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PERSONAL INFORMATION
Address: Friedrich-Ebert Anlage 51D, 69117 Heidelberg, Germany
Email: alison.waller@embl.de
Website: http://alisonwallereng.weebly.com
Phone: +49-6221-914-8187 (home), +49-6221-387-8296 (work)
Citizenship: Canadian
Married with 4 children
AREAS OF EXPERTISE
Analysis of large-scale datasets, in particular, (meta)genomic sequences, microarray data, and
high-throughput chemical genomic and metabolomic data from bacterial mutant libraries
Integration and visualization of multiple datasets
Microbiology and molecular biology of microbial communities
EDUCATION
Ph.D., Dept. of Chemical Engineering and Applied Chemistry,
University of Toronto, Toronto Canada
2008
2002
1999
http://alisonwallereng.weebly.com
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Student Travel Fellowship (~$500, June 2005) American Society for Microbiology
Student Travel Grant (~ $500, April 2005) - International Conference on Microbial
Genomes
Project of the Year Award (2001) Awarded to Geosyntec Consultants from the Strategic
Environmental Research and Development Program (SERDP)
Bioremediation of Perchlorate-Contaminated Groundwater I was the primary
investigator involved in the laboratory component of this project
REFEREED PUBLICATIONS
For the most up-to-date list of publications and citations see: http://scholar.google.ca/citations?
user=9KXjOUkAAAAJ&hl=en
11. Waller, A.S., Yamada T., Kristensen D., Koonin, E.V., and Bork, P. (2014). Taxonomic
Classification and Quantification of Bacteriophage Taxa in Human Gut Metagenomes. ISME
Journal. 2014; 8: 1391-1402 (Cited by 5)
10. Ahsanul Islam M., Waller A.S., Hug L.A., Provart N.J., Mahadevan R., and Edwards E.A.
(2014) New Insights into Dehalococcoides mccartyi Metabolism from a Reconstructed Metabolic
Network-Based Systems-Level Analysis of D. mccartyi Transcriptomes. PLoS One. 2014. 9(4):
e94808. doi:10.1371/journal.pone.0094808 (Cited by 1)
9. Kristensen, D., Waller, A.S., Yamada, T., Bork, P., Mushegian, A., and Koonin, E.V. (2013)
Orthologous gene clusters and taxon signature genes for viruses of prokaryotes. Journal of
Bacteriology. 2013; 195(5): 941-50.(Cited by 21)
8. Schloissnig S., Arumugam M., Sunagawa S., Mitreva M., Tap J., Zhu A., Waller A.S., Mende
D.R., Martin J., Kota K., Sunyaev S.R., Weinstock G.M. and Bork, P. (2012). Genomic variation
landscape of the human gut microbiome: Individuality and temporal stability. Nature. 2012; 493:
4550. (Cited by 157)
7. Alonso-Sez L., Waller A.S., Mende D.R., Bakker K., Farnelid H., Yager P., Lovejoy C.,
Tremblay J-E, Potvin M., Heinrich F., Estrada M., Riemann L., Bork P., Pedrs-Ali C., Bertilsson
S. (2012). A role for urea in nitrification by polar marine archaea. PNAS. 2012; 10(44) 1798917994. (Cited by 62)
6. Yamada T., Waller A.S., Raes J., Zelezniak A., Perchat N., Perret A., Salanoubat M., Patil K.R,
Weissenbach J., and Bork P. (2012) Prediction and identification of sequences coding for orphan
enzymes using genomic and metagenomic neighbours. Molecular Systems Biology. 2012; 8: 581.
(highlighted in Cell June 22 vol 149, No. 7). (Cited by 17)
5. Mende D.R. *, Waller A.S. *, Sunagawa S., Jarvelin A.I., Chan M.M., Arumugam M., Raes J.,
and Bork P. (2012) Assessment of Metagenomic Assembly Using Simulated Next Generation
Sequencing Data. PLoS One. 2012; 7(2): e31386. (Cited by 62)
http://alisonwallereng.weebly.com
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4. Waller A.S., Hug L.A., Mo K., Radford D.R., Maxwell, K.L., and Edwards E.A. (2012).
Transcriptional analysis in a Dehalococcoides-containing microbial consortium reveals prophage
activation. Applied and Environmental Microbiology. 78(2): 1178-1186. (Cited by 15)
3. Waller A.S., Krajmalnik-Brown R., Loffler F.E., and Edwards E.A. (2005) Multiple ReductiveDehalogenase-Homologous Genes Are Simulataneously Transcribed during Dechlorination by
Dehalococcoides-Contining Cultures. Applied and Environmental Microbiology. December;
71(12): 82578264. (cited by 110)
2. Chartrand M.M.G., Waller A.S., Mattes T.E., Elsner M., Lacrampe-Couloume G., Gossett J.M.,
Edwards E.A. and Sherwood Lollar B.(2005) Carbon isotopic fractionation during aerobic vinyl
chloride degradation. Environmental Science and Technology. 39:1064-1070. (Cited by 43)
1. Waller A.S., Cox E.E., and Edwards E.A. (2004) Perchlorate-reducing microorganisms isolated
from contaminated sites. Environmental Microbiology. 2004 May;6(5):517-27. (Cited by 68)
NON-REFEREED PUBLICATIONS
Technical Report
Waller A.S., Allen G.D., and Edwards E.A. (2006) The Potential for Biological Treatment of
Perchlorate in Pulp Mill Effluent Treatment Systems. Prepared for a Pulp and Paper industry
consultant.
Presentations to Consulting Firms
Waller A.S. and Edwards E.A. (February 2007). Nucleic Acid Tools and Biomarkers to
Monitor Reductive Dechlorination. Geosyntec Consultants, Guelph, ON.
Waller A.S.
2011
Delivered a lecture concerning a general introduction to Protein Networks for the participants
in an EU-wide grant DiGtoP (From Disease Genes to Protein Pathways)
Organizer: Advanced Topics for Cytoscape, EMBL
2010
Planned and organized a course for bioinformaticians in the Heidelberg area about advanced
topics for the software Cytoscape (An open source platform for network analysis and
visualization).
Course Lecturer: Environmental Chemistry, University of Toronto (U of T)
2005
Designed and taught a section of an undergraduate course on Environmental Chemistry
Created and marked final examination questions
Teaching Assistant: Calculus and Numerical methods, U of T
2002-2005
Was asked to be the course lecturer for 2005/2006, but declined due to workload
Led tutorials for calculus theory
Led computer laboratories for numerical methods (C++, FORTRAN)
Graded mid-terms tests and quizzes
Teaching Assistant: Physical Chemistry, University of Toronto
http://alisonwallereng.weebly.com
2000-2004
A L I S O N
Led
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