Functional Analysis of Genes

[1] AGI: THE ARABIDOPSIS GENOME INITIATIVE. Analysis of the genome sequence of the flowering plant Arabidopsis thaliana. Nature 2000; 408: 796-81510.1038/35048692Search in Google Scholar

[2] ALTSCHUL SF, GISH W, MILLER W, MYERS EW, LIPMAN DJ. Basic local alignment search tool. J Mol Biol 1990; 215: 403-410.223171210.1016/S0022-2836(05)80360-2Search in Google Scholar

[3] ALTSCHUL SF, MADDEN TL, SCHAFFER AA, ZHANG J, ZHANG Z, MILLER W, LIPMAN DJ. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 1997; 25: 3389-3402.10.1093/nar/25.17.33891469179254694Open DOISearch in Google Scholar

[4] AMBROS V, CHEN X. The regulation of genes and genomes by small RNAs. Development 2007; 134: 1635-16411740911810.1242/dev.00200617409118Search in Google Scholar

[5] BENSON DA, KARSCH-MIZRACHI I, LIPMAN DJ, OSTELL J, WHEELER LD. GenBank: update. Nucleic Acids Res 2005; 32: 23-2610.1093/nar/gkh04530877914681350Search in Google Scholar

[6] BERNSTEIN E, CAUDY AA, HAMMOND SM, HANNON GJ. Role for a bidentate ribonuclease in the initiation step of RNA interference. Nature 2001; 409: 363-366.1120174710.1038/3505311011201747Search in Google Scholar

[7] BĄCZKOWSKI K, MACKIEWICZ K, KOWALCZUK M, BANASZAK J, CEBRAT S. Od sekwencji do funkcji - poszukiwanie genów i ich adnotacje. Biotechnologia 2005; 3: 22-44Search in Google Scholar

[8] CHALMEL F, PRIMIG M. The Annotation, Mapping, Expression and Network (AMEN) suite of tools for molecular systems biology. BMC Bioinformatics 2008; 9: 86.10.1186/1471-2105-9-8618254954237511818254954Open DOISearch in Google Scholar

[9] CHAVAN P, JOSHI K, PATWARDHAN B. DNA Microarrays in Herbal Drug Research. Evid Based Complement Alternat Med 2006; 3: 447-457.10.1093/ecam/nel075169775517173108Search in Google Scholar

[10] DANFORD T, ROLFE A, GOFFORD D. GSE: A comprehensive database system for the representation, retrieval and analysis of microarray data. Pacific Symposium on Biocomputing 2008; 13: 539-550.Search in Google Scholar

[11] FILIPECKI M, MALEPSZY S. Unintended consequences of plant transformation: a molecular insight. J Appl Genet 2006; 47: 277-2861713289210.1007/BF0319463717132892Search in Google Scholar

[12] FUELLEN G. Homology and phylogeny and their automated inference. Naturwissenschaften 2008; 95: 469-48110.1007/s00114-008-0348-11828847118288471Open DOISearch in Google Scholar

[13] FUJITA A, SATO JR, FERREIRA CE, SOGAYAR MC. GEDI: a user-friendly toolbox for analysis of large-scale gene expression data. BMC Bioinformatics 2007; 8: 457.10.1186/1471-2105-8-45718021455Open DOISearch in Google Scholar

[14] GENTLEMAN RC, CAREY VJ, BATES DM, BOLSTAD B, DETTLING M, DUDOIT S, ELLIS B, GAUTIER L, GE Y, GENTRY J, HORNIK K, HOTHORN T, HUBER W, IACUS S, IRIZARRY R, LEISCH F, LI CH, MAECHLER M, ROSSINI AJ, SAWITZKI G, SMITH C, SMYTH G, TIERNEY L, YANG JYH, ZHANG J. Bioconductor: open software development for computational biology and bioinformatics. Genome Biol 2004; 5: R80.10.1186/gb-2004-5-10-r80Open DOISearch in Google Scholar

[15] GIBSON G. Microarrays in ecology and evolution: a preview. Molecular Ecology 2002; 11: 17-2410.1046/j.0962-1083.2001.01425.x11903901Open DOISearch in Google Scholar

[16] GINALSKI K, PAS J, WYRWICZ LS, GROTTHUSS M, BUJNICKI JM, RYCHLEWSKI L. ORFeus: detection of distant homology using sequence profiles and predicted secondary structure. Nucleic Acids Res 2003; 31: 3804-38071282442310.1093/nar/gkg504Search in Google Scholar

[17] GOGARTEN JP, OLENDZENSKI L. Orthologs, paralogs and genome comparisons. Current Opinion in Genetics and Development 1999; 9: 630-63610.1016/S0959-437X(99)00029-5Search in Google Scholar

[18] GOLIAS CH, CHARALABOPOULOS A, STAGIKAS D, GIANNAKOPOULOS X, PESCHOS D, BATISTATOU A, SOFIKITIS N, CHARALABOPOULOS K. Molecular profiling and genomic microarrays in prostate cancer. Exp Oncol 2007; 29: 82-8417704736Search in Google Scholar

[19] GOWRI VS, SANDHYA S. Recent trends in remote homology detection: an Indian Medley. Bioinformation 2006; 3: 94-9610.6026/97320630001094189165817597865Open DOISearch in Google Scholar

[20] GÓRSKA M, KOWALSKI ML. Knock-out genowy- zastosowanie w badaniach medycznych. Alergia, Astma, Immunologia. 1997: 2: 162-169Search in Google Scholar

[21] HOFFMAN BG, JONES SJM. Genome-wide identification of DNA-protein interactions using chromatin immunoprecipitation coupled with flow cell sequencing. J Endocrinol 2009; 201: 1-13.10.1677/JOE-08-05261913661719136617Open DOISearch in Google Scholar

[22] JOHNSON DS, MORTAZAVI A, MYERS RM, WOLD B. Genome-wide mapping of in vivo protein-DNA interactions. Science 2007; 316: 1497-1502.10.1126/science.11413191754086217540862Open DOISearch in Google Scholar

[23] KRYSAN PJ, YOUNG JC, SUSSMAN MR. T-DNA as an insertional mutagen in Arabidopsis. Plant Cel 1999; 11: 2283-229010.1105/tpc.11.12.228314413610590158Open DOISearch in Google Scholar

[24] KUMAR L, FUTSCHIK M. Mfuzz: A software package for soft clustering of microarray data. Bioinformation 2007; 2: 5-7.10.6026/9732063000200518084642213999118084642Open DOISearch in Google Scholar

[25] LARKIN MA, BLACKSHIELDS G, BROWN NP, CHENNA R, MCGETTIGAN PA, MCWILLIAM H, VALENTIN F, WALLACE IM, WILM A, LOPEZ R, THOMPSON JD, GIBSON TJ, HIGGINS DG. Clustal W and Clustal X version 2.0. Bioinformatics 2007; 23: 2947-2948.10.1093/bioinformatics/btm404Search in Google Scholar

[26] LAW JP, CLAUDEL-RENARD C, JOUBERT F, LOUW AI, BERGER DK. MADIBA: A web server toolkit for biological interpretation of Plasmodium and plant gene clusters. BMC Genomics 2008; 9: 105.1830776810.1186/1471-2164-9-105Search in Google Scholar

[27] MACIEJEWSKI H, KONARSKI Ł, JASIŃSKA A, DRATH M. Analiza danych z mikromacierzy DNA- metody, narzędzia. Journal Edited by Medical College- Jagiellonion University 2005; 1: 129-132Search in Google Scholar

[28] MACKIEWICZ P, BĄCZKOWSKI K, SOBCZYŃSKI M, CEBRAT S. Zagadka sierocych otwartych ramek odczytu (ORF-anów). Biotechnologia 2005; 70: 45-56.Search in Google Scholar

[29] MARTIN D, BRUN Ch, REMY E, MOUREN P, THIEFFRY D, JACQ B. GOToolBox: functional analysis of gene datasets based on gene ontology. Genome Biol 2004; 5: R101.10.1186/gb-2004-5-12-r101Open DOISearch in Google Scholar

[30] MARTINEAU HM, PYRAH IT. Review of the Application of RNA interference technology in the pharmaceutical industry. Toxicol Pathol 2007; 35: 327-3361745508010.1080/01926230701197107Search in Google Scholar

[31] MERCHANT S, PROCHNIK S, VALLON O, HARRIS E, KARPOWICZ S, WITMAN G, TERRY A, SALAMOV A, FRITZ-LAYLIN LK, MARECHAL-DROUARD L, MARSHALL W, LIANG-HU Q, NELSON D, SANDERFOOT A, SPALDING M, KAPITONOV V, REN Q, FERIS, LINDQUIST E, SHAPIRO H, LUCAS S, GRIMWOOD J, SCHMUTZ J, CHLAMYDOMONAS ANNOTATION TEAM, JGI ANNOTATION TEAM, GRIGORIEV I, ROKHSAR D, GROSSMAN A. The Chlamydomonas genome reveals the evolution of key animal and plant functions. Science 2007; 318: 245-251.10.1126/science.1143609Open DOISearch in Google Scholar

[32] NISHIMURA K, ABE K, ISHIKAWA S, TSUTSUMI S, HIROTA K, ABURATANI H, HIROSE M. A PCA Based Method of Gene Expression Visual Analysis. Genome Informat 2003; 14: 346-347.Search in Google Scholar

[33] NOWAKOWSKA JA. Detekcja ekspresji genów drzew leśnych za pomocą mikromacierzy DNA. Sylwan 2006; 4: 33-43Search in Google Scholar

[34] NUC P, NUC K. Produkcja rekombinowanych białek w Escherichia coli. Post Bioch 2006; 52: 448-456Search in Google Scholar

[35] PAPROCKA M, WOŁOSZYŃSKA M. Potranskrypcyjne wyciszanie genów u roślin. Kosmos 2004; 53: 193- 200 Search in Google Scholar

[36] POPTSOVA MS, GOGARTEN JP. The power of phylogenetic approaches to detect horizontally transferred genes. BMC Evolutionary Biology 2007; 7:451737623010.1186/1471-2148-7-45Search in Google Scholar

[37] ROMAN I. Mikromacierze DNA- perspektywy wykorzystania w badaniach skuteczności i bezpieczeństwa stosowania leków. Post Bioch 2008; 54: 107-115Search in Google Scholar

[38] SCHMIDT D, WILSON MD, SPYROU CH, BROWN GD, HADFIELD J, ODOM DT. ChIP-seq: Using high-throughput sequencing to discover protein-DNA interactions. Methods 2009; 48 :240-248.1927593910.1016/j.ymeth.2009.03.001Search in Google Scholar

[39] SJÖLANDER K. Phylogenomic inference of protein molecular function: advances and challenges. Bioinformatics 2004; 20: 170-17910.1093/bioinformatics/bth02114734307Open DOISearch in Google Scholar

[40] SORENSEN HP, MORTENSEN KK. Advanced genetic strategies for recombinant protein expression in Eschericha coli. J Biotechnol 2005; 115: 113-12810.1016/j.jbiotec.2004.08.004Open DOISearch in Google Scholar

[41] SZWEYKOWSKA-KULIŃSKA Z, SZARZYŃSKA B. Nagroda Nobla 2006 za fundamentalne odkrycia w regulacji ekspresji genów u Eucariontów. Post Biol Kom 2007; 34: 3-13Search in Google Scholar

[42] VANHECKE D, JANITZ M. Functional genomics using high-throughput RNA interference. Drug Discov Today 2005; 10: 205-212.1570853510.1016/S1359-6446(04)03352-5Search in Google Scholar

[43] WIŚNIEWSKA A, FILIPECKI M. Wyciszanie genów jako strategia badania ich funkcji w roślinach. Post Biol Kom 2003; 30: 339-358Search in Google Scholar

[44] XIONG Q, QIU Y, GU W. PGMapper: a web-based tool linking phenotype to genes. Bioinformatics Advance Access 2008; 10: 1323. Search in Google Scholar