Publications

Please see Rachel’s Google Scholar page for an up-to-date list.

2024

KS Makarova, C Zhang, YI Wolf, S Karamycheva, RJ Whitaker, EV Koonin (2024). Computational analysis of genes with lethal knockout phenotype and prediction of essential genes in archaea. Mbio, e03092-23

2023

Local and Environmental Reservoirs of Salmonella enterica After Hurricane Florence Flooding

Y Mao, M Zeineldin, M Usmani, A Jutla, JL Shisler, RJ Whitaker, …
GeoHealth 7 (11), e2023GH000877
Phage-mediated resolution of genetic conflict alters the evolutionary trajectory of Pseudomonas aeruginosa lysogens

LC Suttenfield, Z Rapti, JH Chandrashekhar, AC Steinlein, JC Vera, T Kim, …
bioRxiv, 2023.10. 24.563318
Genomic insight and physiological characterization of thermoacidophilic Alicyclobacillusisolated from Yellowstone National Park

HW Kim, NK Kim, APR Phillips, DA Parker, P Liu, RJ Whitaker, CV Rao, …
Frontiers in Microbiology 14, 1232587
AJ Collins, RJ Whitaker (2023). CRISPR Comparison Toolkit: Rapid Identification, Visualization, and Analysis of CRISPR Array Diversity

The CRISPR Journal 6 (4), 386-400
JC Kosmopoulos, DE Campbell, RJ Whitaker, EG Wilbanks (2023). Horizontal gene transfer and CRISPR targeting drive phage-bacterial host interactions and coevolution in “pink berry” marine microbial aggregates. Applied and environmental microbiology 89 (7), e00177-23
Sanchez-Nieves, R.L., Zhang, C., and Whitaker, R.J. (2023). Integrated conjugative plasmid drives high frequency chromosomal gene transfer in Sulfolobus islandicus. Front. Microbiol. 14, 1114574. 10.3389/fmicb.2023.1114574.

2022

Collins, A.J., and Whitaker, R.J. (2022). CRISPR comparison toolkit (CCTK): Rapid identification, visualization, and analysis of CRISPR array diversity (Bioinformatics)
10.1101/2022.07.31.502198.
Orazi, G., Collins, A.J., and Whitaker, R.J. (2022). Prediction of prophages and their host ranges in pathogenic and commensal Neisseria species. 2021.12.16.473053.
10.1101/2021.12.16.473053.
DeWerff, S.J., Zhang, C., Schneider, J., and Whitaker, R.J. (2022). Intraspecific antagonism through viral toxin encoded by chronic Sulfolobus spindle-shaped virus. Philosophical Transactions of the Royal Society B: Biological Sciences 377, 20200476.
10.1098/rstb.2020.0476.

2021

Campbell, D.E., Leigh, J.R., Kim, T., England, W.E., Whitaker, R.J., and Degnan, P.H. (2021). Interrogation of the integrated mobile genetic elements in gut-associated Bacteroidaceae with a consensus prediction approach. 2021.09.02.458807. 10.1101/2021.09.02.458807.

2020

Urtecho, G., Campbell, D.E., Hershey, D.M., Hussain, F.A., Whitaker, R.J., and O’Toole, G.A. (2020). Discovering the Molecular Determinants of Phaeobacter inhibens Susceptibility to Phaeobacter Phage MD18. mSphere 5, e00898-20.
10.1128/mSphere.00898-20.
Pilosof, S., Alcalá-Corona, S.A., Wang, T., Kim, T., Maslov, S., Whitaker, R., and Pascual, M. (2020). The network structure and eco-evolutionary dynamics of CRISPR-induced immune diversification. Nat Ecol Evol 4, 1650–1660.
10.1038/s41559-020-01312-z.
Campbell, D.E., Ly, L.K., Ridlon, J.M., Hsiao, A., Whitaker, R.J., and Degnan, P.H. (2020). Infection with Bacteroides Phage BV01 Alters the Host Transcriptome and Bile Acid Metabolism in a Common Human Gut Microbe. Cell Reports 32, 108142.
10.1016/j.celrep.2020.108142.

DeWerff, Samantha J., Maria A. Bautista, Matthew Pauly, Changyi Zhang, and Rachel J. Whitaker. “Killer Archaea: Virus-Mediated Antagonism to CRISPR-Immune Populations Results in  Emergent Virus-Host Mutualism.” MBio 11, no. 2 (April 28, 2020). https://doi.org/10.1128/mBio.00404-20.

Rowland, Elizabeth F., Maria A. Bautista, Changyi Zhang, and Rachel J. Whitaker. “Surface Resistance to SSVs and SIRVs in Pilin Deletions of Sulfolobus Islandicus.” Molecular Microbiology 113, no. 4 (April 2020): 718–27. https://doi.org/10.1111/mmi.14435.

Weitzel, Christopher S., Li Li, Changyi Zhang, Kristen K. Eilts, Nicholas M. Bretz, Alex L. Gatten, Rachel J. Whitaker, and Susan A. Martinis. “Duplication of Leucyl-TRNA Synthetase in an Archaeal Extremophile May Play a Role in  Adaptation to Variable Environmental Conditions.” The Journal of Biological Chemistry 295, no. 14 (April 3, 2020): 4563–76. https://doi.org/10.1074/jbc.RA118.006481.

Athukoralage, Januka S., Stephen A. McMahon, Changyi Zhang, Sabine Grüschow, Shirley Graham, Mart Krupovic, Rachel J. Whitaker, Tracey M. Gloster, and Malcolm F. White. “An Anti-CRISPR Viral Ring Nuclease Subverts Type III CRISPR Immunity.” Nature 577, no. 7791 (January 2020): 572–75. https://doi.org/10.1038/s41586-019-1909-5.

Tsai, Chi-Lin, Patrick Tripp, Shamphavi Sivabalasarma, Changyi Zhang, Marta Rodriguez-Franco, Rebecca L. Wipfler, Paushali Chaudhury, Rachel J. Whitaker, et al. “The Structure of the Periplasmic FlaG-FlaF Complex and Its Essential Role for  Archaellar Swimming Motility.” Nature Microbiology 5, no. 1 (January 2020): 216–25. https://doi.org/10.1038/s41564-019-0622-3.

2019

Clifton, Sara M., Ted Kim, Jayadevi H. Chandrashekhar, George A. O’Toole, Zoi Rapti, and Rachel J. Whitaker. “Lying in Wait: Modeling the Control of Bacterial Infections via Antibiotic-Induced  Proviruses.” MSystems 4, no. 5 (October 1, 2019). https://doi.org/10.1128/mSystems.00221-19.

Zhang, Changyi, Rebecca L. Wipfler, Yuan Li, Zhiyu Wang, Emily N. Hallett, and Rachel J. Whitaker. “Cell Structure Changes in the Hyperthermophilic Crenarchaeon Sulfolobus Islandicus  Lacking the S-Layer.” MBio 10, no. 4 (August 27, 2019). https://doi.org/10.1128/mBio.01589-19.

Pauly, M.D., M.A. Bautista, J.A. Black, and R.J. Whitaker. “Diversified Local CRISPR-Cas Immunity to Viruses of Sulfolobus Islandicus.” Philosophical Transactions of the Royal Society B: Biological Sciences 374, no. 1772 (May 2019): 20180093. https://doi.org/10.1098/rstb.2018.0093.

Weitz, Joshua S., Guanlin Li, Hayriye Gulbudak, Michael H. Cortez, and Rachel J. Whitaker. “Viral Invasion Fitness across a Continuum from Lysis to Latency.” Virus Evolution 5, no. 1 (January 2019): vez006. https://doi.org/10.1093/ve/vez006.

Krause, David J., and Rachel J. Whitaker. “Population Genomics of Archaea: Signatures of Archaeal Biology from Natural Populations.” In Population Genomics: Microorganisms, edited by Martin F. Polz and Om P. Rajora, 145–55. Population Genomics. Cham: Springer International Publishing, 2019. https://doi.org/10.1007/13836_2018_49.

2018

Lab Papers

Zhang, Changyi, Alex P. R. Phillips, Rebecca L. Wipfler, Gary J. Olsen, and Rachel J. Whitaker. “The Essential Genome of the Crenarchaeal Model Sulfolobus Islandicus.” Nature Communications 9, no. 1 (November 21, 2018): 4908. https://doi.org/10.1038/s41467-018-07379-4.

England, Whitney E., Ted Kim, and Rachel J. Whitaker. “Metapopulation Structure of CRISPR-Cas Immunity in Pseudomonas Aeruginosa and Its Viruses.” MSystems 3, no. 5 (October 30, 2018): e00075-18. https://doi.org/10.1128/mSystems.00075-18.

Zhang, Changyi, and Rachel J. Whitaker. “Microhomology-Mediated High-Throughput Gene Inactivation Strategy for the Hyperthermophilic Crenarchaeon Sulfolobus Islandicus.” Appl. Environ. Microbiol. 84, no. 1 (January 1, 2018): e02167-17. https://doi.org/10.1128/AEM.02167-17.

Munson-McGee, Jacob H., Shengyun Peng, Samantha Dewerff, Ramunas Stepanauskas, Rachel J. Whitaker, Joshua S. Weitz, and Mark J. Young. “A Virus or More in (Nearly) Every Cell: Ubiquitous Networks of Virus–Host Interactions in Extreme Environments.” The ISME Journal 12, no. 7 (July 2018): 1706. https://doi.org/10.1038/s41396-018-0071-7.

Ling, Fangqiong, Rachel Whitaker, Mark W. LeChevallier, and Wen-Tso Liu. “Drinking Water Microbiome Assembly Induced by Water Stagnation.” The ISME Journal 12, no. 6 (June 2018): 1520. https://doi.org/10.103/s41396-018-0101-5.

2017

Wagner, Alexander, Rachel J. Whitaker, David J. Krause, Jan-Hendrik Heilers, Marleen van Wolferen, Chris van der Does, and Sonja-Verena Albers. “Mechanisms of Gene Flow in Archaea.” Nature Reviews Microbiology 15, no. 8 (August 2017): 492–501. https://doi.org/10.1038/nrmicro.2017.41.

Anderson, Rika E., Angela Kouris, Christopher H. Seward, Kate M. Campbell, and Rachel J. Whitaker. “Structured Populations of Sulfolobus Acidocaldarius with Susceptibility to Mobile Genetic Elements.” Genome Biology and Evolution 9, no. 6 (June 1, 2017): 1699–1710. https://doi.org/10.1093/gbe/evx104.

Campbell, Kate M., Angela Kouris, Whitney England, Rika E. Anderson, R. Blaine McCleskey, D. Kirk Nordstrom, and Rachel J. Whitaker. “Sulfolobus Islandicus Meta-Populations in Yellowstone National Park Hot Springs.” Environmental Microbiology 19, no. 6 (June 2017): 2334–47. https://doi.org/10.1111/1462-2920.13728.

Bautista, Maria A., Jesse A. Black, Nicholas D. Youngblut, and Rachel J. Whitaker. “Differentiation and Structure in Sulfolobus Islandicus Rod-Shaped Virus Populations.” Viruses 9, no. 5 (May 19, 2017). https://doi.org/10.3390/v9050120.

2016

Zhang, Changyi, Qunxin She, Hongkai Bi, and Rachel J. Whitaker. “The Apt/6-Methylpurine Counterselection System and Its Applications in Genetic Studies of the Hyperthermophilic Archaeon Sulfolobus Islandicus.” Appl. Environ. Microbiol. 82, no. 10 (May 15, 2016): 3070–81. https://doi.org/10.1128/AEM.00455-16.

Whitaker, Rachel J., and Carin K. Vanderpool. “CRISPR-Cas Gatekeeper: Slow on the Uptake but Gets the Job Done.” Cell Host & Microbe 19, no. 2 (February 10, 2016): 135–37. https://doi.org/10.1016/j.chom.2016.01.015.

2015

Lab Papers

Krause, David J., and Rachel J. Whitaker. “Inferring Speciation Processes from Patterns of Natural Variation in Microbial Genomes.” Systematic Biology 64, no. 6 (November 1, 2015): 926–35. https://doi.org/10.1093/sysbio/syv050.

Youngblut, Nicholas D., Joseph S. Wirth, James R. Henriksen, Maria Smith, Holly Simon, William W. Metcalf, and Rachel J. Whitaker. “Genomic and Phenotypic Differentiation among Methanosarcina Mazei Populations from Columbia River Sediment.” The ISME Journal 9, no. 10 (October 2015): 2191–2205. https://doi.org/10.1038/ismej.2015.31.

Bautista, Maria A., Changyi Zhang, and Rachel J. Whitaker. “Virus-Induced Dormancy in the Archaeon Sulfolobus Islandicus.” MBio 6, no. 2 (May 1, 2015): e02565-14. https://doi.org/10.1128/mBio.02565-14.

Smith, Maria W., Richard E. Davis, Nicholas D. Youngblut, Tuomas Kärnä, Lydie Herfort, Rachel J. Whitaker, William W. Metcalf, Bradley M. Tebo, António M. Baptista, and Holly M. Simon. “Metagenomic Evidence for Reciprocal Particle Exchange between the Mainstem Estuary and Lateral Bay Sediments of the Lower Columbia River.” Frontiers in Microbiology 6 (2015). https://doi.org/10.3389/fmicb.2015.01074.

Paver, Sara F., Nicholas D. Youngblut, Rachel J. Whitaker, and Angela D. Kent. “Phytoplankton Succession Affects the Composition of Polynucleobacter Subtypes in Humic Lakes.” Environmental Microbiology 17, no. 3 (2015): 816–28. https://doi.org/10.1111/1462-2920.12529.

2014

Lab Papers

Jasti, Chandana, Barbara Hug, Jillian L. Waters, and Rachel J. Whitaker. “How Do Small Things Make a Big Difference? Activities to Teach about Human–Microbe Interactions.” The American Biology Teacher 76, no. 9 (November 2014): 601–8. https://doi.org/10.1525/abt.2014.76.9.6.

Youngblut, Nicholas D., Mark Dell’Aringa, and Rachel J. Whitaker. “Differentiation between Sediment and Hypolimnion Methanogen Communities in Humic Lakes.” Environmental Microbiology 16, no. 5 (2014): 1411–23. https://doi.org/10.1111/1462-2920.12330.

Krause, David J., Xavier Didelot, Hinsby Cadillo-Quiroz, and Rachel J. Whitaker. “Recombination Shapes Genome Architecture in an Organism from the Archaeal Domain.” Genome Biology and Evolution 6, no. 1 (January 2014): 170–78. https://doi.org/10.1093/gbe/evu003.

Childs, Lauren M., Whitney E. England, Mark J. Young, Joshua S. Weitz, and Rachel J. Whitaker. “CRISPR-Induced Distributed Immunity in Microbial Populations.” PLOS ONE 9, no. 7 (July 7, 2014): e101710. https://doi.org/10.1371/journal.pone.0101710.

Benedict, Matthew N., James R. Henriksen, William W. Metcalf, Rachel J. Whitaker, and Nathan D. Price. “ITEP: An Integrated Toolkit for Exploration of Microbial Pan-Genomes.” BMC Genomics 15, no. 1 (January 3, 2014): 8. https://doi.org/10.1186/1471-2164-15-8.

2013

England, Whitney E., and Rachel J. Whitaker. “Evolutionary Causes and Consequences of Diversified CRISPR Immune Profiles in Natural Populations.” Biochemical Society Transactions 41, no. 6 (December 2013): 1431–36. https://doi.org/10.1042/BST20130243.

Held, Nicole L., Alfa Herrera, and Rachel J. Whitaker. “Reassortment of CRISPR Repeat-Spacer Loci in Sulfolobus Islandicus.” Environmental Microbiology 15, no. 11 (November 2013): 3065–76. https://doi.org/10.1111/1462-2920.12146.

Zhang, Changyi, Tara E. Cooper, David J. Krause, and Rachel J. Whitaker. “Augmenting the Genetic Toolbox for Sulfolobus Islandicus with a Stringent Positive Selectable Marker for Agmatine Prototrophy.” Appl. Environ. Microbiol. 79, no. 18 (September 15, 2013): 5539–49. https://doi.org/10.1128/AEM.01608-13.

Zhang, Changyi, David J. Krause, and Rachel J. Whitaker. “Sulfolobus Islandicus: a Model System for Evolutionary Genomics.” Biochemical Society Transactions 41, no. 1 (February 1, 2013): 458–462. doi:10.1042/BST20120338.

Youngblut, Nicholas D., Ashley Shade, Jordan S. Read, Katherine D. McMahon, and Rachel J. Whitaker. “Lineage-Specific Responses of Microbial Communities to Environmental Change.” Applied and Environmental Microbiology 79, no. 1 (January 2013): 39–47. https://doi.org/10.1128/AEM.02226-12.

Held, Nicole L., Lauren M. Childs, Michelle Davison, Joshua S. Weitz, Rachel J. Whitaker, and Devaki Bhaya. “CRISPR-Cas Systems to Probe Ecological Diversity and Host–Viral Interactions.” In CRISPR-Cas Systems, edited by Rodolphe Barrangou and John van der Oost, 221–250. Springer Berlin Heidelberg, 2013.

2012

Lab Papers

Zhang, Changyi, and Rachel J. Whitaker. “A Broadly Applicable Gene Knockout System for the Thermoacidophilic Archaeon  Sulfolobus Islandicus Based on Simvastatin Selection.” Microbiology (Reading, England) 158, no. Pt 6 (June 2012): 1513–22. https://doi.org/10.1099/mic.0.058289-0.

Cadillo-Quiroz, Hinsby, Xavier Didelot, Nicole L. Held, Alfa Herrera, Aaron Darling, Michael L. Reno, David J. Krause, and Rachel J. Whitaker. “Patterns of Gene Flow Define Species of Thermophilic Archaea.” PLoS Biology 10, no. 2 (February 2012): e1001265. https://doi.org/10.1371/journal.pbio.1001265.

Shade, Ashley, Jordan S. Read, Nicholas D. Youngblut, Noah Fierer, Rob Knight, Timothy K. Kratz, Noah R. Lottig, Rachel J. Whitaker, et al. “Lake Microbial Communities Are Resilient after a Whole-Ecosystem Disturbance.” The ISME Journal 6, no. 12 (December 2012): 2153–67. https://doi.org/10.1038/ismej.2012.56.

Childs, Lauren M., Nicole L. Held, Mark J. Young, Rachel J. Whitaker, and Joshua S. Weitz. “Multiscale Model of CRISPR-Induced Coevolutionary Dynamics: Diversification at the  Interface of Lamarck and Darwin.” Evolution; International Journal of Organic Evolution 66, no. 7 (July 2012): 2015–29. https://doi.org/10.1111/j.1558-5646.2012.01595.x.

2011

Rachel J. Whitaker. “A New Age of Naturalists.” Microbe 6, no. 11 (November 2011): 491-494.

Rachel J. Whitaker. “An appreciation for natural variation.” Environmental Microbiology Reports 3, no. 1 (2011): 25-26.

2010

Held, Nicole L., Alfa Herrera, Hinsby Cadillo-Quiroz, and Rachel J. Whitaker. “CRISPR Associated Diversity within a Population of Sulfolobus Islandicus.” PloS One 5, no. 9 (September 28, 2010). https://doi.org/10.1371/journal.pone.0012988.

Milferstedt, Kim, Nicholas D. Youngblut, and Rachel J. Whitaker. “Spatial Structure and Persistence of Methanogen Populations in Humic Bog Lakes.” The ISME Journal 4, no. 6 (June 2010): 764–76. https://doi.org/10.1038/ismej.2010.7.

2009

Whitaker, Rachel J. “Evolution: Spatial Scaling of Microbial Interactions.” Current Biology : CB 19, no. 20 (November 3, 2009): R954-956. https://doi.org/10.1016/j.cub.2009.09.035.

Reno, Michael L., Nicole L. Held, Christopher J. Fields, Patricia V. Burke, and Rachel J. Whitaker. “Biogeography of the Sulfolobus Islandicus Pan-Genome.” Proceedings of the National Academy of Sciences of the United States of America 106, no. 21 (May 26, 2009): 8605–10. https://doi.org/10.1073/pnas.0808945106.

Held, Nicole L., and Rachel J. Whitaker. “Viral Biogeography Revealed by Signatures in Sulfolobus Islandicus Genomes.” Environmental Microbiology 11, no. 2 (February 2009): 457–66. https://doi.org/10.1111/j.1462-2920.2008.01784.x.

Before 2009

Green, Jessica L., Brendan J. M. Bohannan, and Rachel J. Whitaker. “Microbial Biogeography: From Taxonomy to Traits.” Science 320, no. 5879 (May 23, 2008): 1039–43. https://doi.org/10.1126/science.1153475.

Whitaker, Rachel J. “Allopatric Origins of Microbial Species.” Philosophical Transactions of the Royal Society of London. Series B, Biological  Sciences 361, no. 1475 (November 29, 2006): 1975–84. https://doi.org/10.1098/rstb.2006.1927.

Whitaker, Rachel J., and Jillian F. Banfield. “Population Genomics in Natural Microbial Communities.” Trends in Ecology & Evolution 21, no. 9 (September 2006): 508–16. https://doi.org/10.1016/j.tree.2006.07.001.

Whitaker, Rachel J., Dennis W. Grogan, and John W. Taylor. “Recombination Shapes the Natural Population Structure of the Hyperthermophilic  Archaeon Sulfolobus Islandicus.” Molecular Biology and Evolution 22, no. 12 (December 2005): 2354–61. https://doi.org/10.1093/molbev/msi233.

Whitaker, Rachel J., Dennis W. Grogan, and John W. Taylor. “Geographic Barriers Isolate Endemic Populations of Hyperthermophilic Archaea.” Science 301, no. 5635 (August 15, 2003): 976–78. https://doi.org/10.1126/science.1086909.