, 336 graph-clustering methods 498 – Bioinformatics 305, 334 graph description, chemical 436 hierarchical biochemical systems 482 graph theoretical approach 473 hierarchical clustering 252, 426 graphical user interface 344 high-density DNA arrays 575 graphs 462, 496–498 high-level protein expression 284 – metabolic networks 463 high-molecular-weight DNA, purifying 51 GRAS 15 high-molecular-weight proteins, capillary gray holes 8 electrophoresis 215 green revolution genes 117 high performance computing 577 Gribskov statistic 319 high-performance liquid chromatography 220 GRID 447, 578 high-resolution maps, plants 62 group consent, biobanks 538 high resolution NMR 273 growth factor 94 high-resolution solution NMR 282 GSRMA 422 – cryogenically cooled probes 285 – deuteration 284 H – hardware 285 1H-1H inter-nuclear distance 286 – labeling 284 Hac1p 269 – micro-probes 285 Haemophilus influenzae, model organisms 17 – relaxation decay 284 Haldane’s mapping method 109 – signal-to-noise ratio 285 halophilic archaea 49 – size barrier 283 hanging-drop vapor diffusion 278 – soluble parts of proteins 284 haplotype 89 – super-high-field instruments 285 – analysis 120 – target selection 282–283 – map see human genome high-throughput DNA synthesis 230–232 HAPMap consortium 509 – hardware 575 hapmap project 89–90 – operational constraints 231 hardware, genome research-related 575 – quality-control 232 Harmonization 511 – scale and cost of synthesis 230–231 harmonized ethical frameworks 511 – synthesizers 231 Harvard mouse 548 high-throughput facilities 361 hash tables 399 high-volume tissue banking efforts 542 hay bacterium 10 Hinxton Genome Campus 299 health card 97 Hippocrates 537 health emergencies 519 histidine kinases 20 Health Sector Database, Icelandic 553 HIV Molecular Immunilogy Database 447 Heisenberg’s Uncertainity Principle, DNA HIV/AIDS 512 sequencing 160 HLAB*5701 polymorphism 376 Heliobacter pylori, model organisms 17, 262, 451, HMMER 363 492 HMMTOP 340 helium-neon laser 144 HNPCC see hereditary non-polyposis colorectal Helsinki Declaration 512 cancer hemiascomycete yeast genomes 25 holes, gray 8 hempchromatosis 86 homeostatic 494 hereditary non polyposis colon cancer 86, 93 HomoloGene 120 hereditary sensory and autonomic neuropathy homologs 85 – MutL 12 hERG gene, expression pattern 370 – MutS 12 heritability 83 horizontal gene transfers 49 heterochromatin, Drosophila melanogaster 35 horizontal transfer of DNA 321 heuristic scoring schemes 331 Howard Hughes Medical Institute 118 600 Subject Index

HOX genes, Drosophila melanogaster 35 human neurofibromatosis type 1 gene 117 HOX Pro 447 human reproduction cloning 513 HPLC 232 Human Research Ethics Committee 522 HPRD 440, 447 human rights 513 HREC 522 Human Transcriptome Project 358 Hs1/pro-1 gene 111 Humboldt University 565 HSN2 85 humic substances 46 HTML 385, 438 Huntington disease 84 HTML interface 466 hybrid Petri nets 474 hubs 498 hybridization HUGO 538 – DNA microarrays 235 – Ethics Committee 550 – DNA sequencing 152 – Statement on DNA Sampling: Control and – kinetics, DNA microarrays 250 Access 515 – strategy 163–164 human, perfect 563 hydrodynamic injection, capillary electrophoresis human biological material, ownership 538 212 human body, undesirable commodification 542 hydrogen-bond distance restraints 286 human cancercell lines 373 hypercolesterolemia 95 human clone 562 hyperekplexia 114 human dignity 513, 563 hypertension 95 human disease networks 35 hyperthermophilic organism 19 human diseases 357 hypertrophic cardiomyopathy 95 human genes 433 hypothesis driven research 223 – homologs, Saccharomyces cerevisiae 25 human genetic databases 519 I Human Genetics Commission 543 I2 gene 110 human genome 538 Icarus language 465 – allelic heterogeneity 87 ICAT experiments 211 – altered proteine structure 88 ICBS 448 – carrier screening 86 Iceland, biobanks 538 – Darwinian selection 83 Icelandic Action Biobanks 522 – DNA re-sequencing 90 Icelandic Health Sector Database 553 – genetic testing 86 Iconix Pharmaceutals 369 – haplotype map 90 IFF ultra-zoom gels 324 – inherited diseases 84 IMAGE Consortium 355 – linkage disequilibrium 89 ImageMAster 2D 324 – locus heterogeneity 86 imaging mass spectrometry 187 – multifactorial diseases 87 imaging technologies 581 – mutations 82 immediate property rights, genetic material 528 – non-coding RNA 82 in-gel digestion procedure 196 – polygenic diseases 87 in silicio biology 579 – polymorphisms 88 in-vitro expression 277 –protection 528 InBase 447 – protein coding genes 81 INCLUSive 429 – reference sequence 81 Incyte 454 – risk assessment 86 Indigo 448 – spontaneous mutations 91 indirect labeling method, DNA microarrays 248 – tissue-specific cDNA libraries 84 individual bases, identification, DNA sequencing – variant sites 88 156 Human Genome Mapping Project 321 individualized medicine 510 Human Genome Organization 513 informal consent, blanket 519 Human Genome Project 81, 339, 509, 537 Informax 345 Human Genome Sciences 580 infrared laser semiconductor diodes 144 human heliotype mapping project 357 infusion mode, continuous, mass spectrometry Subject Index 601

198 ISYS 465 inherited diseases, human genome 84 iUDB 469 injection, capillary electrophoresis 212 IUPAC single letter code 436 ink-jet devices 234 ink-jet spotting, DNA microarrays 224 J inkjet technology, DNA microarrays 241 Japanese Bioethics Committee of the Council for insect cells, expression systems 277 Science and Technology 523 insertional mutagenesis 73 Jarnac 479 Institut Curie 546 Java 3D 578 Institute for Systems Biology 361 Java applet 439 Institute Gustave Roussy 546 Java application 465 insulin like growth factor II receptor 94 JAVA-based Apache software 406 IntAct 338, 440, 448 Java programming language 576 intact proteins, analysis 203 JDBC 465 intact RNA, DNA microarrays 246 JDesigner 479 integrated handheld devices 581 Jemboss 321 integrative metabolism system 462 JenPep 448 intellectual property, genetic resources 544–551 JOIN operations 467 inter-gel comparison, Proteomics 326 Jurkat cells 255 Interact 448 interaction, protein-protein 496 k interaction database 433–434, 440 k-means clustering 426 interaction information K-nearest neighbors 370 – abstraction 435–437 k-tuples, Bioinformatics 305 – specific affinity 434 karyotypes, electrophoretic, Saccharomyces interaction networks 433 cerevisiae 21 interaction screening 262 KCNE1 371 intergenic regions, Saccharomyces cerevisiae 23 KCNE2 371 Interleukin 4 366 KCNQ1 see KQT-like voltage-gated potassium International Bioethics Committee 515 channel-1 international collaboration, etical obligation 518 KDD 472 international declaration on human cloning 515 KEGG 338, 359, 449, 462 International Declaration on Human Genetic kinases 363, 367 Data 518 – phylogenetic classification 367 international stewardship, genetic material 526 Kluyveromyces, model organisms 25 interologs 339 knockout 73 InterPro 336 knockout experiments 496 introns 375 knowledge-based simulation 462 – Saccharomyces cerevisiae 23 Kohn Molecular Interaction Maps 449 inducements to participate in genetic research Kosambi’s mapping method 109 550 KQT-like voltage-gated potassium channel-1 371 ion-channel proteins 373 Kyoto Institute of Chemical Research 338 ion trap, mass spectrometry 193 ion-trapping, mass spectrometry 191 L ionisation, mass spectrometry 188 L-tyrosine ammonia-lyase 471 IRDye, DNA sequencing 132 lab-on-a-chip technology 246 Ire1 signaling system 268–269 labeling, DNA microarrays 247–248 iron dependend repressor proteins 20 labeling chemistry, capillary iron metabolism, Bacillus subtilis 15 electrophoresis 214 IS elements, Archaeoglobus fulgidus 18 labeling strategy, DNA sequencing 142–143 isoelectric focusing, capillary electrophoresis 215 laboratory organization 581 isoelectric point, Archaeoglobus fulgidus 19 lane detection, DNA sequencing 153 isoenzymes 371 lane trace profiles, DNA sequencing 155 Israel 529 lane tracker, DNA sequencing 154 602 Subject Index

large B-cell lymphoma, diffuse 245 localized ungapped alignments, Bioinformatics large-scale computational analysis 493 305 large-scale data production 492 LOCkey 339 large-scale database 491 locus heterogeneity, human genome 86 large-scale factories 582 LocusLink 357 large-scale interaction maps 262 log ratio, regreession 422 large-scale population genetic initiatives 552 long coding repeats, Archaeoglobus fulgidus 18 laser 144 long oligonucleotide, DNA microarrays 250 laser-capture microdissection 67, 185 long-patch mismatch repair system 12 laser technology 573 long QT syndrome 96 LaserGene 334, 344 long-term viability of biobank initiatives 551 LC columns, mass spectrometry 200 Longitudinal Study on Aging 538 LC-MS 232 loss-of-function 90 LCDR/MerMade 231 loss-of-interaction mutants 264 LCM see laser-capture microdissection LOWESS 252, 422 LDA 425 lung cancer 91 LDL receptor gene 95 Lutefisk 195 LDLR gene 95 lymphoblastic leukemia, acute 255 left-over samples 518 legal trusts 543 M leptin 343 M. jannaschii see Methanococcus jannaschii leukemia M. thermoautotrophicum see Methanobacterium – lymphoblastic 255 thermoautotrophicum – myeloid 255 MacVector 344 – promyelocytic 373 MAD phasing 274, 281 leukemia-like disease 87 – cryogenic data collection 281 LexAp 262 – software packages 281 licensing fees 545 MADBOX gene 111 LiCor 4200 Global system 576 MAExplorer 420 lifetime discrimination, fluorescence, DNA MAGE-ML 419 sequencing 138 MAGE-OM 420 Limma 425 MAGPIE 228, 383, 578 LIMS 420 – agarose gel simulation 403 linear amplification method 247 – analysis tools summary 396–367 linear discriminant analysis 370 – Assembly Coverage 399, 402 linkage disequilibrium mapping 120 – Base Composition 399 linkage map – coding region displays 391–395 – algorithm 110 – contiguous sequence 394 – construction 108 – expanded tool summary 397–399 – distance between markers 108 – expressed sequence tags 394–395 – DNA markers 108 – function evidence 396–399 – map construction 109 – inter-ORF regions 392 – map distance 109 –manual annotation 387 – single-locus analysis 108 – marker mobility data 404 – three-locus analysis 109 – ORF close-up 395 – two-locus analysis 109 – ORF coloration 392 linkage segments, rice 116 – ORF evidence 391–394 lipoprotein receptor 366 – ORF traits 393 5-Lipoxygenase 373 – overlapping contigs 390 liquid chromatography, mass spectrometry 189 – poorly covered regions 402 liquid handling robots 279 – potential overlaps 394 Listeria monocytogenes, model organisms 12 – purine composition 400 liver, metabolism 371 – rare codons 396 local sequence similarity, Bioinformatics 332 – repeats 400–401 Subject Index 603

– restriction enzyme cuts 402 – MALDI-TOF 189 – sequence ambiguities 401 – monolithic columns 200 – similarity display 398 – MS-MS analyses 198 – states 387 – MS-tag 195 – stop codons 393 – multidimensional LC-MC-MS 201–204 – vector sequence 404 – peak suppression 196 – whole project view 387 – peptide analysis 191 maize, model organisms 28 – protein-degradation methods 191 malaria parasites, model organisms 476 – Proteomics 328 MALDI 580 – quadrupole instruments 189 – see also matrix assisted laser-desorption – quad-TOF instruments 199 ionization – revised tandem affinity purification procedure MALDI-TOF 152 202 – mass spectrometry 189 – sample introduction methods 188 MALDI-TOF MS 68 – sample processing 190–191 Mammalian Gene Collection 355 – small-bore reverded phase LC columns 200 map expansion 107 – tandem in space 191 map unit, genetic 61 –tandem in time 191 Mapmaker 110 – tandem MS data sets 194 marine ecosystems 48 – time of flight 189 marine plankton 48 – TOF 189 marker genes 47 – TOF-TOF-instruments 199 – taxonomic 53 – triple quadrupole 191 market exclusivity, genetic resources 544 – ultra-long chromatographic gradients 200 Markov model, hidden 305, 323, 336 mass spectroscopy 262 markup language, Petri nets 478 mathematical modelers 492 Martinsried Institute of Protein Sequences 22 MatLab 482 Mascot 331 matrix assisted laser-desorption ionization 68 Mascot database searching tools 193 mats, microbial 50 mass action law 475 Max Plank Institute in Cologne 566 mass fingerprinting, Proteomics 329 Maxam 129 mass spectrometer, cyclotron 332 MBEI 422 mass spectrometric analysis 211 MCA methodology 482 mass spectrometry 181–209 MDB 449 – anion-exchange prefractionation 202 MDR see multidrug-resistance proteins – Bioinformatics 193–195 MDR1 gene 117 – capillary electrophoresis 214 Medicago trunculata, model organisms 64 – chemical noise 199 medical genetics 538 – coeluting peptides 200 Medical Research Council Operationsl and Ethical – collisionally induced dissociation 192 Guidelines on Human Tissue and Biological – continuous infusion mode 198 Samples for Research 529 – databases 194 medicine, individualized 510 – electrospray ionization 189 – see also pharmacogenomics – fully automated systems 201 Medline 578 – gas phase 189 MEGABLAST 401 – instrumentation 191–193 Melanie 4 324 – ion trap 193 melting temperature, DNA microarrays 249 – ion trapping 191 membrane proteins 282 – ionisation 188 membrane yeast two-hybrid systems 265–269 – LC-MS-MS 199–200 Meme 344 – liquid chromatography 189 Mendelain patterns 509 – lower-intensity peptide ions 199 Mendelian diseases 84 – m/z values 191 mental disorders 512 – MALDI 188 merging algorithm 251 604 Subject Index

mesophilic crenarchaeota 53 – clustering algorithms 426–428 metabolic data integration 481–481 – data management 420 metabolic enzymes 433 – design phase 419 metabolic fingerprinting, plants 70 – differently expressed genes 423 metabolic networks 461 – dual-labeled 417 – graphs 463 – experimental design 417–419 metabolic pathway 354, 461–490, 499 – false positives 423 – conceptual model 469 – feature selection 425 – database 463 – gene level summaries 422 – database integration 465–472 – general analysis 420–421 – database systems 463–465 – image quality 421–422 – direct reaction graph 463 – noise 425 – editor 481 – normalization 422–423 – online maps 463 – oligonucleotide group 417 – secondary, plants 64 – pin group 416 metabolism in the liver 371 – preprocessing 421 metabolism pathways 360 – robust mulitchip average 422 metabolite fluxes 484 – scaling 423 metabolite profiling, plants 70 – searching for meaning 428–429 metabolomics 291 – significant analysis 424 –plants 70 – single-labeled 417 Metabometrix 360 – spatial bias 422 metabonomics 291, 360 – standards 419–420 MetaCyc 445 – validation of clusters 427 MetaCYG 359 – within-class variation 423 metagenomic 45 microbial communities 46 metagenomic libraries 48 Microbial Genome Program 17 metazoan development 34 microbial mats 50 Methanobacterium thermoautotrophicum, model microdissection, laser-capture 185 organisms 16–17 microfluidic channel gels, Methanococcus jannaschii, model organisms DNA sequencing 146 16–17 microheterogeneity, genomic 48 MGD see Mouse Genome Database microorganisms, uncultivated 48 MGED 254, 419 microRNA 37 MHCPEP 449 microsatellite instability pathway 94 MIAME 254, 419, 576 microscale chromatography 183 mice, model organisms 581 microscopy equipment 576 micellar separation, capillary electrophoresis 217 Ministries of Health in Canada 546 micelle concentration, critical 217 MINT 338, 440, 450 Michaelis-Menten equation 476 MIPS see Martinsried Institute of Protein micro batch under oil 278 Sequences micro dialysis 278 MIPS Comprehensive Yeast Genome Database Microarray Gene Expression Data Society 254 450 microarray sample pool 252 mismatch repair genes 94 MicroArray Suite 421 mismatch repair system, long-patch 12 microarray technologies 416–417 mismatched hybrids, DNA microarrays 250 microarraying robots, DNA microarrays 234 mispairing of bases, DNA microarrays 249 microarrays 415 mitochondrial chromosome 61 – apot quality 421 mitochondrial genome 61 – array-level quality 421 mitochondrion 60 – cDNA 416–417 MLH1 94 – class comparison 423–425 mmCIF 436 – class discovery 418 MMDB 450 – class prediction 418, 425–426 MMR see mismatch repair genes Subject Index 605

MMR function 94 – rice 60, 122 mobility correction, DNA sequencing 156 – Saccharomyces cerevisiae 20, 37, 201, 261–262, MOBY CENTRAL 410 317, 327, 439 model organisms 3 – sea urchin 492 – Apium graveolens 64 – soybean 64 – Aquifex aeolicus 17 – spinach 69 – Arabidopsis 63, 110, 239 – Staphylococcus aureus 354 – Arabidopsis thaliana 4, 25, 59, 411 – strawberry 122 – Archaeoglobus fulgidus 3 – Streptomyces lincolnensis 51 – Asparagales 64 – Streptomyces lividans 53 – Bacillus subtilis 3, 448 – Sulfolobus solfataricus P2 384, 399 – barley 110, 122 – Thermotoga maritima 284 – Brassica 26 – tomato 110 – Brassica spp. 61 – Vibrio harvey 288 – budding yeast 117, 440 – worm 492 – Caenorhabditis briggsae 32 – Yarrowia 25 – Caenorhabditis elegans 4, 29–30, 37, 218, 262, – yeast 8, 428, 492 354, 447, 581 modified nucleoside triphosphates, DNA – Candida albicans 228 sequencing 130 – Cenarchaeum symbiosum 48 moesin 256 – comparative analysis 38 molecular biology 492 – corn 64 molecular chaperones 11 – Corona virus 354 molecular evolution 363 – Deinococcus radiodurans 17, 220 molecular markers 61, 106–108 – Desulfotalea psychrophilia 19 molecular networks – Drosophila melanogaster 4, 29, 34, 37, 262, 354, – conceptual models 466 446 – data integration 467 – Escherichia coli 3, 284, 307, 448, 476, 492 – model extraction 471–472 – Escherichia coli K12 359, 407–408 – model-driven reconstruction 466 – evolution of eukaryotic organisms 38 molecular profiling 542 – fly 492 mono-isotopic standards, Proteomics 329 – Haemophilus influenzae 7, 17 monocots, plants 64 – Heliobacter pylori 17, 262, 451, 492 monolithic columns, mass spectrometry 200 – Kluyveromyces 25 moral competence 568 – Listeria monocytogenes 12 morality clause, genetic patents 547 – maize 28 Morgan 109 – malaria parasites 476 Morgan’s mapping method 109 – Medicago trunculata 64 Mori, H. 8 – Methanobacterium thermoautotrophicum 16–17 morphological markers 106 – Methanococcus jannaschii 16–17 mosaic genome structure 50 – mice 581 mounting, protein crystallography 280 – Mus musculus 81, 354 Mouse Genome Database 117 – Mycoplasma genitalium 17 MPW 481 – Myobacterium smegmatis 360 MS-MS-ToF 580 – Nicotiana attenuata 67 MudPIT see Multidimensional Protein – Ocimum basilicum 64 Identification Technology – Oenothera 61 MudPIT experiments 211 – Oryza sativa 64 mulitchip average, microarrays 422 – Physcomitrella patens 73 multi-color fluorescent labels, DNA microarrays – Populus tremuloides 64, 122 235 – Pseudomonas aeruginosa 200, 318 multi database systems 465 – Pyrobaculum aerophilum 17 multicellularity 30 – Pyrococcus furiosus 17 multicolored multiplexed DIGE 324 – Rattus norvegicus 354 multidimensional protein identification 69 606 Subject Index

Multidimensional Protein Identification NCBI MMDB data specification 436 Technology 201 NCBI-nr 329 multidrug-resistance proteins 372 NCBL 398 multifactorial cardiovascular disease 96 nearest neighbor classification 426 multifactorial diseases, human genome 87 Needleman-Wunsch, Bioinformatics 301 multifunctional genes 8 nervous systems, Caenorhabditis elegans 30 multiparametric fitting 323 NetBiochem 450 multiple wavelength anomalous dispersion 274 NetOGlyc 338 multiplexed DIGE, multicolored 324 NetPhos 338 Mus musculus, model organisms 354 Netwinder 576 mutagenesis, insertional 73 networks, metabolic 461, 463 mutant phenotypes, Drosophila melanogaster 34 networks of objects 469 mutants, collection, Bacillus subtilis 14 neural network analysis, Bioinformatics 334 mutations 90 neural networks 323 – frameshift 11 – Proteomics 338 – human genome 82 newcpgreport 313 MutL homologs 12 newcpgseek 314 MutS homologs 12 Nicotiana attenuata, model organisms 67 Mycoplasma genitalium, model organisms 17 NIH study group 516 myeloid leukemia, acute 255 NMR 70 myGrid 321 – determination of protein fold 289 Myobacterium smegmatis, model organisms 360 – post-structural characterization 287 myosin-binding protein C 95 – pre-structural characterization 287 myosin heavy chain 95 – protein crystallography 282–290 Myriad Genetics 546 – suitability screening 288–289 MySQL 420 – see also nuclear magnetic resonance NNPSI 339 N NOESY 286 NAE 479, 482 non-coding repeats, Archaeoglobus fulgidus 18 naive Bayes classifier 427 non-coding RNA, human genome 82 naive graph 473 non-crosslinked polymers, capillary nanopore filtering, DNA sequencing 161 electrophoresis 216 nanopore filtering strategy, single molecule non-electrophoresis methods, DNA sequencing detection 164 152 nanospray experiment, static, Proteomics 198 non-fluorescence methods, DNA sequencing nanotechnology, biobanks 540 152–156 National Bioethics Commission of the United non-messenger RNA, small 20 States 524 non-monetary benefits, genetic resources 550 – see also NCBI non-yeast hybrid systems, yeast two-hybrid system National Institute for Biotechnology Information 269 62 nonownership language, genetic material 528 National Institute of Environmental Health nontoxic strains, Escherichia coli 9 Sciences 369 normalization, microarrays 422 National Institute of Health 546 normalization of the treatment of DNA 530 national jurisdiction, DNA banking 522 norms, ethical 509 National Statement on Ethical Conduct in Northern blots 249 Research Involving Humans 522 NtrC/NifA family 14 natural-product biosynthesis 53 NubGp 266 natural selection, Bacillus subtilis 12 nuclear magnetic resonance 70, 273 NCBI 62, 118 – see also NMR – see also National Institute for Biotechnology nuclease 269 Information nucleoside triphosphates, modified, DNA NCBI ASN.1 435 sequencing 130 NCBI GI identifier 398 Subject Index 607 nucleotide, chain-terminating, DNA sequencing organic anion-transporting polypeptides 372 130 organic cation transporters 372 nucleotide sequence pattern, Bioinformatics ornithine decarboxylase 471 314–315 Oryza sativa, model organisms 64 Nuffield Council on Bioethics 545 osmotic stress, Bacillus subtilis 11 Nuremberg Code 512 osteoblasts 364 osteoclasts 364 O osteoporosis 364 Oak Ridge National Laboratory 363 osteoporosis gene 364 OAT see organic anion-transporters ovarian cancer 92 OATP see organic anion-transporting OWL 329, 332 polypeptides ownership, genetic material 526 obesity 87 ownership of human biological material 538 OBJ 578 b-oxidation enzymes 19 object fusion 466–467 object oriented concepts 469 object oritented approaches 462 P Occam’s razor 422 P450 isoenzymes 371 Ocimum basilicum, model organisms 64 p53 261 OCT see organic cation transporters – gene 366 ODBC 465 PA SubCell server 339 ODE 479, 482 PAC see phage P1-based artificial chromosomes ODE-NAE 481 PAGE 232 OECD report 546 PAM 426 Oenothera, model organisms 61 Paracel GeneMatcher 384, 577 oil gland secretory cells, plants 64 paralogous gene families, Archaeoglobus fulgidus oligonucleotide arrays, DNA microarrays 229 19 oligonucleotide group, microarrays 417 parametric bootstrap clustering 427 oligonucleotide primer, DNA sequencing 143 paraoxonase 1 / paraoxonase 2 gene 97 oligonucleotide sequences, DNA microarrays Parkinsons’s disease 566 228 partly-recovered genomes 54 oligonucleotides patent databases 544 – bias 12 patent-infringment ligitation 547 – design, DNA microarrays 242 patent law 545 – long 250 patent policy 548 OMG 469 patent reforms 547–548 OMIM see Online Mendelian Inheritance In patenting 527 Man patenting of higher life forms 548 one-hybrid system 264 patents Online Mendelian Inheritance In Man 117 – DNA based 545 Onto-Express 254 – genetic resources 544 ontologies 361, 428 pathway 93 OntoMiner 428 – metabolic 461–490 ooTFD 451 pathway genes, Embden-Meyerhof-Parnas 13 open source effort, Bioinformatics 321 patient access to new technologies 542 open source software 254 patients confidentiality 525 operation UNION 468 patients rights 516 optical tweezers 17 PATIKA 451 OQL 466, 470 pattern-based Oracle 478 – Proteomics 335 ORDB 451 – sequence motifs 335 ordre public, genetic patents 547 patterns, detection 311 organ transplantation 512 PC-style computers 575 organic anion transporters 372 PCR failures, DNA microarrays 230 608 Subject Index

PCR methods, quantitative 358 phosphorylation 182, 436 PCR products, DNA sequencing 141 photobleaching, DNA sequencing 160 PDB 436 photolithography, DNA microarrays 223, 241 PDQuest 324–325 photoperiod sensitivity 117 peak suppression, mass spectrometry 196 PHRAB 31 PED, Petri net tools 477 PHRED 31, 158 PEDANT 578 phylloplane 10 penetrance 88 phylogenetic analysis 366 pentose phosphate pathway 476 phylogenetic classification, kinases 367 peptide analysis, mass spectrometry 191 phylogenetic markers 49 peptide ions, mass spectrometry 199 phylogenetic reconstructions 49 peptide mass fingerprinting 193 Physcomitrella patens, model organisms 73 – Proteomics 328 physical genetic map, Escherichia coli 7 peptides physiological research 576 – coeluting, mass spectrometry 200 Pi-h gene 110 – short, Proteomics 332 Pi-ta2 gene 110 PepTool 334, 341, 345 pI/MW measurements 326 perfect human 563 picoplancton 49 perfect life 566 PICS 286 Perl5 385 PIMdb 452 personal information 513 PIMRider 451 personal life 564 pin group, microarrays 416 personal rights 568 pipetting robots 576 PEST sequence 340 PIR 332, 462 Petri net model 473–479 Pise 321 – virtual cell 486 plankton, marine 48 Petri nets 451, 462 plants – applications 476 – AnnAt1 69 – colored 474 – barley microarray 66 – examples 483 – Calvin cycle enzymes 71 – firing speed 475 – counterparts in other eukaryotic genomes 63 – hybrid 474 – defense against herbivores 67 – markup language 478 – elevated ploidy levels 60 – model construction 478 – EST 64 – modules 481 – forward genetics 72 – self modified 474 – functional genomics 72 – simulation tools 479–483 – gene expression 64, 66 – times 474 – genes in rice 66 – tools 477 – genome annotation 63 Pfam 341 – genome structure 60 – database 336 – glucose 67 PGRL 110 – greening of leaf tissue 69 phage display 441–454 – high-resolution maps 62 phage family 6 – loss-of-function mutants 73 phage P1-based artificial chromosomes 62 – metabolic fingerprinting 70 Pharmacogenomics 509 – metabolite profiling 70 pharmacovigilance 376 – metabolomics 70 phasing, protein crystallography 281 – monocots 64 phenotyping screening limits, positional cloning – multidimensional protein identification 69 112 – multivariate data analysis 71 Phloem tissues, plants 64 – oil gland secretory cells 64 Phoretix 2D 324 – Phloem tissues 64 PhosphoBase 451 – physical map 62 phosphoenolpyruvate-dependent systems 11 – pollen 67 Subject Index 609

– preperation of samples 70 – genes in the critical region 115 – primary metabolism 69 – genetic approaches 112 – protein profiling 68 – model organisms 117 – Proteomics 68 – phenotyping screening limits 112 – putative gene 63 – physical approaches 113 – reverse genetics 73 – region-specific markers 112 – rice genome 64 positional mapping – ripening-inhibitor 72 – comparative maps 116 –rose petals 65 – conserved gene orders 116 – secondary metabolic pathways 64 post-mortem use of samples 520 – secretory pathway 63 post-synthesis arraying, DNA microarrays 224 – sequence-indexed T-DNA insertion-site post-transcriptional gene-silencing 73 database 73 post-transitional changes 436 – stress-induced genes 66 post-translational modifications 181 – sugar signal transduction 67 postgenome era 8 – synteny 64 – Caenorhabditis elegans 33 – TILLING 76 – Saccharomyces cerevisiae 25 plasmid DNA vectors 62 potassium channel 371 plasmid purification kit, DNA sequencing 141 Ppd genes 118 plasminogene-activator inhibitor gene 96 pre-implantation diagnostics 567 plasmon resonance, surface 163 precipitant 278 plastid 60 preconcentration step, Proteomics 187 plastid chromosome 60 PredictProtein Web server 341 plastid genomes 583 prefractionation plastid transit peptides 28 – anion-exchange 202 Plato 537 – protein 187 ploidy levels, elevated, plants 60 premature implementation of new technologies plus/minus method, DNA sequencing 129 542 PML/RAR chimeric gene 373 presumed consent to the storage and use of PNG 385 health data 529 PNK 478 prices of medical products 548 PNML 478 primary interaction experiments 434 pollen, plants 67 primary metabolism, plants 69 poly(ethylene oxide), capillary electrophoresis primer identification tool 229 216 primer walking, DNA sequencing 139 polydot 307 PrimerBank 358 polygenic diseases, human genome 87 principal-component analysis 370, 426 polyketide synthase gene clusters 54 principle of reciprocity 525 polymers, non-crosslinked 216 PRINTS 336 polymorphisms 107 prior art, Myriad Genetics 547 – human genome 88 privacy, biobanks 553 – single-nucleotide 50 privacy and confidentiality 538 polypeptides, anion-transporting 372 private-public funding of research, genetic polyposis phenotype 93 material 528 pooled progeny 112 pro-creation 566 poplar, model organisms 122 probe population genetic research 537 – cryogenically cooled 285 population studies 521 – DNA 416 Populus tremuloides, model organisms 64 – DNA microarrays 234, 240 position-specific scoring matreices 336 ProChart 452 positional candidate method 85 Prodom 341 positional cloning 105, 110–115 profound 331 – analysis of DNA sequences 118 Prohibition of Cloning Human Beings 512 – critical region 111 prokaryotic diversity 45 610 Subject Index

prokaryotic genomes 404 protein quantity loci 121 promoters 383 protein structures 273 promyelocytic leukemia, acute 373 ProteinProspector 331 ProNET 452 proteins 203 propanolol 374 – bait and prey 496 property rights for individuals, genetic material – disease-related 182 528 – high-molecular-weight 215 Proposal on Archived Biological Materials 528 – purification 277 PROSITE 315, 393 – repressor, iron dependend 20 protases 363 – soluble parts 284 Protean 344 – truncated tagged, Bacillus subtilis 13 Protection of the Human Genome by the Council Proteobacteria 49 of Europe 528 proteolytic digests 332 protein chips 328, 580 proteome 181 protein coding genes, human genome 81 – Bacillus subtilis 14 protein crystallazation, structural genomics 278 – cumulative citation 181 protein crystallization factories 577 – historical definition 181 protein crystallography 273–274 Proteomics 10, 181–209, 273, 323–351, 413 – additives 278–279 –2D gel databases 328 – algorithms 287 – analysis of subcellular fractions 186 – attrition 275 – bottom-up 204 – automation of data collection 280 – clinical 187–188 – data base 282 – complex samples 187 – data collection 279–281 – contaminating proteins 330 – expression 279 – database quality 184 – harvesting 280 – direct ms analysis 196–198 – mounting 280 – direct sequencing 332 – mounting loop 280 – dynamic range 187 – NMR 282–290 – enzymatic processing 197 – phasing methods 281 – experimental noise 330 – removal of the affinity tag 278 – Federated 2D gel databases 326 – robotic sample-mounting systems 280 – Federated Gel Database requirements 326 – seeding 279 – fractionation procedures 186 – seleno-methionine 274 – functional definition 181 – serious challanges 281 – fundamental issues 182 – well-diffracting crystals 275 – hyphenated tools 190 – X-ray detectors 274 – inter-gel comparison 326 – X-ray diffraction data 280 – interlaboratory variance 187 protein-degradation methods, mass spectrometry – internally calibrated mono-isotopic standards 191 329 protein domains, predicting, Proteomics 341 – low-micron spatial resolution 188 protein expression 284 – mass fingerprinting software 329 protein fold, determination, NMR 289 – mass spectrometry 328 protein fold-space 273 – ms fingerprint analysis 329 protein identification 324–334 – neural networks 338 – multidimensional, plants 69 – pattern-based sequence motifs 335 protein interaction, Proteomics 338 – peptide mass fingerprinting 328 protein interaction databases 433–459 – plants 68 protein prefractionation 187 – post-translated modification 338 protein production, structural genomics 276 – preconcentration step 187 protein products, predicted, Caenorhabditis elegans – predicting 3D folds 342 32 – predicting active sites 334–337 protein profiling, plants 68 – predicting bulk properties 334 protein-protein interactions 261, 496 – predicting protein domains 341 Subject Index 611

– predicting secondary structure 341–342 PubMed 334, 345 – protein identification from 2D gels 324–328 – identifiers 442 – protein interaction databases 338 pulldown assays 203 – protein interaction information 338 pullulan, capillary electrophoresis 216 – protein property prediction 334–345 purification, target protein, structural genomics – reactor-based digestion 198 277 – reduction of sample complexity 184 purification procedure, mass spectrometry 202 – relationship to genomics 182 purifying high-molecular-weight DNA 51 – sample-driven 195–204 putative functions, Archaeoglobus fulgidus 19 – samples 184 putative gene, plants 63 – sequence databases 332 Pyrobaculum aerophilum, model organisms 17 – sequence of short peptides 332 Pyrococcus furiosus, model organisms 17 – shotgun 201 pyrosequencing 152 – signature sequences 334 – silver staining method 197 Q – single-cell 188 QDA 425 – software tools 324 QTL see qualitative and quantitative trait loci – spectral patterns 188 quadratic discriminant analysis 425 – spot (re)coloring 325 quadrupole instruments, mass spectrometry 189 – spot annotation 325 qualitative and quantitative trait loci 105 – spot detection 325 quality, microarrays 421 – spot editing 325 QuantArray 252 – spot filtering 325 quantization 251 – spot normalization 325 Quebec 530 – spot quantitation 325 – Myriad Genetics 546 – static nanospray experiment 198 query languages 470 – Sub-cellular location 339 quicksort algorithm 399 – validation step 186 – whole cell 186 R – whole gel manipulations 326 R17 bacteriophage RNA 129 proteorhodopsin 49 RADAR 287 proto-oncogenes 90 radiation damage 91 pseudomized 517 radiation hybrid map 114–115 Pseudomonas aeruginosa, model organisms 200, radioactive sequenzing 574 318 Raelian sect 562 PSI 439 random amplified polymorphic DNA 107 PSI-BLAST 333 random selfing 106 PSIBLAST 342 random sequencing, complete genome sequences PSIMI 439 17 PSORT 339 random shotgun sequencing, DNA sequencing PTS see phosphoenolpyruvate-dependent 139 systems randomply amplified polymorphic DNA 62 public confidence and trust 552 RAPD see random amplified polymorphic DNA public consultation, biobanks 553 Rar-1 gene 111 Public Expression Profiling Resource 358 Ras 261 public health research 516 rate constants 472 public involvement 522 rational drug design 273 public opinion 540–541 rational drug target discovery 290 – genetic patents 548–549 – alternate approach 290 – genetic resources 543 Rattus norvegicus, model organisms 354 – genetic technologies 541 reactor-based digestion, Proteomics 198 public perception 583 real-time analysis environments 577 public trust 551 REBASE 315, 439, 452 – biobanks 553 receptors 366 612 Subject Index

– G-protein coupled 362 rice recombinant inbred lines 106 – genes, plants 64, 66 regression, log ratio 422 – model organisms 60, 122 regulatory framework, biobanks 552 rice dwarf mutants, spontaneous 117 regulatory networks 499 rice linkage segments 116 – Archaeoglobus fulgidus 20 right not to know 512 RegulonDB 452 right to live 565 regulons 498 right to withold 521 relationships with the general public, scientists rigth to know 514 583 RIKEN Genomic Science Center 275, 355 relaxation decay, high-resolution solution NMR ripening-inhibitor, plants 72 284 risk assessment, human genome 86 Relibase 452 risk factors, genetic 509 renal salt-reabsorption pathway 95 risk of market failure 542 Renew 478 RmySQL 420 repair RNA – mechanism 312 – genes, Archaeoglobus fulgidus 18 – of double-strand DNA breaks 92 – intact 246 repeat families, Caenorhabditis elegans 33 – non-messenger 20 repetitive DNA 60 RNA expression, antisense 76 replication RNA genes, Caenorhabditis elegans 32 – Bacillus subtilis 12 RNA interference 73 – termination of 8 RNA isolation kits 246 replication strands, leading, Bacillus subtilis 14 RNase 247 repressed transactivator system 264 robotic sample-mounting systems, protein repressor proteins, iron dependend 20 crystallography 280 repressor Tup1p, transcriptional 264 robots reproductive cloning 562 – liquid handling 279 reproductive technologies 512 – microarraying 234 research ethics 510 – pippeting 576 resequencing, DNA sequencing 138, 140 rose petals, plants 66 residual dipolar couplings 287 Rosetta 289 restriction fragment length polymorphism 62, Royal College of Physicians Committee on Ethical 107 Issues in Medicine 516 – see also RFLP Rpg1 gene 116 restriction map, Escherichia coli 7 RPM1 gene 110 restriction mapping, Bioinformatics 315 RPP13 gene 110 retinitis pigmentosa 86 RUBISCO 202 retrotransposons 116 ruke-based systems 462 reverse genetic approaches 60, 365 –plants 73 S reverse primers, DNA microarrays 230 S-PLUS implementation 419 reverse two-hybrid system 263–264 Saccharomyces cerevisiae RFLP 62 – analysis by computer algorithms 22 – see also restriction fragment length – ancient duplication 24 polymorphism – chromosome III 21 RH map 114 – classical mapping methods 22 rhodopsin 49 – cosmid libraries 21 ribonuclease 246 – electrophoretic karyotypes 21 ribosomal RNA 129 – experimental system 20 – Saccharomyces cerevisiae 23 – gene duplications 24 16S-ribosomal RNA 129 – gene expression profiles 25 23S-ribosomal RNA 129 – genes 23 5S-ribosomal RNA 129 – genetic map 21 Subject Index 613

– homologs among human genes 25 SELEX-DB 453 – in silicio analysis 23 self determination 568 – intergenic regions 23 self-determined organization of life 565 – internal genetic redundancy 24 self-modified Petri nets 476 – introns 23 self-organizating maps 426 – Micrograph 21 self responsibility 565 –model organisms 20, 37, 201, 261–262, 317, selfing 106 327, 439 sense RNA, co-suppression 76 – non-chromosomal elements 23 sensory networks, Archaeoglobus fulgidus 20 – periodicity of the GC content 24 separation buffer, capillary electrophoresis 214 – postgenome era 25 separation time, capillary electrophoresis 213 – ribosomal RNA genes 23 separations, two-dimensional, capillary – sequencing strategies 22 electrophoresis 219–220 – subtelomeric regions 24 SeqLab 344 – telomeres 22 seqmatchall 307 – transposeable elements 23 SEQSEE 334, 341 SAGE 358 SEQSITE 336 saltstress response, Bacillus subtilis 15 sequence accession numbers 442 SAM 363, 424 sequence coverage, minimum, Archaeoglobus sample channels, DNA sequencing 147 fulgidus 17 sample complexity, reduction, Proteomics 184 sequence databases sample-mounting systems, robotic 280 – Bioinformatics 354 sample preparation, DNA microarrays 246 – Proteomics 332 sample processing, mass spectrometry 190–191 sequence gaps, complete genome sequences 17 samples, post-mortem use 520 sequence motifs 229 Sanger 129 – pattern-based, Proteomics 335 Sanger Center 31, 321 sequence pattern, nucleotide 314–315 Sanger dideoxy sequencing 130 sequence polymorphisms 106 sbSNP 357 Sequence Retrieval System 397, 462 scaffolds 48 – see also SRS scalable vector graphics 405–406 sequence variations 354 scale-free graphs 501 sequencers, DNA 575 scaling, microarrays 423 sequences SCAMP 479 – amino-modified oligonucleotide 228 ScanArray 235 – cDNA see cDNA sequences scanning, DNA microarrays 234 – complete genome see complete genome scanning devices, confocal 235 sequences scheme integration 466 – oligonucleotide 228 schizophrenia 87 – PEST 340 scientific importance of the research 517 – Shine Dalgarno 383 scoring methods, Bioinformatics 300 – signature 334 screening, genetic 365–366 – splice site consenus 305 screening limits, phenotyping 112 – spliced cDNA 300 sea urchin, model organisms 492 – tentative consensous 118 searching, Bioinformatics 363 – unmodified oligonucleotide 228 second harmonic generation laser 144 – vector 404 secretory cells, oil gland 64 sequencing segments, duplicated, Arabidopsis thaliana 29 – Drosophila melanogaster 35 segregating population 105 – Proteomics 332 selection – random – Darwinian 83 sequencing primer, universal, DNA sequencing – direct cDNA 115 140 – natural, Bacillus subtilis 12 sequencing strategy seleno-methionine, protein crystallography 274 – Arabidopsis thaliana 27 614 Subject Index

– Archaeoglobus fulgidus 18 slide substrates, DNA microarrays 242–243 – Saccharomyces cerevisiae 22 small-bore reverded phase LC columns, mass SEQUEST 331 spectrometry 200 SeqWeb 344 small non-messenger RNA 20 severe acute respiratory syndrome 354 SMART-IDEA 359 severe ADR 376 SmartNotebook 286 sh2-a1 gene 116 Smith, H. O. 18 SH3 domains 433 Smith-Waterman algorithm 363 shearing effects 51 Smith-Waterman alignment, sheath-flow cuvette detector, capillary Bioinformatics 303 electrophoresis 219 SNOMAD 422 Sherenga 195 SNP see single nucleotide polymorphisms Shine-Dalgarno motifs 383, 393 SNP Consortium 371, 509 short peptides, sequence, Proteomics 332 SNP data analysis 372 shuttle cosmid vector 54 SoapLab 321 sib-mating 106 soil libraries 51 sickle-cell disease 86–87 soil sample 50 signal averaging 331 solid state laser 144 signal-to-noise ratio, high-resolution solution solid state NMR 282 NMR 285 solubilization 277 signal-transduction pathways 360, 499 SOS recruitment system 266 signature sequences, Proteomics 334 Southern Alberta Microarry Facility 241 silver staining method, Proteomics 197 Southern blots 223 simple-sequence length polymorphisms 62 SoyBase 453 simulators for metabolic networks 462 soybean, model organisms 64 simultaneous bi-directional sequencing, DNA SPAD 453 sequencing 144 spatial blots 252 simvastatin 357 spatial resolution, low-micron, Proteomics 188 Singapore Bioethics Advisory Ethics Committee special status of genetic material 526 522 spectral patterns, Proteomics 188 single-base extension, DNA sequencing 152 spectrophotometers 576 single-cell analysis, capillary electrophoresis spectroscopy 218–219 – fluorescence 70 single-gene defects 84 – infrared 70 single-gene disorders 510 – ultraviolet 70 single-labeled, microarrays 417 SPIN-PP 453 single-locus analysis, linkage map 108 spinach, model organisms 69 single molecule detection splice site consenus sequences, Bioinformatics – DNA degradation strategy 161–162 305 – DNA hybridization strategy 163–164 spliced cDNA sequences, Bioinformatics 300 – DNA sequencing 160 split-ubiquitin system 266 – DNA synthesis strategy 162–163 spontaneous rice dwarf mutants 117 – fluorescence energy transfer 163 sporadic colon tumors 94 – nanopore filtering strategy 164 spots – surface plasmon resonance 163 – amibigious 252 single-nucleotide polymorphisms 50, 88, 152, – Proteomics 325 354, 356 spotting concentration, DNA microarrays 230 single sequence repeat 107 spotting pins, DNA microarrays 243 single strand conformational polymorphism 107 SQL 465 single stranded DNA template 140 SRS 465, 578 siRNA 581 – see also Sequence Retrieval System siRNA gene knock-downs 261 SRS-6 386 sitting-drop vapor diffusion 278 SSCP see single strand conformational slab gels, DNA sequencing 146, 149–151 polymorphism Subject Index 615

SSLP see simple-sequence length subtelomeric regions, Saccharomyces cerevisiae 24 polymorphisms sugar signal transduction, plants 67 SSR see single sequence repeat suitability screening, NMR 288 Staden package 402 sulfate-reducing organism 16 standards and guidelines, biotechnology 561 sulfate reduction, Archaeoglobus fulgidus 19 Stanford Medical School 6 Sulfolobus solfataricus P2, model organisms 384, Stanford University 115 399 Staphylococcus aureus, model organisms 354 super-high-field instruments, high-resolution start-up companies 582 solution NMR 285 Statement on DNA Sampling: Control and Access support vector machines 339, 425 517 surface plasmon resonance, single molecule static models, systems biology 498 detection 163 static nanospray experiment, Proteomics 198 surfactant, capillary electrophoresis 214 static system models 496 surveys, environmental 46 statins 373 sustainable development, genetic resources 550 statistical programming language R 420 SVG see scalable vector graphics steady-state rate equations 472 SVM see support vector machines Stella, Petri net tools 477 SWISS-2D PAGE 326 stem cell research 516, 540, 566 SWISS-2DPAGE 10 stem cells 512 Swiss-Prot 329, 332, 462 – embryonic 565 synchrotron protein crystallography 273 Stetter, K. O. 17 synchrotron x-ray sources, third generation 274 stigmatization 513 synteny 116 stigmatization by association 510 –plants 64 STKE 453 synthesis, spatially ordered 223 stochastic models 500 synthesis strategy 162–163 stoichiometric matrices 482 SYPEITHI 453 Stokes Shift, DNA sequencing 132 systematic sequencing, Escherichia coli 7 STOP codons 228 Systems Biology 491–505, 582 strains – analysis of static models 498–499 – nontoxic, Escherichia coli 9 – basic concepts 494 – toxic, Escherichia coli 9 – combining data 493 strawberry, model organisms 122 – combining multiple data types 493 Streptomyces lincolnensis, model organisms 51 – connection 493 Streptomyces lividans, model organisms 53 – control mechanisms 494 stress, osmotic, Bacillus subtilis 11 – data fusion 493 stromelysin-1 gene 96 – data types 492–493 structural characterization, NMR 287 – definition 360 structural genomics – diagrammatic representations 495 – cloning of the genes 277 – dynamic models 499–500 – commercial 275 – dynamic properties 494 – correct expression system 277 – error rates 493 – efforts 274 – experimental system 492 – projects 274 – hierarchical modularity 495 – protein crystallazation 278–279 – interactions 493 – protein production 276 – mathematical models 491 – purification of the target protein 277 – modeling formalisms 500 structure based drug design 289 – models 495 structure mining 581 – modularity 495–496 stuctural genomics 273–295 – simple model 494 subcellular fractions, analysis, Proteomics 186 – states 494 SubLoc 339 – static properties 494 substitution matrices, Bioinformatics 333 systems modeling 472 616 Subject Index

T tissue banking 512 T-DNA tagging 73 tissue research, ethical framework 511 t-statistics 253 TissueInformatics 542 TAC see transformation-competent artificial Tm2a gene 110 chromosomes TM4 420 tagged protein, truncated, Bacillus subtilis 13 TM4 software 254 tagging TMHMM 340 – T-DNA 73 TMV gene 110 – transposon 73 TOF see time of flight tagSNP 90 tomato, model organisms 110 TAIR see The Arabidopsis Information Resource tools to educate the public, biobanks 553 TAMBIS 465 top-down approach 468 tandem TopoSNP 357 – in space, mass spectrometry 191 toxic strains, Escherichia coli 9 – in time, mass spectrometry 191 toxicity, compound 369–372 tandem capillary electrophoresis 328 toxicity signatures 369–370 tandem gene knockout 434 toxicogenomics 366–372 tandem repeat regions, Caenorhabditis elegans 32 – optimum dosage 374 tandem repeats 29 – signatures 370 tardive dyskinesia 375 TPMT see thiopurine S-methyltransferase target 416 trace generation, DNA sequencing 155–156 – DNA microarrays 240 tracking, DNA sequencing 153 target protein, purification 277 transaction costs 545 target validation 364 transactivator system, repressed 264 TargetP 339 transcription complex 13 Tatum, E. 6 transcription factors 373, 428, 499 Taverna 321 – Drosophila melanogaster 36 taxonomic marker genes 53 – yeast 262 TD see tardive dyskinesia transcription-translation apparatus 433 telomeres, Saccharomyces cerevisiae 22 transcriptional modules 498 template-primer-polymerase complex, DNA transcriptional repressor Tup1p 264 sequencing 143 transcriptome 357 tentative consensus sequences 118 TRANSFAC 315, 444, 454, 462 termination of replication 8 transferrins, Drosophila melanogaster 36 terminators 383 transformation-competent artificial chromosomes TEV protease 278 62 TGFBR1 gene 94 transforming growth factor receptor type 2 94 Thal, Johannes 25–26 transgenic plants 67 The Arabidopsis Information Resource 27 transit peptides, plastid 28 therapeutic cloning 512, 516, 562 translation 461 thermophiles, extreme 49 translational research 542 Thermotoga maritima, model organisms 284 TRANSPATH 444, 454, 462, 481 thing and person blurring 565 transposeable elements, repeats, Arabidopsis thiopurine S-methyltransferase 372 thaliana 28 third generation synchrotron x-ray sources 274 transposons 116 THORNs, Petri net tools 477 – insertion, DNA sequencing 139 three-hybrid system 264 – tagging 73 three-locus analysis, linkage map 109 trapping, exon 115 throughput, hardware for DNA synthesis 575 TREMBL 332–333 TIGR 17, 118, 580 tricyclic antidepressants 373 TIGR XML 412 triple quadrupole, mass spectrometry 191 TIM-barrel motif 291 TRRD 454 time of flight, mass spectrometry 68, 189 truncated tagged protein, Bacillus subtilis 13 TimeLogic 363, 577 trust in corporate participants 543 Subject Index 617 trypsin 190 vector sequence, MAGPIE 404 Tukey biweight 422 VectorNTI 334 tumor-suppressor genes 90 vectors, plasmid DNA 62 tumor suppressors 182 very short patch repair mechanism 312 Tup1p, transcriptional repressor 264 Vibrio harvey, model organisms 288 two-dimensional electrophoresis 211 view concepts 472 two-dimensional separations, capillary violacein 53 electrophoresis 219–220 virtual cell 482 two-locus analysis, linkage map 109 – Petri net model 486 two-phase electrophoresis 51 virtual reality environments, automated 578 type 1 TGF/Beta receptor 94 virus-induced gene silencing 76 type II Albers-Schonberg disease 364 vitamin K epoxide reductase complex subunit 1 374 U VKORC1 374 UAS-URA3 growth reporter 263 VON++, Petri net tools 477 Ubiquitin 266 VRML 578 UDB system 479 UGTA1A1 see uridine diphosphate W glucuronosyltransferase 1A1 W2H 321 UK Biobank Ethics and Governance Framework warfarin 374 525 Washington University in St. Louis 118, 580 UK Biobank Limited 528–529 water 303 ultra-zoom gels, IFF 324 Watson-Crick base-pairing 240 UltraScan, Petri net tools 477 web-based computing 575 unassigned 1H,15N RDC 289 web services 578 uncultivated microorganisms 48 WebGel 326 undesirable commodification of the human body well-diffracting crystals, protein crystallography 542 275 UNESCO 513, 538 Wellcometrust Sanger Institute 580 – Declaration on Genetic Data 515 Western blotting 326 ungapped alignments, localized 305 Whitehead Institute 115 UniGene database 240 WHO 513 UniProt 332–333 WHO Genetic Databases report and United Kingdom, biobanks 538 recommandations 515 United States, biobanks 538 whole cell visualization 435 Universal Declaration on the Human Genome whole gel manipulations, Proteomics 326 and Human Rights 513 whole-genome shotgun assembly, DNA universal sequencing primer, DNA sequencing sequencing 139 140 Wilms tumors 255 University of Calgary 243 WIT 440, 454 unmodified oligonucleotide sequences 228 WIT/EMP 462 untouchable human being 563 Woese, Carl R. 17 unwarranted information 515 wordcount 310 urea cycle 485 wordmatch 306 – pathway 484 World-2-DPAGE 327 uridine diphosphate glucuronosyltransferase 1A1 World Health Organization 512 372 worm, model organisms 492 US National Bioethics Advisory Comission 511 UV absorbance, capillary electrophoresis 214 X X-ray crystallography 275 V X-ray detectors, protein crystallography 274 validation step, Proteomics 186 X-ray sources, synchrotron 274 vapor diffusion 278 Xgrail 118 vector, shuttle cosmid 54 XLink standard, Bluejay 411 618 Subject Index

XML 438, 466 yeast transcription factor Gal4p 262 – see also extensible markup language yeast two-hybrid network 441 XML language 578 yeast two-hybrid system 261–272 XML Schema 439 – bait 262 XSL schemes 478 –classical 262 XSLT stylesheet 410 – false negatives 270 – false positives 270 Y – interpretation 269–270 YAC see yeast artificial chromosome – non-yeast hybrid systems 269 Yarrowia, model organisms 25 – prey 262 YASMA 422 yMGV 420 yeast, model organisms 428, 492 YPD 454 yeast artificial chromosomes 62, 114 yeast genomes, hemiascomycetes 25 Z yeast interactome 182 zyxin 256