Current Awareness
Open Access
Current Awareness
First published: 19 December 2001
Abstract
In order to keep subscribers up-to-date with the latest developments in their field, this current awareness service is provided by John Wiley & Sons and contains newly-published material on comparative and functional genomics. Each bibliography is divided into 16 sections. 1 Reviews & symposia; 2 General; 3 Large-scale sequencing and mapping; 4 Genome evolution; 5 Comparative genomics; 6 Gene families and regulons; 7 Pharmacogenomics; 8 Large-scale mutagenesis programmes; 9 Functional complementation; 10 Transcriptomics; 11 Proteomics; 12 Protein structural genomics; 13 Metabolomics; 14 Genomic approaches to development; 15 Technological advances; 16 Bioinformatics. Within each section, articles are listed in alphabetical order with respect to author. If, in the preceding period, no publications are located relevant to any one of these headings, that section will be omitted
Current Awareness
- 1. Reviews & symposia
- (2001). Special issue: From Genome to Proteome Proceedings of the Vth Siena Two-Dimensional Electrophoresis Meeting - Siena, Italy - September 4-7, 2000. Electrophoresis 22,
- (2001). Special issue on genomic approaches to interactions of plants with pathogens and symbionts. Curr Opin Plant Biol 4,
- Altman RB, Raychaudhuri S. (2001). Whole-genome expression analysis: Challenges beyond clustering. Curr Opin Struct Biol 11, 340
- Anderson NG, Matheson A, Anderson NL. (2001). Back to the future: The human protein index (HPI) and the agenda for post-proteomic biology. Proteomics 1, 3
- Anisimov SV, Lakatta EG, Boheler KR. (2001). Discovering altered genomic expression patterns in heart: Transcriptome determination by serial analysis of gene expression (Review). Eur J Heart Fail 3, 271
- Arrell DK, Neverova I, Van Eyk JE. (2001). Cardiovascular proteomics: Evolution and potential (Review). Circ Res 88, 763
- Bancroft I. (2001). Duplicate and diverge: The evolution of plant genome microstructure (Review). Trends Genet 17, 89
- Battersby BJ, Lawrie GA, Trau M. (2001). Optical encoding of microbeads for gene screening: Alternatives to microarrays (Review). Drug Discov Today 6, S19
- Bertucci F, Loriod B, Tagett R, Granjeaud S, Birnbaum D, Nguyen C, Houlgatte R. (2001). DNA arrays: Technological aspects and applications (French, English Abstract). Bull Cancer 88, 243
- Bjorkholm BM, Oh JD, Falk PG, Engstrand LG, Gordon JI. (2001). Genomics and proteomics converge on Helicobacter pylori. Curr Opin Microbiol 4, 237
- Boucher Y, Nesbo CL, Doolittle WF. (2001). Microbial genomes: Dealing with diversity. Curr Opin Microbiol 4, 285
- Bremer C, Weissleder R. (2001). In vivo imaging of gene expression: MR and optical technologies. Acad Radiol 8, 15
- Burgess JK. (2001). Gene expression studies using microarrays. Clin Exp Pharmacol Physiol 28, 321
- Califano A. (2001). Advances in sequence analysis. Curr Opin Struct Biol 11, 330
- Charlesworth D, Charlesworth B, McVean GAT. (2001). Genome sequences and evolutionary biology, a two-way interaction (Review). Trends Ecol Evol 16, 235
- Charron P, Komajda M. (2001). Are we ready for pharmacogenomics in heart failure? (Review). Eur J Pharmacol 417, 1
- Cooper CS. (2001). Applications of microarray technology in breast cancer research (Review). Breast Cancer Res Treat 3, 158
- Cunningham MJ. (2000). Genomics and proteomics: The new millenium of drug discovery and development. J Pharmacol Toxicol Methods 44, 291
- Davidson D, Baldock R. (2001). Bioinformatics beyond sequence: Mapping gene function in the embryo (Review). Nat Rev Genet 2, 409
- Delseny M, Salses J, Cooke R, Sallaud C, Regad F, Lagoda P, Guiderdoni E, Ventelon M, Brugidou C, Ghesquiere A. (2001). Rice genomics: Present and future. Plant Physiol Biochem 39, 323
- Devaux F, Marc P, Jacq C. (2001). Transcriptomes, transcription activators and microarrays (Minireview). FEBS Lett 498, 140
- Deyholos MK, Galbraith DW. (2001). High density microarrays for gene expression analysis (Review). Cytometry 43, 229
10.1002/1097-0320(20010401)43:4<229::AID-CYTO1055>3.0.CO;2-2 CAS PubMed Web of Science® Google Scholar
- Ehrat M, Kresbach GM. (2001). DNA and protein microarrays and their contributions to proteomics and genomics. Chimia 55, 35
- Fisch I. (2001). Peptide display in functional genomics. Comb Chem High Throughput Scr 4, 157
- Franken P, Requena N. (2001). Analysis of gene expression in arbuscular mycorrhizas: New approaches and challenges (Review). New Phytol 150, 517
- Gaasterland T, Oprea M. (2001). Whole-genome analysis: Annotations and updates. Curr Opin Struct Biol 11, 377
- Godovac-Zimmerman J, Brown KL. (2001). Perspectives for mass spectrometry and functional proteomics. Mass Spectrom Rev 20, 1
- Grabherr R, Ernst W. (2001). The baculovirus expression system as a tool for generating diversity by viral surface display. Comb Chem High Throughput Scr 4, 185
- Grandi G. (2001). Antibacterial vaccine design using genomics and proteomics (Review). Trends Biotechnol 19, 181
- Grant WN, Viney ME. (2001). Post-genomic nematode parasitology. Int J Parasitol 31, 879
- Graveley BR. (2001). Alternative splicing: Increasing diversity in the proteomic world (Review). Trends Genet 17, 100
- Gull K. (2001). The biology of kinetoplastid parasites: Insights and challenges from genomics and post-genomics. Int J Parasitol 31, 443
- Hancock WS. (2001). Contribution of ion trap mass spectrometers to proteomics. Am Lab 33, 18
- Hanke J. (2000). Genomics and new technologies as catalysts for change in the drug discovery paradigm. J Law Med Ethics 28, 15
- Harvey DJ. (2001). Identification of protein-bound carbohydrates by mass spectrometry (Review). Proteomics 1, 311
- Jenkins RE, Pennington SR. (2001). Arrays for protein expression profiling: Towards a viable alternative to two-dimensional gel electrophoresis? Proteomics 1, 13
- Joussen AM, Huang S. (2001). Gene expression profiling using cDNA microarrays (Survey) (German, English Abstract). Ophthalmologe 98, 568
- Kagnoff MF, Eckmann L. (2001). Analysis of host responses to microbial infection using gene expression profiling. Curr Opin Microbiol 4, 246
- Kaufmann H, Bailey JE, Fussenegger M. (2001). Use of antibodies for detection of phosphorylated proteins separated by two-dimensional gel electrophoresis (Review). Proteomics 1, 194
- Kerr MK, Churchill GA. (2001). Statistical design and the analysis of gene expression microarray data (Review). Genet Res 77, 123
- Koehl P. (2001). Protein structure similarities. Curr Opin Struct Biol 11, 348
- Kriventseva EV, Biswas M, Apweiler R. (2001). Clustering and analysis of protein families. Curr Opin Struct Biol 11, 334
- Kuster B, Krogh TN, Mortz E, Harvey DJ. (2001). Glycosylation analysis of gel-separated proteins (Review). Proteomics 1, 350
- Lagudah ES, Dubcovsky J, Powell W. (2001). Wheat genomics. Plant Physiol Biochem 39, 335
- Laurell T, Nilsson J, Marko-Varga G. (2001). Proteomics-protein profiling technology: The trend towards a microfabricated toolbox concept. Trends Anal Chem 20, 225
- Lee KH. (2001). Proteomics: A technology-driven and technology-limited discovery science (Review). Trends Biotechnol 19, 217
- Leeder JS. (2001). Pharmacogenetics and pharmacogenomics. Pediatr Clin North Am 48, 765
- Lengeling A, Pfeffer K, Balling R. (2001). The battle of two genomes: Genetics of bacterial host-pathogen interactions in mice (Review). Mamm Genome 12, 261
- Lieschke GJ. (2001). Zebrafish: An emerging genetic model for the study of cytokines and hematopoiesis in the era of functional genomics. Int J Hematol 73, 23
- Lucchini S, Thompson A, Hinton JCD. (2001). Microarrays for microbiologists (Review). Microbiology 147, 1403
- Maggio ET, Ramnarayan K. (2001). Recent developments in computational proteomics (Review). Trends Biotechnol 19, 266
- Martienssen R, McCombie WR. (2001). The first plant genome (Minireview). Cell 105, 571
- Martin JB. (2000). Genomics and degenerative diseases of the nervous system. J Law Med Ethics 28, 30
- McLeod HL, Evans WE. (2001). Pharmacogenomics: Unlocking the human genome for better drug therapy. Annu Rev Pharmacol Toxicol 41, 101
- Meltzer PS. (2001). Spotting the target: Microarrays for disease gene discovery. Curr Opin Genet Dev 11, 258
- Miklos GLG, Maleszka R. (2001). Integrating molecular medicine with functional proteomics: Realities and expectations. Proteomics 1, 30
- Miklos GLG, Maleszka R. (2001). Protein functions and biological contexts (Overview). Proteomics 1, 169
- Miller W. (2001). Comparison of genomic DNA sequences: Solved and unsolved problems (Review). Bioinformatics 17, 391
- Nedelkov D, Nelson RW. (2001). Biomolecular interaction analysis mass spectrometry: A comprehensive microscale proteomics approach. Am Lab 33, 22
- Niculescu AB, Kelsoe JR. (2001). Convergent functional genomics: Application to bipolar disorder. Ann Med 33, 263
- Norton RM. (2001). Clinical pharmacogenomics: Applications in pharmaceutical R&D(Review). Drug Discov Today 6, 180
- O'Donovan C, Apweiler R, Bairoch A. (2001). The human proteomics initiative (HPI) (Review). Trends Biotechnol 19, 178
- Ondrej M. (2001). Transgenosis of Arabidopsis thaliana for understanding plant gene structure and functions (Review). Biologia 56, 1
- Payne DJ, Warren PV, Holmes DJ, Ji YD, Lonsdale JT. (2001). Bacterial fatty-acid biosynthesis: A genomics-driven target for antibacterial drug discovery (Review). Drug Discov Today 6, 537
- Quackenbush J. (2001). Computational analysis of microarray data (Review). Nat Rev Genet 2, 418
- Raychaudhuri S, Sutphin PD, Chang JT, Altman RB. (2001). Basic microarray analysis: Grouping and feature reduction (Review). Trends Biotechnol 19, 189
- Read SJ, Parsons AA, Harrison DC, Philpott K, Kabnick K, O'Brien S, Clark S, Brawner M, Bates S, Gloger I, Legos JJ, Barone FC. (2001). Stroke genomics: Approaches to identify, validate, and understand ischemic stroke gene expression. J Cereb Blood Flow Metab 21, 755
- Rice MC, Czymmek K, Kmiec EB. (2001). The potential of nucleic acid repair in functional genomics (Review). Nat Biotechnol 19, 321
- Rohlff C. (2001). Proteomics in neuropsychiatric disorders. Int J Neuropsychopharmacol 4, 93
- Saito H, Nakajima T, Matsumoto K. (2001). Human mast cell transcriptome project (Review). Int Arch Allergy Immunol 125, 1
- Schmitz G, Aslanidis C, Lackner KJ. (2001). Pharmacogenomics: Implications for laboratory medicine. Clin Chim Acta 308, 43
- Schulz-Knappe P, Zucht HD, Heine C, Jurgens M, Hess R, Schrader M. (2001). Peptidomics: The comprehensive analysis of peptides in complex biological mixtures. Comb Chem High Throughput Scr 4, 207
- Sreekumar KR, Aravind L, Koonin EV. (2001). Computational analysis of human disease-associated genes and their protein products. Curr Opin Genet Dev 11, 247
- Sternberg PW. (2001). Working in the post-genomic C. elegans world (Minireview). Cell 105, 173
- Taniguchi N, Ekuni A, Ko JH, Miyoshi E, Ikeda Y, Ihara Y, Nishikawa A, Honke K, Takahashi M. (2001). A glycomic approach to the identification and characterization of glycoprotein function in cells transfected with glycosyltransferase genes (Review). Proteomics 1, 239
- Tarleton RL, Kissinger J. (2001). Parasite genomics: Current status and future prospects. Curr Opin Immunol 13, 395
- Teichmann SA, Murzin AG, Chothia C. (2001). Determination of protein function, evolution and interactions by structural genomics. Curr Opin Struct Biol 11, 354
- Thebault S, Machour N, Perrot F, Jouenne T, Lange C, Hubert M, Fontaine M, Tron F, Charlionet R. (2001). Object and methodological development of proteomics. M S-Med Sci 17, 609
- Ubarretxena-Belandia I, Engelman DM. (2001). Helical membrane proteins: Diversity of functions in the content of simple architecture. Curr Opin Struct Biol 11, 370
- Van Belle D, Andre B. (2001). A genomic view of yeast membrane transporters (Review). Curr Opin Cell Biol 13, 389
- Van Oostrum J, Hoving S, Muller D, Schindler P, Steinmetz M, Towbin H, Voshol H, Wirth U. (2001). Proteomics: From protein identification to biological function. Chimia 55, 354
- Van Wijk KJ. (2001). Challenged and prospects of plant proteomics. Plant Physiol 126, 501
- Vandenbunder B. (2001). From DNA arrays to transcriptional regulatory networks (French, English Abstract). Bull Cancer 88, 253
- Vaucheret H, Fagard M. (2001). Transcriptional gene silencing in plants: Targets, inducers and regulators (Review). Trends Genet 17, 29
- Vitkup D, Melamud E, Moult J, Sander C. (2001). Completeness in structural genomics. Nat Struct Biol 8, 559
- Walch A, Specht K, Smida J, Aubele M, Zitelsberger H, Hofler H, Werner M. (2001). Tissue microdissection techniques in quantitative genome and gene expression analyses (Review). Histochem Cell Biol 115, 269
- Walsh UF, Morrissey JP, O'Gara F. (2001). Pseudomonas for biocontrol of phytopathogens: From functional genomics to commercial exploitation. Curr Opin Biotechnol 12, 289
- Walter G, Konthur Z, Lehrach H. (2001). High-throughput screening of surface displayed gene products. Comb Chem High Throughput Scr 4, 193
- Wieczorek SJ, Tsongalis GJ. (2001). Pharmacogenomics: Will it change the field of medicine? Clin Chim Acta 308, 1
- Zabarovsky ER. (2001). Alternative approaches to genome mapping and sequencing. Mol Biol-Engl Tr 35, 183
- 3. Large-scale sequencing and mapping
- Akopyants NS, Clifton SW, Martin J, Pape D, Wylie T, Li L, Kissinger JC, Roos DS, Beverley SM. (2001). A survey of the Leishmania major Friedlin strain V1 genome by shotgun sequencing: A resource for DNA microarrays and expression profiling. Mol Biochem Parasitol 113, 337
- Aubourg S, Rouze P. (2001). Genome annotation. Plant Physiol Biochem 39, 181
- Bahr U, Darai G. (2001). Analysis and characterization of the complete genome of Tupala (tree shrew) herpesvirus. J Virol 75, 4854
- Blazewicz J, Formanowicz P, Kasprzak M, Jaroszewski M, Markiewicz WT. (2001). Construction of DNA restriction maps based on a simplified experiment. Bioinformatics 17, 398
- Bolotin A, Wincker P, Mauger S, Jaillon O, Malarme K, Weissenbach J, Ehrlich SD, Sorokin A. (2001). The complete genome sequence of the lactic acid bacterium Lactococcus lactis spp lactis IL1403. Genome Res 11, 731
- Casaregola S, Nguyen HV, Lapathitis G, Kotyk A, Gaillardin C. (2001). Analysis of the constitution of the beer yeast genome by PCR, sequencing and subtelomeric sequence hybridization. Int J Syst Evol Microbiol 51, 1607
- Chambaud I, Heilig R, Ferris S, Barbe V, Samson D, Galisson F, Moszer I, Dybvig K, Wroblewski H, Viari A, Rocher EPC, Blanchard A. (2001). The complete genome sequence of the murine respiratory pathogen Mycoplasma pulmonis. Nucleic Acids Res 29, 2145
- Ferretti JJ, McShan WM, Ajdic D, Savic DJ, Lyon K, Primeaux C, Sezate S, Suvorov AN, Kenton S, Lai HS, Lin SP, Qian YD, Jia HG, Najar FZ, Ren Q, Zhu H, Song L, White J, Yuan XL, Clifton SW, Roe BA, McLaughlin R. (2001). Complete genome sequence of an M1 strain of Streptococcus pyogenes. Proc Natl Acad Sci U S A 98, 4658
- Frohme M, Camargo AA, Czink C, Matsukuma AY, Simpson AJG, Hoheisel JD, Verjovski-Almeida S. (2001). Directed gap closure in large-scale sequencing projects. Genome Res 11, 901
- Glusman G, Yanai I, Rubin I, Lancet D. (2001). The complete human olfactory subgenome. Genome Res 11, 685
- Gordon SV, Eiglmeier K, Garnier T, Brosch R, Parkhill J, Barrell B, Cole ST, Hewinson RG. (2001). Genomics of Mycobacterium bovis. Tuberculosis 81, 157
- Gray WL, Starnes B, White MW, Mahalingam R. (2001). The DNA sequence of the simian varicella virus genome. Virology 284, 123
- Hall D, Bhandarkar SM, Arnold J, Jiang TZ. (2001). Physical mapping with automatic capture of hybridization data. Bioinformatics 17, 205
- Harley E, Bonner A, Goodman N. (2001). Uniform integration of genome mapping data using intersection graphs. Bioinformatics 17, 487
- Hauser NC, Fellenberg K, Gil R, Bastuck S, Hoheisel JD, Perez-Ortin JE. (2001). Whole genome analysis of a wine yeast strain. Comp Funct Genom 2, 69
- Janssen CS, Barrett MP, Lawson D, Quail MA, Harris D, Bowman S, Phillips RS, Turner CMR. (2001). Gene discovery in Plasmodium chabaudi by genome survey sequencing. Mol Biochem Parasitol 113, 251
- Karlin S, Bergman A, Gentles AJ. (2001). Annotation of the Drosophila genome. Nature 411, 259
- Kerscher S, Durstewitz G, Casaregola S, Gaillardin C, Brandt U. (2001). The complete mitochondrial genome of Yarrowia lipolytica. Comp Funct Genom 2, 80
- Kuroda M, Ohta T, Uchiyama I, Baba T, Yuzawa H, Kobayashi I, Cui LZ, Oguchi A, Aoki K, Nagai Y, Lian JQ, Ito T, Kanamori M, Matsumaru H, Murayama A, Murakami H, Hosoyama A, Mizutani-Ui Y, Takahashi NK, Sawano T, Inoue R, Kaito C, Sekimizu K, Hirakawa H, Kuhara S, Goto S, Yabuzaki J, Kanehisa M, Yamashita A, Ogasawara N, Hayashi H, Hiramatsu K. (2001). Whole genome sequencing of meticillin-resistant Staphylococcus aureus. Lancet 357, 1225
- Louis A, Ollivier E, Aude JC, Risler EL. (2001). Massive sequence comparisons as a help in annotating genomic sequences. Genome Res 11, 1296
- Maddox JF, Davies KP, Crawford AM, Hulme DJ, Vaiman D, Cribiu EP, Freking BA, Beh KJ, Cockett NE, Kang N, Riffkin CD, Drinkwater R, Moore SS, Dodds KG, Lumsden JM, Van Stijn TC, Phua SH, Adelson DL, Burkin HR, Brrom JE, Buitkamp J, Cambridge L, Cushwa WT, Gerard E, Galloway SM, Harrison B, Hawken RJ, Hiendleder S, Henry SM, Medrano JF, Paterson KA, Schibler L, Stone RT, Van Hest B. (2001). An enhanced linkage map of the sheep genome comprising more than 1000 loci. Genome Res 11, 1275
- McCarter JP, Bird DM, Clifton SW, Waterston RH. (2000). Nematode gene sequences, December 2000 update. J Nematol 32, 331
- Ming R, Moore PH, Zee F, Abbey CA, Ma H, Paterson AH. (2001). Construction and characterization of a papaya BAC library as a foundation for molecular dissection of a tree-fruit genome. Theor Appl Genet 102, 892
- Nouzova M, Neumann P, Navratilova A, Galbraith DW, Macas J. (2001). Microarray-based survey of repetitive genomic sequences in Vicia spp. Plant Mol Biol 45, 229
- Samretwanich K, Kittipakom K, Chiemsombat P, Ikegami M. (2001). Complete nucleotide sequence and genome organization of soybean crinkle leaf virus. J Phytopathol 149, 333
- Seki M, Narusaka M, Yamaguchi-Shinozaki K, Carninci P, Kawai J, Hayashizaki Y, Shinozaki K. (2001). Arabidopsis encyclopedia using full-length cDNAs and its application. Plant Physiol Biochem 39, 211
- She Q, Singh RK, Confalonieri F, Zivanovic Y, Allard G, Awayez MJ, Chan-Weiher CCY, Clausen IG, Curtis BA, De Moors A, Erauso G, Fletcher C, Gordon PMK, Heikamp-de Jong I, Jeffries AC, Kozera CJ, Medina N, Peng X, Thi-Ngoe HP, Redder P, Scheuk ME, Theriault C, Tolstrup N, Charlebois RL, Doolittle WF, Duguet M, Gaasterland T, Garrett RA, Ragan MA, Sensen CW, Van der Oost J. (2001). The complete genome of the crenarchaeon Sulfolobus solfataricus P2. Proc Natl Acad Sci U S A 98, 7835
- Tettelin H, Nelson KE, Paulsen IT, Eisen JA, Read TD, Peterson S, Heidelberg J, De Boy RT, Haft DH, Dodson RJ, Durkin AS, Gwinn M, Kolonay JF, Nelson WC, Peterson JD, Umayam LA, White O, Salzberg SL, Lewis MR, Radune D, Holtzapple E, Khouri H, Wolf AM, Utterback TR, Hansen CL, McDonald LA, Feldblyum TV, Angiuoli S, Dickinson T, Hickey EK, Holt IE, Loftus BJ, Yang F, Smitt HO, Venter JC, Dougherty BA, Morrison DA, Hollingshead SK, Fraser CM. (2001). Complete genome sequence of a virulent isolate of Streptococcus pneumoniae. Science 293, 498
- Von Nickisch-Rosenegk M, Brown WM, Boore JL. (2001). Complete sequence of the mitochondrial genome of the tapeworm Hymenolepsis diminuta: Gene arrangements indicate that platyhelminths are eutrochozoans. Mol Biol Evol 18, 721
- Zhang HB, Wu CC. (2001). BAC as tools for genome sequencing. Plant Physiol Biochem 39, 195
- 4. Evolutionary genomics
- Baisnee PF, Baldi P, Brunak S, Pedersen AG. (2001). Flexibility of the genetic code with respect to DNA structure. Bioinformatics 17, 237
- Handa N, Nakayama Y, Sadykov M, Kobayashi I. (2001). Experimental genome evolution: Large-scale genome rearrangements associated with resistance to replacement of a chromosomal restriction-modification gene complex. Mol Microbiol 40, 932
- Jakobsen IB, Saleeba JA, Poidinger M, Littlejohn TG. (2001). TreeGeneBrowser: Phylogenetic data mining of gene sequences from public databases. Bioinformatics 17, 535
- Kreil DP, Ouzounis CA. (2001). Identification of thermophilic species by the amino acid compositions deduced from their genomes. Nucleic Acids Res 29, 1608
- Kundu S, Bandyopadhyay D, Thakur AR. (2001). Sequence-based structural signatures of genome evolution. Indian J Biochem Biophys 38, 104
- Lecompte O, Ripp R, Puzos-Barbe V, Duprat S, Heilig R, Dietrich J, Thierry JC, Poch O. (2001). Genome evolution at the genus level: Comparison of three complete genomes of hyperthermophilic Archaea. Genome Res 11, 981
- Ledent V, Vervoort M. (2001). The basic helix-loop-helix protein family: Comparative genomics and phylogenetic analysis. Genome Res 11, 754
- Marais G, Mouchiroud D, Duret L. (2001). Does recombination improve selection on codon usage? Lessons from nematode and fly complete genomes. Proc Natl Acad Sci U S A 98, 5688
- McGuire G, Denham MC, Balding DJ. (2001). MAC5: Bayesian inference of phylogenetic trees from DNA sequences incorporating gaps. Bioinformatics 17, 479
- Nevo E. (2001). Evolution of genome-phenome diversity under environmental stress. Proc Natl Acad Sci U S A 98, 6233
- Rocha EPC, Danchin A, Viari A. (2001). Evolutionary role of restriction/modification systems as revealed by comparative genome analysis. Genome Res 11, 946
- Ronneberg TA, Freeland SJ, Landweber LF. (2001). Genview and Gencode: A pair of programs to test theories of genetic code evolution. Bioinformatics 17, 280
- Rujan T, Martin W. (2001). How many genes in Arabidopsis come from cyanobacteria? An estimate from 386 protein phylogenies. Trends Genet 17, 113
- Salzberg SL, White O, Peterson J, Eisen JA. (2001). Microbial genes in the human genome: Lateral transfer or gene loss? Science 292, 1903
- Suyama M, Bork P. (2001). Evolution of prokaryotic gene order: Genome rearrangements in closely related species. Trends Genet 17, 10
- Tolou HJG, Couissinier-Paris P, Durand JP, Mercier V, De Pina JJ, De Micco P, Billoir F, Charrel RN, De Lamballerie X. (2001). Evidence for recombination in natural populations of dengue virus type 1 based on the analysis of complete genome sequences. J Gen Virol 82, 1283
- Tu ZC, Dewhirst FE, Blaser MJ. (2001). Evidence that the Campylobacter fetus sap locus is an ancient genomic constituent with origins before mammals and reptiles diverged. Infect Immun 69, 2237
- Vicient CM, Jaaskelainen MJ, Kalendar R, Schulman AH. (2001). Active retrotransposons are a common feature of grass genomes. Plant Physiol 125, 1283
- Zoldos V, Siljak-Yakovlev S, Papes D, Sarr A, Panaud O, Zoldos V, Papes D. (2001). Representational difference analysis reveals genomic differences between Q. robur and Q. suber: Implications for the study of genome evolution in the genus Quercus. Mol Genet Genomics 265, 234
- 5. Comparative genomics
- Akin A, Lin TL, Wu CC, Bryan TA, Hooper T, Schrader D. (2001). Nucleocapsid protein gene sequence analysis reveals close genomic relationship between turkey coronavirus and avian infectious bronchitis virus. Acta Virol 45, 31
- Desiere F, Mahanivong C, Hillier AJ, Chandry PS, Davidson BE, Brussow H. (2001). Comparative genomics of lactococcal phages: Insight from the complete genome sequence of Lactococcus lactis phase BK5-T. Virology 283, 240
- Draye X, Lin YR, Qian XY, Bowers JE, Burow GB, Morrell PL, Peterson DG, Presting GG, Ren SX, Wing RA, Paterson AH. (2001). Toward integration of comparative genetic, physical, diversity, and cytomolecular maps for grasses and grains, using the sorghum genome as a foundation. Plant Physiol 125, 1325
- Dubcovsky J, Ramakrishna W, San Miguel PJ, Busso CS, Yan LL, Shiloff BA, Bennetzen JL. (2001). Comparative sequence analysis of colinear barley and rice bacterial artificial chromosomes. Plant Physiol 125, 1342
- Ito H, Sugiyama M, Masubuchi K, Mori Y, Minamoto N. (2001). Complete nucleotide sequence of a group A avian rotavirus genome and a comparison with its counterparts of mammalian rotaviruses. Virus Res 75, 123
- Janke B, Dobrindt U, Hacker J, Blum-Oehler G. (2001). A subtractive hybridisation analysis of genomic differences between the uropathogenic E. coli strain 536 and the E. coli K12 strain MG1655. FEMS Microbiol Lett 199, 61
- Mayer K, Murphy G, Tarchini R, Wambutt R, Volckaert G, Pohl T, Dusterhoft A, Stiekema W, Entian KD, Terryn N, Lemcke K, Haase D, Hall CR, Van Dodeweerd AM, Tingey SV, Mewes HW, Bevan MW, Bancroft I. (2001). Conservation of microstructure between a sequenced region of the genome of rice and multiple segments of the genome of Arabidopsis thaliana. Genome Res 11, 1167
- Rossberg M, Theres K, Acarkan A, Herrero R, Schmitt T, Schumacher K, Schmitz G, Schmidt R. (2001). Comparative sequence analysis reveals extensive microcolinearity in the lateral suppressor regions of the tomato, Arabidopsis, and Capsella genomes. Plant Cell 13, 979
- Schmidt R, Acarkan A, Boivin K. (2001). Comparative structural genomics in the Brassicaceae family. Plant Physiol Biochem 39, 253
- Yanai I, Derti A, De Lisi C. (2001). Genes linked by fusion events are generally of the same functional category: A systematic analysis of 30 microbial genomes. Proc Natl Acad Sci U S A 98, 7940
- 6. Pathways, gene families and regulons
- Heger A, Holm L. (2001). Picasso: Generating a covering set of protein family profiles. Bioinformatics 17, 272
- Mayfield JA, Fiebig A, Johnstone SE, Preuss D. (2001). Gene families from the Arabidopsis thaliana protein pollen coat proteome. Science 292, 2482
- Myung K, Chen C, Kolodner RD. (2001). Multiple pathways co-operate in the suppression of genome instability in Saccharomyces cerevisiae. Nature 411, 1073
- Park J, Lappe M, Teichmann SA. (2001). Mapping protein family interactions: Intramolecular and intermolecular protein family interaction repertoires in the PDB and yeast. J Mol Biol 307, 929
- Robinson-Rechavi M, Marchand O, Escriva H, Bardet PL, Zelus D, Hughes S, Laudet V. (2001). Euteleost fish genomes are characterized by expansion of gene families. Genome Res 11, 781
- Shoop E, Silverstein KAT, Johnson JE, Retzel EF. (2001). MetaFam: A unified classification of protein families. II. Schema and query capabilities. Bioinformatics 17, 262
- Silverstein KAT, Shoop E, Johnson JE, Retzel EF. (2001). MetaFam: A unified classification of protein families. I. Overview and statistics. Bioinformatics 17, 249
- Suzuki Y, Tsunoda T, Sese J, Taira H, Mizushima-Sugano J, Hata H, Ota T, Isogai T, Tanaka T, Nakamura Y, Suyama A, Sakaki Y, Morishita S, Okubo K, Sugano S. (2001). Identification and characterization of the potential promoter regions of 1031 kinds of human genes. Genome Res 11, 677
- 7. Pharmacogenomics
- Akiyoshi S, Ishii M, Nemoto N, Kawabata M, Aburatani H, Miyazono K. (2001). Targets of transcriptional regulation by transforming growth factor-β: Expression profile analysis using oligonucleotide arrays. Jpn J Cancer Res 92, 257
- Behr MA. (2001). Correlation between BCG genomics and protective efficacy. Scand J Infec Dis 33, 249
- Behr MA. (2001). Comparative genomics of BCG vaccines. Tuberculosis 81, 165
- Bertucci F, Houlgatte R, Nguyen C, Benziane A, Nasser V, Granjeaud S, Tagett B, Loriod B, Giaconia A, Jacquemier J, Viens P, Birnbaum D. (2001). Molecular typing of breast cancer: Transcriptomics and DNA microarrays (French English Abstract). Bull Cancer 88, 277
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- 8. Large-scale mutagenesis programmes
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- 9. Functional genomics
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- Cliften PF, Hillier LW, Fulton L, Graves T, Miner T, Gish WR, Waterston RH, Johnston M. (2001). Surveying Saccharomyces genomes to identify functional elements by comparative DNA sequence analysis. Genome Res 11, 1175
- Frankenberg N, Mukougawa K, Kohchi T, Lagarias JC. (2001). Functional genomic analysis of the HY2 family of ferredoxin-dependent bilin reductases from oxygenic photosynthesis organisms. Plant Cell 13, 965
- Hishigaki H, Nakai K, Ono T, Tanigami A, Takagi T. (2001). Assessment of prediction accuracy of protein function from protein-protein interaction data. Yeast 18, 523
- Ishimaru K, Yano M, Aoki N, Ono K, Hirose T, Lin SY, Monna L, Sasaki T, Ohsugi R. (2001). Toward the mapping of physiological and agronomic characters on a rice function map: QTL analysis and comparison between QTLs and expressed sequence tags. Theor Appl Genet 102, 793
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- King RD, Karwath A, Clare A, Dehaspe L. (2001). The utility of different representations of protein sequence for predicting functional class. Bioinformatics 17, 445
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- Lau GW, Haataja S, Lonetto M, Kensit SE, Marra A, Bryant AP, McDevitt D, Morrison DA, Holden DW. (2001). A functional genomic analysis of type 3 Streptococcus pneumoniae virulence. Mol Microbiol 40, 555
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- Paustian ML, May BJ, Kapur V. (2001). Pasteurella multocida gene expression in response to iron limitation. Infect Immun 69, 4109
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- Rabitsch KP, Toth A, Galova M, Schleiffer A, Schaffner G, Aigner E, Rupp C, Penkner AM, Moreno-Borchart AC, Primig M, Esposito RE, Klein F, Knop M, Nasmyth K. (2001). A screen for genes required for meiosis and spore formation based on whole-genome expression. Curr Biol 11, 1001
- Reymond P. (2001). DNA microarrays and plant defence. Plant Physiol Biochem 39, 313
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- 10. Transcriptomics
- Becker B, Vogt T, Landthaler M, Stolz W. (2001). Detection of differentially regulated genes in keratinocytes by cDNA array hybridization: Hsp27 and other novel players in response to artificial ultraviolet radiation. J Investig Dermatol 116, 983
- Blader IJ, Manger ID, Boothroyd JC. (2001). Microarray analysis reveals previously unknown changes in Toxoplasma gondii-infected human cells. J Biol Chem 276, 24223
- Brown AJP, Planta RJ, Restuhadi F, Bailey DA, Butler PR, Cadahia JL, Cerdan ME, De Jonge M, Gardner DCJ, Gent ME, Hayes A, Kolen CP, Lombardia LJ, Murad AM, Oliver RA, Sefton M, Thevelein JM, Tournu H, Van Delft YJ, Verbart DJ, Winderickx J, Oliver SG. (2001). Transcript analysis of 1003 novel yeast genes using high-throughput northern hybridizations. EMBO J 20, 3177
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- Hihara Y, Kamei A, Kanehisa M, Kaplan A, Ikeuchi M. (2001). DNA microarray analysis of cyanobacterial gene expression during acclimation to high light. Plant Cell 13, 793
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- Hughes TR, Mao M, Jones AR, Burchard J, Marton MJ, Shannon KW, Lefkowitz SM, Ziman M, Schelter JM, Meyer MR, Kabayashi S, Davis C, Dai HY, He YDD, Stephaniants SB, Cavet G, Walker WL, West A, Coffey E, Shoemaker DD, Stoughton R, Blanchard AP, Friend SH, Linsley PS. (2001). Expression profiling using microarrays fabricated by an ink-jet oligonucleotide synthesizer. Nat Biotechnol 19, 342
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- Kawasaki S, Borchert C, Deyholos M, Wang H, Brazille S, Kawai K, Galbraith D, Bohnert HJ. (2001). Gene expression profiles during the initial phase of salt stress in rice. Plant Cell 13, 889
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- Nagasawa Y, Takenaka M, Kaimori J, Matsuoka Y, Akagi Y, Tsujie M, Imai E, Hori M. (2001). Rapid and diverse changes of gene expression in the kidneys of protein-overload proteinuria mice detected by microarray analysis. Nephrol Dial Transplant 16, 923
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- Scandurro AB, Weldon CW, Figueroa YG, Alam J, Beckman BS. (2001). Gene microarray analysis reveals a novel hypoxia signal transduction pathway in human hepatocellular carcinoma cells. Int J Oncol 19, 129
- Smith EJ, Shi L, Drummond P, Rodriguez L, Hamilton R, Ramlal S, Smith G, Pierce K, Foster J. (2001). Expressed sequence tags for the chicken genome from a normalized 10-day-old white leghorn whole embryo cDNA library: I. DNA sequence characterization and linkage analysis. J Hered 92, 1
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- Van der Merwe GK, Van Vuuren HJJ, Cooper TG. (2001). Cis-acting sites contributing to expression of divergently transcribed DAL1 and DAL4 genes in S. cerevisiae: A word of caution when correlating cis-acting sequences with genome-wide expression analyses. Curr Genet 39, 156
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- 11. Proteomics
- Alaiya AA, Oppermann M, Langridge J, Roblick U, Egevad L, Brandstedt S, Hellstrom M, Linder S, Bergman T, Jornvall H, Auer G. (2001). Identification of proteins in human prostate tumor material by two-dimensional gel electrophoresis and mass spectrometry. Cell Mol Life Sci 58, 307
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- Derhami K, Zheng J, Li L, Wolfaardt JF, Scott PG. (2001). Proteomic analysis of human skin fibroblasts grown on titanium: Novel approach to study molecular biocompatibility. J Biomed Mater Res 56, 234
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- 13. Metabolomics
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- 14. Genomic approaches to development
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- Liu HC, He ZM, Rosenwaks Z. (2001). Application of complementary DNA microarray (DNA chip) technology in the study of gene expression profiles during folliculogenesis. Fertil Steril 75, 947
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- 15. Technological advances
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- 16. Bioinformatics
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