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Song J, Q Xu, R Olsen, WF Loomis, G Shaulsky, A Kuspa, and R Sucgang. 2005. Comparing the Dictyostelium and Entamoeba Genomes Reveals an Ancient Split in the Conosa Lineage. PLoS Computational Biology 1(7):e71

Supplemental Information
Booth EO, Van Driessche N, Zhuchenko O, Kuspa A, Shaulsky G. Bioinformatics 2005 Oct 18; [Epub] Modes of Gene Expression, also supplementary materials.
Eichinger L, Pachebat JA, Glöckner G, Rajandream MA, Sucgang R, Berriman M, Song J, Olsen R, Szafranski K, Xu Q, Tunggal B, Kummerfeld S, Madera M, Konfortov BA, Rivero F, Bankier AT, Lehmann R, Hamlin N, Davies R, Gaudet P, Fey P, Pilcher K, Chen G, Saunders D, Sodergren E, Davis P, Kerhornou A, Nie X, Hall N, Anjard C, Hemphill L, Bason N, Farbrother P, Desany B, Just E, Morio T, Rost R, Churcher C, Cooper J, Haydock S, van Driessche N, Cronin A, Goodhead I, Muzny D, Mourier T, Pain A, Lu M, Harper D, Lindsay R, Hauser H, James K, Quiles M, Madan Babu M, Saito T, Buchrieser C, Wardroper A, Felder M, Thangavelu M, Johnson D, Knights A, Loulseged H, Mungall K, Oliver K, Price C, Quail MA, Urushihara H, Hernandez J, Rabbinowitsch E, Steffen D, Sanders M, Ma J, Kohara Y, Sharp S, Simmonds M, Spiegler S, Tivey A, Sugano S, White B, Walker D, Woodward J, Winckler T, Tanaka Y, Shaulsky G, Schleicher M, Weinstock G, Rosenthal A, Cox EC, Chisholm RL, Gibbs R, Loomis WF, Platzer M, Kay RR, Williams J, Dear PH, Noegel AA, Barrell B, Kuspa A. Nature. 2005 May 5; 435(7038): 43-57 Link to Nature Website Supplementary Materials
Katoh M, Shaw C, Xu Q, Van Driessche N, Morio T, Kuwayama H, Obara S, Urushihara H, Tanaka Y, Shaulsky G: An orderly retreat: Dedifferentiation is a regulated process Proc Natl Acad Sci U S A. 2004 May 4; 101(18): 7005-10 PNAS

6_Quant.zip; 7_Norm.zip; Katoh_supplement.zip

Demsar J, B Zupan, I Bratko, A Kuspa, JA Halter, RJ Beck, and G Shaulsky: GenePath: a computer program for genetic pathway discovery from mutant data. Medinfo 2001, 10:956-9. GenePath Website
Van Driessche N, C Shaw, M Katoh, T Morio, R Sucgang, M Ibarra, H Kuwayama, T Saito, H Urushihara, M Maeda, I Takeuchi, H Ochiai, W Eaton, J Tollett, J Halter, A Kuspa, Y Tanaka, and G Shaulsky: A transcriptional profile of multicellular development in Dictyostelium discoideum. Development 2002, 129:1543-52.
Van Driessche N, J Demsar, EO Booth, P Hill, P Juvan, B Zupan, A Kuspa, and G Shaulsky: Epistasis analysis with global transcriptional phenotypes. Nat Genet 2005, 37:471-7. supp_info.zip
Xu Q, M Ibarra, D Mahadeo, C Shaw, E Huang, A Kuspa, D Cotter, and G Shaulsky: Transcriptional transitions during Dictyostelium spore germination. Eukaryot Cell 2004, 3:1101-10. Germ_Suppl.tar.gz; Germ_Suppl.zip
Zupan B, I Bratko, J Demsar, P Juvan, T Curk, U Borstnik, JR Beck, J Halter, A Kuspa, and G Shaulsky: GenePath: a system for inference of genetic networks and proposal of genetic experiments. Artif Intell Med 2003, 29:107-30. GenePath Website
Zupan B, J Demsar, I Bratko, P Juvan, JA Halter, A Kuspa, and G Shaulsky: GenePath: a system for automated construction of genetic networks from mutant data. Bioinformatics 2003, 19:383-9.
Sucgang R, G Shaulsky, and A Kuspa: Toward the functional analysis of the Dictyostelium discoideum genome. J Eukaryot Microbiol 2000, 47:334-9.
Sucgang R, G Chen, W Liu, R Lindsay, J Lu, D Muzny, G Shaulsky, W Loomis, R Gibbs, and A Kuspa: Sequence and structure of the extrachromosomal palindrome encoding the ribosomal RNA genes in Dictyostelium. Nucleic Acids Res 2003, 31:2361-8.
Kuspa A, R Sucgang, and G Shaulsky: The promise of a protist: the Dictyostelium genome project. Funct Integr Genomics 2001, 1:279-93.
 
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