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Home → Our Research → Publications

Publications

The members of the Scripps Genome Center have a long history of contributing to scientific literature. The list below contains selected publications of interest.

  1. Ule J; Stefani G; Mele A; Ruggiu M; Wang X; Taneri B; Gaasterland T; Blencowe BJ; Darnell RB. An RNA map predicting Nova-dependent splicing regulation. Nature 2006, 444, 580-6.   Abstract
  2. Sea Urchin Genome Sequencing Consortium; Sodergren E; Weinstock GM; Davidson EH; Cameron RA; Gibbs RA; Angerer RC; Angerer LM; Arnone MI; Burgess DR; Burke RD; Coffman JA; Dean M; Elphick MR; Ettensohn CA; Foltz KR; Hamdoun A; Hynes RO; Klein WH; Marzluff W; McClay DR; Morris RL; Mushegian A; Rast JP; Smith LC; Thorndyke MC; Vacquier VD; Wessel GM; Wray G; Zhang L; Elsik CG; Ermolaeva O; Hlavina W; Hofmann G; Kitts P; Landrum MJ; Mackey AJ; Maglott D; Panopoulou G; Poustka AJ; Pruitt K; Sapojnikov V; Song X; Souvorov A; Solovyev V; Wei Z; Whittaker CA; Worley K; Durbin KJ; Shen Y; Fedrigo O; Garfield D; Haygood R; Primus A; Satija R; Severson T; Gonzalez-Garay ML; Jackson AR; Milosavljevic A; Tong M; Killian CE; Livingston BT; Wilt FH; Adams N; Belle R; Carbonneau S; Cheung R; Cormier P; Cosson B; Croce J; Fernandez-Guerra A; Geneviere AM; Goel M; Kelkar H; Morales J; Mulner-Lorillon O; Robertson AJ; Goldstone JV; Cole B; Epel D; Gold B; Hahn ME; Howard-Ashby M; Scally M; Stegeman JJ; Allgood EL; Cool J; Judkins KM; McCafferty SS; Musante AM; Obar RA; Rawson AP; Rossetti BJ; Gibbons IR; Hoffman MP; Leone A; Istrail S; Materna SC; Samanta MP; Stolc V; Tongprasit W; Tu Q; Bergeron KF; Brandhorst BP; Whittle J; Berney K; Bottjer DJ; Calestani C; Peterson K; Chow E; Yuan QA; Elhaik E; Graur D; Reese JT; Bosdet I; Heesun S; Marra MA; Schein J; Anderson MK; Brockton V; Buckley KM; Cohen AH; Fugmann SD; Hibino T; Loza-Coll M; Majeske AJ; Messier C; Nair SV; Pancer Z; Terwilliger DP; Agca C; Arboleda E; Chen N; Churcher AM; Hallbook F; Humphrey GW; Idris MM; Kiyama T; Liang S; Mellott D; Mu X; Murray G; Olinski RP; Raible F; Rowe M; Taylor JS; Tessmar-Raible K; Wang D; Wilson KH; Yaguchi S; Gaasterland T; Galindo BE; Gunaratne HJ; Juliano C; Kinukawa M; Moy GW; Neill AT; Nomura M; Raisch M; Reade A; Roux MM; Song JL; Su YH; Townley IK; Voronina E; Wong JL; Amore G; Branno M; Brown ER; Cavalieri V; Duboc V; Duloquin L; Flytzanis C; Gache C; Lapraz F; Lepage T; Locascio A; Martinez P; Matassi G; Matranga V; Range R; Rizzo F; Rottinger E; Beane W; Bradham C; Byrum C; Glenn T; Hussain S; Manning FG; Miranda E; Thomason R; Walton K; Wikramanayke A; Wu SY; Xu R; Brown CT; Chen L; Gray RF; Lee PY; Nam J; Oliveri P; Smith J; Muzny D; Bell S; Chacko J; Cree A; Curry S; Davis C; Dinh H; Dugan-Rocha S; Fowler J; Gill R; Hamilton C; Hernandez J; Hines S; Hume J; Jackson L; Jolivet A; Kovar C; Lee S; Lewis L; Miner G; Morgan M; Nazareth LV; Okwuonu G; Parker D; Pu LL; Thorn R; Wright R. The genome of the sea urchin Strongylocentrotus purpuratus. Science 2006, 314, 941-52.   Abstract
  3. Landry DM; Gaasterland T; Palenik BP. Molecular Characterization of a Phosphate-Regulated Cell-Surface Protein from the Coccolithophorid, Emiliania huxleyi (Prymnesiophyceae). Journal of Phycology 2006, 42, 814.
  4. Barabote RD; Tamang DG; Abewardena SN; Fallah NS; Fu JYC; Mirhosseini P; Pezeshk R; Podell S; Salampessy ML; Thever MD; Saier MH. Extra Domains in Secondary Transport Carriers. Biochim. Biophys. Acta, in press.
  5. Cui C; Griffiths A; Li G; Silva LM; Kramer MF; Gaasterland T; Wang XJ; Coen DM. Prediction and identification of herpes simplex virus 1-encoded microRNAs. J. Virol. 2006, 80, 5499-508.   Abstract
  6. Gopal S; Awadalla S; Gaasterland T; Cross GA. A computational investigation of kinetoplastid trans-splicing. Genome Biol. 2005, 6, R95.   Abstract
  7. Bonanno JB; Almo SC; Bresnick A; Chance MR; Fiser A; Swaminathan S; Jiang J; Studier FW; Shapiro L; Lima CD; Gaasterland TM; Sali A; Bain K; Feil I; Gao X; Lorimer D; Ramos A; Sauder JM; Wasserman SR; Emtage S; D'Amico KL; Burley SK. New York-Structural GenomiX Research Consortium (NYSGXRC): a large scale center for the protein structure initiative. J. Struct. Funct. Genomics 2005, 6, 225-32.   Abstract
  8. Wang XJ; Gaasterland T; Chua NH. Genome-wide prediction and identification of cis-natural antisense transcripts in Arabidopsis thaliana. Genome Biol. 2005, 6, R30.   Abstract
  9. Taneri B; Snyder B; Novoradovsky A; Gaasterland T. Alternative splicing of mouse transcription factors affects their DNA-binding domain architecture and is tissue specific. Genome Biol. 2004, 5, R75.   Abstract
  10. Wang XJ; Reyes JL; Chua NH; Gaasterland T. Prediction and identification of Arabidopsis thaliana microRNAs and their mRNA targets. Genome Biol. 2004, 5, R65.   Abstract
  11. Podell S; Gribskov M. Predicting N-terminal myristoylation sites in plant proteins. BMC Genomics 2004, 5, 37.   Abstract
  12. Hoth S; Ikeda Y; Morgante M; Wang X; Zuo J; Hanafey MK; Gaasterland T; Tingey SV; Chua NH. Monitoring genome-wide changes in gene expression in response to endogenous cytokinin reveals targets in Arabidopsis thaliana. FEBS Lett. 2003, 554, 373-80.   Abstract
  13. Gopal S; Cross GA; Gaasterland T. An organism-specific method to rank predicted coding regions in Trypanosoma brucei. Nucleic Acids Res. 2003, 31, 5877-85.   Abstract
  14. Aravin AA; Lagos-Quintana M; Yalcin A; Zavolan M; Marks D; Snyder B; Gaasterland T; Meyer J; Tuschl T. The small RNA profile during Drosophila melanogaster development. Dev. Cell 2003, 5, 337-50.   Abstract
  15. Kim U; Siegel R; Ren X; Gunther CS; Gaasterland T; Roeder RG. Identification of transcription coactivator OCA-B-dependent genes involved in antigen-dependent B cell differentiation by cDNA array analyses. Proc. Natl. Acad. Sci. U.S.A. 2003, 100, 8868-73.   Abstract
  16. Ravasi T; Huber T; Zavolan M; Forrest A; Gaasterland T; Grimmond S; Hume DA; RIKEN GER Group; GSL Members. Systematic characterization of the zinc-finger-containing proteins in the mouse transcriptome. Genome Res. 2003, 13, 1430-42.   Abstract
  17. Zavolan M; Kondo S; Schonbach C; Adachi J; Hume DA; Hayashizaki Y; Gaasterland T; RIKEN GER Group; GSL Members. Impact of alternative initiation; splicing; and termination on the diversity of the mRNA transcripts encoded by the mouse transcriptome. Genome Res. 2003, 13, 1290-300.   Abstract
  18. Zavolan M; Socci ND; Rajewsky N; Gaasterland T. SMASHing regulatory sites in DNA by human-mouse sequence comparisons. Proc IEEE Comput Soc Bioinform Conf. 2003, 2, 277-86.   Abstract
  19. Okazaki Y; Furuno M; Kasukawa T; Adachi J; Bono H; Kondo S; Nikaido I; Osato N; Saito R; Suzuki H; Yamanaka I; Kiyosawa H; Yagi K; Tomaru Y; Hasegawa Y; Nogami A; Schonbach C; Gojobori T; Baldarelli R; Hill DP; Bult C; Hume DA; Quackenbush J; Schriml LM; Kanapin A; Matsuda H; Batalov S; Beisel KW; Blake JA; Bradt D; Brusic V; Chothia C; Corbani LE; Cousins S; Dalla E; Dragani TA; Fletcher CF; Forrest A; Frazer KS; Gaasterland T; Gariboldi M; Gissi C; Godzik A; Gough J; Grimmond S; Gustincich S; Hirokawa N; Jackson IJ; Jarvis ED; Kanai A; Kawaji H; Kawasawa Y; Kedzierski RM; King BL; Konagaya A; Kurochkin IV; Lee Y; Lenhard B; Lyons PA; Maglott DR; Maltais L; Marchionni L; McKenzie L; Miki H; Nagashima T; Numata K; Okido T; Pavan WJ; Pertea G; Pesole G; Petrovsky N; Pillai R; Pontius JU; Qi D; Ramachandran S; Ravasi T; Reed JC; Reed DJ; Reid J; Ring BZ; Ringwald M; Sandelin A; Schneider C; Semple CA; Setou M; Shimada K; Sultana R; Takenaka Y; Taylor MS; Teasdale RD; Tomita M; Verardo R; Wagner L; Wahlestedt C; Wang Y; Watanabe Y; Wells C; Wilming LG; Wynshaw-Boris A; Yanagisawa M; Yang I; Yang L; Yuan Z; Zavolan M; Zhu Y; Zimmer A; Carninci P; Hayatsu N; Hirozane-Kishikawa T; Konno H; Nakamura M; Sakazume N; Sato K; Shiraki T; Waki K; Kawai J; Aizawa K; Arakawa T; Fukuda S; Hara A; Hashizume W; Imotani K; Ishii Y; Itoh M; Kagawa I; Miyazaki A; Sakai K; Sasaki D; Shibata K; Shinagawa A; Yasunishi A; Yoshino M; Waterston R; Lander ES; Rogers J; Birney E; Hayashizaki Y; FANTOM Consortium; RIKEN Genome Exploration Research Group Phase I & II Team. Analysis of the mouse transcriptome based on functional annotation of 60,770 full-length cDNAs. Nature 2002, 420, 563-73.   Abstract
  20. Ball CA; Sherlock G; Parkinson H; Rocca-Sera P; Brooksbank C; Causton HC; Cavalieri D; Gaasterland T; Hingamp P; Holstege F; Ringwald M; Spellman P; Stoeckert CJ Jr; Stewart JE; Taylor R; Brazma A; Quackenbush J; Microarray Gene Expression Data. The underlying principles of scientific publication. Bioinformatics 2002, 18, 1409.
  21. Ball CA; Sherlock G; Parkinson H; Rocca-Sera P; Brooksbank C; Causton HC; Cavalieri D; Gaasterland T; Hingamp P; Holstege F; Ringwald M; Spellman P; Stoeckert CJ Jr; Stewart JE; Taylor R; Brazma A; Quackenbush J; Microarray Gene Expression Data (MGED) Society. Standards for microarray data. Science 2002, 298, 539.
  22. Zavolan M; van Nimwegen E; Gaasterland T. Splice variation in mouse full-length cDNAs identified by mapping to the mouse genome. Genome Res. 2002, 12, 1377-85.   Abstract
  23. Gaasterland T; Orengo CA. Genomic insights into evolution. Curr. Opin. Struct. Biol. 2002, 12, 345-7.
  24. Arisue N; Hashimot T; Lee JA; Moore DV; Gordon P; Sensen CW; Gaasterland T; Hasegawa M; Muller M. The phylogenetic position of the pelobiont Mastigamoeba balamuthi based on sequences of rDNA and translation elongation factors EF-1alpha and EF-2. J Eukaryot. Microbiol. 2002, 49, 1-10.   Abstract
  25. Bapteste E; Brinkmann H; Lee JA; Moore DV; Sensen CW; Gordon P; Durufle L; Gaasterland T; Lopez P; Muller M; Philippe H. The analysis of 100 genes supports the grouping of three highly divergent amoebae: Dictyostelium; Entamoeba; and Mastigamoeba. Proc. Natl. Acad. Sci. U.S.A. 2002, 99, 1414-9.   Abstract
  26. Gunther CS; Gaasterland T. Characterizing the relationship between protein-fusion and gene co-expression. Genome Inform. Ser. Workshop Genome Inform. 2001, 12, 34-43.   Abstract
  27. Brazma A; Hingamp P; Quackenbush J; Sherlock G; Spellman P; Stoeckert C; Aach J; Ansorge W; Ball CA; Causton HC; Gaasterland T; Glenisson P; Holstege FC; Kim IF; Markowitz V; Matese JC; Parkinson H; Robinson A; Sarkans U; Schulze-Kremer S; Stewart J; Taylor R; Vilo J; Vingron M. Minimum information about a microarray experiment (MIAME)-toward standards for microarray data. Nat. Genet. 2001, 29, 365-71.   Abstract
  28. Muller M; Lee JA; Gordon P; Gaasterland T; Sensen CW. Presence of prokaryotic and eukaryotic species in all subgroups of the PP(i)-dependent group II phosphofructokinase protein family. J. Bacteriol. 2001, 183, 6714-6.   Abstract
  29. Ehrt S; Schnappinger D; Bekiranov S; Drenkow J; Shi S; Gingeras TR; Gaasterland T; Schoolnik G; Nathan C. Reprogramming of the macrophage transcriptome in response to interferon-gamma and Mycobacterium tuberculosis: signaling roles of nitric oxide synthase-2 and phagocyte oxidase. J. Exp. Med. 2001, 194, 1123-40.   Abstract
  30. Serres MH; Gopal S; Nahum LA; Liang P; Gaasterland T; Riley M. A functional update of the Escherichia coli K-12 genome. Genome Biol. 2001, 2, research0035.   Abstract
  31. Altmann CR; Bell E; Sczyrba A; Pun J; Bekiranov S; Gaasterland T; Brivanlou AH. Microarray-based analysis of early development in Xenopus laevis. Dev. Biol. 2001, 236, 64-75.   Abstract
  32. She Q; Singh RK; Confalonieri F; Zivanovic Y; Allard G; Awayez MJ; Chan-Weiher CC; Clausen IG; Curtis BA; De Moors A; Erauso G; Fletcher C; Gordon PM; Heikamp-de Jong I; Jeffries AC; Kozera CJ; Medina N; Peng X; Thi-Ngoc HP; Redder P; Schenk ME; Theriault C; Tolstrup N; Charlebois RL; Doolittle WF; Duguet M; Gaasterland T; Garrett RA; Ragan MA; Sensen CW; Van der Oost J. The complete genome of the crenarchaeon Sulfolobus solfataricus P2. Proc. Natl. Acad. Sci. U.S.A. 2001, 98, 7835-40.   Abstract
  33. Gaasterland T; Oprea M. Whole-genome analysis: annotations and updates. Curr. Opin. Struct. Biol. 2001, 11, 377-81.   Abstract
  34. Gopal S; Schroeder M; Pieper U; Sczyrba A; Aytekin-Kurban G; Bekiranov S; Fajardo JE; Eswar N; Sanchez R; Sali A; Gaasterland T. Homology-based annotation yields 1,042 new candidate genes in the Drosophila melanogaster genome. Nat. Genet. 2001, 27, 337-40.   Abstract
  35. Kawai J; Shinagawa A; Shibata K; Yoshino M; Itoh M; Ishii Y; Arakawa T; Hara A; Fukunishi Y; Konno H; Adachi J; Fukuda S; Aizawa K; Izawa M; Nishi K; Kiyosawa H; Kondo S; Yamanaka I; Saito T; Okazaki Y; Gojobori T; Bono H; Kasukawa T; Saito R; Kadota K; Matsuda H; Ashburner M; Batalov S; Casavant T; Fleischmann W; Gaasterland T; Gissi C; King B; Kochiwa H; Kuehl P; Lewis S; Matsuo Y; Nikaido I; Pesole G; Quackenbush J; Schriml LM; Staubli F; Suzuki R; Tomita M; Wagner L; Washio T; Sakai K; Okido T; Furuno M; Aono H; Baldarelli R; Barsh G; Blake J; Boffelli D; Bojunga N; Carninci P; de Bonaldo MF; Brownstein MJ; Bult C; Fletcher C; Fujita M; Gariboldi M; Gustincich S; Hill D; Hofmann M; Hume DA; Kamiya M; Lee NH; Lyons P; Marchionni L; Mashima J; Mazzarelli J; Mombaerts P; Nordone P; Ring B; Ringwald M; Rodriguez I; Sakamoto N; Sasaki H; Sato K; Schonbach C; Seya T; Shibata Y; Storch KF; Suzuki H; Toyo-oka K; Wang KH; Weitz C; Whittaker C; Wilming L; Wynshaw-Boris A; Yoshida K; Hasegawa Y; Kawaji H; Kohtsuki S; Hayashizaki Y; RIKEN Genome Exploration Research Group Phase II Team and the FANTOM Consortium. Functional annotation of a full-length mouse cDNA collection. Nature 2001, 409, 685-90.   Abstract
  36. Hannaert V; Brinkmann H; Nowitzki U; Lee JA; Albert MA; Sensen CW; Gaasterland T; Muller M; Michels P; Martin W. Enolase from Trypanosoma brucei; from the amitochondriate protist Mastigamoeba balamuthi; and from the chloroplast and cytosol of Euglena gracilis: pieces in the evolutionary puzzle of the eukaryotic glycolytic pathway. Mol. Biol. Evol. 2000, 17, 989-1000.   Abstract
  37. Gaasterland T; Sczyrba A; Thomas E; Aytekin-Kurban G; Gordon P; Sensen CW. MAGPIE/EGRET annotation of the 2.9-Mb Drosophila melanogaster Adh region. Genome Res. 2000, 10, 502-10.   Abstract
  38. Charlebois RL; Singh RK; Chan-Weiher CC; Allard G; Chow C; Confalonieri F; Curtis B; Duguet M; Erauso G; Faguy D; Gaasterland T; Garrett RA; Gordon P; Jeffries AC; Kozera C; Kushwaha N; Lafleur E; Medina N; Peng X; Penny SL; She Q; St Jean A; van der Oost J; Young F; Zivanovic Y; Doolittle WF; Ragan MA; Sensen CW. Gene content and organization of a 281-kbp contig from the genome of the extremely thermophilic archaeon; Sulfolobus solfataricus P2. Genome 2000, 43, 116-36.   Abstract
  39. Gaasterland T; Bekiranov S. Making the most of microarray data. Nat. Genet. 2000, 24, 204-6.
  40. Gaasterland T. Archaeal genomics. Curr. Opin. Microbiol. 1999, 2, 542-7.   Abstract
  41. Burley SK; Almo SC; Bonanno JB; Capel M; Chance MR; Gaasterland T; Lin D; Sali A; Studier FW; Swaminathan S. Structural genomics: beyond the human genome project. Nat. Genet. 1999, 23, 151-7.   Abstract
  42. Romine MF; Stillwell LC; Wong KK; Thurston SJ; Sisk EC; Sensen C; Gaasterland T; Fredrickson JK; Saffer JD. Complete sequence of a 184-kilobase catabolic plasmid from Sphingomonas aromaticivorans F199. J. Bacteriol. 1999, 181, 1585-602.   Abstract
  43. Ragan MA; Gaasterland T. Microbial genescapes: a prokaryotic view of the yeast genome. Microb. Comp. Genomics 1998, 3, 219-35.   Abstract
  44. Gaasterland T; Ragan MA. Microbial genescapes: phyletic and functional patterns of ORF distribution among prokaryotes. Microb. Comp. Genomics 1998, 3, 199-217.   Abstract
  45. Sensen CW; Charlebois RL; Chow C; Clausen IG; Curtis B; Doolittle WF; Duguet M; Erauso G; Gaasterland T; Garrett RA; Gordon P; de Jong IH; Jeffries AC; Kozera C; Medina N; De Moors A; van der Oost J; Phan H; Ragan MA; Schenk ME; She Q; Singh RK; Tolstrup N. Completing the sequence of the Sulfolobus solfataricus P2 genome. Extremophiles 1998, 2, 305-12.   Abstract
  46. Gaasterland T; Ragan MA. Constructing multigenome views of whole microbial genomes. Microb. Comp. Genomics 1998, 3, 177-92.   Abstract
  47. Gaasterland T. Structural genomics: bioinformatics in the driver's seat. Nat. Biotechnol. 1998, 16, 625-7.
  48. Gaasterland T. Structural genomics taking shape. Trends Genet. 1998, 14, 135.
  49. Deckert G; Warren PV; Gaasterland T; Young WG; Lenox AL; Graham DE; Overbeek R; Snead MA; Keller M; Aujay M; Huber R; Feldman RA; Short JM; Olsen GJ; Swanson RV. The complete genome of the hyperthermophilic bacterium Aquifex aeolicus. Nature 1998, 392, 353-8.   Abstract
  50. Sensen CW; Klenk HP; Singh RK; Allard G; Chan CC; Liu QY; Penny SL; Young F; Schenk ME; Gaasterland T; Doolittle WF; Ragan MA; Charlebois RL. Organizational characteristics and information content of an archaeal genome: 156 kb of sequence from Sulfolobus solfataricus P2. Mol. Microbiol. 1996, 22, 175-91.   Abstract
  51. Charlebois RL; Gaasterland T; Ragan MA; Doolittle WF; Sensen CW. The Sulfolobus solfataricus P2 genome project. FEBS Lett. 1996, 389, 88-91.   Abstract
  52. Gaasterland T; Sensen CW. MAGPIE: automated genome interpretation. Trends Genet. 1996, 12, 76-8.
  53. Gaasterland T; Sensen CW. Fully automated genome analysis that reflects user needs and preferences. A detailed introduction to the MAGPIE system architecture. Biochimie 1996, 78, 302-10.   Abstract
  54. Selkov E; Basmanova S; Gaasterland T; Goryanin I; Gretchkin Y; Maltsev N; Nenashev V; Overbeek R; Panyushkina E; Pronevitch L; Selkov E Jr; Yunus I. The metabolic pathway collection from EMP: the enzymes and metabolic pathways database. Nucleic Acids Res. 1996, 24, 26-8.   Abstract
  55. Gaasterland T; Selkov E. Reconstruction of metabolic networks using incomplete information. Proc. Int. Conf. Intell. Syst. Mol. Biol. 1995, 3, 127-35.   Abstract
  56. Gaasterland T; Maltsev N; Lobo J; Chen GH. Assigning function to CDS through qualified query answering: beyond alignment and motifs. Proc. Int. Conf. Intell. Syst. Mol. Biol. 1994, 2, 130-7.   Abstract
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