Current Awareness
Open Access
Current Awareness
First published: 19 August 2002
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
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- Aardema MJ, MacGregor JT. (2002). Toxicology and genetic toxicology in the new era of ‘toxicogenomics’: impact of ‘-omics’ technologies. Mutat Res 499, 13
- Adams MD, Sekelsky JJ. (2002). From sequence to phenotype: Reverse genetics in Drosophila melanogaster. Nat Rev Genet 3, 189
- Allsop A, Illingworth R. (2002). The impact of genomics and related technologies on the search for new antibiotics. J Appl Microbiol 92, 7
- Altman RB, Klein TE. (2002). Challenges for biomedical informatics and pharmacogenomics. Annu Rev Pharmacol Toxicol 42, 113
- Andersen JS, Lyon CE, Fox AH, Leung AKL, Lam YW, Steen H, Mann M, Lamond AI. (2002). Directed proteomic analysis of the human nucleolus (Review). Curr Biol 12, 1
- Arcellana-Panlilio M, Robbins SM. (2002). Cutting-edge technology: I. Global gene expression profiling using DNA microarrays. Am J Physiol 282, G397
- Arya P, Joseph R, Chou DTH. (2002). Toward high-throughout synthesis of complex natural product-like compounds in the genomics and proteomics age (Review). Chem Biol 9, 145
- Austin MJF, Kreiner T. (2002). Integrating genomics technologies in health care: Practice and policy challenges and opportunities. Physiol Genomics 8, 33
- Azuaje F. (2002). Advancing post-genome data and system integration through machine learning (Conference Review). Comp Funct Genom 3, 28
- Barnes MR. (2002). SNP and mutation data on the Web - Hidden treasures for uncovering (Review). Comp Funct Genom 3, 67
- Barnes S. (2002). Comparing Arabidopsis to other flowering plants. Curr Opin Plant Biol 5, 128
- Beckers J, De Angelis MH. (2002). Large-scale mutational analysis for the annotation of the mouse genome. Curr Opin Chem Biol 6, 17
- Blackshaw S, Livesey R. (2002). Applying genomics technologies to neural development. Curr Opin Neurobiol 12, 110
- Brizuela L, Braun P, La Baer J. (2001). FLEXGene repository: From sequenced genomes to gene repositories for high-throughput functional biology and proteomics (Review). Mol Biochem Parasitol 118, 155
- Brussow H, Hendrix RW. (2002). Phage genomics: Small is beautiful (Mini-Review). Cell 108, 13
- Buckler ES, Thornberry JM. (2002). Plant molecular diversity and applications to genomics. Curr Opin Plant Biol 5, 107
10.1016/S1369-5266(02)00238-8 Google Scholar
- Camargo AA, De Souza SJ, Brentani RR, Simpson AJG. (2002). Human gene discovery through experimental definition of transcribed regions of the human genome. Curr Opin Chem Biol 6, 13
- Chung TP, Laramie JM, Province M, Cobb JP. (2002). Functional genomics of critical illness and injury. Crit Care Med 30, S51
- Cirelli C. (2002). How sleep deprivation affects gene expression in the brain: A review of recent findings. J Appl Physiol 92, 394
- Conrads TP, Issaq HJ, Veenstra TD. (2002). New tools for quantitative phosphoproteome analysis. Biochem Biophys Res Commun 290, 885
- Copley RR, Letunic I, Bork P. (2002). Genome and protein evolution in eukaryotes. Curr Opin Chem Biol 6, 39
- Copley RR, Doerks T, Letunic I, Bork P. (2002). Protein domain analysis in the era of complete genomes. FEBS Lett 513, 129
- Coppel RL. (2001). Bioinformatics and the malaria genome: Facilitating access and exploitation of sequence information (Review). Mol Biochem Parasitol 118, 139
- Croston GE. (2002). Functional cell-based µHTS in chemical genomic drug discovery (Review). Trends Biotechnol 20, 110
- Davidson EH, Rast JP, Oliveri P, Ransick A, Calestani C, Yuh CH, Minokawa T, Amore G, Hinman V, Arenas-Mena C, Otim O, Brown CT, Livi CB, Lee PY, Revilla R, Rust AG, Pan Z, Schilstra MJ, Clarke PJ, Arnone MI, Rowen L, Cameron RA, McClay DR, Hood L, Bolouri H. (2002). A genomic regulatory network for development (Review). Science 295, 1669
- Eiglmeier K, Simon S, Garnier T, Cole ST. (2001). The integrated genome map of Mycobacterium leprae. Lepr Rev 72, 462
- Emmanuel E, Levy AA. (2002). Tomato mutants as tools for functional genomics. Curr Opin Plant Biol 5, 112
- Gilbert M, Albala JS. (2002). Accelerating code to function: Sizing up the protein production line. Curr Opin Chem Biol 6, 102
- Glueck SB, Dzau VJ. (2002). Physiological genomics: Implications in hypertension research. Hypertension 39, 310
- Gmuender H. (2002). Perspectives and challenges for DNA microarrays in drug discovery and development. Biotechniques 32, 152
- Goodman N. (2002). Biological data becomes computer literate: New advances in bioinformatics. Curr Opin Biotechnol 13, 68
- Granucci F, Castagnoli PR, Rogge L, Sinigaglia F. (2001). Gene expression profiling in immune cells using microarray (Review). Int Arch Allergy Immunol 126, 257
- Greene AS. (2002). Application of physiological genomics to the microcirculation. Microcirculation 9, 3
- Grivet L, Arruda P. (2002). Sugarcane genomics: Depicting the complex genome of an important tropical crop. Curr Opin Plant Biol 5, 122
- Grosset JH, Cole ST. (2001). Genomics and the chemotherapy of leprosy. Lepr Rev 72, 429
- Gull K. (2002). The cell biology of parasitism in Trypansoma brucei: Insights and drug targets from genomic approaches? Curr Pharm Design 8, 241
- Haberkorn U, Altmann A, Eisenhut M. (2002). Functional genomics and proteomics: The role of nuclear medicine. Eur J Nucl Med 29, 115
- Harwood CR, Moszer I. (2002). From gene regulation to gene function: Regulatory networks in Bacillus subtilis (Conference Review). Comp Funct Genom 3, 37
- Hawkins TL, Detter JC, Richardson PM. (2002). Whole genome amplification: Applications and advances. Curr Opin Biotechnol 13, 65
- Hayaishi O. (2002). Functional genomics of sleep and circadian rhythm: Molecular genetic studies on sleep-wake regulation, with special emphasis on the prostaglandin D2 system (Review). J Appl Physiol 92, 863
- Hermjakob H, Apweiler R. (2002). TEMBLOR - Perspectives of EBI database services (Conference Review). Comp Funct Genom 3, 47
- Jacob HJ, Kwitek AE. (2002). Rat genetics: Attaching physiology and pharmacology to the genome. Nat Rev Genet 3, 33
- James P. (2001). Protein expression analysis: From ‘tip of the iceberg’ to a global method. Dis Marker 17, 235
- Jenkins S, Gibson N. (2002). High-throughput SNP genotyping (Review). Comp Funct Genom 3, 57
- Karst U, REALIS Consortium. (2002). REALIS: Postgenomic analysis of Listeria monocytogenes (Conference Review). Comp Funct Genom 3, 32
- Kennelly PJ. (2002). Protein kinases and protein phosphatases in prokaryotes: A genomic perspective (Minireview). FEMS Microbiol Lett 206, 1
- Kloos DU, Choi C, Wingender E. (2002). The TGF-β-Smad network: Introducing bioinformatic tools (Review). Trends Genet 18, 96
- Korke R, Rink A, Seow TK, Chung MCM, Beattie CW, Hu WS. (2002). Genomic and proteomic perspectives in cell culture engineering. J Biotechnol 94, 73
- Lechner D, Lathrop GM, Gut IG. (2002). Large-scale genotyping by mass spectrometry: Experience, advances and obstacles. Curr Opin Chem Biol 6, 31
- Li XM, Gu WK, Mohan S, Baylink DJ. (2002). DNA microarrays: Their use and misuse. Microcirculation 9, 13
- Lilley KS, Razzaq A, Dupree P. (2002). Two-dimensional gel electrophoresis: Recent advances in sample preparation, detection and quantitation. Curr Opin Chem Biol 6, 46
- Ma DH, Li M. (2001). Applications of display technologies to proteomic analyses. J Cell Biochem 84, 34
- MacCoss MJ, Yates JR. (2001). Proteomics: Analytical tools and techniques. Curr Opin Clin Nutr Metab Care 4, 369
- Meyerowitz EM. (2002). Comparative genomics: Plants compared to animals: The broadest comparative study of development (Review). Science 295, 1482
- Mirzabekov A, Kolchinsky A. (2002). Emerging array-based technologies in proteomics. Curr Opin Chem Biol 6, 70
- Mouradian S. (2002). Lab-on-a-chip: Applications in proteomics. Curr Opin Chem Biol 6, 51
- Mousses S, Kallioniemi A, Kauraniemi P, Elkahloun A, Kallioniemi OP. (2002). Clinical and functional target validation using tissue and cell microarrays. Curr Opin Chem Biol 6, 97
- Mullet JE, Klein RR, Klein PE. (2002). Sorghum bicolor: An important species for comparative grass genomics and a source of beneficial genes for agriculture. Curr Opin Plant Biol 5, 118
- Newmark PA, Alvarado AS. (2002). Not your father's planarian: A classic model enters the era of functional genomics. Nat Rev Genet 3, 210
- Nolan JP, Mandy FF. (2001). Suspension array technology: New tools for gene and protein analysis. Cell Mol Biol (Noisy-le-Grand) 47, 1241
- Norin M, Sundstrom M. (2002). Structural proteomics: Developments in structure-to-function predictions (Review). Trends Biotechnol 20, 79
- Oliver DJ, Nikolau B, Wurtele ES. (2002). Functional genomics: High-throughput mRNA, protein, and metabolite analyses. Metab Eng 4, 98
- Osterlund MT, Paterson AH. (2002). Applied plant genomics: The secret is integration. Curr Opin Plant Biol 5, 141
- Panisko EA, Conrads TP, Goshe MB, Veenstra TD. (2002). The postgenomic age: Characterization of proteomes. Exp Hematol 30, 97
- Patton WF, Beechem JM. (2002). Rainbow's end: The quest for multiplexed fluorescence quantitative analysis in proteomics. Curr Opin Chem Biol 6, 63
- Pellegrini M, Thompson M, Fierro J, Bowers P. (2001). Computational method to assign microbial genes to pathways. J Cell Biochem 84, 106
- Phelps TJ, Palumbo AV, Beliaev AS. (2002). Metabolomics and microarrays for improved understanding of phenotypic characteristics controlled by both genomics and environmental constraints. Curr Opin Biotechnol 13, 20
- Rappsilber J, Mann M. (2002). What does it mean to identify a protein in proteomics? Trends Biochem Sci 27, 74
- Rathod PK, Ganesan K, Hayward RE, Bozdech Z, De Risi JL. (2002). DNA microarrays for malaria. Trends Parasitol 18, 39
- Reidhaar-Olson JF, Rhees BK, Hammer J. (2001). Genomics approaches to drug discovery. J Cell Biochem 84, 110
- Rice P, Jassal B, De Daruvar A. (2002). RIBDB: An SRS based infrastructure for REALIS (Conference Review). Comp Funct Genom 3, 35
- Ronaghi M, Elahi E. (2002). Discovery of single nucleotide polymorphisms and mutations by pyrosequencing (Review). Comp Funct Genom 3, 51
- Sassetti C, Rubin EJ. (2002). Genomic analyses of microbial virulence. Curr Opin Microbiol 5, 27
- Schoolnik GK. (2002). Functional and comparative genomics of pathogenic bacteria. Curr Opin Microbiol 5, 20
- Schweitzer B, Kingsmore SF. (2002). Measuring proteins on microarrays. Curr Opin Biotechnol 13, 14
- Shields DC, O'Halloran AM. (2002). Integrating genotypic data with transcriptomic and proteomic data (Conference Review). Comp Funct Genom 3, 22
- Stephenson JL, McLuckey SA, Reid GE, Wells JM, Bundy JL. (2002). Ion/ion chemistry as a top-down approach for protein analysis. Curr Opin Biotechnol 13, 57
- Stevens R. (2002). Ontology based document enrichment in bioinformatics (Conference Review). Comp Funct Genom 3, 42
- Stoll D, Templin MF, Schrenk M, Traub PC, Vohringer CF, Joos TO. (2002). Protein microarray technology. Front Biosci 7, C13
- Strosberg AD. (2001). Functional proteomics to exploit genome sequences. Cell Mol Biol (Noisy-le-Grand) 47, 1295
- Thalmann I. (2001). Proteomics and the inner ear. Dis Marker 17, 259
- Thompson J, Janse CJ, Waters AP. (2001). Comparative genomics in Plasmodium: A tool for the identification of genes and functional analysis (Review). Mol Biochem Parasitol 118, 147
- Uetz P. (2002). Two-hybrid arrays. Curr Opin Chem Biol 6, 57
- Warner EE, Dieckgraefe BK. (2002). Application of genome-wide gene expression profiling by high-density DNA arrays to the treatment and study of inflammatory bowel disease (Review). Inflamm Bowel Dis 8, 140
- Weinberger SR, Dalmasso EA, Fung ET. (2002). Current achievements using ProteinChip® array technology. Curr Opin Chem Biol 6, 86
- Wheeler PR. (2001). The microbial physiologist's guide to the leprosy genome. Lepr Rev 72, 399
- Wild CP, Law GR, Roman E. (2002). Molecular epidemiology and cancer: Promising areas for future research in the post-genomic era. Mutat Res 499, 3
- Wilson DS, Nock S. (2002). Functional protein microarrays. Curr Opin Chem Biol 6, 81
- Zheng XFS, Chan TF. (2002). Chemical genomics in the global study of protein functions (Review). Drug Discov Today 7, 197
- 3. Large-scale sequencing and mapping
- Coe E, Cone K, McMullen M, Chen SS, Davis G, Gardiner J, Liscum E, Polacco M, Paterson A, Sanchez-Villeda H, Soderlund C, Wing R. (2002). Access to the maize genome: An integrated physical and genetic map. Plant Physiol 128, 9
- Del Vecchio VG, Kapatral V, Redkar RJ, Patra G, Mujer C, Los T, Ivanova N, Anderson I, Bhattacharyya A, Lykidis A, Reznik G, Jablonski L, Larsen N, D'Souza M, Bernal A, Mazur M, Goltsman E, Selkov E, Elzer PH, Hagius S, O'Callaghan D, Letesson JJ, Haselkorn R, Kyrpides N, Overbeek R. (2002). The genome sequence of the faculative intracellular pathogen Brucella melitensis. Proc Natl Acad Sci U S A 99, 443
- Schulte U, Becker I, Mewes HW, Mannhaupt G. (2002). Large scale analysis of sequences from Neurospora crassa. J Biotechnol 94, 3
- Wood V, Gwilliam R, Rajandream MA, Lyne M, Lyne R, Stewart A, Sgouros J, Peat N, Hayles J, Baker S, Basham D, Bowman S, Brooks K, Brown D, Brown S, Chillingworth T, Churcher C, Collins M, Connor R, Cronin A, Davis P, Feltwell T, Fraser A, Gentles S, Goble A, Hamlin N, Harris D, Hidalgo J, Hodgson G, Holroyd S, Hornsby T, Howarth S, Huckle EJ, HuntS, Jagels K, James K, Jones L, Jones M, Leather S, McDonald S, McLean J, Mooney P, Moule S, Mungall K, Murphy L, Niblett D, Odell C, Oliver K, O'Neil S, Pearson D, Quail MA, Rabbinowitsch E, Rutherford K, Rutter S, Saunders D, Seeger K, Sharp S, Skelton J, Simmonds M, Squares R, Squares S, Stevens K, Taylor K, Taylor RG, Tivey A, Walsh S, Warren T, Whitehead S, Woodward J, Volckaert G, Aert R, Robben J, Grymonprez B, Weltjens I, Vanstreels E, Rieger M, Schafer M, Muller-Auer S, Gabel C, Fuchs M, Fritzc C, Holzer E, Moestl D, Hilbert H, Borzym K, Langer I, Beck A, Lehrach H, Reinhardt R, Pohl TM, Eger P, Zimmermann W, Wedler H, Wambutt R, Purnelle B, Goffeau A, Cadieu E, Dreano S, Gloux S, Lelaure V,Mottier S, Galibert F, Aves SJ, Xiang Z, Hunt C, Moore K, Hurst SM, Lucas M, Rochet M, Gaillardin C, Tallada VA, Garzon A, Thode G, Daga RR, Cruzado L, Jimenez J, Sanchez M, Del Rey F, Benito J, Dominguez A, Revuelta JL, Moreno S, Armstrong J, Forsburg SL, Cerrutti L, Lowe T, McCombie WR, Paulsen I, Potashkin J, Shpakovski GV, Ussery D, Barrell BG, Nurse P. (2002). The genome sequence of Schizosaccharomyces pombe. Nature 415, 871
- Zabarovska VI, Gizatullin RZ, Al Amin AN, Podowski R, Protopopov AI, Lofdahl S, Wahlestedt C, Winberg G, Kashuba VI, Ernberg I, Zabarovsky ER. (2002). A new approach to genome mapping and sequencing: Slalom libraries (Electronic paper). Nucleic Acids Res 30, E6
- 4. Evolutionary genomics
- Dai LX, Zimmerly S. (2002). Compilation and analysis of group II intron insertions in bacterial genomes: Evidence for retroelement behavior. Nucleic Acids Res 30, 1091
- Fay JC, Wyckoff GJ, Wu CI. (2002). Testing the neutral theory of molecular evolution with genomic data from Drosophila. Nature 415, 1024
- Hansen-Wester I, Stecher B, Hensel M. (2002). Analyses of the evolutionary distribution of Salmonella translocated effectors. Infect Immun 70, 1619
- Hartman H, Fedorov A. (2002). The origin of the eukaryotic cell: A genomic investigation. Proc Natl Acad Sci U S A 99, 1420
- Krakauer DC, Plotkin JB. (2002). Redundancy, antiredundancy, and the robustness of genomes. Proc Natl Acad Sci U S A 99, 1405
- 5. cOMPARATIVE GENOMICS
- Bapteste E, Brinkmann H, Lee JA, Moore DV, Sensen CW, Gordon P, Durufle L, Gaasterland T, Lopez P, Muller M, Philippe H. (2002). The analysis of 100 genes supports the grouping of three highly divergent amoebae: Dictyostelium, Entamoeba, and Mastigamoeba. Proc Natl Acad Sci U S A 99, 1414
- Carlton JMR, Muller R, Yowell CA, Fluegge MR, Sturrock KA, Pritt JR, Vargas-Serrato E, Galinski MR, Barnwell JW, Mulder N, Kanapin A, Cawley SE, Hide WA, Dame JB. (2001). Profiling the malaria genome: A gene survey of three species of malaria parasite with comparison to other apicomplexan species. Mol Biochem Parasitol 118, 201
- Dziejman M, Balon E, Boyd D, Fraser CM, Heidelberg JF, Mekalanos JJ. (2002). Comparative genomic analysis of Vibrio cholerae: Genes that correlate with cholera endemic and pandemic disease. Proc Natl Acad Sci U S A 99, 1556
- Gu ZL, Cavalcanti A, Chen FC, Bouman P, Li WH. (2002). Extent of gene duplication in the genomes of Drosophila, nematode, and yeast. Mol Biol Evol 19, 256
- Sebban M, Mokrousov I, Rastogi N, Sola C. (2002). A data-mining approach to spacer oligonucleotide typing of Mycobacterium tuberculosis. Bioinformatics 18, 235
- Thomas JW, Touchman JW. (2002). Vertebrate genome sequencing: Building a backbone for comparative genomics. Trends Genet 18, 104
- 6. Pathways, gene families and regulons
- Shmulevich I, Dougherty ER, Kim S, Zhang W. (2002). Probabilistic Boolean networks: A rule-based uncertainty model for gene regulatory networks. Bioinformatics 18, 261
- Wagner A. (2002). Estimating coarse gene network structure from large-scale gene perturbation data. Genome Res 12, 309
- 7. Pharmacogenomics
- Belbin TJ, Singh B, Barber I, Socci N, Wenig B, Smith R, Prystowsky MB, Childs G. (2002). Molecular classification of head and neck squamous cell carcinoma using cDNA microarrays. Cancer Res 62, 1184
- Bosetti F, Seemann R, Bell JM, Zahorchak R, Friedman E, Rapoport SI, Manickam P. (2002). Analysis of gene expression with cDNA microarrays in rat brain after 7 and 42 days of oral lithium administration. Brain Res Bull 57, 205
- Chauhan D, Auclair D, Robinson EK, Hideshima T, Li GL, Podar K, Gupta D, Richardson P, Schlossman RL, Krett N, Chen LB, Munshi NC, Anderson KC. (2002). Identification of genes regulated by dexamethasone in multiple myeloma cells using oligonucleotide arrays. Oncogene 21, 1346
- Cristillo AD, Bierer BE. (2002). Identification of novel targets of immunosuppressive agents by cDNA-based microarray analysis. J Biol Chem 277, 4465
- Dan S, Tsunoda T, Kitahara O, Yanagawa R, Zembutsu H, Katagiri T, Yamazaki K, Nakamura Y, Yamori T. (2002). An integrated database of chemosensitivity to 55 anticancer drugs and gene expression profiles of 39 human cancer cell lines. Cancer Res 62, 1139
- De Wit NJW, Burtscher HJ, Weidle UH, Ruiter DJ, Van Muijen GNP. (2002). Differentially expressed genes identified in human melanoma cell lines with different metastatic behaviour using high density oligonucleotide arrays. Melanoma Res 12, 57
- Dong Y, Ganther HE, Stewart C, Ip C. (2002). Identification of molecular targets associated with selenium-induced growth inhibition in human breast cells using cDNA microarrays. Cancer Res 62, 708
- Eyster KM, Boles AL, Brannian JD, Hansen KA. (2002). DNA microarray analysis of gene expression markers of endometriosis. Fertil Steril 77, 38
- Fink L, Kohlhoff S, Stein MM, Hanze J, Weissmann N, Rose F, Akkayagil E, Manz D, Grimminger F, Seeger W, Bohle RM. (2002). cDNA array hybridization after laser-assisted microdissection from nonneoplastic tissue. Am J Pathol 160, 81
- Galon J, Franchimont D, Hiroi N, Frey G, Boettner A, Ehrhart-Bornstein M, O'Shea JJ, Chrousos GP, Bornstein SR. (2001). Gene profiling reveals unknown enhancing and suppressive actions of glucocorticoids on immune cells. FASEB J 16, 61
- Goldenberg D, Ayesh S, Schneider T, Pappo O, Jurim O, Eid A, Fellig Y, Dadon T, Ariel I, De Groot N, Hochberg A, Galun E. (2002). Analysis of differentially expressed genes in hepatocellular carcinoma using cDNA arrays. Mol Carcinog 33, 113
- Hanash S, Brichory F, Beer D. (2001). A proteomic approach to the identification of lung cancer markers. Dis Marker 17, 295
- Hippo Y, Taniguchi H, Tsutsumi S, Machida N, Chong JM, Fukayama M, Kodama T, Aburtani H. (2002). Global gene expression analysis of gastric cancer by oligonucleotide microarrays. Cancer Res 62, 233
- Hofmann WK, De Vos S, Elashoff D, Gschaidmeier H, Hoelzer D, Koeffler HP, Ottmann OG. (2002). Relation between resistance of Philadelphia-chromosome-positive acute lymphoblastic leukaemia to the tyrosine kinase inhibitor ST1571 and gene-expression profiles: A gene-expression study. Lancet 359, 481
- Hui ABY, Lo KW, Teo PML, To KF, Huang DP. (2002). Genome wide detection of oncogene amplifications in nasopharyngeal carcinoma by array based comparative genomic hybridization. Int J Oncol 20, 467
- Leerkes MR, Caballero OL, Mackay A, Torloni H, O'Hare MJ, Simpson AJG, De Souza SJ. (2002). In silico-comparison of the transcriptome derived from purified normal breast cells and breast tumor cell lines reveals candidate upregulated genes in breast tumor cells. Genomics 79, 257
- Luo JH, Yu YP, Cieply K, Lin F, Deflavia P, Dhir R, Finkelstein S, Michalopoulos G, Becich M. (2002). Gene expression analysis of prostate cancers. Mol Carcinog 33, 25
- Miller JC, Butler EB, Teh BS, Haab BB. (2001). The application of protein microarrays to serum diagnostics: Prostate cancer as a test case. Dis Marker 17, 225
- Moore SM, Nelson PS. (2002). Gene expression profiling of the human prostate androgen response program. J Androl 23, 163
- Mori M, Mimori K, Yoshikawa Y, Shibuta K, Utsunomiya T, Sadanaga F, Tanaka F, Matsuyama A, Inoue H, Sugimachi K. (2002). Analysis of the gene-expression profile regarding the progression of human gastric carcinoma. Surgery 131, S39
- Noel-Georis I, Bernard A, Falmagne P, Wattiez R. (2001). Proteomics as the tool to search for lung disease markers in bronchoalveolar lavage. Dis Marker 17, 271
- Paweletz CP, Trock B, Pennanen M, Tsangaris T, Magnant C, Liotta LA, Petricoin EF. (2001). Proteomic patterns of nipple aspirate fluids obtained by SELDI-TOF: Potential for new biomarkers to aid in the diagnosis of breast cancer. Dis Marker 17, 301
- Petricoin EF, Ardekani AM, Hitt BA, Levine PJ, Fusaro VA, Steinberg SM, Mills GB, Simone C, Fishman DA, Kohn EC, Liotta LA. (2002). Use of proteomic patterns in serum to identify ovarian cancer. Lancet 359, 572
- Schubert EL, Hsu L, Cousens LA, Glogovac J, Self S, Reid BJ, Rabinovitch PS, Porter PL. (2002). Single nucleotide polymorphism array analysis of flow-sorted epithelial cells from frozen versus fixed tissues for whole genome analysis of allelic loss in breast cancer. Am J Pathol 160, 73
- Selaru FM, Zou T, Xu Y, Shustova V, Yin J, Mori Y, Sato F, Wang S, Olaru A, Shibata D, Greenwald BD, Krasna MJ, Abraham JM, Meltzer SJ. (2002). Global gene expression profiling in Barrett's esophagus and esophageal cancer: A comparative analysis using cDNA microarrays. Oncogene 21, 475
- Shalhoub P, Kern S, Girard S, Beretta L. (2001). Proteomic-based approach for the identification of tumor markers associated with hepatocellular carcinoma. Dis Marker 17, 217
- Tabuchi Y, Kondo T, Ogawa R, Mori H. (2002). DNA microarray analyses of genes elicited by ultrasound in human U937 cells. Biochem Biophys Res Commun 290, 498
- Tannapfel A, Geissler F, Witzigmann H, Hauss J, Wittekind C. (2001). Analysis of liver allograft rejection related genes using cDNA-microarrays in liver allograft specimen. Transpl Proc 33, 3283
- Ten Hagen KG, Balys MM, Tabak LA, Melvin JE. (2002). Analysis of isoproterenol-induced changes in parotid gland gene expression. Physiol Genomics 8, 107
- Tsuji T, Shimohama S. (2001). Analysis of the proteomic profiling of brain tissue in Alzheimer's disease. Dis Marker 17, 247
- Wai DH, Schaefer KL, Schramm A, Korsching E, Van Valen F, Ozaki T, Boecker W, Schweigerer L, Dockhorn-Dworniczak B, Poremba C. (2002). Expression analysis of pediatric solid tumor cell lines using oligonucleotide microarrays. Int J Oncol 20, 441
- Zembutsu H, Ohnishi Y, Tsunoda T, Furukawa Y, Katagiri T, Ueyama Y, Tamaoki N, Nomura T, Kitahara O, Yanagawa R, Hirata K, Nakamura Y. (2002). Genome-wide cDNA microarray screening to correlate gene expression profiles with sensitivity of 85 human cancer xenografts to anticancer drugs.Cancer Res 62, 518
- 8. EST, cDNA and other clone resources
- Carson DL, Huckett BI, Botha FC. (2002). Sugarcane ESTs differentially expressed in immature and maturing internodal tissue. Plant Sci 162, 289
- Jia L, Young MF, Powell J, Yang LM, Ho NC, Hotchkiss R, Robey PG, Francomano CA. (2002). Gene expression profile of human marrow stromal cells: High-throughput expressed sequence tag sequencing analysis. Genomics 79, 7
- Michalek W, Weschke W, Pleissner KP, Graner A. (2002). EST analysis in barley defines a unigene set comprising 4,000 genes. Theor Appl Genet 104, 97
- Yao J, Burton JL, Saama P, Sipkovsky S, Coussens PM. (2001). Generation of EST and cDNA microarray resources for the study of bovine immunobiology. Acta Vet Scand 42, 391
- 9. Functional genomics
- Avaro S, Belgareh-Touze N, Sibella-Arguelles C, Volland C, Haguenauer-Tsapis R. (2002). Mutants defective in secretory/vacuolar pathways in the EUROFAN collection of yeast disruptants. Yeast 19, 351
- Briza P, Bogengruber E, Thur A, Rutzler M, Munsterkotter M, Dawes IW, Breitenbach M. (2002). Systematic analysis of sporulation phenotypes in 624 non-lethal homozygous deletion strains of Saccharomyces cerevisiae. Yeast 19, 403
- Cujec TP, Medeiros PF, Hammond P, Rise C, Kreider BL. (2002). Selection of v-abl tyrosine kinase substrate sequences from randomized peptide and cellular proteomic libraries using mRNA display. Chem Biol 9, 253
- Featherstone DE, Broadie K. (2002). Wrestling with pleiotropy: Genomic and topological analysis of the yeast gene expression network. Bioessays 24, 267
- Higgins VJ, Alic N, Thorpe GW, Breitenbach M, Larsson V, Dawes IW. (2002). Phenotypic analysis of gene deletant strains for sensitivity to oxidative stress. Yeast 19, 203
- Klevecz RR, Murray DB. (2001). Genome wide oscillations in expression: Wavelet analysis of time series data from yeast expression arrays uncovers the dynamic architecture of phenotype. Mol Biol Rep 28, 73
- Marra A, Asundi J, Bartilson M, Lawson S, Fang F, Christine J, Wiesner C, Brigham D, Schneider WP, Hromockyj AE. (2002). Differential fluorescence induction analysis of Streptococcus pneumoniae identifies genes involved in pathogenesis. Infect Immun 70, 1422
- Reid RJD, Sunjevaric I, Kedacche M, Rothstein R. (2002). Efficient PCR-based gene disruption in Saccharomyces strains using intergenic primers. Yeast 19, 319
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- 10. Transcriptomics
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- 11. Proteomics
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- Fountoulakis M, Berndt P, Langen H, Suter L. (2002). The rat liver mitochondrial proteins. Electrophoresis 23, 311
- Harris RA, Yang A, Stein RC, Lucy K, Brusten L, Herath A, Parekh R, Waterfield MD, O'Hare MJ, Neville MA, Page MJ, Zvelebil MJ. (2002). Cluster analysis of an extensive human breast cancer cell line protein expression map database. Proteomics 2, 212
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- Karlsen AE, Sparre T, Nielsen K, Nerup J, Pociot F. (2001). Proteome analysis: A novel approach to understand the pathogenesis of type 1 diabetes mellitus. Dis Marker 17, 205
- Kim SI, Kim SJ, Nam MH, Kim SH, Ha KS, Oh KH, Yoo JS, Park YM. (2002). Proteome analysis of aniline-induced proteins in Acinetobacter lwoffii K24. Curr Microbiol 44, 61
- Maltman DJ, Simon WJ, Wheeler CH, Dunn MJ, Wait R, Slabas AR. (2002). Proteomic analysis of the endoplasmic reticulum from developing and germinating seed of castor (Ricinus communis). Electrophoresis 23, 626
- Martin SAM, Cash P, Blaney S, Houlihan DF. (2001). Proteome analysis of rainbow trout (Oncorhynchus mykiss) liver proteins during short term starvation. Fish Physiol Biochem 24, 259
- Musante L, Candiano C, Bruschi M, Zennaro C, Carraro M, Artero M, Giuffrida MG, Conti A, Santucci A, Ghiggeri GM. (2002). Characterization of plasma factors that alter the permeability to albumin within isolated glomeruli. Proteomics 2, 197
- Park SG, Kho CW, Cho S, Lee DH, Kim SH, Park BC. (2002). A functional proteomic analysis of secreted fibrinolytic enzymes from Bacillus subtilis 168 using a combined method of two-dimensional gel electrophoresis and zymography. Proteomics 2, 206
- Peltier JB, Emanuelsson O, Kalume DE, Ytterberg J, Friso G, Rudella A, Liberles DA, Soderberg L, Roepstorff P, Von Heijne G, Van Wijk KJ. (2002). Central functions of the lumenal and peripheral thylakoid proteome of Arabidopsis determined by experimentation and genome-wide prediction.Plant Cell 14, 211
- Piubelli C, Galvani M, Hamdan M, Domenici E, Righetti PG. (2002). Proteome analysis of rat polymorphonuclear leukocytes: A two-dimensional electrophoresis/mass spectrometry approach. Electrophoresis 23, 298
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- Roos C, Kolmer M, Mattila P, Renkonen R. (2002). Composition of Drosophila melanogaster proteome involved in fucosylated glycan metabolism. J Biol Chem 277, 3168
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- Shaw AC, Gevaert K, Demol H, Hoorelbeke B, Vandekerckhove J, Larsen MR, Roepstorff P, Holm A, Christiansen G, Birkelund S. (2002). Comparative proteome analysis of Chlamydia trachomatis serovar A, D and L2. Proteomics 2, 164
- Sherman NE, Stefansson B, Fox JW, Goldberg JB. (2001). Pseudomonas aeruginosa and a proteomic approach to bacterial pathogenesis. Dis Marker 17, 285
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- Werhahn W, Braun HP. (2002). Biochemical dissection of the mitochondrial proteome from Arabidopsis thaliana by three-dimensional gel electrophoresis. Electrophoresis 23, 640
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- 12. Protein structural genomics
- Yee A, Chang XQ, Pineda-Lucena A, Wu B, Semesi A, Le B, Ramelot T, Lee GM, Bhattacharyya S, Gutierrez P, Denisov A, Lee CH, Cort JR, Kozlov G, Liao J, Finak G, Chen L, Wishart D, Lee W, McIntosh LP, Gehring K, Kennedy MA, Edwards AM, Arrowsmith CH. (2002). An NMR approach to structural proteomics. Proc Natl Acad Sci U S A 99, 1825
- 13. Metabolomics
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- 14. Genomic approaches to development
- Cho KS, Choi JG, Ha CM, Son YJ, Choi WS, Lee BJ. (2002). Comparison of gene expression in old versus young rat hippocampus by cDNA array. Neuroreport 13, 285
- Doi M, Nagano A, Nakamura Y. (2002). Genome-wide screening by cDNA microarray of genes associated with matrix mineralization by human mesenchymal stem cells in vitro. Biochem Biophys Res Commun 290, 381
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- 15. Technological advances
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- 16. Bioinformatics
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