Software Usage References

--- MadMapper 2009 ---
Drost DR, Novaes E, Boaventura-Novaes C, Benedict CI, Brown RS, Yin T, Tuskan GA, Kirst M.
A microarray-based genotyping and genetic mapping approach for highly heterozygous outcrossing species enables localization of a large fraction of the unassembled Populus trichocarpa genome sequence.
Plant J. 2009 Jun;58(6):1054-67. Epub 2009 Feb 10.

--- GenomePixelizer 2007 ---
Yang S, Jiang K, Araki H, Ding J, Yang YH, Tian D.
A molecular isolation mechanism associated with high intra-specific diversity in rice.
Gene. 2007 Jun 1;394(1-2):87-95. Epub 2007 Feb 24.

--- SNP Discovery Pipeline 2007 ---
Fierro AC, Thuret R, Coen L, Perron M, Demeneix BA, Wegnez M, Gyapay G, Weissenbach J, Wincker P, Mazabraud A, Pollet N.
Exploring nervous system transcriptomes during embryogenesis and metamorphosis in Xenopus tropicalis using EST analysis.
BMC Genomics. 2007 May 16;8:118.

--- GenomePixelizer 2007 ---
Dardick C, Chen J, Richter T, Ouyang S, Ronald P.
The rice kinase database. A phylogenomic database for the rice kinome.
Plant Physiol. 2007 Feb;143(2):579-586. Epub 2006 Dec 15.

--- GenoPix2D Plotter 2006 ---
Stajich JE, Lapp H.
Open source tools and toolkits for bioinformatics: significance, and where are we?
Brief Bioinform. 2006 Sep;7(3):287-96. Epub 2006 Aug 9.

--- CheckMatrix - MadMapper 2006 ---
Fu Y, Wen TJ, Ronin YI, Chen HD, Guo L, Mester DI, Yang Y, Lee M, Korol AB, Ashlock DA, Schnable PS.
Genetic dissection of intermated recombinant inbred lines using a new genetic map of maize that includes 1,329 novel PCR-based genic markers.
Genetics. 2006 Nov;174(3):1671-1683. Epub 2006 Sep 1.

--- GenomePixelizer 2006 ---
Timms L, Jimenez R, Chase M, Lavelle D, McHale L, Kozik A, Lai Z, Heesacker A, Knapp S, Rieseberg L, Michelmore R, Kesseli R.
Analyses of synteny between Arabidopsis thaliana and species in the Asteraceae reveal a complex network of small syntenic
Genetics. 2006 Aug;173(4):2227-2235.

--- TkLife 2006 ---
Kliebenstein DJ, West MA, van Leeuwen H, Loudet O, Doerge RW, St Clair DA.
Identification of QTLs controlling gene expression networks defined a priori.
BMC Bioinformatics. 2006 Jun 16;7:308.
BMC Bioinformatics web site

--- CheckMatrix - MadMapper 2006 ---
West MA, van Leeuwen H, Kozik A, Kliebenstein DJ, Doerge RW, St Clair DA, Michelmore RW.
High-density haplotyping with microarray-based expression and single feature polymorphism markers in Arabidopsis.
Genome Res. 2006 Jun;16(6):787-95.
Genome Research web site

--- GenomePixelizer 2006 ---
Dardick C, Ronald P.
Plant and animal pathogen recognition receptors signal through non-RD kinases.
PLoS Pathog. 2006 Jan;2(1):e2.
PLoS web site (supplemental data)

--- Blast Parser 2005 ---
Torres MJ, Tomilov AA, Tomilova N, Reagan RL, Yoder JI.
Pscroph, a parasitic plant EST database enriched for parasite associated transcripts.
BMC Plant Biol. 2005 Nov 16;5:24.
BMC Plant Biology web site

--- GenomePixelizer 2005 ---
Feuk L, MacDonald JR, Tang T, Carson AR, Li M, Rao G, Khaja R, Scherer SW.
Discovery of human inversion polymorphisms by comparative analysis of human and chimpanzee DNA sequence assemblies.
PLoS Genet. 2005 Oct;1(4):e56.
PLoS web site

--- PhyloGrapher 2005 ---
Vasconcelos AT, Ferreira HB, Bizarro CV, Bonatto SL, Carvalho MO, Pinto PM, Almeida DF, Almeida LG, Almeida R, Alves-Filho L, ... ... ... Vainstein MH, Zuccherato LW, Simpson AJ, Zaha A.
Swine and poultry pathogens: the complete genome sequences of two strains of Mycoplasma hyopneumoniae and a strain of Mycoplasma synoviae.
J Bacteriol. 2005 Aug;187(16):5568-5577.
Journal of Bacteriology web site

--- GenomePixelizer 2005 ---
Guyot R, Cheng X, Su Y, Cheng Z, Schlagenhauf E, Keller B, Ling HQ.
Complex organization and evolution of the tomato pericentromeric region at the FER gene locus.
Plant Physiol. 2005 Jul;138(3):1205-1215.
Plant Physiology web site (supplemental data)

--- GenomePixelizer 2005 ---
Fritz-Laylin LK, Krishnamurthy N, Tor M, Sjolander KV, Jones JD.
Phylogenomic analysis of the receptor-like proteins of rice and Arabidopsis.
Plant Physiol. 2005 Jun;138(2):611-623.
Plant Physiology web site

--- GenoPix2D Plotter 2005 ---
Silverstein KA, Graham MA, Paape TD, VandenBosch KA.
Genome organization of more than 300 defensin-like genes in Arabidopsis.
Plant Physiol. 2005 Jun;138(2):600-610.
Plant Physiology web site

--- PhyloGrapher 2005 ---
Jeffrey L. Brown, Clayton S. Ferner, Thomas C. Hudson, Ann E. Stapleton, Ronald J. Vetter, Tristan Carland, Andrew Martin, Jerry Martin, Allen Rawls, William J. Shipman, and Michael Wood.
GridNexus: A Grid Services Scientific Workflow System
International Journal of Computer Information Science (IJCIS), Vol 6, No 2; June 20, 2005: 72-82. web site

--- GenomePixelizer 2005 ---
Wisser RJ, Sun Q, Hulbert SH, Kresovich S, Nelson RJ.
Identification and characterization of regions of the rice genome associated with broad-spectrum, quantitative disease resistance.
Genetics. 2005 Apr;169(4):2277-2293.
Genetics web site

--- GenomePixelizer 2004 ---
Guyot R, Keller B.
Ancestral genome duplication in rice.
Genome. 2004 Jun;47(3):610-614.

--- GenomePixelizer 2004 ---
Zhou T, Wang Y, Chen JQ, Araki H, Jing Z, Jiang K, Shen J, Tian D.
Genome-wide identification of NBS genes in japonica rice reveals significant expansion of divergent non-TIR NBS-LRR genes.
Mol Genet Genomics. 2004 May;271(4):402-415.

--- PhyloGrapher 2004 ---
Oliveira de Carvalho M, Silva JC, Loreto EL.
Analyses of P-like transposable element sequences from the genome of Anopheles gambiae.
Insect Mol Biol. 2004 Feb;13(1):55-63.

--- GenomePixelizer 2003 ---
Marshall SD, Putterill JJ, Plummer KM, Newcomb RD.
The carboxylesterase gene family from Arabidopsis thaliana.
J Mol Evol. 2003 Nov;57(5):487-500.

--- PhyloGrapher 2003 ---
Farnum MA, Xu H, Agrafiotis DK.
Exploring the nonlinear geometry of protein homology.
Protein Sci. 2003 Aug;12(8):1604-1612.
Protein Science web site

--- PhyloGrapher 2003 ---
Richly E, Dietzmann A, Biehl A, Kurth J, Laloi C, Apel K, Salamini F, Leister D.
Covariations in the nuclear chloroplast transcriptome reveal a regulatory master-switch.
EMBO Rep. 2003 May;4(5):491-498.

--- GenomePixelizer 2003 ---
Hammond-Kosack KE, Parker JE.
Deciphering plant-pathogen communication: fresh perspectives for molecular resistance breeding.
Curr Opin Biotechnol. 2003 Apr;14(2):177-193.

--- GenomePixelizer 2003 ---
Ureta-Vidal A, Ettwiller L, Birney E.
Comparative genomics: genome-wide analysis in metazoan eukaryotes.
Nat Rev Genet. 2003 Apr;4(4):251-262.

--- GenomePixelizer 2003 ---
Scherer SW, Cheung J, MacDonald JR, Osborne LR,
Human chromosome 7: DNA sequence and biology.
Science. 2003 May 2;300(5620):767-772.

--- GenomePixelizer 2003 ---
Cheung J, Wilson MD, Zhang J, Khaja R, MacDonald JR, Heng HH, Koop BF, Scherer SW.
Recent segmental and gene duplications in the mouse genome.
Genome Biol. 2003;4(8):R47.
GenomeBiology web site

--- GenomePixelizer 2003 ---
Cheung J, Estivill X, Khaja R, MacDonald JR, Lau K, Tsui LC, Scherer SW.
Genome-wide detection of segmental duplications and potential assembly errors in the human genome sequence.
Genome Biol. 2003;4(4):R25.
GenomeBiology web site

--- GenomePixelizer 2003 ---
Meyers BC, Kozik A, Griego A, Kuang H, Michelmore RW.
Genome-wide analysis of NBS-LRR-encoding genes in Arabidopsis.
Plant Cell. 2003 Apr;15(4):809-834.
Plant Cell web site

--- GenomePixelizer 2003 ---
Gimelli G, Pujana MA, Patricelli MG, Russo S, Giardino D, Larizza L, Cheung J, Armengol L, Schinzel A, Estivill X, Zuffardi O.
Genomic inversions of human chromosome 15q11-q13 in mothers of Angelman syndrome patients with class II (BP2/3) deletions.
Hum Mol Genet. 2003 Apr 15;12(8):849-858.
Human Molecular Genetics web site

--- GenomePixelizer 2003 ---
Thomas K. Mitchell, Michael R. Thon, Jun-Seop Jeong, Doug Brown, Jixin Deng, Ralph A. Dean
The rice blast pathosystem as a case study for the development of new tools and raw materials for genome analysis of fungal plant pathogens.
New Phytologist. 2003 July;159(1):53-61.
New Phytologist web site

--- GenomePixelizer 2002 ---
Estivill X, Cheung J, Pujana MA, Nakabayashi K, Scherer SW, Tsui LC.
Chromosomal regions containing high-density and ambiguously mapped putative single nucleotide polymorphisms (SNPs) correlate with segmental duplications in the human genome.
Hum Mol Genet. 2002 Aug 15;11(17):1987-1995.
Human Molecular Genetics web site

--- GenomePixelizer 2002 ---
Gagne JM, Downes BP, Shiu SH, Durski AM, Vierstra RD.
The F-box subunit of the SCF E3 complex is encoded by a diverse superfamily of genes in Arabidopsis.
Proc Natl Acad Sci U S A. 2002 Aug 20;99(17):11519-11524.
PNAS web site

email: Alexander Kozik

Last modified, October 2010