Helen V. Cook
Computational Biology and Visualization
I am a computer scientist, biologist and artist living in Copenhagen, Denmark.
Currently, I am an M.Sc. student at the Technical University of Denmark (DTU) in Systems Biology. In short, this means that I use techniques from a wide range of fields to model, predict and visualize biological systems.
Prior to going back to school, I worked as both a Software Engineer and as a Technical Program Manager at Amazon.com, and I spent several years as a programmer at startups in Vancouver, BC.
My undergraduate degree is in Mathematics and Philosophy from UBC.
Download my resume as a PDF, and see my photography portfolio below.
Papers
Sigma factors in a thousand E. coli genomes
Everyone working with bacterial genomics is familiar with the phrase 'too much data'. In this Genome Update, we discuss two methods for helping to deal with this explosion of genomic information. First, we introduce the concept of calculating a quality score for each sequenced genome, and second, we describe a method to quickly sort through genomes for a particular set of protein families. We apply these two methods to all of the current Escherichia coli genomes available in the The National Center for Biotechnology Information database. Out of the 2074 E. coli / Shigella genomes listed (June, 2013), only less than half (983) are of sufficient quality to use in comparative genomic work. Unfortunately, even some of the 'complete' E. coli genomes are in pieces, and a few 'draft' genomes are good quality. Six of the seven known sigma factors in E. coli strain K-12 are extremely well conserved; the iron-regulating sigma factor FecI (sigma-19) is missing in most genomes. Surprisingly, the E. coli strain CFT073 genome does not encode a functional RpoD (sigma-70), which is obviously essential, and this is likely due to poor genome assembly/annotation. We find a possible novel sigma factor present in more than a hundred E. coli genomes.
Everyone working with bacterial genomics is familiar with the phrase 'too much data'. In this Genome Update, we discuss two methods for helping to deal with this explosion of genomic information. First, we introduce the concept of calculating a quality score for each sequenced genome, and second, we describe a method to quickly sort through genomes for a particular set of protein families. We apply these two methods to all of the current Escherichia coli genomes available in the The National Center for Biotechnology Information database. Out of the 2074 E. coli / Shigella genomes listed (June, 2013), only less than half (983) are of sufficient quality to use in comparative genomic work. Unfortunately, even some of the 'complete' E. coli genomes are in pieces, and a few 'draft' genomes are good quality. Six of the seven known sigma factors in E. coli strain K-12 are extremely well conserved; the iron-regulating sigma factor FecI (sigma-19) is missing in most genomes. Surprisingly, the E. coli strain CFT073 genome does not encode a functional RpoD (sigma-70), which is obviously essential, and this is likely due to poor genome assembly/annotation. We find a possible novel sigma factor present in more than a hundred E. coli genomes.
Preventing the Fusogenic Transition of Hemagglutinin H10
In this project, we studied inhibiting influenza infection via preventing the low pH fusogenic transition of hemagglutinin. The antibody HC63 has been shown to bind to HA of subtype H3 and prevent the fusogenic transition. Inspired by this work, we sought to mutate the antibody to enable it to bind to HA of the subtype H10.
In this project, we studied inhibiting influenza infection via preventing the low pH fusogenic transition of hemagglutinin. The antibody HC63 has been shown to bind to HA of subtype H3 and prevent the fusogenic transition. Inspired by this work, we sought to mutate the antibody to enable it to bind to HA of the subtype H10.
The importance of the 16S rRNA for species definition and growth rate of Prokaryotes
In this paper, we generate the standard 16S tree of members of the Vibrionaceae and compare it to a tree generated from amino acid sequence comparisons of the L3 ribosomal proteins. We find that the L3 tree is a less computationally complex method of constructing a phylogenetic tree compared to the pan-genome tree, and the L3 tree produces more reliable results than the 16S rRNA tree. Additionally, our data indicates that prokaryotes from aquatic habitats might use their multiple rRNA operons in distinct environmental conditions.
In this paper, we generate the standard 16S tree of members of the Vibrionaceae and compare it to a tree generated from amino acid sequence comparisons of the L3 ribosomal proteins. We find that the L3 tree is a less computationally complex method of constructing a phylogenetic tree compared to the pan-genome tree, and the L3 tree produces more reliable results than the 16S rRNA tree. Additionally, our data indicates that prokaryotes from aquatic habitats might use their multiple rRNA operons in distinct environmental conditions.
Projects
iGEM 2013
I am participating in the iGEM synthetic biology competition with the team from DTU. Our project aims to reclaim energy from waste water. See our team wiki for more details.
I am participating in the iGEM synthetic biology competition with the team from DTU. Our project aims to reclaim energy from waste water. See our team wiki for more details.
Translation: the amino acid card game
A card game that revolves around translation of mRNA to amino acids. It can be used as a tool to learn the amino acids, and it is genuinely fun to play.
A card game that revolves around translation of mRNA to amino acids. It can be used as a tool to learn the amino acids, and it is genuinely fun to play.
Metagenome Assembly Game
Each player is handed a fragment of a metagenomic sample. Players need to work together to assemble the fragments, translate the sequences, and unscramble the hidden message. The script requires a config file (here is a sample) and the header and footer files to generate latex output.
Each player is handed a fragment of a metagenomic sample. Players need to work together to assemble the fragments, translate the sequences, and unscramble the hidden message. The script requires a config file (here is a sample) and the header and footer files to generate latex output.
Nowhere2Nowhere Monorail
Nowhere2Nowhere was a 500ft long wooden monorail that was built and installed for Burning Man 2010 (theme: Metropolis). It ran for one night, then we burned it to the ground.
Nowhere2Nowhere was a 500ft long wooden monorail that was built and installed for Burning Man 2010 (theme: Metropolis). It ran for one night, then we burned it to the ground.
Photography
