@article{mclaren_nearing_willis_lloyd_callahan_2022, title={Implications of taxonomic bias for microbial differential-abundance analysis}, url={https://doi.org/10.1101/2022.08.19.504330}, DOI={10.1101/2022.08.19.504330}, abstractNote={Abstract}, author={McLaren, Michael R. and Nearing, Jacob T. and Willis, Amy D. and Lloyd, Karen G. and Callahan, Benjamin J.}, year={2022}, month={Aug} }
 @article{fletcher_pike_parsons_rivera_foley_mclaren_montgomery_theriot_2021, title={Clostridioides difficile exploits toxin-mediated inflammation to alter the host nutritional landscape and exclude competitors from the gut microbiota}, volume={12}, ISSN={["2041-1723"]}, url={https://doi.org/10.1038/s41467-020-20746-4}, DOI={10.1038/s41467-020-20746-4}, abstractNote={Abstract}, number={1}, journal={NATURE COMMUNICATIONS}, author={Fletcher, Joshua R. and Pike, Colleen M. and Parsons, Ruth J. and Rivera, Alissa J. and Foley, Matthew H. and McLaren, Michael R. and Montgomery, Stephanie A. and Theriot, Casey M.}, year={2021}, month={Jan} }
 @misc{nguyen_bakerlee_mckelvey_rose_norman_joseph_manheim_mclaren_jiang_barnes_et al._2021, title={Evaluating Use Cases for Human Challenge Trials in Accelerating SARS-CoV-2 Vaccine Development}, volume={72}, ISSN={["1537-6591"]}, DOI={10.1093/cid/ciaa935}, abstractNote={Abstract}, number={4}, journal={CLINICAL INFECTIOUS DISEASES}, author={Nguyen, Linh Chi and Bakerlee, Christopher W. and McKelvey, T. Greg and Rose, Sophie M. and Norman, Alexander J. and Joseph, Nicholas and Manheim, David and McLaren, Michael R. and Jiang, Steven and Barnes, Conor F. and et al.}, year={2021}, month={Feb}, pages={710–715} }
 @article{thanissery_mclaren_rivera_reed_betrapally_burdette_winston_jacob_callahan_theriot_2020, title={Clostridioides difficile carriage in animals and the associated changes in the host fecal microbiota}, volume={66}, ISSN={["1095-8274"]}, DOI={10.1016/j.anaerobe.2020.102279}, abstractNote={The relationship between the gut microbiota and Clostridioides difficile, and its role in the severity of C. difficile infection in humans is an area of active research. Intestinal carriage of toxigenic and non-toxigenic C. difficile strains, with and without clinical signs, is reported in animals, however few studies have looked at the risk factors associated with C. difficile carriage and the role of the host gut microbiota. Here, we isolated and characterized C. difficile strains from different animal species (predominantly canines (dogs), felines (cats), and equines (horses)) that were brought in for tertiary care at North Carolina State University Veterinary Hospital. C. difficile strains were characterized by toxin gene profiling, fluorescent PCR ribotyping, and antimicrobial susceptibility testing. 16S rRNA gene sequencing was done on animal feces to investigate the relationship between the presence of C. difficile and the gut microbiota in different hosts. Here, we show that C. difficile was recovered from 20.9% of samples (42/201), which included 33 canines, 2 felines, and 7 equines. Over 69% (29/42) of the isolates were toxigenic and belonged to 14 different ribotypes including ones known to cause CDI in humans. The presence of C. difficile results in a shift in the fecal microbial community structure in both canines and equines. Commensal Clostridium hiranonis was negatively associated with C. difficile in canines. Further experimentation showed a clear antagonistic relationship between the two strains in vitro, suggesting that commensal Clostridia might play a role in colonization resistance against C. difficile in different hosts.}, journal={ANAEROBE}, author={Thanissery, R. and McLaren, M. R. and Rivera, A. and Reed, A. D. and Betrapally, N. S. and Burdette, T. and Winston, J. A. and Jacob, M. and Callahan, B. J. and Theriot, C. M.}, year={2020}, month={Dec} }
 @article{mclaren_callahan_2020, title={Pathogen resistance may be the principal evolutionary advantage provided by the microbiome}, volume={375}, url={https://doi.org/10.1098/rstb.2019.0592}, DOI={10.1098/rstb.2019.0592}, abstractNote={To survive, plants and animals must continually defend against pathogenic microbes that would invade and disrupt their tissues. Yet they do not attempt to extirpate all microbes. Instead, they tolerate and even encourage the growth of commensal microbes, which compete with pathogens for resources and via direct inhibition. We argue that hosts have evolved to cooperate with commensals in order to enhance the pathogen resistance this competition provides. We briefly describe competition between commensals and pathogens within the host, consider how natural selection might favour hosts that tilt this competition in favour of commensals, and describe examples of extant host traits that may serve this purpose. Finally, we consider ways that this cooperative immunity may have facilitated the adaptive evolution of non-pathogen-related host traits. On the basis of these observations, we argue that pathogen resistance vies with other commensal-provided benefits for being the principal evolutionary advantage provided by the microbiome to host lineages across the tree of life.}, number={1808}, journal={Philosophical Transactions of the Royal Society B: Biological Sciences}, publisher={The Royal Society}, author={McLaren, Michael R. and Callahan, Benjamin J.}, year={2020}, month={Sep}, pages={20190592} }
 @article{berman_mclaren_callahan_2020, title={Understanding and interpreting community sequencing measurements of the vaginal microbiome}, volume={127}, url={https://doi.org/10.1111/1471-0528.15978}, DOI={10.1111/1471-0528.15978}, abstractNote={Community‐wide high‐throughput sequencing has transformed the study of the vaginal microbiome, and clinical applications are on the horizon. Here we outline the three main community sequencing methods: (1) amplicon sequencing, (2) shotgun metagenomic sequencing, and (3) metatranscriptomic sequencing. We discuss the advantages and limitations of community sequencing generally, and the unique strengths and weaknesses of each method. We briefly review the contributions of community sequencing to vaginal microbiome research and practice. We develop suggestions for critically interpreting research results and potential clinical applications based on community sequencing of the vaginal microbiome.}, number={2}, journal={BJOG: An International Journal of Obstetrics & Gynaecology}, publisher={Wiley}, author={Berman, HL and McLaren and Callahan, BJ}, year={2020}, month={Jan}, pages={139–146} }
 @article{thanissery_mclaren_rivera_reed_betrapally_burdette_winston_jacob_callahan_theriot_2019, title={Characterization of C. difficile strains isolated from companion animals and the associated changes in the host fecal microbiota}, url={http://europepmc.org/abstract/PPR/PPR100283}, DOI={10.1101/822577}, abstractNote={Abstract}, author={Thanissery, R and McLaren, M and Rivera, A and Reed, AD and Betrapally, N and Burdette, T and Winston, J and Jacob, M and Callahan, B and Theriot, C}, year={2019}, month={Oct} }
 @article{mclaren_willis_callahan_2019, title={Consistent and correctable bias in metagenomic sequencing experiments}, url={https://doi.org/10.7554/eLife.46923}, DOI={10.7554/eLife.46923}, abstractNote={Marker-gene and metagenomic sequencing have profoundly expanded our ability to measure biological communities. But the measurements they provide differ from the truth, often dramatically, because these experiments are biased toward detecting some taxa over others. This experimental bias makes the taxon or gene abundances measured by different protocols quantitatively incomparable and can lead to spurious biological conclusions. We propose a mathematical model for how bias distorts community measurements based on the properties of real experiments. We validate this model with 16S rRNA gene and shotgun metagenomics data from defined bacterial communities. Our model better fits the experimental data despite being simpler than previous models. We illustrate how our model can be used to evaluate protocols, to understand the effect of bias on downstream statistical analyses, and to measure and correct bias given suitable calibration controls. These results illuminate new avenues toward truly quantitative and reproducible metagenomics measurements.}, journal={eLife}, author={McLaren, Michael R and Willis, Amy D and Callahan, Benjamin J}, year={2019}, month={Sep} }
 @article{mclaren_willis_callahan_2019, title={Consistent and correctable bias in metagenomic sequencing measurements}, volume={2}, url={https://www.biorxiv.org/content/10.1101/559831v1}, DOI={10.1101/559831}, abstractNote={Abstract}, journal={bioRxiv}, publisher={Cold Spring Harbor Laboratory}, author={McLaren, Michael R. and Willis, Amy D. and Callahan, Benjamin J.}, year={2019}, month={Feb}, pages={559831} }
 @article{sakowski_uritskiy_cooper_gomes_mclaren_meisel_mickol_mintz_mongodin_pop_et al._2019, title={Current State of and Future Opportunities for Prediction in Microbiome Research: Report from the Mid-Atlantic Microbiome Meet-up in Baltimore on 9 January 2019.}, volume={10}, url={http://europepmc.org/abstract/med/31594828}, DOI={10.1128/mSystems.00392-19}, abstractNote={Accurate predictions across multiple fields of microbiome research have far-reaching benefits to society, but there are few widely accepted quantitative tools to make accurate predictions about microbial communities and their functions. More discussion is needed about the current state of microbiome analysis and the tools required to overcome the hurdles preventing development and implementation of predictive analyses.}, journal={mSystems}, author={Sakowski, E and Uritskiy, G and Cooper, R and Gomes, M and McLaren and Meisel, JS and Mickol, RL and Mintz, CD and Mongodin, EF and Pop, M and et al.}, year={2019}, month={Oct} }
 @article{mclaren_callahan_2018, title={In Nature, There Is Only Diversity}, volume={9}, ISSN={["2150-7511"]}, url={http://www.ncbi.nlm.nih.gov/pubmed/29295915}, DOI={10.1128/mbio.02149-17}, abstractNote={ABSTRACT}, number={1}, journal={MBIO}, publisher={American Society for Microbiology}, author={McLaren, Michael R. and Callahan, Benjamin J.}, year={2018} }
 @article{mclaren_2016, title={Fitness-valley crossing in subdivided asexual populations}, url={http://biorxiv.org/content/early/2016/10/08/079624}, DOI={10.1101/079624}, abstractNote={Abstract}, journal={bioRxiv}, publisher={Cold Spring Harbor Laboratory Press}, author={McLaren, Michael R.}, year={2016} }
 @article{the atacama cosmology telescope: cosmological parameters from three seasons of data_2013, volume={2013}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-84888090276&partnerID=MN8TOARS}, DOI={10.1088/1475-7516/2013/10/060}, abstractNote={We present constraints on cosmological and astrophysical parameters from high-resolution microwave background maps at 148 GHz and 218 GHz made by the Atacama Cosmology Telescope (ACT) in three seasons of observations from 2008 to 2010. A model of primary cosmological and secondary foreground parameters is fit to the map power spectra and lensing deflection power spectrum, including contributions from both the thermal Sunyaev-Zeldovich (tSZ) effect and the kinematic Sunyaev-Zeldovich (kSZ) effect, Poisson and correlated anisotropy from unresolved infrared sources, radio sources, and the correlation between the tSZ effect and infrared sources. The power ℓ2Cℓ/2π of the thermal SZ power spectrum at 148 GHz is measured to be 3.4±1.4 μK2 at ℓ = 3000, while the corresponding amplitude of the kinematic SZ power spectrum has a 95% confidence level upper limit of 8.6 μK2. Combining ACT power spectra with the WMAP 7-year temperature and polarization power spectra, we find excellent consistency with the LCDM model. We constrain the number of effective relativistic degrees of freedom in the early universe to be Neff = 2.79±0.56, in agreement with the canonical value of Neff = 3.046 for three massless neutrinos. We constrain the sum of the neutrino masses to be Σmν < 0.39 eV at 95% confidence when combining ACT and WMAP 7-year data with BAO and Hubble constant measurements. We constrain the amount of primordial helium to be Yp = 0.225±0.034, and measure no variation in the fine structure constant α since recombination, with α/α0 = 1.004±0.005. We also find no evidence for any running of the scalar spectral index, dns/dln k = −0.004±0.012.}, number={10}, journal={Journal of Cosmology and Astroparticle Physics}, year={2013} }
 @article{hand_appel_battaglia_richard bond_das_devlin_dunkley_dünner_essinger-hileman_fowler_et al._2011, title={The Atacama cosmology telescope: Detection of Sunyaev-Zel'dovich decrement in groups and clusters associated with luminous red galaxies}, volume={736}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-80051485713&partnerID=MN8TOARS}, DOI={10.1088/0004-637X/736/1/39}, abstractNote={We present a detection of the Sunyaev–Zel'dovich (SZ) decrement associated with the luminous red galaxy (LRG) sample of the Sloan Digital Sky Survey. The SZ data come from 148 GHz maps of the equatorial region made by the Atacama Cosmology Telescope. The LRG sample is divided by luminosity into four bins, and estimates for the central SZ temperature decrement are calculated through a stacking process. We detect and account for a bias of the SZ signal due to weak radio sources. We use numerical simulations to relate the observed decrement to Y200 and clustering properties to relate the galaxy luminosity to halo mass. We also use a relation between brightest cluster galaxy luminosity and cluster mass based on stacked gravitational lensing measurements to estimate the characteristic halo masses. The masses are found to be around 1014 M☉.}, number={1}, journal={Astrophysical Journal}, author={Hand, N. and Appel, J.W. and Battaglia, N. and Richard Bond, J. and Das, S. and Devlin, M.J. and Dunkley, J. and Dünner, R. and Essinger-Hileman, T. and Fowler, J.W. and et al.}, year={2011} }