Current Awareness on Comparative and Functional Genomics

2001. Special issue: From Genome to Proteome. Proceedings of the Vth Siena Two-Dimensional Electrophoresis Meeting Siena, Italy September 4-7, 2000. Electrophoresis 22: (9) 2001. Special issue on genomic approaches to interactions of plants with pathogens and symbionts. Curr Opin Plant Biol 4: (4) Altman RB, Raychaudhuri S. 2001. Stanford Med Information, 251 Campus Dr, Stanford, Ca 95305, USA. Whole-genome expression analysis: challenges beyond clustering. Curr Opin Struct Biol 11: (3) 340. Anderson NG, Matheson A, Anderson NL*. 2001. *Large Scale Proteomics Corp, 9620 Med Ctr Dr, Rockville, Md 20850, USA. Back to the future: The human protein index (HPI) and the agenda for post-proteomic biology. Proteomics 1: (1) 3. Anisimov SV, Lakatta EG, Boheler KR*. 2001. *NIH/NIA, Cardiovasc Sci Lab, Baltimore, Md 21224, USA. Discovering altered genomic expression patterns in heart: Transcriptome determination by serial analysis of gene expression (Review). Eur J Heart Fail 3: (3) 271. Arrell DK, Neverova I, Van Eyk JE*. 2001. *Queen’s Univ, Dept Physiol, 429 Botterell Hall, Kingston, Ontario, Canada K7L 3N6. Cardiovascular proteomics: Evolution and potential (Review). Circ Res 88: (8) 763. Bancroft I. 2001. John Innes Ctr Plant Sci Res, Dept Brassica & Oilseeds Res, Norwich Res Pk, Norwich NR4 7UH, England. Duplicate and diverge: The evolution of plant genome microstructure (Review). Trends Genet 17: (2) 89. Battersby BJ, Lawrie GA, Trau M. 2001. Univ Queensland, Dept Chem, Ctr Nanotechnol & Biomaterials, St Lucia, Qld 4072, Australia. Optical encoding of microbeads for gene screening: Alternatives to microarrays (Review). Drug Discov Today 6: (12 Suppl S1) S19. Bertucci F, Loriod B, Tagett R, Granjeaud S, Birnbaum D, Nguyen C, Houlgatte R*. 2001. *Inst J Paoli-Calmettes, Lab Biol Tumeurs, FR-13009 Marseille, France. DNA arrays: Technological aspects and applications (French, English Abstract). Bull Cancer 88: (3) 243. Bjorkholm BM, Oh JD, Falk PG, Engstrand LG, Gordon JI*. 2001. *Washington Univ, Sch Med, Dept Mol Biol & Pharmacol, Box 8103, 660 Sth Euclid Ave, St Louis, Mo 63110, USA. Genomics and proteomics converge on Helicobacter pylori. Curr Opin Microbiol 4: (3) 237. Boucher Y, Nesbo CL, Doolittle WF*. 2001. *Dalhousie Univ, Dept Biochem & Mol Biol, Inst Adv Res Program Evolutionary Biol, Halifax, Nova Scotia, Canada BSH 4H7. Microbial genomes: Dealing with diversity. Curr Opin Microbiol 4: (3) 285. Bremer C, Weissleder R*. 2001. *MGH, Ctr Mol Imaging Res, Bldg 149, 13th St, Boston, Ma 02129, USA. In vivo imaging of gene expression: MR and optical technologies. Acad Radiol 8: (1) 15. Burgess JK. 2001. Univ Sydney, Dept Pharmacol, Resp Res Grp, Bosch Bldg, Sydney, NSW 2006, Australia. Gene expression studies using microarrays. Clin Exp Pharmacol Physiol 28: (4) 321. Califano A. 2001. First Genet Trust Inc, 9 Polito Ave, Suite 930, Lyndhurst, NJ 07071, USA. Advances in sequence analysis. Curr Opin Struct Biol 11: (3) 330. Charlesworth D, Charlesworth B, McVean GAT. 2001. Univ Edinburgh, Inst Cell Anim & Populat Biol, Ashworth Lab, West Mains Rd, Kings Bldg, Edinburgh EH9 3JT, Scotland. Genome sequences and evolutionary biology, a two-way interaction (Review). Trends Ecol Evol 16: (5) 235. Charron P, Komajda M*. 2001. *Univ Paris 06, Hop La Pitie Salpetriere, Serv Cardiol, 47-83 Blvd Hop, FR-75013 Paris, France. Are we ready for pharmacogenomics in heart failure? (Review). Eur J Pharmacol 417: (1-2) 1. Cooper CS. 2001. Inst Canc Res, Haddow Labs, Cotswold Rd, Sutton SM2 5NG, England. Applications of microarray technology in breast cancer research (Review). Breast Cancer Res Treat 3: (3) 158. Cunningham MJ. 2000. Genometrix Inc, 2700 Res Forest Dr, The Woodlands, Tx 77381, USA. Genomics and proteomics: The new millenium of drug discovery and development. J Pharmacol Toxicol Methods 44: (1) 291. Davidson D, Baldock R. 2001. Western Gen Hosp, MRC Human Genet Unit, Crewe Rd, Edinburgh EH4 2XU, Scotland. Bioinformatics beyond sequence: Mapping gene function in the embryo (Review). Nat Rev Genet 2: (6) 409. Delseny M, Salses J, Cooke R, Sallaud C, Regad F, Lagoda P, Guiderdoni E, Ventelon M, Brugidou C, Ghesquiere A. 2001. Univ Perpignan, CNRS UMR 5096, Lab Genome & Dev Plantes, 52 Ave Villeneuve, FR-66860 Perpignan, France. Rice genomics: Present and future. Plant Physiol Biochem 39: (3-4) 323. Devaux F, Marc P, Jacq C*. 2001. *Ecole Normale Super, Mol Genet Lab, 46 rue Ulm, FR-75005 Paris, France. Transcriptomes, transcription activators and microarrays (Minireview). FEBS Lett 498: (2-3) 140. Deyholos MK, Galbraith DW*. 2001. *Univ Arizona, Dept Plant Sci, 1145 East 4th St, Tucson, Az 85721, USA. High density microarrays for gene expression analysis (Review). Cytometry 43: (4) 229. Ehrat M, Kresbach GM. 2001. Zeptosens AG, Benkenstr 254, CH-4018 Witterswil, Switzerland. DNA and protein microarrays and their contributions to proteomics and genomics. Chimia 55: (1-2) 35. Fisch I. 2001. Ecole Polytech Fed Lausanne, DC IGC, Ctr Biotechnol, Swiss Fed Inst Technol, SELEXIS SA, CBUE-LBTM, CH-1015 Lausanne, Switzerland. Peptide display in functional genomics. Comb Chem High Throughput Scr 4: (2) 157. Franken P, Requena N. 2001. Univ Marburg, Max-Planck-Inst Terr Mikrobiol, Karl von Frisch Str, DE-35043 Marburg, Germany. Analysis of gene expression in arbuscular mycorrhizas: New approaches and challenges (Review). New Phytol 150: (3) 517. Gaasterland T, Oprea M. 2001. Rockefeller Univ, Lab Computat Genomics, 1230 York Ave, New York, NY 10021, USA. Whole-genome analysis: Annotations and updates. Curr Opin Struct Biol 11: (3) 377. Godovac-Zimmerman J, Brown KL. 2001. UCL, Ctr Molec Med, 5 Univ St, London WC1E 6JJ, England. Perspectives for mass spectrometry and functional proteomics. Mass Spectrom Rev 20: (1) 1. Grabherr R, Ernst W. 2001. Agr Univ Vienna, Inst Appl Microbiol, Muthgasse 18, AU-1190 Vienna, Austria. The baculovirus expression system as a tool for generating diversity by viral surface display. Comb Chem High Throughput Scr 4: (2) 185. Grandi G. 2001. Chiron SpA, Dept Biol Mol, via Florentina 1, IT-53100 Siena, Italy. Antibacterial vaccine design using genomics and proteomics (Review). Trends Biotechnol 19: (5) 181. Grant WN, Viney ME. 2001. AgRes Ltd, Wallaceville Anim Res Ctr, Ward St, POB 40063, Upper Hutt, New Zealand. Post-genomic nematode parasitology. Int J Parasitol 31: (9) 879. Graveley BR. 2001. Univ Connecticut, Ctr Hlth, Dept Genet & Dev Biol, Farmington, Ct 06030, USA. Alternative splicing: Increasing diversity in the proteomic world (Review). Trends Genet 17: (2) 100. Gull K. 2001. University Manchester, School Biology Science, 2.205 Stopford Bldg, Manchester M13 9PT, England. The biology of kinetoplastid parasites: Insights and challenges from genomics and Comparative and Functional Genomics Comp. Funct. Genom. 2001; 2: 401–412 DOI:10.1002/cfg.60

[1]  I Fisch,et al.  Peptide display in functional genomics. , 2012, Combinatorial chemistry & high throughput screening.

[2]  H. Lehrach,et al.  High-throughput screening of surface displayed gene products. , 2012, Combinatorial chemistry & high throughput screening.

[3]  K. Ramnarayan,et al.  Recent developments in computational proteomics. , 2001, Drug discovery today.

[4]  C. Gaillardin,et al.  Analysis of the constitution of the beer yeast genome by PCR, sequencing and subtelomeric sequence hybridization. , 2001, International journal of systematic and evolutionary microbiology.

[5]  M. Moran,et al.  Mass spectrometry for the study of protein-protein interactions. , 2001, Methods.

[6]  B. Bochner,et al.  Phenotype microarrays for high-throughput phenotypic testing and assay of gene function. , 2001, Genome research.

[7]  S. Bates,et al.  Stroke Genomics: Approaches to Identify, Validate, and Understand Ischemic Stroke Gene Expression , 2001, Journal of cerebral blood flow and metabolism : official journal of the International Society of Cerebral Blood Flow and Metabolism.

[8]  M. Oh,et al.  Issues in cDNA microarray analysis: quality filtering, channel normalization, models of variations and assessment of gene effects. , 2001, Nucleic acids research.

[9]  M. Borodovsky,et al.  GeneMarkS: a self-training method for prediction of gene starts in microbial genomes. Implications for finding sequence motifs in regulatory regions. , 2001, Nucleic acids research.

[10]  D. Lockhart,et al.  Arrays of arrays for high-throughput gene expression profiling. , 2001, Genome research.

[11]  J S Leeder,et al.  Pharmacogenetics and pharmacogenomics. , 2001, Pediatric clinics of North America.

[12]  Peter D. Karp,et al.  Database verification studies of SWISS-PROT and GenBank , 2001, Bioinform..

[13]  Ari Löytynoja,et al.  SOAP, cleaning multiple alignments from unstable blocks , 2001, Bioinform..

[14]  Charlotte M. Deane,et al.  SCORE: predicting the core of protein models , 2001, Bioinform..

[15]  W. Kim,et al.  One-step PCR amplification of complete arthropod mitochondrial genomes. , 2001, Molecular phylogenetics and evolution.

[16]  D. Engelman,et al.  Helical membrane proteins: diversity of functions in the context of simple architecture. , 2001, Current opinion in structural biology.

[17]  Pierre Baldi,et al.  A Bayesian framework for the analysis of microarray expression data: regularized t -test and statistical inferences of gene changes , 2001, Bioinform..

[18]  Kate Johnson,et al.  MAPS: a microarray project system for gene expression experiment information and data validation , 2001, Bioinform..

[19]  Burkhard Morgenstern,et al.  The HIB database of annotated UniGene clusters , 2001, Bioinform..

[20]  R Apweiler,et al.  Clustering and analysis of protein families. , 2001, Current opinion in structural biology.

[21]  C. Chothia,et al.  Determination of protein function, evolution and interactions by structural genomics. , 2001, Current opinion in structural biology.

[22]  Zheng Xie,et al.  AMADA: analysis of microarray data , 2001, Bioinform..

[23]  F. O'Gara,et al.  Pseudomonas for biocontrol of phytopathogens: from functional genomics to commercial exploitation. , 2001, Current opinion in biotechnology.

[24]  Tiee-Jian Wu,et al.  Statistical Measures of DNA Sequence Dissimilarity under Markov Chain Models of Base Composition , 2001, Biometrics.

[25]  A. Thompson,et al.  Microarrays for microbiologists. , 2001, Microbiology.

[26]  K. Turteltaub,et al.  Attomole quantitation of protein separations with accelerator mass spectrometry , 2001, Electrophoresis.

[27]  Russ B. Altman,et al.  Missing value estimation methods for DNA microarrays , 2001, Bioinform..

[28]  P Dupree,et al.  Quantitative and reproducible two‐dimensional gel analysis using Phoretix 2D Full , 2001, Electrophoresis.

[29]  A. Jamie Cuticchia,et al.  Compositional symmetries in complete genomes , 2001, Bioinform..

[30]  P. Righetti,et al.  Alkylation kinetics of proteins in preparation for two‐dimensional maps: A matrix assisted laser desorption/ionization‐mass spectrometry investigation , 2001, Electrophoresis.

[31]  Malay Kumar Basu,et al.  SeWeR: a customizable and integrated dynamic HTML interface to bioinformatics services , 2001, Bioinform..

[32]  John M. Ward,et al.  Identification of novel families of membrane proteins from the model plant Arabidopsis thaliana , 2001, Bioinform..

[33]  G. Tsongalis,et al.  Pharmacogenomics: will it change the field of medicine? , 2001, Clinica chimica acta; international journal of clinical chemistry.

[34]  George M. Church,et al.  Aligning gene expression time series with time warping algorithms , 2001, Bioinform..

[35]  Philippe Soriano,et al.  A gene trap vector system for identifying transcriptionally responsive genes , 2001, Nature Biotechnology.

[36]  J Tong,et al.  Software scripts for quality checking of high-throughput nucleic acid sequencers. , 2001, BioTechniques.

[37]  A. Danchin,et al.  Description and application of a rapid method for genomic DNA direct sequencing. , 2001, FEMS microbiology letters.

[38]  R. Mahalingam,et al.  The DNA sequence of the simian varicella virus genome. , 2001, Virology.

[39]  M E Belov,et al.  High-throughput proteomics using high-efficiency multiple-capillary liquid chromatography with on-line high-performance ESI FTICR mass spectrometry. , 2001, Analytical chemistry.

[40]  N. Niikawa,et al.  Isolation of novel heart-specific genes using the BodyMap database. , 2001, Genomics.

[41]  P. Warren,et al.  Bacterial fatty-acid biosynthesis: a genomics-driven target for antibacterial drug discovery. , 2001, Drug discovery today.

[42]  M. Hogan,et al.  DNA microarrays based on noncovalent oligonucleotide attachment and hybridization in two dimensions. , 2001, Analytical biochemistry.

[43]  J A Blake,et al.  Program description: Strategies for biological annotation of mammalian systems: implementing gene ontologies in mouse genome informatics. , 2001, Genomics.

[44]  E. Rocha,et al.  The complete genome sequence of the murine respiratory pathogen Mycoplasma pulmonis. , 2001, Nucleic acids research.

[45]  C. Mirkin,et al.  Two-color labeling of oligonucleotide arrays via size-selective scattering of nanoparticle probes. , 2001, Journal of the American Chemical Society.

[46]  Rainer Fuchs,et al.  Analysis of temporal gene expression profiles: clustering by simulated annealing and determining the optimal number of clusters , 2001, Bioinform..

[47]  Brian T. Foley,et al.  Retrieval and on-the-fly alignment of sequence fragments from the HIV database , 2001, Bioinform..

[48]  Jacek Blazewicz,et al.  Construction of DNA restriction maps based on a simplified experiment , 2001, Bioinform..

[49]  G. McVean,et al.  Genome sequences and evolutionary biology, a two-way interaction. , 2001, Trends in ecology & evolution.

[50]  Jeremy Buhler,et al.  Efficient large-scale sequence comparison by locality-sensitive hashing , 2001, Bioinform..

[51]  Jonas S. Almeida,et al.  Analysis of genomic sequences by Chaos Game Representation , 2001, Bioinform..

[52]  Thomas Laurell,et al.  Proteomics–protein profiling technology: the trend towards a microfabricated toolbox concept , 2001 .

[53]  C. Huber,et al.  High-performance liquid chromatography-electrospray ionization mass spectrometry using monolithic capillary columns for proteomic studies. , 2001, Analytical chemistry.

[54]  S. Hoving,et al.  Proteomics: From Protein Identification to Biological function , 2001, CHIMIA.

[55]  P. Sternberg,et al.  Working in the Post-Genomic C. elegans World , 2001, Cell.

[56]  E Pauws,et al.  Heterogeneity in polyadenylation cleavage sites in mammalian mRNA sequences: implications for SAGE analysis. , 2001, Nucleic acids research.

[57]  S. Clifton,et al.  A survey of the Leishmania major Friedlin strain V1 genome by shotgun sequencing: a resource for DNA microarrays and expression profiling. , 2001, Molecular and biochemical parasitology.

[58]  M. Quail,et al.  Gene discovery in Plasmodium chabaudi by genome survey sequencing. , 2001, Molecular and biochemical parasitology.

[59]  Inge Jonassen,et al.  J-Express: exploring gene expression data using Java , 2001, Bioinform..

[60]  Michael Gribskov,et al.  Use of keyword hierarchies to interpret gene expression patterns , 2001, Bioinform..

[61]  T. Rognes,et al.  ParAlign: a parallel sequence alignment algorithm for rapid and sensitive database searches. , 2001, Nucleic acids research.

[62]  Ka Yee Yeung,et al.  Validating clustering for gene expression data , 2001, Bioinform..

[63]  Cédric Notredame,et al.  Mocca: semi-automatic method for domain hunting , 2001, Bioinform..

[64]  Eran Eyal,et al.  MutaProt: a web interface for structural analysis of point mutations , 2001, Bioinform..

[65]  A. Chenchik,et al.  Reverse transcriptase template switching: a SMART approach for full-length cDNA library construction. , 2001, BioTechniques.

[66]  B. Chait,et al.  Enrichment analysis of phosphorylated proteins as a tool for probing the phosphoproteome , 2001, Nature Biotechnology.

[67]  S. Balaji,et al.  PALI: a database of alignments and phylogeny of homologous protein structures , 2001, Bioinform..

[68]  Ioannis Xenarios,et al.  Mining literature for protein-protein interactions , 2001, Bioinform..

[69]  Martin Vingron,et al.  Limits of homology detection by pairwise sequence comparison , 2001, Bioinform..

[70]  Jonathan Crabtree,et al.  A relational schema for both array-based and SAGE gene expression experiments , 2001, Bioinform..

[71]  Steven J. M. Jones,et al.  PhyloBLAST: facilitating phylogenetic analysis of BLAST results , 2001, Bioinform..

[72]  Jörg D. Hoheisel,et al.  Whole Genome Analysis of a Wine Yeast Strain , 2001, Comparative and functional genomics.

[73]  A. Shevchenko,et al.  Archived polyacrylamide gels as a resource for proteome characterization by mass spectrometry , 2001, Electrophoresis.

[74]  R Reid,et al.  Recovering filter-based microarray data for pathways analysis using a multipoint alignment strategy. , 2001, BioTechniques.

[75]  M. Stoeckli,et al.  Imaging mass spectrometry: A new technology for the analysis of protein expression in mammalian tissues , 2001, Nature Medicine.

[76]  R. Leimgruber,et al.  Practical aspects of fluorescent staining for proteomic applications , 2001, Electrophoresis.

[77]  Erik L. L. Sonnhammer,et al.  NIFAS: visual analysis of domain evolution in proteins , 2001, Bioinform..

[78]  Pjotr Prins,et al.  GenEST, a powerful bidirectional link between cDNA sequence data and gene expression profiles generated by cDNA-AFLP. , 2001, Nucleic acids research.

[79]  M. Steinmetz,et al.  Isotope-tagged cross-linking reagents. A new tool in mass spectrometric protein interaction analysis. , 2001, Analytical chemistry.

[80]  P. Bork,et al.  Charting the proteomes of organisms with unsequenced genomes by MALDI-quadrupole time-of-flight mass spectrometry and BLAST homology searching. , 2001, Analytical chemistry.

[81]  Kurt S. Thorn,et al.  ASEdb: a database of alanine mutations and their effects on the free energy of binding in protein interactions , 2001, Bioinform..

[82]  R. W. Gracy,et al.  Chemiluminescent standards for quantitive comparison of two‐dimensional electrophoresis western blots , 2001, Proteomics.

[83]  Adam Godzik,et al.  Clustering of highly homologous sequences to reduce the size of large protein databases , 2001, Bioinform..

[84]  F. Bertucci,et al.  [DNA arrays: technological aspects and applications]. , 2001, Bulletin du cancer.

[85]  Matthew Davison,et al.  Validation and development of fluorescence two‐dimensional differential gel electrophoresis proteomics technology , 2001, Proteomics.

[86]  Chris Mellish,et al.  Basic Gene Grammars and DNA-ChartParser for language processing of Escherichia coli promoter DNA sequences , 2001, Bioinform..

[87]  R. Wait,et al.  A combined radiolabelling and silver staining technique for improved visualisation, localisation, and identification of proteins separated by two‐dimensional gel electrophoresis , 2001, Proteomics.

[88]  Suchendra M. Bhandarkar,et al.  Physical mapping with automatic capture of hybridization data , 2001, Bioinform..

[89]  G. Kresbach,et al.  DNA and Protein Microarrays and their Contributions to Proteomics and Genomics , 2001, CHIMIA.

[90]  P. Roepstorff,et al.  Phospho‐proteomics: Evaluation of the use of enzymatic de‐phosphorylation and differential mass spectrometric peptide mass mapping for site specific phosphorylation assignment in proteins separated by gel electrophoresis , 2001, Proteomics.

[91]  H. Nakanishi,et al.  Ion intensity analysis of post‐source decay fragmentation in curved‐field reflectron matrix‐assisted laser desorption/ionization time‐of‐flight mass spectrometry of carbohydrates: For structural characterization of glycosylation in proteome analysis , 2001, Proteomics.

[92]  J. Rohrer,et al.  Protein variant separations using cation exchange chromatography on grafted, polymeric stationary phases , 2001, Proteomics.

[93]  P. de Knijff,et al.  A powerful and rapid approach to human genome scanning using small quantities of genomic DNA. , 2001, Genetical research.

[94]  M. Fussenegger,et al.  Use of antibodies for detection of phosphorylated proteins separated by two‐dimensional gel electrophoresis , 2001, Proteomics.

[95]  A. Stensballe,et al.  Characterization of phosphoproteins from electrophoretic gels by nanoscale Fe(III) affinity chromatography with off‐line mass spectrometry analysis , 2001, Proteomics.

[96]  Catherine A. Cooper,et al.  GlycoMod – A software tool for determining glycosylation compositions from mass spectrometric data , 2001, Proteomics.

[97]  Roland Luethy,et al.  Towards defining the urinary proteome using liquid chromatography‐tandem mass spectrometry II.Limitations of complex mixture analyses , 2001, Proteomics.

[98]  G. L. Gabor Miklos,et al.  Integrating molecular medicine with functional proteomics: Realities and expectations , 2001, Proteomics.

[99]  D. Gerber,et al.  Single molecule detector for mass spectrometry with mass independent detection efficiency , 2001, Proteomics.

[100]  S. Pennington,et al.  Arrays for protein expression profiling: Towards a viable alternative to two‐dimensional gel electrophoresis? , 2001, Proteomics.

[101]  P. Stockwell,et al.  ToothPrint, a proteomic database for dental tissues , 2001, Proteomics.

[102]  S. Oliver,et al.  Chromatographic separations as a prelude to two‐dimensional electrophoresis in proteomics analysis , 2001, Proteomics.

[103]  Michael Karas,et al.  Matrix‐assisted laser desorption ionization mass spectrometry , 1991 .

[104]  H. Vaucheret,et al.  Transcriptional gene silencing in plants: targets, inducers and regulators. , 2001, Trends in genetics : TIG.

[105]  M. Mann,et al.  Use of mass spectrometry-derived data to annotate nucleotide and protein sequence databases. , 2001, Trends in biochemical sciences.

[106]  A. Bairoch,et al.  Annotation of glycoproteins in the SWISS-PROT database. , 2001, Proteomics.

[107]  W. Hancock.  Contribution of ion trap mass spectrometers to proteomics , 2001 .

[108]  Kelvin H. Lee.  Proteomics : a technology-driven and technology-limited discovery science , 2001 .

[109]  J. Hanke.  Genomics and new technologies as catalysts for change in the drug discovery paradigm. , 2000, The Journal of law, medicine & ethics : a journal of the American Society of Law, Medicine & Ethics.