Alex Crits-Christoph

I am an undergraduate in Biophysics at Johns Hopkins University. My interests include genomics, microbiome research, bioinformatics, ecology and evolution, biotechnology, web development, and statistics.

Experience

Since January 2015, I have worked as a Data Analyst for Second Genome, both analyzing and creating visualization tools for microbiome research, and worked there full-time from May-August 2015.

Since 2012, I have been working with Dr. Jocelyne DiRuggiero's lab in microbial genomics at Johns Hopkins, where I characterize and study microbiomes of extreme environments. I use current software in computational ecology such as QIIME to analyze diversity and taxonomic composition of large datasets of 16S rRNA samples, and I infer statistical correlations and patterns in this data using R.

I also analyze metagenomic data and infer metabolic properties of microbial communities from metagenomic data. This work involves metagenomic assembly, genome reconstruction, gene annotation, and metabolic profiling.

In Summer 2014, I was accepted to Google Summer of Code, and as part of this program I designed and developed an exploratory web interface for the Cancer Variants Database (Can-VD), a dataset created by the Bader Lab at the University of Toronto.

In 2013, I worked with Dr. Rachel Karchin's lab at the Institute for Computational Medicine on a project analyzing networks of mutation relationships in TEM B-lactamase from an ancestral phylogeny in order to describe the evolution of antibiotic resistance.

In Summer 2011, I collaborated with the Plotkin Research Group at the University of Pennsylvania on computing entropy of the Influenza HA protein using protein sequence and structure data.

Awards

Spring 2014: JHU Business Plan Competition (General Business) - 1st place, $6,000.

Summer 2013: Johns Hopkins Provost Undergraduate Research Award, $2,500 - for an independent research project on exposure of endolithic communities to UV light.

Fall 2013: HopHacks - Best Social Innovation Hack at the Hopkins 2013 Fall Hackathon for co-creating a web app to help researchers access genomic data.

Projects

Can-VD - The Cancer Variants Database allows users to explore the effects of over 800,000 missense mutations on PPI interactions, as mediated by wildtype and variants protein sequences.

SequeBase - A bioinformatics project seeking to improve the way researchers access genomic and proteomic data.

An experimental augmented reality AdBlock, created using a custom head-mounted display and OpenCV image processing with Python. Placed in top 30 hacks @ PennApps. Read more: VICE, Wired, HackerNews Discussion

Aezon - A team of Johns Hopkins students selected as one of 10 finalists in the $10 million Qualcomm Tricorder X-Prize, a competition to built a medical system capable of diagnosing a user of 15 diseases and conditions. I was in charge of development and operations of the servers which store and analyze patient data.

Novel Mycobacteriophage characterization

Publications

Crits‐Christoph, Alexander, Diego R. Gelsinger, Bing Ma, Jacek Wierzchos, Jacques Ravel, Alfonso Davila, M. Cristina Casero, and Jocelyne DiRuggiero. "Functional interactions of archaea, bacteria, and viruses in a hypersaline endolithic community." Environmental Microbiology (2016).

Crits-Christoph, Alexander, Courtney K Robinson, Bing Ma, Jacques Ravel, Jacek Wierzchos, Carmen Ascaso, Octavio Artieda, Virginia Souza-Egipsy, M. Cristina Casero, and Jocelyne DiRuggiero. "Phylogenetic and functional substrate specificity for endolithic microbial communities in hyper-arid environments." Frontiers in Microbiology (2016).

McCall, M. N., Baras, A. S., Crits-Christoph, A., Ingersoll, R., McAlexander, M. A., Witwer, K. W., & Halushka, M. K. (2016). A benchmark for microRNA quantification algorithms using the OpenArray platform. BMC Bioinformatics, 17(1), 1–13. http://doi.org/10.1186/s12859-016-0987-8

Crits-Christoph, Alexander, Courtney K. Robinson, Tyler Barnum, W. Florian Fricke, Alfonso F. Davila, Bruno Jedynak, Christopher P. McKay, and Jocelyne DiRuggiero. "Colonization patterns of soil microbial communities in the Atacama Desert." Microbiome 1, no. 1 (2013): 28.

Robinson, Courtney K., Jacek Wierzchos, Celeste Black, Alexander Crits-Christoph, Bing Ma, Jacques Ravel, Carmen Ascaso et al. "Microbial diversity and the presence of algae in halite endolithic communities are correlated to atmospheric moisture in the hyper-arid zone of the Atacama Desert". Environmental Microbiology. (2014).