Alex Crits-Christoph

I am currently a Senior Scientist in Computational Biology at Cultivarium, a non-profit focused research organization creating open source tools for microbiology.
I received my PhD in Microbiology from the University of California, Berkeley in 2021, working in the laboratory of Jill Banfield.
BA in Biophysics from Johns Hopkins (2016),
past experience:
2021-2022 - postdoc @ Johns Hopkins School of Public Health in the Suez lab,
2021 - computational biologist @ Pattern Ag,
2015-2016 - data analysis @ Second Genome,
2012-2016 - microbial genomics @ DiRuggiero lab at JHU

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.

Selected 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

Crits-Christoph, Alexander, Rose S. Kantor, Matthew R. Olm, Oscar N. Whitney, Basem Al-Shayeb, Yue Clare Lou, Avi Flamholz et al. "Genome sequencing of sewage detects regionally prevalent SARS-CoV-2 variants."
MBio 12, no. 1 (2021): e02703-20.

Olm, Matthew R., Alexander Crits-Christoph, Keith Bouma-Gregson, Brian A. Firek, Michael J. Morowitz, and Jillian F. Banfield. "inStrain profiles population microdiversity from metagenomic data and sensitively detects shared microbial strains."
Nature Biotechnology 39, no. 6 (2021): 727-736.

Holmes, Edward C., Stephen A. Goldstein, Angela L. Rasmussen, David L. Robertson, Alexander Crits-Christoph, Joel O. Wertheim, Simon J. Anthony et al. "The origins of SARS-CoV-2: A critical review."
Cell 184, no. 19 (2021): 4848-4856.

Rubin, Benjamin E., Spencer Diamond, Brady F. Cress, Alexander Crits-Christoph, Yue Clare Lou, Adair L. Borges, Haridha Shivram et al. "Species-and site-specific genome editing in complex bacterial communities."
Nature Microbiology 7, no. 1 (2022): 34-47.

Crits-Christoph, Alexander, Matthew R. Olm, Spencer Diamond, Keith Bouma-Gregson, and Jillian F. Banfield. "Soil bacterial populations are shaped by recombination and gene-specific selection across a grassland meadow."
The ISME Journal 14, no. 7 (2020): 1834-1846.

Crits-Christoph, Alexander, Nicholas Bhattacharya, Matthew R. Olm, Yun S. Song, and Jillian F. Banfield. "Transporter genes in biosynthetic gene clusters predict metabolite characteristics and siderophore activity."
Genome Research 31, no. 2 (2021): 239-250.

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): 1-13.

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.

Chen, Lin-Xing, Raphaël Méheust, Alexander Crits-Christoph, Katherine D. McMahon, Tara Colenbrander Nelson, Gregory F. Slater, Lesley A. Warren, and Jillian F. Banfield. "Large freshwater phages with the potential to augment aerobic methane oxidation."
Nature Microbiology 5, no. 12 (2020): 1504-1515.