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PERSONAL INFORMATION
Address: Friedrich-Ebert Anlage 51D, 69117 Heidelberg, Germany
Email: alison.sara.waller@gmail.com
Website: http://alisonwallersysbio.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

M.A.Sc, Dept. of Chemical Engineering and Applied Chemistry,

University of Toronto, Toronto Canada

2002

B.A.Sc., Dept. of Civil Engineering,

McGill University, Montreal Canada

1999

Relevant Courses: Graduate - Bioinformatics, Proteomics and Functional Genomics,

Phylogenetics, Environmental Microbiology, Wastewater Treatment Processes, Environmental Isotope
Geochemistry, Environmental Pathways.
RESEARCH EXPERIENCE
Post Doctoral Fellow, Genome Biology, European Molecular Biology Laboratory 2013 present
Supervisor: Dr. Nassos Typas
Leading a project analysing a metabolomics data set from a Pseudomonas aeruginosa genomewide single-gene knockout library
Developed a data analysis pipeline for data from high-throughput chemical genomics
screening of bacterial single-gene knockout libraries
Collaborated with colleagues to perform network analyses of datasets
Integrated chemical genomics data with Orphan Enzyme predictions to predict gene function
Post Doctoral Fellow, Bioinformatics, European Molecular Biology Laboratory
2009 2013
Supervisor: Dr. Peer Bork
Performed assembly, annotation and comparative analysis of metagenomic sequences from
human gut and marine systems
Developed a pipeline to quantify and classify prophages in metagenomic sequencing data
Developed a technique to differentiate lytic and lysogenic states of prophages in metagenomic
sequences and to identify the bacterial host
Performed statistical analyses to identify biomarkers for conditions of the human host
Compared assembly and annotation methods for different next-generation sequencing methods
through the development and analysis of simulated metagenomes
Used genomic and pathway adjacency information to determine candidate sequences for
Orphan Enzymes (characterized enzymes that lack cognate gene sequences)
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Ph.D. Candidate, Dept. of Chemical Engineering, University of Toronto

2003 - 2008
Supervisor: Dr. Elizabeth A. Edwards
Thesis title: Molecular Investigation of Chloroethene Reductive Dehalogenation by the
Dehalococcoides-Containing Microbial Culture KB-1
Performed microarray experiments, and data analysis, of custom shotgun
metagenome arrays
Developed a database to manage sequence and functional information for
the array spots
Co-ordinated a metagenomic sequencing project with the Joint Genome
Institute
Integrated data from microarray experiments, metagenomic sequencing
and genome-scale metabolic modeling to identify prophage activation in
response to specific contaminant levels, and to elucidate interspecies
interaction such as one involving cobalamin
Elucidated reductive dehalogenase genes, quantified gene transcription
during dechlorination of different compounds and designed specific
quantitative PCR primers and protocols to be used as biomarkers at
contaminated sites
M.A.Sc Candidate, Dept. of Chemical Engineering, University of Toronto
2000 2002
Supervisor: Dr. Elizabeth A. Edwards
Thesis title: Bioremediation of Perchlorate-Contaminated Groundwater
Isolated 16 novel micro-organisms capable of degrading perchlorate
Determined the phylogeny of these isolates using molecular techniques and sequence analysis
Studied the kinetics of perchlorate reduction
Performed microcosm studies to study perchlorate-degrading organisms at contaminated sites
Worked with Geosyntec Consultants to implement In-Situ perchlorate-remediation
technologies
B.A.Sc. Summer Research Student, Dept. Civil Engineering, McGill University
1999
Supervisor: Dr. Subhasis Ghoshal
Wrote a computer-program that used numerical methods to approximate the dissolution of a
NAPL in groundwater
Set up a new laboratory with equipment such as an anaerobic glove-box
B.A.Sc. Thesis Student, Dept. Civil Engineering, McGill University
1999
Supervisor: Dr. Ronald Gehr
Performed experiments to test different methods for removing dyes from waste-water of a
textile-dyeing plant
Presented a remediation strategy to the textile-dyeing company
ACADEMIC SCHOLARSHIPS AND AWARDS
Post-Doctoral Fellowship - National Science and Engineering Research Council (NSERC):
$80,000 (2009/2011)
Ontario Graduate Scholarship: $15,000 (2006/2007) & (2005/2006)
Ontario Graduate Scholarships in Science and Technology: $15,000 (2004/2005) &
(2003/2004)
Ontario Graduate Scholarship $15,000 (2002/2003)
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Ontario Graduate Scholarships in Science and Technology $15,000 (2000/2001)

University of Toronto Open Fellowship $10,000 (01/2000-08/2000)
McGill University Entrance Scholarship (1995/1996)
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 12)
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 2)
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 24)
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 178)
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 73)
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 18)
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 71)

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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 17)
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 111)
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 71)
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.

and Edwards E.A. (October 2005) Differential Gene Expression in a

Dehalococcoides-Containing Culture KB-1. Geosyntec Consultants, Guelph, ON.
TEACHING EXPERIENCE
Lecturer: Introduction to Protein Networks, EMBL

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
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tutorials and graded quizzes

LEADERSHIP AND ADMINISTRATIVE EXPERIENCE

Member of the Parents Panel for the EMBL Kindergarten
Co-chairperson of the Chemical Engineering Graduate Student Association (CEGSA)
(2005/2006)
Graduate Student representative on the conference organizational committee for the
Canadian Society for Chemical Engineering 2005 Conference
o Organized the first Graduate Student Poster Competition
Graduate Student member of the search committee for the new Departmental Chair
(2005/2006)
CEGSA Social Director (2003/2004-2004/2005)
o Designed and implemented first technology tour for graduate students
Graduate Student member of a faculty search committee (2004/2005)
Captain of the University of Toronto Womens Ultimate Frisbee Team (2005/2006)
Member of the University of Toronto Gardening Collective (2002-2004)
o Organized a food bank
REFERENCES
Dr. Nassos Typas (post-doctoral supervisor)
Group Leader, Genome Biology and Structural and Computational Biology
European Molecular Biology Laboratory
Meyerhofstrae 1, 69117 Heidelberg, Germany
Tel: +49 6221 387-8156
e-mail:typas@embl.de
Dr. Peer Bork (post-doctoral supervisor)
Joint Head of Unit, Senior Scientist and Strategic Head of Bioinformatics, EMBL Heidelberg
Structural and Computational Biology, EMBL Heidelberg
Meyerhofstrae 1, 69117 Heidelberg, Germany
Tel: +49-6221-387-8526.
e-mail: bork@embl.de
Dr. Elizabeth Edwards (doctoral supervisor)
Professor and Director of Biozone
Department of Chemical Engineering and Applied Chemistry, University of Toronto
200 College Street, Toronto, ON, M5S 3E5
Tel: 416 946 3506. Fax: 416 978 8605. e-mail: elizabeth.edwards@utoronto.ca
Dr. David Major (Industrial Collaborator during graduate research)
Principal Environmental Scientist and Adjunt Professor (Uof T)
Geosyntec Consulting
130 Research Lane, Suite 2, Guelph, ON, N1G 5G3, CAN
Tel.: 519 822 2230. Fax: 519 822 3151 e-mail: dmajor@geosyntec.com.

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