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GAASTERLAND, THERESA

Professor of Computational Biology and Genomics

Director, Scripps Genome Center

Degrees:

• B.S., Duke University
• M.S., University of Maryland
• Ph.D., University of Maryland

Research Interests:

• Microbial Genome Annotation; Comparison of whole genomes in closely related organisms and identification of laterally transferred genes using comparative operon structure for gene function and assignment
• Alternative Splicing in Eukaryotic Genes in humans, mice and rats. Impact on protein structure, emphasis on transcription factors. Impact in cancer related genes and genes expressed in embryonic development
• Regulation of RNA; Comparative identification of microRNA genes, prediction of mRNA targets of microRNA genes, prediction of pre-mRNA targets of RNA binding proteins, reconstruction of regulatory networks for RNA expression

Courses Recently Taught:

• SIO 296: Special Topics/Marine Biology
• SIO 297: Marine Biology Seminar
• SIO242A: Marine Biotechnology I

Honors and Awards:

• Mayor’s Award for Excellence in Science and Technology, 2003
• Presidential Early Career Award in Science and Engineering, 2000-2005
• Burroughs Wellcome New Investigator Award, 2000-2002
• Sinsheimer Foundation Fellowship, 1999-2002
• Mallinkrodt Foundation Fellowship, 1999-2001
• NSF CAREER Award, 1999
• NSF Postdoctoral Fellowship, 1992
• DOE Enrico Fermi Fellowship, 1992-1994
• Angier B. Duke Scholar, Oxford University, 1983
• Valedictorian, Winston Churchill High School, 1980
• Angier B. Duke Scholar, Duke University, 1980-1984

Mentoring:

• Shokirev, Max (Graduate; 2009-2009)
• Wu, Allan (Graduate; 2009-2009)
• Yost, Shawn (Graduate; 2009-2009)
• Chaisson, Mark (Graduate; 2007-2009)
• Hutt, Kasey (Graduate; 2004-2009)
• Norden-Krichmar, Trina (Graduate; 2004-2009)
• Bracht, John (Graduate; 2003-2009)
• Neill, Anna (Graduate; 2003-2005)
• Novorodovsky, Alexey (Post Doc; 2003-2005)
• Taneri, Bahar (Graduate; 2002-2005)
• Wang, Xiujie (Graduate; 2002-2005)
• Chang, Emmanuel (Graduate; 2001-2005)
• Fajardo, Eduardo (Graduate; 2001-2003)
• Gopal, Shuba (Graduate; 2001-2003)
• Gunther, Cary (Graduate; 2001-2003)
• Bean, James (Graduate; 2000-2005)
• Zavolan, Mihaela (Post Doc; 2000-2004)
• Kurbin, Gulriz (Graduate; 1998-2002)

S. Podell, T. Gaasterland, E.E. Allen. A database of phylogenetically atypical genes in archaeal and bacterial genomes, identified using the DarkHorse algorithm. BMC Bioinformatics. 2008;9:419.

G.J. Dick, S. Podell, H.A. Johnson, Y. Rivera-Espinoza, R. Bernier-Latmani, J.K. McCarthy, J.W. Torpey, B.G. Clement, T. Gaasterland, B.M. Tebo. Genomic insights into Mn(II) oxidation by the marine alphaproteobacterium Aurantimonas sp. strain SI85-9A1. Appl Environ Microbiol. 2008;74:2646-58.

J.C. Robidart, S.R. Bench, R.A. Feldman, A. Novoradovsky, S.B. Podell, T. Gaasterland, E.E. Allen, H. Felbeck. Metabolic versatility of the Riftia pachyptila endosymbiont revealed through metagenomics. Environ Microbiol. 2008;10:727-37.

T.M. Norden-Krichmar, J. Holtz, A.E. Pasquinelli, T. Gaasterland. Computational prediction and experimental validation of Ciona intestinalis microRNA genes. BMC Genomics. 2007;8:445.

E.J. Chang, R. Begum, B.T. Chait, T. Gaasterland. Prediction of cyclin-dependent kinase phosphorylation substrates. PLoS One. 2007;2(7):e656.

B. Palenik, J. Grimwood, A. Aerts, P. Rouzé, A. Salamov, N. Putnam, C. Dupont, R. Jorgensen, E. Derelle, S. Rombauts, K. Zhou, R. Otillar, S.S. Merchant, S. Podell, T. Gaasterland, C. Napoli, K. Gendler, A. Manuell, V. Tai, O. Vallon, G. Piganeau, S. Jancek, M. Heijde, K. Jabbari, C. Bowler, M. Lohr, S. Robbens, G. Werner, I. Dubchak, G.J. Pazour, Q. Ren, I. Paulsen, C. Delwiche, J. Schmutz, D. Rokhsar, Y. Van de Peer, H. Moreau, I.V. Grigoriev. The tiny eukaryote Ostreococcus provides genomic insights into the paradox of plankton speciation. Proc Natl Acad Sci U S A. 2007;104:7705-10.

X. Li, X. J. Wang, J. Tannenhauser, S. Podell, P. Mukherjee, M. Hertel, J. Biane, S. Masuda, F. Nottebohm, T. Gaasterland. Genomic resources for songbird research and their use in characterizing gene expression during brain development. Proc Natl Acad Sci U S A. 2007;104:6834-9.

H. Zhang, Y. Hou, L. Miranda, D.A. Campbell, N.R. Sturm, T. Gaasterland, S. Lin. Spliced leader RNA trans-splicing in dinoflagellates. Proc Natl Acad Sci U S A. 2007;104:4618-23.

S. Podell, T. Gaasterland. DarkHorse: a method for genome-wide prediction of horizontal gene transfer. Genome Biol. 2007;8(2):R16.

R.G. Sobral, A.E. Jones, S.G. Des Etages, T.J. Dougherty, R.M. Peitzsch, T. Gaasterland, A.M. Ludovice, H. de Lencastre, A. Tomasz. Extensive and genome-wide changes in the transcription profile of Staphylococcus aureus induced by modulating the transcription of the cell wall synthesis gene murF. J Bacteriol. 2007;189:2376-91.

E. Sodergren and 229 co-authors. The genome of the sea urchin Strongylocentrotus purpuratus. Science 2006;314:941-52.

J. Ule, G. Stefani, A. Mele, M. Ruggiu, X. Wang, B. Taneri, T. Gaasterland, B.J. Blencowe, R.B. Darnell. An RNA map predicting Nova-dependent splicing regulation. Nature 2006;444:580-6.

D.M. Landry, T. Gaasterland, B.P. Palenik. Molecular Characterization of a Phosphate-Regulated Cell-Surface Protein from the Coccolithophorid, Emiliania huxleyi (Prymnesiophyceae). Journal of Phycology 2006;42:814-21.

C. Cui, A. Griffiths, G. Li, L.M. Silva, M.F. Kramer, T. Gaasterland, X.J. Wang, D.M. Coen. Prediction and identification of herpes simplex virus 1-encoded microRNAs. J Virol. 2006;80:5499-508.

S. Gopal, S. Awadalla, T. Gaasterland, G.A. Cross. A computational investigation of kinetoplastid trans-splicing. Genome Biol. 2005;6(11):R95.

J.B. Bonanno, S.C. Almo, A. Bresnick, M.R. Chance, A. Fiser, S. Swaminathan, J. Jiang, F.W. Studier, L. Shapiro, C.D. Lima, T. Gaasterland, A. Sali, K. Bain, I. Feil, X. Gao, D. Lorimer, A. Ramos, J.M. Sauder, S.R. Wasserman, S. Emtage, K.L. D'Amico, S.K. Burley. New York-Structural GenomiX Research Consortium (NYSGXRC): a large scale center for the protein structure initiative. J Struct Funct Genomics 2005;6:225-32.

X.J. Wang, T. Gaasterland, N.H. Chua. Genome-wide prediction and identification of cis-natural antisense transcripts in Arabidopsis thaliana. Genome Biol. 2005;6:R30.

B. Taneri, B. Snyder, A. Novoradovsky, T. Gaasterland. Alternative splicing of mouse transcription factors affects their DNA-binding domain architecture and is tissue specific. Genome Biol. 2004;5:R75.

X.J. Wang, J.L. Reyes, N.H. Chua, T. Gaasterland. Prediction and identification of Aabidopsis thaliana microRNAs and their mRNA targets. Genome Biol. 2004;5:R65.

S. Hoth, Y. Ikeda, M. Morgante, X. Wang, J. Zuo, M.K. Hanafey, T. Gaasterland, S.V. Tingey, N.H. Chua. Monitoring genome-wide changes in gene expression in response to endogenous cytokinin reveals targets in Arabidopsis thaliana. FEBS Lett. 2003;554:373-80.

S. Gopal, G.A. Cross, T. Gaasterland. An organism-specific method to rank predicted coding regions in Trypanosoma brucei. Nucleic Acids Res. 2003;31:5877-85.

A.A. Aravin, M. Lagos-Quintana, A. Yalcin, M. Zavolan, D. Marks, B. Snyder, T. Gaasterland, J. Meyer, T. Tuschl. The small RNA profile during Drosophila melanogaster development. Dev Cell 2003;5:337-50.

T. Ravasi, T. Huber, M. Zavolan, A. Forrest, T. Gaasterland, S. Grimmond, D.A. Hume; RIKEN GER Group; GSL Members. Systematic characterization of the zinc-finger-containing proteins in the mouse transcriptome. Genome Res. 2003;13:1430-42.

M. Zavolan, S. Kondo, C. Schonbach, J. Adachi, D.A. Hume, Y. Hayashizaki, T. Gaasterland; 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.

Y. Okazaki, M. Furuno, T. Kasukawa, J. Adachi, H. Bono, S. Kondo, I. Nikaido, N. Osato, R. Saito, H. Suzuki, I. Yamanaka, H. Kiyosawa, K. Yagi, Y. Tomaru, Y. Hasegawa, A. Nogami, C. Schonbach, T. Gojobori, R. Baldarelli, D.P. Hill, C. Bult, D.A. Hume, J. Quackenbush, L.M. Schriml, A. Kanapin, H. Matsuda, S. Batalov, K.W. Beisel, J.A. Blake, D. Bradt, V. Brusic, C. Chothia, L.E. Corbani, S. Cousins, E. Dalla, T.A. Dragani, C.F. Fletcher, A. Forrest, K.S. Frazer, T. Gaasterland, M. Gariboldi, C. Gissi, A. Godzik, J. Gough, S. Grimmond, S. Gustincich, N. Hirokawa, I.J. Jackson, E.D. Jarvis, A. Kanai, H. Kawaji, Y. Kawasawa, R.M. Kedzierski, B.L. King, A. Konagaya, I.V. Kurochkin, Y. Lee, B. Lenhard, P.A. Lyons, D.R. Maglott, L. Maltais, L. Marchionni, L. McKenzie, H. Miki, T. Nagashima, K. Numata, T. Okido, W.J. Pavan, G. Pertea, G. Pesole, N. Petrovsky, R. Pillai, J.U. Pontius, D. Qi, S. Ramachandran, T. Ravasi, J.C. Reed, D.J. Reed, J. Reid, B.Z. Ring, M. Ringwald, A. Sandelin, C. Schneider, C.A. Semple, M. Setou, K. Shimada, R. Sultana, Y. Takenaka, M.S. Taylor, R.D. Teasdale, M. Tomita, R. Verardo, L. Wagner, C. Wahlestedt, Y. Wang, Y. Watanabe, C. Wells, L.G. Wilming, A. Wynshaw-Boris, M. Yanagisawa, I. Yang, L. Yang, Z. Yuan, M. Zavolan, Y. Zhu, A. Zimmer, P. Carninci, N. Hayatsu, T. Hirozane-Kishikawa, H. Konno, M. Nakamura, N. Sakazume, K. Sato, T. Shiraki, K. Waki, J. Kawai, K. Aizawa, T. Arakawa, S. Fukuda, A. Hara, W. Hashizume, K. Imotani, Y. Ishii, M. Itoh, I. Kagawa, A. Miyazaki, K. Sakai, D. Sasaki, K. Shibata, A. Shinagawa, A. Yasunishi, M. Yoshino, R. Waterston, E.S. Lander, J. Rogers, E. Birney, Y. Hayashizaki; 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.

M. Zavolan, E. van Nimwegen, T. Gaasterland. Splice variation in mouse full-length cDNAs as indicated by their mapping to the mouse genome. Genome Research 2002;12:1377-85.

N. Arisue, T. Hashimot, J. Lee, D. Moore, P. Gordon, C.W.Sensen, T. Gaasterland, M. Hasegawa, M. Muller. 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.

E. Bapteste, H. Brinkmann, J.A.Lee, D. Moore, C.W. Sensen, P. Gordon, L. Durufle, T. Gaasterland, P. Lopez, M. Muller, H. Philippe. 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.

C.S. Gunther, T. Gaasterland. Characterizing the relationship between protein-fusion and gene co-expression. Genome Informatics 2001;12:34-43.

A. Brazma, P. Hingamp, J. Quackenbush, G. Sherlock, P. Spellman, C. Stoeckert, J. Aach, W. Ansorge, C.A. Ball, H.C. Causton, T. Gaasterland, P. Glenisson, F.C. Holstege, I.F. Kim, V. Markowitz, J.C. Matese, H. Parkinson, A. Robinson, U. Sarkans, S. Schulze-Kremer, J. Stewart, R. Taylor, J. Vilo, M. Vingron. Minimum information about a microarray experiment (MIAME)-toward standards for microarray data. Nat Genet. 2001;29:365-71.

M. Muller, J.A. Lee, P. Gordon, T. Gaasterland, C.W. Sensen. Presence of prokaryotic and eukaryotic species in all subgroups of the pp(i)-dependent group ii phosphofructokinase protein family. J Bact 2001;183:6714-6.

S. Ehrt, D. Schnappinger, S. Bekiranov, J. Drenkow, S. Shi, T.R. Gingeras, T. Gaasterland, G. Schoolnik, C. Nathan. 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.

M.H. Serres, S. Gopal, L.A. Nahum, P. Liang, T. Gaasterland, M. Riley. A functional update of the Escherichia coli K-12 genome. Genome Biol. 2001;2:RESEARCH0035.1-0035.7.

J. Kawai, A. Shinagawa, K. Shibata, M. Yoshino, M. Itoh, Y. Ishii, T. Arakawa, A. Hara, Y. Fukunishi, H. Konno, J. Adachi, S. Fukuda, K. Aizawa, M. Izawa, K. Nishi, H. Kiyosawa, S. Kondo, I. Yamanaka, T. Saito, Y. Okazaki, T. Gojobori, H. Bono, T. Kasukawa, R. Saito, K. Kadota, Matsuda A. , M. Ashburner, S. Batalov, T. Casavant, W. Fleischmann, T. Gaasterland, C. Gissi, B. King, H. Kochiwa, P. Kuehl, S. Lewis, Y. Matsuo, I. Nikaido, G. Pesole, J. Quackenbush, L. Schriml, F. Staubli, R. Suzuki, M. Tomita, L. Wagner, T. Washio, K. Sakai, T. Okido, M. Furuno, H. Aono, R. Baldarelli, G. Barsh, J. Blake, D. Bo elli, N. Bojunga, P. Carninci, F. de Bonaldo, J. Brownstein, C. Bult, C. Fletcher, M. Fujita, M. Gariboldi, S. Gustincich, D. Hill, M. Hofmann, D. Hume, M. Kamiya, H. Lee, P. Lyons, L. Marchionni, J. Mashima, J. Mazzarelli, P. Mombaerts, P. Nordone, B. Ring, M. Ringwald, I. Rodriguez, N. Sakamoto, H. Sasaki, K. Sato, C. Schonbach, T. Seya, Y. Shibata, K. Storch, H. Suzuki, K. Toyo-oka, H.Wang, C.Weitz, C. Whittaker, L. Wilming, A. Wynshaw-Boris, K. Yoshida, Y. Hasegawa, H. Kawaji, S. Kohtsuki, and Y. Hayashizaki. Functional annotation of a full-length mouse cDNA collection. Nature 2001;409:685-90.

C. Altmann, E. Bell, A. Sczyrba, J. Pun, S. Bekiranov, T. Gaasterland, A. Brivanlou. Microarray based analysis of early development in Xenopus laevis. Developmental Biology 2001;236:64-75.

Q. She, R. Singh, F. Confalonieri, Y. Zivanovic, G. Allard, M. Awayez, C. Chan-Weiher, I. Clausen, B. Curtis, A. De Moors, G. Erauso, C. Fletcher, P. Gordon, I. Heikamp-de Jong, A. Jeffries, C. Kozera, N. Medina, X. Peng, H. Thi-Ngoc, P. Redder, M. Schenk, C. Theriault, N. Tolstrup, R. Charlebois, W. Doolittle, M. Duguet, T. Gaasterland, R. Garrett, M. Ragan, W. Sensen, J. Van der Oost. The complete genome of the crenarchaeon Sulfolobus solfataricus P2. Proc Natl Acad Sci U S A 2001;98:7835-40.

S. Gopal M. Schroeder, U. Pieper, A. Sczyrba, G. Aytekin-Kurban, S. Bekiranov, J. Eduardo Fajardo, N. Eswar, R. Sanchez, A. Sali, T. Gaasterland. Homology-based annotation yields 1,042 new candidate genes in the Drosophila melanogaster genome. Nature Genetics 2001;27:337-40.

T. Gaasterland, A. Sczyrba, E. Thomas, G. Aytekin-Kurban, P. Gordon, C. Sensen. MAGPIE/EGRET Annotation of the 2.91Mb Drosophila melanogaster ADH Region. Genome Research 2000;10:502-510.

V. Hanneart, H. Brinkmann, U. Nowitzki, J. Lee, M. Albert, C. Sensen, T. Gaasterland, M. Mller, P. Michels, W. Martin. Enolase from Trypanosoma brucei, from the amitochondriate protist Mastigamoeba bala muthi, and from the chloroplast and cytosol of Euglena gracilis. Mol. Biol. Evol. 2000;17:989-1000.

R. Charlebois, R-K. Singh, C. Chan, G. Allard, C. Chow, F. Confalonieri, B. Curtis, M. Duget, G. Erauso, D. Faguy, T. Gaasterland, R. Garret, P. Gordon, A. Je ries, C. Kozera, N. Kushwara, E. Lafleur, N. Medina, X. Peng, S. Penny, Q. She, A. St. Jean, J. van der Oost, F. Young, Y. Zivanovic, W.F. Doolittle, M. Ragan, C. Sensen. Gene content and organization of a 281 Kbp contig from the genome of the extremely thermophilic archaeon, Sulfolobus solfataricus P2. Genome 2000;43:116-136.

T. Gaasterland and S. Bekiranov. Making the Most of Microarray Data. Nature Genetics 2000;24:204-206.

S. Burley, S. Almo, J. Bonanno, M. Capel, M. Chance, T. Gaasterland, D. Lin, A. Sali, F. Studier, S. Swaminathan. Structural Genomics: beyond the Human Genome Project. Nature Genetics 1999;23:151-157.

M. Romine, L. Stilwell, K.-K.Wong, S.J. Thurston, E.C. Sisk, C.W. Sensen, T. Gaasterland, J.D. Saffer, J.K. Frederickson. Complete Sequence of a 184 kb Catabolic Plasmid from Sphingomonas aromaticivorans Strain F199. Journal of Bacteriology 1999;181:1585-1602.

T. Gaasterland and M. Ragan. Constructing Multi-Genome Views of Whole Microbial Genomes. Journal of Microbial and Comparative Genomics 1998;3:177-192.

M. Ragan and T. Gaasterland. Microbial Genescapes: A Prokaryotic View of the Yeast Genome. Journal of Microbial and Comparative Genomics 1998;3:219-235.

T. Gaasterland and M. Ragan. Microbial Genescapes: Phyletic and Functional Patterns of ORF Distribution Among Prokaryotes. Journal of Microbial and Comparative Genomics 1998;3:199-217. C.W. Sensen, T. Gaasterland, et al. Completing the sequence of the Sulfolobus solfataricus P2 genome. Extremophiles 1998;2:305-312.

G. Deckert, P. Warren, T. Gaasterland, W.G.Young, A.L. Lenox, D. Graham, R. Overbeek, M. Snead, M. Keller, M. Aujay, R. Huber, R. Feldman, J. Short, G. Olsen, R. Swanson. The complete genome of the hyperthermophilic bacterium Aquifex aeolicus. Nature 1998;392:352-358.