Alex Crits-Christoph

I am currently a graduate student in Microbiology in the Banfield Lab at University of Calfornia, Berkeley.
Affiliations: Plant and Microbial Biology, Innovative Genomics Institute

Interests
Computational analysis of microbial communities; evolution and ecology of microbes and viruses; CRISPR genome editing; bioinformatics software and web development; statistics and machine learning applied to genomics.
My past
BA in Biophysics from Johns Hopkins (2016)
2015-2016 - data analysis @ Second Genome,
2016 summer - genome informatics @ Caribou Biosciences,
2012-2016 - microbial genomics @ DiRuggiero lab at JHU,
2014 - Google Summer of Code.

In the past I have collaborated on individual projects with Marc Halushka, Gary Bader and Mohammed Helmy, and Rachel Karchin. My email and Github are at the top of this page.

Publications
For the complete and up to date list, see my Google Scholar.

Crits-Christoph, Alexander, Spencer Diamond, Cristina N. Butterfield, Brian C. Thomas, & Jillian F. Banfield. "Novel soil bacteria possess diverse genes for secondary metabolite biosynthesis." Nature (2018). doi:10.1038/s41586-018-0207-y

Olm, Matthew R., Alexander Crits-Christoph, Spencer Diamond, Adi Lavy, Paula B. Matheus Carnevali, and Jillian F. Banfield. "Consistent Metagenome-Derived Metrics Verify and Delineate Bacterial Species Boundaries." mSystems 5, no. 1 (2020).

Olm, Matthew R., Nicholas Bhattacharya, Alexander Crits-Christoph, Brian A. Firek, Robyn Baker, Yun S. Song, Michael J. Morowitz, and Jillian F. Banfield. "Necrotizing enterocolitis is preceded by increased gut bacterial replication, Klebsiella, and fimbriae-encoding bacteria." Science Advances 5, no. 12 (2019): eaax5727.

Steen, Andrew D., Alexander Crits-Christoph, Paul Carini, Kristen M. DeAngelis, Noah Fierer, Karen G. Lloyd, and J. Cameron Thrash. "High proportions of bacteria and archaea across most biomes remain uncultured." The ISME Journal 13, no. 12 (2019): 3126-3130.

Diamond, Spencer, Peter F. Andeer, Zhou Li, Alexander Crits-Christoph, David Burstein, Karthik Anantharaman, Katherine R. Lane et al. "Mediterranean grassland soil C–N compound turnover is dependent on rainfall and depth, and is mediated by genomically divergent microorganisms." Nature Microbiology 4, no. 8 (2019): 1356-1367.

Berg, Maureen, David Monnin, Juhyun Cho, Lydia Nelson, Alex Crits-Christoph, and Michael Shapira. "TGFβ/BMP immune signaling affects abundance and function of C. elegans gut commensals." Nature Communications 10, no. 1 (2019): 1-12.

Helmy, Mohamed, Alexander Crits-Christoph, & Gary D. Bader. "Ten Simple Rules for Developing Public Biological Databases." PLoS Comput Biol 12, no. 11 (2016): e1005128.

Crits‐Christoph, Alexander, Diego R. Gelsinger, Bing Ma, Jacek Wierzchos, Jacques Ravel, Alfonso Davila, M. Cristina Casero, & 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, & Jocelyne DiRuggiero. "Phylogenetic and functional substrate specificity for endolithic microbial communities in hyper-arid environments." Frontiers in Microbiology 7 (2016).

McCall, Matthew N., Alexander S. Baras, Alexander Crits-Christoph, Roxann Ingersoll, Melissa A. McAlexander, Kenneth W. Witwer, & Marc K. Halushka. "A benchmark for microRNA quantification algorithms using the OpenArray platform." BMC Bioinformatics 17, no. 1 (2016): 1.

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

Projects

InStrain: A Python package for population genomic analysis from metagenomic data and rigorous detection of identical microbial strains. (BioRxiv) Original repository is here; Current version was developed into a full feature program and is maintained by Matthew Olm.

DV-IMPACT (Disease Variants' Impacts on Domain-based Protein Interactions) allows users to explore the effects of over 800,000 missense mutations on PPI interactions, as mediated by wildtype and variants protein sequences.

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

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

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.