Current awareness on comparative and functional genomics.

* Reviews & symposia

2004. Special issue: Genomes and evolution. Curr Opin Genet Dev 14: (6)

2004. Special issue: Proceedings of the First Annual Conference of the MidSouth Computational Biology and Bioinformatics Society, November 13-15 2003, Little Rock, Ar, USA. DNA Cell Biol 23: (10)

2004. Special issue: Linking Functional Genomics with Physiology for Global Change Research. Field Crop Res 90: (1)

Bar-Joseph Z. 2004. Analyzing time series gene expression data (Review). Bioinformatics 20: (16) 2493.

Bennetzen JL, Coleman C, Liu RY, Ma JX, Ramakrishna W. 2004. Consistent over-estimation of gene number in complex plant genomes. Curr Opin Plant Biol 7: (6) 732.

Burt DW. 2004. The chicken genome and the developmental biologist. Mech Dev 121: (9) 1129.

Causler B. 2004. Studying the interactome with the yeast two-hybrid system and mass spectrometry. Mass Spectrom Rev 23: (5) 350.

Chignard N, Beretta L. 2004. Proteomics for hepatocellular carcinoma marker discovery. Gastroenterology 127: (5 Suppl 1) S120.

Darvas F, Dorman G, Krajcsi P, Puskas LG, Kovari Z, Lorincz Z, Urge L. 2004. Recent advances in chemical genomics. Curr Med Chem 11: (23) 3119.

Dharmadi Y, Gonzalez R. 2004. DNA microarrays: Experimental issues, data analysis, and application to bacterial systems (Review). Biotechnol Prog 20: (5) 1309.

Engstrom Y, Loseva O, Theopold U. 2004. Proteomics of the Drosophila immune response (Review). Trends Biotechnol 22: (11) 600.

Eyers L, George I, Schuler L, Stenuit B, Agathos SN, El Fantroussi S. 2004. Environmental genomics: Exploring the unmined richness of microbes to degrade xenobiotics (Review). Appl Microbiol Biotechnol 66: (2) 123.

Fey MF. 2004. Genomics and proteomics: Expression arrays in clinical oncology. Ann Oncol 15: (Suppl 4) iv163.

Friedman A, Perrimon N. 2004. Genome-wide high-throughput screens in functional genomics. Curr Opin Genet Dev 14: (5) 470.

Guenet JL. 2004. Chemical mutagenesis of the mouse genome: An overview. Genetica 122: (1) 9.

Hachey DL, Chaurand P. 2004. Proteomics in reproductive medicine: The technology for separation and identification of proteins. J Reprod Immunol 63: (1) 61.

Haraguchi N, Inoue H, Mimori K, Tanaka F, Utsunomiya T, Yoshikawa K, Mori M. 2004. Analysis of gastric cancer with cDNA microarray. Cancer Chemother Pharmacol 54: (Suppl 1) S21.

Haubold B, Wiehe T. 2004. Comparative genomics: Methods and applications (Review). Naturwissenschaften 91: (9) 405.

Kabuyama Y, Resing KA, Ahn NG. 2004. Applying proteomics to signaling networks. Curr Opin Genet Dev 14: (5) 492.

Korpelainen H. 2004. The evolutionary processes of mitochondrial and chloroplast genomes differ from those of nuclear genomes (Review). Naturwissenschaften 91: (11) 505.

Kramer R, Cohen D. 2004. Functional genomics to new drug targets. Nat Rev Drug Discov 3: (11) 965.

Lee JS, Thorgeirsson SS. 2004. Genome-scale profiling of gene expression in hepatocellular carcinoma: Classification, survival prediction, and identification of therapeutic targets. Gastroenterology 127: (5 Suppl 1) S51.

Leitner A, Lindner W. 2004. Current chemical tagging strategies for proteome analysis by mass spectrometry (Review). J Chromatogr B 813: (1-2) 1.

Lenz HJ. 2004. Pharmacogenomics and colorectal cancer. Ann Oncol 15: (Suppl 4) iv173.

Liew CC, Dzau VJ. 2004. Molecular genetics and genomics of heart failure. Nat Rev Genet 5: (11) 811.

Llinas M, DeRisi JL. 2004. Pernicious plans revealed: Plasmodium falciparum genome wide expression analysis. Curr Opin Microbiol 7: (4) 382.

Lundstrom K. 2004. Structural genomics on membrane proteins: Mini review. Comb Chem High Throughput Scr 7: (5) 431.

Mestres J. 2004. Computational chemogenomics approaches to systematic knowledge-based drug discovery. Curr Opin Drug Discov Dev 7: (3) 304.

Motyka SA, Englund PT. 2004. RNA interference for analysis of gene function in trypanosomatids. Curr Opin Microbiol 7: (4) 362.

Muller-Hagen G, Beinert T, Sommer A. 2004. Aspects of lung cancer gene expression profiling. Curr Opin Drug Discov Dev 7: (3) 290.

O'Donnell R, Holland JW, Deeth HC, Alewood P. 2004. Milk proteomics (Review). Int Dairy J 14: (12) 1013.

Parsons L, Orban J. 2004. Structural genomics and the metabolome: Combining computational and NMR methods to identify target ligands. Curr Opin Drug Discov Dev 7: (1) 62.

Penkett CJ, Bahler J. 2004. Navigating public microarray databases (Review). Comp Funct Genom 5: (6-7) 471.

Prentice H, Webster KA. 2004. Genomic and proteomic profiles of heart disease (Review). Trends Cardiovasc Med 14: (7) 282.

Preuss TM, Caceres M, Oldham MC, Geschwind DH. 2004. Human brain evolution: Insights from microarrays. Nat Rev Genet 5: (11) 850.

Rupp S. 2004. Proteomics on its way to study host-pathogen interaction in Candida albicans. Curr Opin Microbiol 7: (4) 330.

Scobioala S, Klocke R, Michel G, Kuhlmann M, Nikol S. 2004. Proteomics: State of the art and its application in cardiovascular research. Curr Med Chem 11: (24) 3203.

Sellheyer K, Belbin TJ. 2004. DNA microarrays: From structural genomics to functional genomics. The applications of gene chips in dermatology and dermatopathology. J Am Acad Dermatol 51: (5) 681.

Simillion C, Vandepoele K, Van de Peer Y. 2004. Recent developments in computational approaches for uncovering genomic homology. Bioessays 26: (11) 1225.

Stathopoulos A, Levine M. 2004. Whole-genome analysis of Drosophila gastrulation. Curr Opin Genet Dev 14: (5) 477.

Stevens EV, Posadas EM, Davidson B, Kohn EC. 2004. Proteomics in cancer. Ann Oncol 15: (Suppl 4) iv167.

Thiede B, Rudel T. 2004. Proteome analysis of apoptotic cells. Mass Spectrom Rev 23: (5) 333.

Williams K, Wu T, Colangelo C, Nairn AC. 2004. Recent advances in neuroproteomics and potential application to studies of drug addiction. Neuropharmacology 47: (Suppl) 148.

3 Large-scale sequencing and mapping

Baliga NS, Bonneau R, Facciotti MT, Pan M, Glusman G, Deutsch EW, Shannon P, Chiu YL, Gan RR, Hung PL et al. 2004. Genome sequence of Haloarcula marismortui: A halophilic archaeon from the Dead Sea. Genome Res 14: (11) 2221.

Costantini M. 2004. An analysis of sponge genomes. Gene 342: (2) 321.

Fu Y, Hsia AP, Guo L, Schnable PS. 2004. Types and frequencies of sequencing errors in methyl-filtered and high [C.sub.0]t maize genome survey sequences. Plant Physiol 135: (4) 2040.

Hendrickson EL, Kaul R, Zhou Y, Bovee D, Chapman P, Chung J, De Macario EC, Dodsworth JA, Gillett W, Graham DE et al. 2004. Complete genome sequence of the genetically tractable hydrogenotrophic methanogen Methanococcus maripaludis. J Bacteriol 186: (20) 6956.

Ihara N, Takasuga A, Mizoshita K, Takeda H, Sugimoto M, Mizoguchi Y, Hirano T, Itoh T, Watanabe T, Reed KM et al. 2004. A comprehensive genetic map of the cattle genome based on 3802 microsatellites. Genome Res 14: (10A) 1987.

Messing J, Bharti AK, Karlowski WM, Gundlach H, Kim HR, Yu Y, Wei FS, Fuks G, Soderlund CA, Mayer KFX et al. 2004. Sequence composition and genome organization of maize. Proc Natl Acad Sci U S A 101: (40) 14349.

Monosi B, Wisser RJ, Pennill L, Hulbert SH. 2004. Full-genome analysis of resistance gene homologues in rice. Theor Appl Genet 109: (7) 1434.

Monteiro-Vitorello CB, Camargo LEA, Van Sluys MA, Kitajima JP, Truffi D, Do Amaral AM, Harakava R, De Oliveira JCF, Wood D, De Oliveira MC et al. 2004. The genome sequence of the Gram-positive sugarcane pathogen Leifsonia xyli subsp xyli. Mol Plant Microbe Interact 17: (8) 827.

Munkvold JD, Greene RA, Bermudez-Kandianis CE, La Rota CM, Edwards H, Sorrells SF, Dake T, Benscher D, Kantety R, Linkiewicz AM et al. 2004. Group 3 chromosome bin maps of wheat and their relationship to rice chromosome 1. Genetics 168: (2) 639.

Wallis JW, Aerts J, Groenen MAM, Crooijmans RPMA, Layman D, Graves TA, Scheer DE, Kremitzki C, Fedele MJ, Mudd NK et al. 2004. A physical map of the chicken genome. Nature 432: (7018) 761.

Xia QY, Zhou ZY, Lu C, Cheng DJ, Dai FY, Li B, Zhao P, Zha XF, Cheng TC, Chai CL et al. 2004. A draft sequence for the genome of the domesticated silkworm (Bombyx mori). Science 306: (5703) 1937.

Zhou SG, Kile A, Kvikstad E, Bechner M, Severin J, Forrest D, Runnheim R, Churas C, Anantharaman TS, Myler P et al. 2004. Shotgun optical mapping of the entire Leishmania major Friedlin genome. Mol Biochem Parasitol 138: (1) 97.

4 Evolutionary genomics

Bengtsson BO. 2004. Modelling the evolution of genomes with integrated external and internal functions. J Theor Biol 231: (2) 271.

Drnevich JM, Reedy MM, Ruedi EA, Rodriguez-Zas S, Hughes KA. 2004. Quantitative evolutionary genomics: Differential gene expression and male reproductive success in Drosophila melanogaster. Proc R Soc Lond B Biol Sci 271: (1554) 2267.

Gao LZ, Innan H. 2004. Very low gene duplication rate in the yeast genome. Science 306: (5700) 1367.

Hillier LW, Miller W, Birney E, Warren W, Hardison RC, Ponting CP, Bork P, Burt DW, Groenen MAM, Delany ME et al. 2004. Sequence and comparative analysis of the chicken genome provide unique perspectives on vertebrate evolution. Nature 432: (7018) 695.

Kim KJ, Lee HL. 2004. Complete chloroplast genome sequences from Korean ginseng (Panax schinseng Nees) and comparative analysis of sequence evolution among 17 vascular plants. DNA Res 11: (4) 247.

Ovcharenko I, Stubbs L, Loots GG. 2004. Interpreting mammalian evolution using Fugu genome comparisons.…