Ines Thiele

Graduate Student

Assistant Professor at the Center for Systems Biology, Iceland

Please also visit my new website.

I came to the Palsson lab in January 2004 to do a 8 month long master thesis with the title: Candidate metabolic network states in human mitochondria. Impact of diabetes, ischemia, and diet.. In Fall 2004, I obtained my Master of Science degree in Biotechnology and Molecular/Cellular Biology from the European School of Biotechnology, Strasbourg (France). After spending a year as research visitor, I entered the PhD program in Bioinformatics in Fall 2005.

Currently, I am in my fourth year. My research work concentrates on the development of reconstruction technologies for metabolic networks and other cellular functions. In particular, I have been leading or participating the reconstruction and mathematical analysis of the following networks:

  • human cardiac mitochondrion, Thiele et al., 2005.
  • human pathogen Helicobacter pylori, Thiele et al, 2005 and Price et al, 2006.
  • human metabolic network, Duarte et al, 2007.
  • pollutant degradative bacterium Pseudomonas putida, Nogales et al., 2008 - Highly accessed.
  • thermophilic bacterium Thermotoga maritima, Zhang et al, in preparation.
  • human Toll-Like Receptor (TLR) signaling network, Fan et al, in press.
  • transcriptional and translational machinery of the model organism Escherichia coli, Thiele et al., in press.

Recent reviews and book chapters that have concentrated on the reconstruction approach and the determination of functional states of condition-specific models:

  • Thiele and Palsson, Bringing genomes to life. Chapter 2, Ed. S. Choi in Introduction to Systems Biology, Humana Press, (2007).
  • Reconstruction approach: Reed et al., 2006; and Feist et al., to appear.
  • Constraint-based modeling techniques: Price et al..
  • Constraint-based modeling tools: Becker et al..

I am intending to graduate in Spring 2009. Please find my detailed CV here.

Education

Ph.D. candidate in Bioinformatics - University of California, San Diego, since September 2005. Expected Graduation: Spring 2009.

M.S. in Bioinformatics - University of California, San Diego, 2007.

M.S. in Biotechnology and Diploma of Advanced Studies (DEA) in Molecular and Cellular Biology - Ecole Superieure de Biotechnologie Strasbourg, France, 2001 - 2004.

B.S. in Technical Biology - (Vordiplom), University of Stuttgart, Germany, 1999 - 2001.

Research Experience

Oct 2004 – Aug 2005: Research Scholar, Systems Biology Research Group, University of California, San Diego

Jan - Aug 2004: Master thesis - Sampling of Biological Networks, Systems Biology Research Group, University of California, San Diego

Dec 2003: Life Cell Imaging: Analysis of current microscopy techniques for rapid 4D imaging of Mal3 and TIP1in Fission yeast, Prof. Jan De Mey, ESBS, France, In colaboration with Dr. D. Brunner (EMBL, Heidelberg), Dr. T. Zimmermann (EMBL, Heidelberg). [4 weeks]

Teaching Experience

Co-organizer and Co-instructor, Systems Biology Short Course (Network reconstruction and systems analysis), University of Iceland, Reykjavik, Iceland, September 2008

Co-instructor, Systems Biology Short Course (Network reconstruction and systems analysis), University of Iceland, Reykjavik, Iceland, October 2007

Teaching assistant for BENG 212: Biology & Bioengineering II: Network Reconstruction (Spring 2007)

Teaching assistant for BENG 213: Systems Biology & Bioengineering III: Building and simulating large-scale in silico models (Winter 2007)

Co-instructor, Systems Biology Short Course (Network reconstruction and systems analysis), UCSD Extension, San Diego, January 2006

Co-instructor, Systems Biology Short Course (Network reconstruction and systems analysis), UCSD Extension, San Diego, July 2005

Teaching assistant for "Structure and Function of Cells: Zoology (Oct 2000 - Feb 2001, University of Stuttgart, Germany)

Tutor for mathematics, physics, chemistry, languages for high school students (1997 - 1999, 2000 - 2001, 2002 - 2003, Germany)

Coursework

Biology: Biochemistry, Molecular Biology, Genetics, Cell Biology, Microbiology, Neurobiology, Immunology, Virology, Human Physiology, Toxicology, Pharmacology, Botany, Zoology.

Chemistry: General Chemistry, Organic Chemistry, and Physical Chemistry.

Engineering: Genetic Engineering, Process Engineering, Metabolic Engineering, Bioinfomatics (BENG 201-204), Electronics and Biophysics, Physics, Applied Statistics (MATH 282B), Systems Biology (BENG 211-213), Algorithm Design.

Language Skills

German: mother tongue

English: Fluent

French: Fluent

Publications

Fleming, R.M.T., Thiele, I., Nasheuer, H.P., Palsson, B.Ø., "Quantitative assignment of reaction directionality in constraint-based models of metabolism.", Submitted.

Zhang, Y.*, Thiele, I.*, Weekes, D., Li, Z., Jaroszewski, L., Ginalski, K., Deacon, A.M., Wooley, J., Lesley, S.A., Wilson, I.A., Palsson, B. Ø., Osterman, A., Godzik, A., "Structural genomics of the Thermotoga maritima sets the stage for the molecular level analysis of its metabolic network.", Submitted.

Thiele, I., Palsson, B.O. , "A protocol for generating a high-quality genome-scale metabolic reconstruction.", Submitted.

Thiele, I., Palsson, B.O. , "Fundamentals of Constraint-Based Methods.", Submitted.

Thiele, I., Palsson, B.O. , "2D genome annotation jamborees: A community effort in systems biology.", Submitted.

Thiele, I., Jamshidi, N., Fleming, R.M.T., Palsson, B.Ø., "Genome-scale reconstruction of E. coli's transcriptional and translational machinery: A knowledge-base, its mathematical formulation, and its functional characterization", PLoS Comput Biol 5(3): e1000312. doi:10.1371/journal.pcbi.1000312.

Li, F., Thiele, I., Jamshidi, N., Palsson, B.Ø., Identification of Potential Pathway Mediation Targets in Toll-like Receptor Signaling, PLOS Comput Biol. 5:e1000292. doi:10.1371/journal.pcbi.1000292 (2009).

Nogales, J. , Palsson, B.Ø., and Thiele, I., "A genome-scale metabolic reconstruction of Pseudomonas putida KT2440: iJN746 as a cell factory.", BMC Syst Biol, 2:79. (2008). - Highly accessed.

Feist, A.M., Herrgard, M.J., Thiele, I., Reed, J.L., Palsson, B.Ø., "Reconstruction of Biochemical Networks in Microbial Organisms". Nature Reviews Microbiology, 7(2)(2009).

Yeung, M., Thiele, I., and Palsson, B.Ø., "Estimation of the number of extreme pathways for metabolic networks.", BMC Bioinformatics, 8(1): 363. (2007). - Highly accessed.

Duarte, N.D., Becker, S.A., Jamshidi, N., Thiele, I., Mo, M.L., Vo, T.D., Srivas, R., Palsson, B.Ø., "Global reconstruction of the human metabolic network based on genomic and bibliomic data", Proc Natl Acad. Sci U S A, 104(6):1777-82 (2007).

Price, N.D., Thiele, I., and Palsson, B.Ø., "Candidate states of Helicobacter pylori's genome-scale metabolic network upon application of "loop law" thermodynamic constraints.", Biophys. J., 90(11): 3919-28 (2006).

Reed , J.L., Famili, I., Thiele, I., and Palsson, B.Ø., "Towards Multidimensional Genome Annotation", Nat. Rev. Genet., 7(2): 130-141. (2006)

Overbeek, R., Begley, T., Butler, R.M., Choudhuri, J.V., Chuang, H-Y., Cohoon, M., de Crécy-Lagard, V., Diaz, N., Disz, T., Edwards, R., Fonstein, M., Frank, E.D., Gerdes, S., Glass, E.M., Goesmann, A., Hanson, A., Iwata-Reuyl, D., Jensen, R., Jamshidi, N., Krause, L., Kubal, M., Larsen, N., Linke, B., McHardy, A.C., Meyer, F., Neuweger, H., Olsen, G., Olson, R., Ostermann, A., Portnoy, V., Pusch, G.D., Rodionov, D.A., Rückert, C., Steiner, J., Stevens, R., Thiele, I., Vassieva, O., Ye, Y., Zagnitko, O., and Vonstein, V., "The Subsystems Approach to Genome Annotation and its Use in the Project to Annotate 1000 Genomes", Nucl. Ac. Res., 33(17): 5691-5702 (2005)

Thiele, I.*, Vo, T.D.*, Price, N.D. and Palsson, B.Ø., "An Expanded Metabolic Reconstruction of Helicobacter pylori (iIT341 GSM/GPR): An in silico genome-scale characterization of single and double deletion mutants", Journal of Bacteriology, 187(16): 5818-5830 (2005).

Thiele, I., Price, N.D., Vo, T.D. and Palsson, B.Ø., "Candidate metabolic network states in human mitochondria: Impact of diabetes, ischemia, and diet", Journal of Biological Chemistry, 280(12): 11683-11695 (2005).

  • authors contributed equally to this work.

Book Chapter

Feist A.M., Thiele, I., Palsson, B.Ø., "Genome-scale reconstruction, modeling, and simulation of E. coli’s metabolic network" in Systems biology and biotechnology of E. coli Eds: Lee, S.Y., Springer, To appear

Lewis, N.E., Jamshidi, N., Thiele, I., Palsson, B.O.. "Metabolic systems biology: a constraint-based approach." In "The Encyclopedia of Complexity and Systems Science." In press.

Thiele, I. and Palsson, B.Ø., "Bringing Genomes to Life: The Use of Genome-Scale in silico Models", Chapter 2, Ines Thiele and Bernhard Ø. Palsson, "Introduction to Systems Biology", "Humana Press". (2007).

Invited Talks

Genome-scale reconstruction of E. coli 's transcriptional and translational machinery: A knowledge-base, its mathematical formulation, and its functional characterization", 1st Bioinfo Expo, San Diego, February 2009.

"Systems Biology Research Group", Bioinformatics Prospect Weekend, San Diego, March 2008

"Genome-scale Reconstruction of Metabolism of Thermotoga maritima", Thermotoga 2007 Workshop, San Diego, July 2007.

"Towards a whole cell model of E. coli", Bioinformatics Prospect Weekend, San Diego, March 2007.

"The transcriptional and translational machinery of E. coli", 2007 UCSD All-Grad Research Symposium, San Diego, February 2007.

"Constraint-based Modeling of Genome-scale Metabolic Networks: An Unbiased Assessment of Candidate Metabolic Network States", Interface 2006 - 38th Symposium on the interface of statistics, computing science, and applications, Pasadena, CA, May 2006.

"Metabolic capabilities in silico of the human pathogen Helicobacter pylori", 2006 UCSD All-Grad Research Symposium, San Diego, February 2006.

Poster Presentations

"Genome-Scale reconstruction of the transcriptional and translational machinery in Escherichia coli: A knowledge-database and its mathematical formulation", 1st Bioinfo Expo, San Diego, February 2009, Ines Thiele, Neema Jamshidi, Ronan M.T. Fleming, and Bernhard Ø. Palsson

"Genome-Scale reconstruction of the transcriptional and tr anslational machinery in Escherichia coli: A knowledge-database and its mathematical formulation", 16th Annual International Conference on Microbial Genomes, Lake Arrowhead, September 2008, Ines Thiele, Neema Jamshidi, Ronan M.T. Fleming, and Bernhard Ø. Palsson

"From Network to Function: Systematic annotation of gene function using metabolic network reconstructions.", Workshop on the Biological Annotation of Novel Proteins, San Diego, March 2008, Ines Thiele and Bernhard Ø. Palsson.

"Genome-Scale reconstruction of the transcriptional and translational machinery in Escherichia coli: A knowledge-database and its mathematical formulation", ICSB 2007, Long Beach, October 2007, Ines Thiele, Neema Jamshidi, Ronan M.T. Fleming, and Bernhard Ø. Palsson

"Extending the predictive potential of metabolic genome-scale reconstructions by accounting for the transcriptional and translational network", ICSB 2007, Long Beach, October 2007, Aarash Bordbar, Ines Thiele, and Bernhard Ø. Palsson

"Genome-scale reconstruction of the transcriptional and translational machinery of E. coli: The "Dogma Matrix"", Algorithmic Biology 2006, San Diego, November 2006, Ines Thiele, Neema Jamshidi, Matthew Yeung, and Bernhard Ø. Palsson

"Genome-scale reconstruction of the transcriptional and translational machinery of E. coli: The "Dogma Matrix"." The 3rd International E. coli Alliance Conference on Systems Biology 2006, Jeju Island, Republic of Korea, November 2006, Ines Thiele, Neema Jamshidi, Matthew Yeung, and Bernhard Ø. Palsson

"Homo sapiens Build 1: A genome-scale reconstruction of human cellular metabolism.", Satellite Session of the International Society for Applied Cardiovascular Biology, San Diego, CA, March 2006, Natalie Duarte, Scott Becker, Neema Jamshidi, Monica Mo, Ines Thiele, Thuy Vo, Bernhard Ø. Palsson presented by Ines Thiele

"Homo sapiens Build 1: A genome-scale reconstruction of human cellular metabolism.", UCSD Jacobs School of Engineering 25th Annual Research Expo, San Diego, CA, February 2006, Natalie Duarte, Scott Becker, Neema Jamshidi, Monica Mo, Ines Thiele, Thuy Vo, Bernhard Ø. Palsson, presented by Ines Thiele

"Metabolic capabilities in silico of the human pathogen Helicobacter pylori", Systems to Synthesis - First Annual Symposium on the Study and Understanding of Complex Biological Systems, San Diego, CA, January 2006, Ines Thiele, Nathan D. Price, Thuy D. Vo, Bernhard Ø. Palsson

"Metabolic capabilities in silico of the human pathogen Helicobacter pylori", The First Annual RECOMB Satellite Workshop on Systems Biology, The Second Annual RECOMB Satellite Workshop on Regulatory Genomics, San Diego, CA, December 2005, Ines Thiele, Nathan D. Price, Thuy D. Vo, Bernhard Ø. Palsson

"Metabolic capabilities in silico of the human pathogen Helicobacter pylori", 13th Annual International Conference on Microbial Genomes, Madison, WI, September 2005, Ines Thiele, Nathan D. Price, Thuy D. Vo, Bernhard Ø. Palsson

Contact Information

Email Address: ines.thiele@gmail.com

Phone: (858)822-3181

Mailing Address: 9500 Gilman Drive Mail Code 0412 La Jolla, CA 92093-0412

Location

Location

417 Powell-Focht Bioengineering Hall

9500 Gilman Drive La Jolla, CA 92093-0412

Contact Us

Contact Us

In Silico Lab:  858-822-1144

Wet Lab:  858-246-1625

FAX:   858-822-3120

Website Concerns: sbrgit@ucsd.edu

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