Gaasterland Lab
Terry Gaasterland
Intro Vitae Recent Papers
Selected peer-reviewed publications

  1. 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 Nov 20;554(3):373-80.
  2. Gopal S, Cross GA, Gaasterland T. An organism-specific method to rank predicted coding regions in Trypanosoma brucei. Nucleic Acids Res. 2003 Oct 15;31(20):5877-85.
  3. Aravin AA, Lagos-Quintana M, Yalcin A, Zavolan M, Marks D, Snyder B, Gaasterland T, Meyer J, Tuschl T. The small RNA profile during D. melanogaster development. Dev Cell. 2003 5(2):337-50.
  4. 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 Jul 22;100(15):8868-73. Epub 2003 Jul 11.
  5. 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 Jun;13(6B):1430-42.
  6. 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 Jun;13(6B):1290-300.
  7. Okazaki Y, 134 co-authors, and 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 Dec 5;420(6915):563-73.
  8. 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 Oct 18;298(5593):539.
  9. Zavolan M, Van Nimwegen E, Gaasterland T. Splice Variation in Mouse Full-Length cDNAs Identified by Mapping to the Mouse Genome. Genome Res. 2002 Sep;12(9):1377-85.
  10. 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 Feb 5;99(3):1414-9.
  11. 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 Jan-Feb;49(1):1-10.
  12. 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 Dec;29(4):365-71.
  13. 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 Nov;183(22):6714-6.
  14. 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 Oct 15;194(8):1123-40.
  15. 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(9):RESEARCH0035.
  16. Gopal S, Schroeder M, Pieper U, Sczyrba A, 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. Nature Genetics, 27(3):337-40, 2001.
  17. Kawai J, 93 co-authors and Hayashizaki Y. Functional annotation of a full-length mouse cDNA collection. Nature, 409(6821):685-90, 2001.
  18. 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 Aug 1;236(1):64-75.
  19. She Q, 30 co-authors and Van der Oost J. The complete genome of the crenarchaeon Sulfolobus solfataricus P2. Proc Natl Acad Sci U S A. 2001 Jul 3;98(14):7835-40.
  20. Gaasterland T, Sczyrba A, Thomas E, Kurban G, Gordon P, Sensen CW. MAGPIE/EGRET Annotation of the 2.91Mb Drosophila melanogaster ADH Region Genome Research, Vol. 10 Issue 4 (April 2000), pp 502-510.
  21. Gaasterland T and Bekiranov S. Making the Most of Microarray Data. Nature Genetics, 24:204-206, 2000.
  22. Hanneart V, Brinkmann H, Nowitzki U, Lee J, Albert M, Sensen CW, Gaasterland T, Miller M, Michels P, Martin W. Enolase from Trypanosoma brucei, from the amitochondriate protist Mastigamoeba balamuthi, and from the chloroplast and cytosol of Euglena gracilis. Mol. Biol. Evol., 17:989-1000, 2000.
  23. Romine M, Stilwell L, Wong K-K, Thurston SJ, Sisk EC, Sensen CW, Gaasterland T, Saffer JD, Frederickson JK. Complete Sequence of a 184 kb Catabolic Plasmid from Sphingomonas aromaticivorans Strain F199, Journal of Bacteriology, 181(5):1585-1602, 1999.
  24. Gaasterland and Ragan M. Constructing Multi-Genome Views of Whole Microbial Genomes, Journal of Microbial and Comparative Genomics, 3(3), 1998.
  25. Gaasterland T and Ragan M. A Prokaryotic View of the Yeast Genome, Journal of Microbial and Comparative Genomics, 3(4):219-235, 1998.
  26. Gaasterland T and Ragan M. Phyletic and Functional Patterns of ORF Distribution Among Prokaryotes, Journal of Microbial and Comparative Genomics, 3(4):199-217, 1998.
  27. Gaasterland T. Structural Genomics: Bioinformatics in the drivers seat. Nature Biotechnology, 16:625-627, July 1998.
  28. Sensen CW, Gaasterland T et al. Sulfolobus solfataricus: Sequencing and Annotation of the First Complete Megabase, Extremophiles, 2:305-312, 1998.
  29. Deckert G, P. Warren P, Gaasterland T, Young W.G, Lenox A, Graham D, Overbeek R, Snead M, Keller M, Aujay R, Huber R, Feldman R, Short J, Olsen G, Swanson R. The Aquifex aeolicus Genome, Nature 392(353):352-358, March 26, 1998.
  30. Gaasterland T. Structural Genomics Taking Shape,Trends in Genetics, March 1998.
  31. Gaasterland T and Lobo J. Qualifying Answers According to User Needs and Preferences, Fundamenta Informatica, November 1997.
  32. Gaasterland T. Cooperative Answering Through Controlled Query Relaxation, IEEE Expert, 12(5):48-59, Sept/Oct 1997.
  33. Sensen CW, Klenk H-P, Singh R-K, Allard G, Chan C, Liu Q, Penny S, Young F, Schenk M, Gaasterland T, Doolittle WF, Ragan M, and Charlebois R. Organizational Characteristics and Information Content of and Archaeal Genome: 156 Kbp of Sequence from Sulfolobus solfataricus P2, Journal of Molecular Microbiology, 22:175-191, 1996.
Terry Gaasterland
Gaasterland Bio/CV Current Research in the Lab Publications: Abstracts and Links Lab Members Computational Resources