PUB - Publikationen an der Universität Bielefeld

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2 Einträge gefunden, die diesen Artikel zitieren

PILER: identification and classification of genomic repeats.
Edgar RC, Myers EW., Bioinformatics 21 Suppl 1(), 2005
PMID: 15961452

AUGUSTUS: a web server for gene prediction in eukaryotes that allows user-defined constraints.
Stanke M, Morgenstern B., Nucleic Acids Res. 33(Web Server issue), 2005
PMID: 15980513

Independent ancient polyploidy events in the sister families Brassicaceae and Cleomaceae.
Schranz ME, Mitchell-Olds T., Plant Cell 18(5), 2006
PMID: 16617098

Following tetraploidy in an Arabidopsis ancestor, genes were removed preferentially from one homeolog leaving clusters enriched in dose-sensitive genes.
Thomas BC, Pedersen B, Freeling M., Genome Res. 16(7), 2006
PMID: 16760422

FPC: a system for building contigs from restriction fingerprinted clones.
Soderlund C, Longden I, Mott R., Comput. Appl. Biosci. 13(5), 1997
PMID: 9367125

The genome of black cottonwood, Populus trichocarpa (Torr. & Gray).
Tuskan GA, Difazio S, Jansson S, Bohlmann J, Grigoriev I, Hellsten U, Putnam N, Ralph S, Rombauts S, Salamov A, Schein J, Sterck L, Aerts A, Bhalerao RR, Bhalerao RP, Blaudez D, Boerjan W, Brun A, Brunner A, Busov V, Campbell M, Carlson J, Chalot M, Chapman J, Chen GL, Cooper D, Coutinho PM, Couturier J, Covert S, Cronk Q, Cunningham R, Davis J, Degroeve S, Dejardin A, Depamphilis C, Detter J, Dirks B, Dubchak I, Duplessis S, Ehlting J, Ellis B, Gendler K, Goodstein D, Gribskov M, Grimwood J, Groover A, Gunter L, Hamberger B, Heinze B, Helariutta Y, Henrissat B, Holligan D, Holt R, Huang W, Islam-Faridi N, Jones S, Jones-Rhoades M, Jorgensen R, Joshi C, Kangasjarvi J, Karlsson J, Kelleher C, Kirkpatrick R, Kirst M, Kohler A, Kalluri U, Larimer F, Leebens-Mack J, Leple JC, Locascio P, Lou Y, Lucas S, Martin F, Montanini B, Napoli C, Nelson DR, Nelson C, Nieminen K, Nilsson O, Pereda V, Peter G, Philippe R, Pilate G, Poliakov A, Razumovskaya J, Richardson P, Rinaldi C, Ritland K, Rouze P, Ryaboy D, Schmutz J, Schrader J, Segerman B, Shin H, Siddiqui A, Sterky F, Terry A, Tsai CJ, Uberbacher E, Unneberg P, Vahala J, Wall K, Wessler S, Yang G, Yin T, Douglas C, Marra M, Sandberg G, Van de Peer Y, Rokhsar D., Science 313(5793), 2006
PMID: 16973872

The ABC's of comparative genomics in the Brassicaceae: building blocks of crucifer genomes.
Schranz ME, Lysak MA, Mitchell-Olds T., Trends Plant Sci. 11(11), 2006
PMID: 17029932

Elaboration of B gene function to include the identity of novel floral organs in the lower eudicot Aquilegia.
Kramer EM, Holappa L, Gould B, Jaramillo MA, Setnikov D, Santiago PM., Plant Cell 19(3), 2007
PMID: 17400892

The evolutionary significance of ancient genome duplications.
Van de Peer Y, Maere S, Meyer A., Nat. Rev. Genet. 10(10), 2009
PMID: 19652647

Gene and genome duplications: the impact of dosage-sensitivity on the fate of nuclear genes.
Edger PP, Pires JC., Chromosome Res. 17(5), 2009
PMID: 19802709

Pistillata--duplications as a mode for floral diversification in (Basal) asterids.
Viaene T, Vekemans D, Irish VF, Geeraerts A, Huysmans S, Janssens S, Smets E, Geuten K., Mol. Biol. Evol. 26(11), 2009
PMID: 19679752

Flower symmetry evolution: towards understanding the abominable mystery of angiosperm radiation.
Busch A, Zachgo S., Bioessays 31(11), 2009
PMID: 19847818

Molecular phylogenetics, temporal diversification, and principles of evolution in the mustard family (Brassicaceae).
Couvreur TL, Franzke A, Al-Shehbaz IA, Bakker FT, Koch MA, Mummenhoff K., Mol. Biol. Evol. 27(1), 2010
PMID: 19744998

A new role for the SHATTERPROOF genes during Arabidopsis gynoecium development.
Colombo M, Brambilla V, Marcheselli R, Caporali E, Kater MM, Colombo L., Dev. Biol. 337(2), 2009
PMID: 19900437

De novo assembly of human genomes with massively parallel short read sequencing.
Li R, Zhu H, Ruan J, Qian W, Fang X, Shi Z, Li Y, Li S, Shan G, Kristiansen K, Li S, Yang H, Wang J, Wang J., Genome Res. 20(2), 2009
PMID: 20019144

The ABC model and the diversification of floral organ identity.
Litt A, Kramer EM., Semin. Cell Dev. Biol. 21(1), 2009
PMID: 19948236

The development of Arabidopsis as a model plant.
Koornneef M, Meinke D., Plant J. 61(6), 2010
PMID: 20409266

Transcriptional regulation of the CRK/DUF26 group of receptor-like protein kinases by ozone and plant hormones in Arabidopsis.
Wrzaczek M, Brosche M, Salojarvi J, Kangasjarvi S, Idanheimo N, Mersmann S, Robatzek S, Karpinski S, Karpinska B, Kangasjarvi J., BMC Plant Biol. 10(), 2010
PMID: 20500828

Evidence for the involvement of Globosa-like gene duplications and expression divergence in the evolution of floral morphology in the Zingiberales.
Bartlett ME, Specht CD., New Phytol. 187(2), 2010
PMID: 20456055

Dated molecular phylogenies indicate a Miocene origin for Arabidopsis thaliana.
Beilstein MA, Nagalingum NS, Clements MD, Manchester SR, Mathews S., Proc. Natl. Acad. Sci. U.S.A. 107(43), 2010
PMID: 20921408

Aligning short sequencing reads with Bowtie.
Langmead B., Curr Protoc Bioinformatics Chapter 11(), 2010
PMID: 21154709

Cabbage family affairs: the evolutionary history of Brassicaceae.
Franzke A, Lysak MA, Al-Shehbaz IA, Koch MA, Mummenhoff K., Trends Plant Sci. 16(2), 2010
PMID: 21177137

Sequence-based physical mapping of complex genomes by whole genome profiling.
van Oeveren J, de Ruiter M, Jesse T, van der Poel H, Tang J, Yalcin F, Janssen A, Volpin H, Stormo KE, Bogden R, van Eijk MJ, Prins M., Genome Res. 21(4), 2011
PMID: 21324881

The Arabidopsis lyrata genome sequence and the basis of rapid genome size change.
Hu TT, Pattyn P, Bakker EG, Cao J, Cheng JF, Clark RM, Fahlgren N, Fawcett JA, Grimwood J, Gundlach H, Haberer G, Hollister JD, Ossowski S, Ottilar RP, Salamov AA, Schneeberger K, Spannagl M, Wang X, Yang L, Nasrallah ME, Bergelson J, Carrington JC, Gaut BS, Schmutz J, Mayer KF, Van de Peer Y, Grigoriev IV, Nordborg M, Weigel D, Guo YL., Nat. Genet. 43(5), 2011
PMID: 21478890

Ancestral polyploidy in seed plants and angiosperms.
Jiao Y, Wickett NJ, Ayyampalayam S, Chanderbali AS, Landherr L, Ralph PE, Tomsho LP, Hu Y, Liang H, Soltis PS, Soltis DE, Clifton SW, Schlarbaum SE, Schuster SC, Ma H, Leebens-Mack J, dePamphilis CW., Nature 473(7345), 2011
PMID: 21478875

Screening synteny blocks in pairwise genome comparisons through integer programming.
Tang H, Lyons E, Pedersen B, Schnable JC, Paterson AH, Freeling M., BMC Bioinformatics 12(), 2011
PMID: 21501495

The genome of the extremophile crucifer Thellungiella parvula.
Dassanayake M, Oh DH, Haas JS, Hernandez A, Hong H, Ali S, Yun DJ, Bressan RA, Zhu JK, Bohnert HJ, Cheeseman JM., Nat. Genet. 43(9), 2011
PMID: 21822265

The genome of the mesopolyploid crop species Brassica rapa.
Wang X, Wang H, Wang J, Sun R, Wu J, Liu S, Bai Y, Mun JH, Bancroft I, Cheng F, Huang S, Li X, Hua W, Wang J, Wang X, Freeling M, Pires JC, Paterson AH, Chalhoub B, Wang B, Hayward A, Sharpe AG, Park BS, Weisshaar B, Liu B, Li B, Liu B, Tong C, Song C, Duran C, Peng C, Geng C, Koh C, Lin C, Edwards D, Mu D, Shen D, Soumpourou E, Li F, Fraser F, Conant G, Lassalle G, King GJ, Bonnema G, Tang H, Wang H, Belcram H, Zhou H, Hirakawa H, Abe H, Guo H, Wang H, Jin H, Parkin IA, Batley J, Kim JS, Just J, Li J, Xu J, Deng J, Kim JA, Li J, Yu J, Meng J, Wang J, Min J, Poulain J, Wang J, Hatakeyama K, Wu K, Wang L, Fang L, Trick M, Links MG, Zhao M, Jin M, Ramchiary N, Drou N, Berkman PJ, Cai Q, Huang Q, Li R, Tabata S, Cheng S, Zhang S, Zhang S, Huang S, Sato S, Sun S, Kwon SJ, Choi SR, Lee TH, Fan W, Zhao X, Tan X, Xu X, Wang Y, Qiu Y, Yin Y, Li Y, Du Y, Liao Y, Lim Y, Narusaka Y, Wang Y, Wang Z, Li Z, Wang Z, Xiong Z, Zhang Z; Brassica rapa Genome Sequencing Project Consortium, Wang X, Wang H, Wang J, Sun R, Wu J, Liu S, Bai Y, Mun JH, Bancroft I, Cheng F, Huang S, Li X, Hua W, Wang J, Wang X, Freeling M, Chris Pires J, Paterson AH, Chalhoub B, Wang B, Hayward A, Sharpe AG, Park BS, Weisshaar B, Liu B, Li B, Liu B, Tong C, Song C, Duran C, Peng C, Geng C, Koh C, Lin C, Edwards D, Mu D, Shen D, Soumpourou E, Li F, Fraser F, Conant G, Lassalle G, King GJ, Bonnema G, Tang H, Wang H, Belcram H, Zhou H, Hirakawa H, Abe H, Guo H, Wang H, Jin H, Parkin IA, Batley J, Kim JS, Just J, Li J, Xu J, Deng J, Kim JA, Li J, Yu J, Meng J, Wang J, Min J, Poulain J, Wang J, Hatakeyama K, Wu K, Wang L, Fang L, Trick M, Links MG, Zhao M, Jin M, Ramchiary N, Drou N, Berkman PJ, Cai Q, Huang Q, Li R, Tabata S, Cheng S, Zhang S, Zhang S, Huang S, Sato S, Sun S, Kwon SJ, Choi SR, Lee TH, Fan W, Zhao X, Tan X, Xu X, Wang Y, Qiu Y, Yin Y, Li Y, Du Y, Liao Y, Lim Y, Narusaka Y, Wang Y, Wang Z, Li Z, Wang Z, Xiong Z, Zhang Z., Nat. Genet. 43(10), 2011
PMID: 21873998

Evolution of the S-locus region in Arabidopsis relatives.
Guo YL, Zhao X, Lanz C, Weigel D., Plant Physiol. 157(2), 2011
PMID: 21810962

Rapid copy number expansion and recent recruitment of domains in S-receptor kinase-like genes contribute to the origin of self-incompatibility.
Zhang X, Wang L, Yuan Y, Tian D, Yang S., FEBS J. 278(22), 2011
PMID: 21914128

The Pfam protein families database.
Punta M, Coggill PC, Eberhardt RY, Mistry J, Tate J, Boursnell C, Pang N, Forslund K, Ceric G, Clements J, Heger A, Holm L, Sonnhammer EL, Eddy SR, Bateman A, Finn RD., Nucleic Acids Res. 40(Database issue), 2011
PMID: 22127870

i-ADHoRe 3.0--fast and sensitive detection of genomic homology in extremely large data sets.
Proost S, Fostier J, De Witte D, Dhoedt B, Demeester P, Van de Peer Y, Vandepoele K., Nucleic Acids Res. 40(2), 2011
PMID: 22102584

Characterization of MADS-domain transcription factor complexes in Arabidopsis flower development.
Smaczniak C, Immink RG, Muino JM, Blanvillain R, Busscher M, Busscher-Lange J, Dinh QD, Liu S, Westphal AH, Boeren S, Parcy F, Xu L, Carles CC, Angenent GC, Kaufmann K., Proc. Natl. Acad. Sci. U.S.A. 109(5), 2012
PMID: 22238427

Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks.
Trapnell C, Roberts A, Goff L, Pertea G, Kim D, Kelley DR, Pimentel H, Salzberg SL, Rinn JL, Pachter L., Nat Protoc 7(3), 2012
PMID: 22383036

Corolla monosymmetry: evolution of a morphological novelty in the Brassicaceae family.
Busch A, Horn S, Muhlhausen A, Mummenhoff K, Zachgo S., Mol. Biol. Evol. 29(4), 2011
PMID: 22135189

Ancient whole genome duplications, novelty and diversification: the WGD Radiation Lag-Time Model.
Schranz ME, Mohammadin S, Edger PP., Curr. Opin. Plant Biol. 15(2), 2012
PMID: 22480429

MrBayes 3.2: efficient Bayesian phylogenetic inference and model choice across a large model space.
Ronquist F, Teslenko M, van der Mark P, Ayres DL, Darling A, Hohna S, Larget B, Liu L, Suchard MA, Huelsenbeck JP., Syst. Biol. 61(3), 2012
PMID: 22357727

The tomato genome sequence provides insights into fleshy fruit evolution.
Tomato Genome Consortium, Sato S, Tabata S, Hirakawa H, Asamizu E, Shirasawa K, Isobe S, Kaneko T, Nakamura Y, Shibata D, Aoki K, Egholm M, Knight J, Bogden R, Li C, Shuang Y, Xu X, Pan S, Cheng S, Liu X, Ren Y, Wang J, Albiero A, Dal Pero F, Todesco S, Van Eck J, Buels RM, Bombarely A, Gosselin JR, Huang M, Leto JA, Menda N, Strickler S, Mao L, Gao S, Tecle IY, York T, Zheng Y, Vrebalov JT, Lee J, Zhong S, Mueller LA, Stiekema WJ, Ribeca P, Alioto T, Yang W, Huang S, Du Y, Zhang Z, Gao J, Guo Y, Wang X, Li Y, He J, Li C, Cheng Z, Zuo J, Ren J, Zhao J, Yan L, Jiang H, Wang B, Li H, Li Z, Fu F, Chen B, Feng Q, Fan D, Wang Y, Ling H, Xue Y, Ware D, McCombie WR, Lippman ZB, Chia JM, Jiang K, Pasternak S, Gelley L, Kramer M, Anderson LK, Chang SB, Royer SM, Shearer LA, Stack SM, Rose JK, Xu Y, Eannetta N, Matas AJ, McQuinn R, Tanksley SD, Camara F, Guigo R, Rombauts S, Fawcett J, Van de Peer Y, Zamir D, Liang C, Spannagl M, Gundlach H, Bruggmann R, Mayer K, Jia Z, Zhang J, Ye Z, Bishop GJ, Butcher S, Lopez-Cobollo R, Buchan D, Filippis I, Abbott J, Dixit R, Singh M, Singh A, Pal JK, Pandit A, Singh PK, Mahato AK, Gaikwad VD, Sharma RR, Mohapatra T, Singh NK, Causse M, Rothan C, Schiex T, Noirot C, Bellec A, Klopp C, Delalande C, Berges H, Mariette J, Frasse P, Vautrin S, Zouine M, Latche A, Rousseau C, Regad F, Pech JC, Philippot M, Bouzayen M, Pericard P, Osorio S, Fernandez del Carmen A, Monforte A, Granell A, Fernandez-Munoz R, Conte M, Lichtenstein G, Carrari F, De Bellis G, Fuligni F, Peano C, Grandillo S, Termolino P, Pietrella M, Fantini E, Falcone G, Fiore A, Giuliano G, Lopez L, Facella P, Perotta G, Daddiego L, Bryan G, Orozco M, Pastor X, Torrents D, van Schriek MG, Feron RM, van Oeveren J, de Heer P, daPonte L, Jacobs-Oomen S, Cariaso M, Prins M, van Eijk MJ, Janssen A, van Haaren MJ, Jungeun Kim SH, Kwon SY, Kim S, Koo DH, Lee S, Hur CG, Clouser C, Rico A, Hallab A, Gebhardt C, Klee K, Jocker A, Warfsmann J, Gobel U, Kawamura S, Yano K, Sherman JD, Fukuoka H, Negoro S, Bhutty S, Chowdhury P, Chattopadhyay D, Datema E, Smit S, Schijlen EG, van de Belt J, van Haarst JC, Peters SA, van Staveren MA, Henkens MH, Mooyman PJ, Hesselink T, van Ham RC, Jiang G, Droege M, Choi D, Kang BC, Kim BD, Park M, Kim S, Yeom SI, Lee YH, Choi YD, Li G, Gao J, Liu Y, Huang S, Fernandez-Pedrosa V, Collado C, Zuniga S, Wang G, Cade R, Dietrich RA, Rogers J, Knapp S, Fei Z, White RA, Thannhauser TW, Giovannoni JJ, Botella MA, Gilbert L, Gonzalez R, Goicoechea JL, Yu Y, Kudrna D, Collura K, Wissotski M, Wing R, Meyers BC, Gurazada AB, Green PJ, Vyas SM, Solanke AU, Kumar R, Gupta V, Sharma AK, Khurana P, Khurana JP, Tyagi AK, Dalmay T, Mohorianu I, Walts B, Chamala S, Barbazuk WB, Li J, Guo H, Lee TH, Wang Y, Zhang D, Paterson AH, Wang X, Tang H, Barone A, Chiusano ML, Ercolano MR, D'Agostino N, Di Filippo M, Traini A, Sanseverino W, Frusciante L, Seymour GB, Elharam M, Fu Y, Hua A, Kenton S, Lewis J, Lin S, Najar F, Lai H, Qin B, Qu C, Shi R, White D, White J, Xing Y, Yang K, Yi J, Yao Z, Zhou L, Roe BA, Vezzi A, D'Angelo M, Zimbello R, Schiavon R, Caniato E, Rigobello C, Campagna D, Vitulo N, Valle G, Nelson DR, De Paoli E, Szinay D, de Jong HH, Bai Y, Visser RG, Klein R, Beasley H, McLaren K, Nicholson C, Riddle C, Gianese G., Nature 485(7400), 2012
PMID: 22660326

Insights into salt tolerance from the genome of Thellungiella salsuginea.
Wu HJ, Zhang Z, Wang JY, Oh DH, Dassanayake M, Liu B, Huang Q, Sun HX, Xia R, Wu Y, Wang YN, Yang Z, Liu Y, Zhang W, Zhang H, Chu J, Yan C, Fang S, Zhang J, Wang Y, Zhang F, Wang G, Lee SY, Cheeseman JM, Yang B, Li B, Min J, Yang L, Wang J, Chu C, Chen SY, Bohnert HJ, Zhu JK, Wang XJ, Xie Q., Proc. Natl. Acad. Sci. U.S.A. 109(30), 2012
PMID: 22778405

Decoding plant and animal genome plasticity from differential paleo-evolutionary patterns and processes.
Murat F, Van de Peer Y, Salse J., Genome Biol Evol 4(9), 2012
PMID: 22833223

Gamma paleohexaploidy in the stem lineage of core eudicots: significance for MADS-box gene and species diversification.
Vekemans D, Proost S, Vanneste K, Coenen H, Viaene T, Ruelens P, Maere S, Van de Peer Y, Geuten K., Mol. Biol. Evol. 29(12), 2012
PMID: 22821009

The Capsella rubella genome and the genomic consequences of rapid mating system evolution.
Slotte T, Hazzouri KM, Agren JA, Koenig D, Maumus F, Guo YL, Steige K, Platts AE, Escobar JS, Newman LK, Wang W, Mandakova T, Vello E, Smith LM, Henz SR, Steffen J, Takuno S, Brandvain Y, Coop G, Andolfatto P, Hu TT, Blanchette M, Clark RM, Quesneville H, Nordborg M, Gaut BS, Lysak MA, Jenkins J, Grimwood J, Chapman J, Prochnik S, Shu S, Rokhsar D, Schmutz J, Weigel D, Wright SI., Nat. Genet. 45(7), 2013
PMID: 23749190

An atlas of over 90,000 conserved noncoding sequences provides insight into crucifer regulatory regions.
Haudry A, Platts AE, Vello E, Hoen DR, Leclercq M, Williamson RJ, Forczek E, Joly-Lopez Z, Steffen JG, Hazzouri KM, Dewar K, Stinchcombe JR, Schoen DJ, Wang X, Schmutz J, Town CD, Edger PP, Pires JC, Schumaker KS, Jarvis DE, Mandakova T, Lysak MA, van den Bergh E, Schranz ME, Harrison PM, Moses AM, Bureau TE, Wright SI, Blanchette M., Nat. Genet. 45(8), 2013
PMID: 23817568

KEGG: kyoto encyclopedia of genes and genomes.
Kanehisa M, Goto S., Nucleic Acids Res. 28(1), 2000
PMID: 10592173

Gene ontology: tool for the unification of biology. The Gene Ontology Consortium.
Ashburner M, Ball CA, Blake JA, Botstein D, Butler H, Cherry JM, Davis AP, Dolinski K, Dwight SS, Eppig JT, Harris MA, Hill DP, Issel-Tarver L, Kasarskis A, Lewis S, Matese JC, Richardson JE, Ringwald M, Rubin GM, Sherlock G., Nat. Genet. 25(1), 2000
PMID: 10802651

Analysis of the genome sequence of the flowering plant Arabidopsis thaliana.
Arabidopsis Genome Initiative., Nature 408(6814), 2000
PMID: 11130711

Development of floral organ identity: stories from the MADS house.
Theissen G., Curr. Opin. Plant Biol. 4(1), 2001
PMID: 11163172

InterProScan--an integration platform for the signature-recognition methods in InterPro.
Zdobnov EM, Apweiler R., Bioinformatics 17(9), 2001
PMID: 11590104

Comparison of the expression patterns of two small gene families of S gene family receptor kinase genes during the defence response in Brassica oleracea and Arabidopsis thaliana.
Pastuglia M, Swarup R, Rocher A, Saindrenan P, Roby D, Dumas C, Cock JM., Gene 282(1-2), 2002
PMID: 11814694

MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform.
Katoh K, Misawa K, Kuma K, Miyata T., Nucleic Acids Res. 30(14), 2002
PMID: 12136088

The SWISS-PROT protein knowledgebase and its supplement TrEMBL in 2003.
Boeckmann B, Bairoch A, Apweiler R, Blatter MC, Estreicher A, Gasteiger E, Martin MJ, Michoud K, O'Donovan C, Phan I, Pilbout S, Schneider M., Nucleic Acids Res. 31(1), 2003
PMID: 12520024

A recent polyploidy superimposed on older large-scale duplications in the Arabidopsis genome.
Blanc G, Hokamp K, Wolfe KH., Genome Res. 13(2), 2003
PMID: 12566392

Comparisons with Caenorhabditis (approximately 100 Mb) and Drosophila (approximately 175 Mb) using flow cytometry show genome size in Arabidopsis to be approximately 157 Mb and thus approximately 25% larger than the Arabidopsis genome initiative estimate of approximately 125 Mb.
Bennett MD, Leitch IJ, Price HJ, Johnston JS., Ann. Bot. 91(5), 2003
PMID: 12646499

Unravelling angiosperm genome evolution by phylogenetic analysis of chromosomal duplication events.
Bowers JE, Chapman BA, Rong J, Paterson AH., Nature 422(6930), 2003
PMID: 12660784

Locating sequence on FPC maps and selecting a minimal tiling path.
Engler FW, Hatfield J, Nelson W, Soderlund CA., Genome Res. 13(9), 2003
PMID: 12915486

OrthoMCL: identification of ortholog groups for eukaryotic genomes.
Li L, Stoeckert CJ Jr, Roos DS., Genome Res. 13(9), 2003
PMID: 12952885

GeneWise and Genomewise.
Birney E, Clamp M, Durbin R., Genome Res. 14(5), 2004
PMID: 15123596

The genetic, developmental, and molecular bases of fruit size and shape variation in tomato.
Tanksley SD., Plant Cell 16 Suppl(), 2004
PMID: 15131251

Four DEF-like MADS box genes displayed distinct floral morphogenetic roles in Phalaenopsis orchid.
Tsai WC, Kuoh CS, Chuang MH, Chen WH, Chen HH., Plant Cell Physiol. 45(7), 2004
PMID: 15295066

PerlPrimer: cross-platform, graphical primer design for standard, bisulphite and real-time PCR.
Marshall OJ., Bioinformatics 20(15), 2004
PMID: 15073005

A superfamily of S locus-related sequences in Arabidopsis: diverse structures and expression patterns.
Dwyer KG, Kandasamy MK, Mahosky DI, Acciai J, Kudish BI, Miller JE, Nasrallah ME, Nasrallah JB., Plant Cell 6(12), 1994
PMID: 7866027

tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence.
Lowe TM, Eddy SR., Nucleic Acids Res. 25(5), 1997
PMID: 9023104

The self-incompatibility (S) haplotypes of Brassica contain highly divergent and rearranged sequences of ancient origin.
Boyes DC, Nasrallah ME, Vrebalov J, Nasrallah JB., Plant Cell 9(2), 1997
PMID: 9061954

Gapped BLAST and PSI-BLAST: a new generation of protein database search programs.
Altschul SF, Madden TL, Schaffer AA, Zhang J, Zhang Z, Miller W, Lipman DJ., Nucleic Acids Res. 25(17), 1997
PMID: 9254694

Sea anemone genome reveals ancestral eumetazoan gene repertoire and genomic organization.
Putnam NH, Srivastava M, Hellsten U, Dirks B, Chapman J, Salamov A, Terry A, Shapiro H, Lindquist E, Kapitonov VV, Jurka J, Genikhovich G, Grigoriev IV, Lucas SM, Steele RE, Finnerty JR, Technau U, Martindale MQ, Rokhsar DS., Science 317(5834), 2007
PMID: 17615350

LTR_FINDER: an efficient tool for the prediction of full-length LTR retrotransposons.
Xu Z, Wang H., Nucleic Acids Res. 35(Web Server issue), 2007
PMID: 17485477

Cleome, a genus closely related to Arabidopsis, contains species spanning a developmental progression from C(3) to C(4) photosynthesis.
Marshall DM, Muhaidat R, Brown NJ, Liu Z, Stanley S, Griffiths H, Sage RF, Hibberd JM., Plant J. 51(5), 2007
PMID: 17692080

The grapevine genome sequence suggests ancestral hexaploidization in major angiosperm phyla.
Jaillon O, Aury JM, Noel B, Policriti A, Clepet C, Casagrande A, Choisne N, Aubourg S, Vitulo N, Jubin C, Vezzi A, Legeai F, Hugueney P, Dasilva C, Horner D, Mica E, Jublot D, Poulain J, Bruyere C, Billault A, Segurens B, Gouyvenoux M, Ugarte E, Cattonaro F, Anthouard V, Vico V, Del Fabbro C, Alaux M, Di Gaspero G, Dumas V, Felice N, Paillard S, Juman I, Moroldo M, Scalabrin S, Canaguier A, Le Clainche I, Malacrida G, Durand E, Pesole G, Laucou V, Chatelet P, Merdinoglu D, Delledonne M, Pezzotti M, Lecharny A, Scarpelli C, Artiguenave F, Pe ME, Valle G, Morgante M, Caboche M, Adam-Blondon AF, Weissenbach J, Quetier F, Wincker P; French-Italian Public Consortium for Grapevine Genome Characterization., Nature 449(7161), 2007
PMID: 17721507

The 2R hypothesis: an update.
Kasahara M., Curr. Opin. Immunol. 19(5), 2007
PMID: 17707623

Control of corolla monosymmetry in the Brassicaceae Iberis amara.
Busch A, Zachgo S., Proc. Natl. Acad. Sci. U.S.A. 104(42), 2007
PMID: 17940055

B-class MADS-box genes in trioecious papaya: two paleoAP3 paralogs, CpTM6-1 and CpTM6-2, and a PI ortholog CpPI.
Ackerman CM, Yu Q, Kim S, Paull RE, Moore PH, Ming R., Planta 227(4), 2007
PMID: 17985156

Using RepeatMasker to identify repetitive elements in genomic sequences.
Chen N., Curr Protoc Bioinformatics Chapter 4(), 2004
PMID: 18428725

The draft genome of the transgenic tropical fruit tree papaya (Carica papaya Linnaeus).
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Interactions of B-class complex proteins involved in tepal development in Phalaenopsis orchid.
Tsai WC, Pan ZJ, Hsiao YY, Jeng MF, Wu TF, Chen WH, Chen HH., Plant Cell Physiol. 49(5), 2008
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Analyzing real-time PCR data by the comparative C(T) method.
Schmittgen TD, Livak KJ., Nat Protoc 3(6), 2008
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Automatically extracting functionally equivalent proteins from SwissProt.
McMillan LE, Martin AC., BMC Bioinformatics 9(), 2008
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InterPro: the integrative protein signature database.
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Assessing the gene space in draft genomes.
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Evolution of floral symmetry: a state of the art.
Jabbour F, Nadot S, Damerval C., C. R. Biol. 332(2-3), 2008
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The MIQE guidelines: minimum information for publication of quantitative real-time PCR experiments.
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TopHat: discovering splice junctions with RNA-Seq.
Trapnell C, Pachter L, Salzberg SL., Bioinformatics 25(9), 2009
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Infernal 1.0: inference of RNA alignments.
Nawrocki EP, Kolbe DL, Eddy SR., Bioinformatics 25(10), 2009
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Old dogs, new tricks: regulatory evolution in conserved genetic modules leads to novel morphologies in plants.
Rosin FM, Kramer EM., Dev. Biol. 332(1), 2009
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Why are orchid flowers so diverse? Reduction of evolutionary constraints by paralogues of class B floral homeotic genes.
Mondragon-Palomino M, Theissen G., Ann. Bot. 104(3), 2009
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Gene duplication and evolutionary novelty in plants.
Flagel LE, Wendel JF., New Phytol. 183(3), 2009
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TigrScan and GlimmerHMM: two open source ab initio eukaryotic gene-finders.
Majoros WH, Pertea M, Salzberg SL., Bioinformatics 20(16), 2004
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Natural variation in expression of self-incompatibility in Arabidopsis thaliana: implications for the evolution of selfing.
Nasrallah ME, Liu P, Sherman-Broyles S, Boggs NA, Nasrallah JB., Proc. Natl. Acad. Sci. U.S.A. 101(45), 2004
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Activation of hypersensitive cell death by pathogen-induced receptor-like protein kinases from Arabidopsis.
Chen K, Fan B, Du L, Chen Z., Plant Mol. Biol. 56(2), 2004
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A gene expression map of Arabidopsis thaliana development.
Schmid M, Davison TS, Henz SR, Pape UJ, Demar M, Vingron M, Scholkopf B, Weigel D, Lohmann JU., Nat. Genet. 37(5), 2005
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