text:
@inproceedings{AnGhRe16,
Author = {Anari, N. and Gharan, S O and Rezaei, A},
Booktitle = {Conference on Learning Theory},
Pages = {23--26},
Title = {{Monte-Carlo Markov chain algorithms for sampling strongly Rayleigh distributions and determinantal point processes}},
arxivId = {1602.05242},
url = {https://arxiv.org/abs/1602.05242},
Year = {2016}}

@inproceedings{AfKuFo13,
abstract = {Determinantal point processes (DPPs) are appealing models for subset selection prob-lems where diversity is desired. They offer surprisingly efficient inference, including sam-pling in O(N 3) time and O(N 2) space, where N is the number of base items. However, in some applications, N may grow so large that sampling from a DPP becomes compu-tationally infeasible. This is especially true in settings where the DPP kernel matrix can-not be represented by a linear decomposition of low-dimensional feature vectors. In these cases, we propose applying the Nystr{\"{o}}m approximation to project the kernel matrix into a low-dimensional space. While theoretical guarantees for the Nystr{\"{o}}m approximation in terms of standard matrix norms have been previously established, we are concerned with probabilistic measures, like total variation dis-tance between the DPP and its Nystr{\"{o}}m ap-proximation, that behave quite differently. In this paper we derive new error bounds for the Nystr{\"{o}}m-approximated DPP and present em-pirical results to corroborate them. We then demonstrate the Nystr{\"{o}}m-approximated DPP by applying it to a motion capture summa-rization task.},
address = {Scottsdale, AZ, USA},
author = {Affandi, R. and Kulesza, A. and Fox, E. B and Taskar, B.},
booktitle = {International Conference on Artificial Intelligence and Statistics},
keywords = {dblp},
pages = {85--98},
title = {{Nystrom Approximation for Large-Scale Determinantal Processes.}},
url = {http://jmlr.org/proceedings/papers/v31/affandi13a.html},
volume = {31},
year = {2013}
}

@article{AvGa13,
abstract = {Consider a finite weighted oriented graph. We study a probability measure on the set of spanning rooted oriented forests on the graph. We prove that the set of roots sampled from this measure is a determinantal process, characterized by a possibly non-symmetric kernel with complex eigenvalues. We then derive several results relating this measure to the Markov process associated with the starting graph, to the spectrum of its generator and to hitting times of subsets of the graph. In particular, the mean hitting time of the set of roots turns out to be independent of the starting point, conditioning or not to a given number of roots. Wilson's algorithm provides a way to sample this measure and, in absence of complex eigenvalues of the generator, we explain how to get samples with a number of roots approximating a prescribed integer. We also exploit the properties of this measure to give some probabilistic insight into the proof of an algebraic result due to Micchelli and Willoughby [13]. Further, we present two different related coalescence and fragmentation processes.},
author = {Avena, L. and Gaudilliere, A.},
journal = {e-prints},
keywords = {05C81,05C85 Keywords,15A15,15A18,60J20,Finite networks,MSC 2010,Wilson's algorithm,coalescence and frag-mentation,determinantal processes,hit-ting times,local equilibria,primary,random partitions,random sets,secondary,spanning forests},
title = {{On some random forests with determinantal roots}},
url = {http://citeseerx.ist.psu.edu/viewdoc/download?doi=10.1.1.740.6173{\&}rep=rep1{\&}type=pdf},
year = {2013}
}

@article{BaHa16,
abstract = {We show that repulsive random variables can yield Monte Carlo methods with faster convergence rates than the typical {\$}N{\^{}}{\{}-1/2{\}}{\$}, where {\$}N{\$} is the number of integrand evaluations. More precisely, we propose stochastic numerical quadratures involving determinantal point processes associated with multivariate orthogonal polynomials, and we obtain root mean square errors that decrease as {\$}N{\^{}}{\{}-(1+1/d)/2{\}}{\$}, where {\$}d{\$} is the dimension of the ambient space. First, we prove a central limit theorem (CLT) for the linear statistics of a class of determinantal point processes, when the reference measure is a product measure supported on a hypercube, which satisfies the Nevai-class regularity condition, a result which may be of independent interest. Next, we introduce a Monte Carlo method based on these determinantal point processes, and prove a CLT with explicit limiting variance for the quadrature error, when the reference measure satisfies a stronger regularity condition. As a corollary, by taking a specific reference measure and using a construction similar to importance sampling, we obtain a general Monte Carlo method, which applies to any measure with continuously derivable density. Loosely speaking, our method can be interpreted as a stochastic counterpart to Gaussian quadrature, which, at the price of some convergence rate, is easily generalizable to any dimension and has a more explicit error term.},
archivePrefix = {arXiv},
arxivId = {1605.00361},
author = {Bardenet, R. and Hardy, A.},
eprint = {1605.00361},
journal = {ArXiv e-prints},
title = {{Monte Carlo with Determinantal Point Processes}},
year = {2016}
}

@ARTICLE{Bor09,
   author = {{Borodin}, A.},
    title = "{Determinantal point processes}",
  journal = {ArXiv e-prints},
archivePrefix = "arXiv",
   eprint = {0911.1153},
 primaryClass = "math.PR",
 keywords = {Mathematics - Probability, Mathematical Physics},
     year = {2009},
    month = {nov},
   adsurl = {http://adsabs.harvard.edu/abs/2009arXiv0911.1153B}
}

@ARTICLE{BoDiFu10,
author = {Borodin, A. and Diaconis, P. and Fulman, J.},
title = "{On adding a list of numbers (and other one-dependent determinantal processes)}",
journal = {ArXiv e-prints},
archivePrefix = "arXiv",
eprint = {0904.3740},
primaryClass = "math.PR",
keywords = {Mathematics - Probability, Mathematics - Combinatorics},
year = {2009},
month = {apr},
adsurl = {http://adsabs.harvard.edu/abs/2009arXiv0904.3740B},
adsnote = {Provided by the SAO/NASA Astrophysics Data System}
}

@ARTICLE{DFL13,
author = {Decreusefond, L. and Flint, I. and Low, K.~C.},
title = "{Perfect Simulation of Determinantal Point Processes}",
journal = {ArXiv e-prints},
archivePrefix = "arXiv",
eprint = {1311.1027},
primaryClass = "math.PR",
keywords = {Mathematics - Probability, Mathematics - Statistics Theory},
year = {2013},
month = {nov},
adsurl = {http://adsabs.harvard.edu/abs/2013arXiv1311.1027D},
adsnote = {Provided by the SAO/NASA Astrophysics Data System}
}

@article{DuEd02,
Author = {Dumitriu, I. and Edelman, A.},
Journal = {Journal of Mathematical Physics},
Number = {11},
Pages = {5830-5847},
Title = {Matrix models for beta ensembles},
Url = {https://sites.math.washington.edu/~dumitriu/JMathPhys_43_5830.pdf},
Volume = {43},
Year = {2002},
}

@ARTICLE{DuEd15,
author = {Dubbs, A. and Edelman, A.},
title = "{Infinite Random Matrix Theory, Tridiagonal Bordered Toeplitz Matrices, and the Moment Problem}",
journal = {ArXiv e-prints},
archivePrefix = "arXiv",
eprint = {1502.04931},
primaryClass = "math.PR",
keywords = {Mathematics - Probability},
year = {2015},
month = {feb},
adsnote = {Provided by the SAO/NASA Astrophysics Data System}
}

@inproceedings{GaBaVa17,
abstract = {Determinantal point processes (DPPs) are distributions over sets of items that model diversity using kernels. Their applications in machine learning include summary extraction and recommendation systems. Yet, the cost of sampling from a DPP is prohibitive in large-scale applications, which has triggered an effort towards efficient approximate samplers. We build a novel MCMC sampler that combines ideas from combinatorial geometry, linear programming, and Monte Carlo methods to sample from DPPs with a fixed sample cardinality, also called projection DPPs. Our sampler leverages the ability of the hit-and-run MCMC kernel to efficiently move across convex bodies. Previous theoretical results yield a fast mixing time of our chain when targeting a distribution that is close to a projection DPP, but not a DPP in general. Our empirical results demonstrate that this extends to sampling projection DPPs, i.e., our sampler is more sample-efficient than previous approaches which in turn translates to faster convergence when dealing with costly-to-evaluate functions, such as summary extraction in our experiments.},
address = {Sydney, Australia},
archivePrefix = {arXiv},
arxivId = {1705.10498},
author = {Gautier, G. and Bardenet, R. and Valko, M.},
booktitle = {International Conference on Machine Learning},
editor = {Precup, Doina and Teh, Yee Whye},
eprint = {1705.10498},
pages = {1223--1232},
publisher = {PMLR},
title = {{Zonotope hit-and-run for efficient sampling from projection DPPs}},
url = {http://proceedings.mlr.press/v70/gautier17a/gautier17a.pdf},
year = {2017}
}

@article{Gil14,
Author = {Gillenwater, J.},
Journal = {Publicly Accessible Penn Dissertations. 1285.},
Title = {{Approximate inference for determinantal point processes}},
url = {https://repository.upenn.edu/edissertations/1285},
Year = {2014}}

@article{HKPV06,
Author = {Hough, J. B. and Krishnapur, M. and Peres, Y. and Virag, B.},
Journal = {Probability surveys},
Title = {{Determinantal processes and independence}},
arxivId = {0503110},
url = {http://arxiv.org/abs/0503110},
Year = {2006}}

@article{KiNe04,
Author = {Killip, R. and Nenciu, I.},
Doi = {10.1155/S1073792804141597},
Journal = {International Mathematics Research Notices},
Number = {50},
Pages = {2665-2701},
Title = {Matrix models for circular ensembles},
Url = {+ http://dx.doi.org/10.1155/S1073792804141597},
Volume = {2004},
Year = {2004}
}

@article{LaGaDe18,
author = {Launay, C. and Galerne, B. and Desolneux, A.},
title = "{Exact Sampling of Determinantal Point Processes without Eigendecomposition}",
journal = {ArXiv e-prints},
archivePrefix = "arXiv",
eprint = {1802.08429},
primaryClass = "stat.ML",
keywords = {Statistics - Machine Learning},
year = {2018},
month = {feb},
adsurl = {http://adsabs.harvard.edu/abs/2018arXiv180208429L},
adsnote = {Provided by the SAO/NASA Astrophysics Data System}
}

@article{KuTa12,
abstract = {Determinantal point processes (DPPs) are elegant probabilistic models of repulsion that arise in quantum physics and random matrix theory. In contrast to traditional structured models like Markov random fields, which become intractable and hard to approximate in the presence of negative correlations, DPPs offer efficient and exact algorithms for sampling, marginalization, conditioning, and other inference tasks. We provide a gentle introduction to DPPs, focusing on the intuitions, algorithms, and extensions that are most relevant to the machine learning community, and show how DPPs can be applied to real-world applications like finding diverse sets of high-quality search results, building informative summaries by selecting diverse sentences from documents, modeling non-overlapping human poses in images or video, and automatically building timelines of important news stories.},
annote = {NULL},
archivePrefix = {arXiv},
arxivId = {1207.6083},
author = {Kulesza, A. and Taskar, B.},
doi = {10.1561/2200000044},
eprint = {1207.6083},
issn = {1935-8237},
journal = {Foundations and Trends in Machine Learning},
month = {jul},
number = {2-3},
pages = {123--286},
title = {{Determinantal Point Processes for Machine Learning}},
volume = {5},
year = {2012}
}

@article{Joh06,
Abstract = {We survey recent results on determinantal processes, random growth, random tilings and their relation to random matrix theory.},
Archiveprefix = {arXiv},
Arxivid = {math-ph/0510038},
Author = {Johansson, K.},
Doi = {10.1016/S0924-8099(06)80038-7},
Eprint = {0510038},
File = {:Users/ggautier/Library/Application Support/Mendeley Desktop/Downloaded/Johansson - 2006 - Course 1 Random matrices and determinantal processes.pdf:pdf},
Issn = {09248099},
Journal = {Les Houches Summer School Proceedings},
Number = {C},
Pages = {1--56},
Primaryclass = {math-ph},
Title = {{Course 1 Random matrices and determinantal processes}},
Volume = {83},
Year = {2006}
}

@article{Kon05,
author = {Konig, W.},
doi = {10.1214/154957805100000177},
fjournal = {Probability Surveys},
journal = {Probab. Surveys},
pages = {385--447},
publisher = {The Institute of Mathematical Statistics and the Bernoulli Society},
title = {Orthogonal polynomial ensembles in probability theory},
url = {https://doi.org/10.1214/154957805100000177},
volume = {2},
year = {2005}
}

@article{LaMoRu15,
abstract = {Statistical models and methods for determinantal point processes (DPPs) seem largely unexplored. We demonstrate that DPPs provide useful models for the description of spatial point pattern datasets where nearby points repel each other. Such data are usually modelled by Gibbs point processes, where the likelihood and moment expressions are intractable and simulations are time consuming. We exploit the appealing probabilistic properties of DPPs to develop parametric models, where the likelihood and moment expressions can be easily evaluated and realizations can be quickly simulated. We discuss how statistical inference is conducted using the likelihood or moment properties of DPP models, and we provide freely available software for simulation and statistical inference.},
archivePrefix = {arXiv},
arxivId = {1205.4818},
author = {Lavancier, F. and Moller, K. and Rubak, E.},
doi = {10.1111/rssb.12096},
eprint = {1205.4818},
issn = {14679868},
journal = {Journal of the Royal Statistical Society. Series B: Statistical Methodology},
keywords = {Maximum-likelihood-based inference,Point process density,Product densities,Repulsiveness,Simulation,Spectral approach},
number = {4},
pages = {853--877},
title = {{Determinantal point process models and statistical inference}},
volume = {77},
year = {2015}
}
@inproceedings{LiJeSr17,
abstract = {We study dual volume sampling, a method for selecting k columns from an n*m short and wide matrix (n {\textless}= k {\textless}= m) such that the probability of selection is proportional to the volume of the parallelepiped spanned by the rows of the induced submatrix. This method was studied in [3], who motivated it as a promising method for column subset selection. However, the development of polynomial time sampling algorithms -- exact or approximate -- has been since open. We close this open problem by presenting (i) an exact (randomized) polynomial time sampling algorithm; (ii) its derandomization that samples subsets satisfying the desired properties deterministically; and (iii) an efficient approximate sampling procedure using Markov chains that are provably fast mixing. Our algorithms can thus benefit downstream applications of dual volume sampling, such as column subset selection and experimental design.},
address = {Long Beach, CA, USA},
annote = {NULL},
archivePrefix = {arXiv},
arxivId = {1703.02674},
author = {Li, C. and Jegelka, S. and Sra, S.},
booktitle = {Neural Information Processing Systems},
eprint = {1703.02674},
month = {mar},
title = {{Column Subset Selection via Polynomial Time Dual Volume Sampling}},
year = {2017}
}
@inproceedings{LiJeSr16a,
abstract = {Determinantal Point Processes (DPPs) provide probabilistic models over finite sets of items that help model repulsion and diversity. Applicability of DPPs to large sets of data is, however, hindered by the expensive matrix operations involved, especially when sampling. We therefore propose a new efficient approximate two-stage sampling algorithm for finite k-DPPs. As opposed to previous approximations, our algorithm aims at minimizing the variational distance to the original distribution. Experiments indicate that the resulting sampling algorithm works well on large data and yields more accurate samples than previous approaches.},
address = {Cadiz, Spain},
archivePrefix = {arXiv},
arxivId = {1509.01618},
author = {Li, C. and Jegelka, S. and Sra, S.},
booktitle = {International Conference on Artificial Intelligence and Statistics},
eprint = {1509.01618},
pages = {1--14},
title = {{Efficient Sampling for k-Determinantal Point Processes}},
url = {http://proceedings.mlr.press/v51/li16f.pdf},
volume = {51},
year = {2016}
}
@inproceedings{LiJeSr16b,
abstract = {The Nystr{\"{o}}m method has long been popular for scaling up kernel methods. Its theoretical guarantees and empirical performance rely critically on the quality of the landmarks selected. We study landmark selection for Nystr{\"{o}}om using Determinantal Point Processes (DPPs), finite probability models that allow tractable generation of diverse samples. We prove that landmarks selected via DPPs guarantee bounds on approximation errors; subsequently, we analyze implications for kernel ridge regression. Contrary to prior reservations due to cubic complexity of DPPsampling, we show that (under certain conditions) Markov chain DPP sampling requires only linear time in the size of the data. We present several empirical results that support our theoretical analysis, and demonstrate the superior performance of DPP-based landmark selection compared with existing approaches.},
address = {New York, USA},
archivePrefix = {arXiv},
arxivId = {1603.06052},
author = {Li, C. and Jegelka, S. and Sra, S.},
booktitle = {International Conference on Machine Learning},
eprint = {1603.06052},
isbn = {9781510829008},
pages = {2061--2070},
title = {{Fast DPP Sampling for Nystr{\"{o}}om with Application to Kernel Methods}},
url = {http://proceedings.mlr.press/v48/lih16.html},
volume = {48},
year = {2016}
}
@inproceedings{LiJeSr16c,
abstract = {We study probability measures induced by set functions with constraints. Such measures arise in a variety of real-world settings, where prior knowledge, resource limitations, or other pragmatic considerations impose constraints. We consider the task of rapidly sampling from such constrained measures, and develop fast Markov chain samplers for them. Our first main result is for MCMC sampling from Strongly Rayleigh (SR) measures, for which we present sharp polynomial bounds on the mixing time. As a corollary, this result yields a fast mixing sampler for Determinantal Point Processes (DPPs), yielding (to our knowledge) the first provably fast MCMC sampler for DPPs since their inception over four decades ago. Beyond SR measures, we develop MCMC samplers for probabilistic models with hard constraints and identify sufficient conditions under which their chains mix rapidly. We illustrate our claims by empirically verifying the dependence of mixing times on the key factors governing our theoretical bounds.},
address = {Barcelona, Spain},
annote = {NULL},
archivePrefix = {arXiv},
arxivId = {1608.01008},
author = {Li, C. and Jegelka, S. and Sra, S.},
booktitle = {Neural Information Processing Systems},
eprint = {1608.01008},
issn = {10495258},
number = {2},
title = {{Fast Mixing Markov Chains for Strongly Rayleigh Measures, DPPs, and Constrained Sampling}},
url = {https://papers.nips.cc/paper/6182-fast-mixing-markov-chains-for-strongly-rayleigh-measures-dpps-and-constrained-sampling},
year = {2016}
}
@article{LiJeSr16d,
abstract = {In this note we consider sampling from (non-homogeneous) strongly Rayleigh probability measures. As an important corollary, we obtain a fast mixing Markov Chain sampler for Determinantal Point Processes.},
archivePrefix = {arXiv},
arxivId = {1607.03559},
author = {Li, C. and Jegelka, S. and Sra, S.},
eprint = {1607.03559},
journal = {ArXiv e-prints},
title = {Fast Sampling for Strongly Rayleigh Measures with Application to Determinantal Point Processes},
year = {2016}
}

@article{Mac75,
Abstract = {The structure of the probability space associated with a general point process, when regarded as a counting process, is reviewed using the coincidence formalism. The rest of the paper is devoted to the class of regular point processes for which all coincidence probabilities admit densities. It is shown that their distribution is completely specified by the system of coincidence densities. The specification formalism is stressed for 'completely' regular point processes. A construction theorem gives a characterization of the system of coincidence densities of such a process. It permits the study of most models of point processes. New results on the photon process, a particular type of conditioned Poisson process, are derived. New examples are exhibited, including the Gauss-Poisson process and the 'fermion' process that is suitable whenever the points are repulsive.},
Author = {Macchi, O.},
Issn = {00018678},
Journal = {Advances in Applied Probability},
Number = {1},
Pages = {83-122},
Publisher = {Applied Probability Trust},
Title = {The Coincidence Approach to Stochastic Point Processes},
Url = {http://www.jstor.org/stable/1425855},
Volume = {7},
Year = {1975}
}

@article{Mez06,
author = {Mezzadri, F.},
title = "{How to generate random matrices from the classical compact groups}",
journal = {ArXiv Mathematical Physics e-prints},
eprint = {math-ph/0609050},
keywords = {Mathematical Physics, Mathematics - Numerical Analysis, 1502,15A52, 65F25},
year = {2006},
month = {sep},
adsurl = {http://adsabs.harvard.edu/abs/2006math.ph...9050M},
adsnote = {Provided by the SAO/NASA Astrophysics Data System}
}

@book{MoWa04,
Abstract = {Spatial point processes play a fundamental role in spatial statistics and today they are an active area of research with many new applications. Although other published works address different aspects of spatial point processes, most of the classical literature deals only with nonparametric methods, and a thorough treatment of the theory and applications of simulation-based inference is difficult to find. Written by researchers at the top of the field, this book collects and unifies recent theoretical advances and examples of applications. The authors examine Markov chain Monte Carlo algorithms and explore one of the most important recent developments in MCMC: perfect simulation procedures.},
Author = {Moller, J. and Waagepetersen, R. R.},
Doi = {10.1201/9780203496930},
File = {:Users/ggautier/Documents/Mendeley Desktop/M{\o}ller, Waagepetersen - 2004 - Statistical inference and simulation for spatial point processes.pdf:pdf},
Isbn = {1584882654},
Issn = {0277-6715},
Keywords = {point processes,spatial analysis (Statistics)},
Pages = {320},
Title = {{Statistical inference and simulation for spatial point processes}},
Volume = {23},
publisher = {CHAPMAN & HALL/CRC},
Year = {2004}
}

@article{Sos00,
Abstract = {This paper contains an exposition of both recent and rather old results on determinantal random point fields. We begin with some general theorems includ- ing proofs of necessary and sufficient conditions for the existence of a determinantal random point field with Hermitian kernel and of a criterion for weak convergence of its distribution. In the second section we proceed with examples of determinantal random fields in quantum mechanics, statistical mechanics, random matrix theory, probability theory, representation theory, and ergodic theory. In connection with the theory of renewal processes, we characterize all Hermitian determinantal random point fields on R1 and Z1 with independent identically distributed spacings. In the third section we study translation-invariant determinantal random point fields and prove the mixing property for arbitrary multiplicity and the absolute continuity of the spectra. In the last section we discuss proofs of the central limit theorem for the number of particles in a growing box and of the functional central limit theorem for the empirical distribution function of spacings.},
Archiveprefix = {arXiv},
Arxivid = {math/0002099v4},
Author = {Soshnikov, A.},
Doi = {10.1070/RM2000v055n05ABEH000321},
Eprint = {math/0002099v4},
Issn = {0042-1316},
Journal = {Russian Mathematical Surveys},
Number = {5},
Pages = {923--975},
Primaryclass = {math},
Title = {{Determinantal random point fields}},
Volume = {55},
Year = {2000}
}

@article{TrAmBa17a,
abstract = {We present a new random sampling strategy for k-bandlimited signals defined on graphs, based on determinantal point processes (DPP). For small graphs, ie, in cases where the spectrum of the graph is accessible, we exhibit a DPP sampling scheme that enables perfect recovery of bandlimited signals. For large graphs, ie, in cases where the graph's spectrum is not accessible, we investigate, both theoretically and empirically, a sub-optimal but much faster DPP based on loop-erased random walks on the graph. Preliminary experiments show promising results especially in cases where the number of measurements should stay as small as possible and for graphs that have a strong community structure. Our sampling scheme is efficient and can be applied to graphs with up to {\$}10{\^{}}6{\$} nodes.},
archivePrefix = {arXiv},
arxivId = {1703.01594},
author = {Tremblay, N. and Amblard, P. O. and Barthelme, S.},
eprint = {1703.01594},
journal = {ArXiv e-prints},
title = {{Graph sampling with determinantal processes}},
year = {2017}
}

@inproceedings{TrBaAm17b,
abstract = {R{\'e}sum{\'e} – Nous consid{\'e}rons l echantillonnage de signaux sur graph{\`e} a bande limit{\'e}e k , i . e . , les combinaisons lin{\'e}aires des k premiers modes de Fourier du graphe . Il existe k noeuds du graphe qui permettent leur reconstruction parfaite , les trouver n{\'e}cessite cependant une diagonalisation partielle de la matrice laplacienne , trop co{\^{u}}teus{\`e} a grande dimension . Nous proposons une nouvelle m{\'e}thode rapide d echantillonnage bas{\'e}e sur des processus d{\'e}terminantaux qui permet la reconstructio a partir d ' un nombre d echantillons de l ' ordre de k . Abstract – We consider the problem of sampling k - bandlimited graph signals , i . e . , linear combinations of the first k graph Fourier modes . We know that a set of k nodes embedding all k - bandlimited signals always exists , thereby enabling their perfect reconstruction after sampling . Unfortunately , to exhibit such a set , one needs to partially diagonalize the graph Laplacian , which becomes prohibitive at large scale . We propose a novel strategy based on determinantal point processes that side - steps partial diagonalisation and enables reconstruction with only O (k) samples .},
archivePrefix = {arXiv},
arxivId = {1704.02239},
author = {Tremblay, N. and Barthelme, S. and Amblard, P. O.},
booktitle = {GRETSI},
eprint = {1704.02239},
title = {{{\'{E}}chantillonnage de signaux sur graphes via des processus d{\'e}terminantaux}},
url = {https://hal.archives-ouvertes.fr/hal-01503736},
year = {2017}
}
@ARTICLE{TrBaAm18,
author = {Tremblay, N. and Barthelme, S. and Amblard, P. O.},
title = "{Optimized Algorithms to Sample Determinantal Point Processes}",
journal = {ArXiv e-prints},
archivePrefix = "arXiv",
eprint = {1802.08471},
primaryClass = "stat.CO",
keywords = {Statistics - Computation, Computer Science - Learning, Statistics - Machine Learning},
year = {2018},
month = {feb},
adsurl = {http://adsabs.harvard.edu/abs/2018arXiv180208471T},
adsnote = {Provided by the SAO/NASA Astrophysics Data System}
}

@article{Wig67,
author = {Wigner, E.},
title = {Random Matrices in Physics},
journal = {SIAM Review},
volume = {9},
number = {1},
pages = {1--23},
year = {1967},
doi = {10.1137/1009001},
URL = {https://doi.org/10.1137/1009001},
eprint = {https://doi.org/10.1137/1009001}
}

repository: ttaburet/DPPy

repo_name: ttaburet/DPPy


text:
@article{mejia2022arrayed,
  title={An Arrayed Transposon Library of \emph{Ruegeria pomeroyi} {DSS-3}},
  author={Mejia, Catalina and Trujillo Rodriguez, Lidimarie and Poudel, Ravin and Ellington, Adam and Rivers, Adam R and Reisch, Christopher},
  journal={bioRxiv},
  pages={2022--09},
  year={2022},
  publisher={Cold Spring Harbor Laboratory}
}

@article{coatsworth2022intrinsic,
  title={Intrinsic variation in the vertically transmitted core virome of the mosquito \emph{Aedes aegypti}},
  author={Coatsworth, Heather and Bozic, Jovana and Carrillo, Juliana and Buckner, Eva A and Rivers, Adam R and Dinglasan, Rhoel R and Mathias, Derrick K},
  journal={Molecular Ecology},
  volume={31},
  number={9},
  pages={2545--2561},
  year={2022}
}

@article{vaughn2022graph,
  title={Graph-based pangenomics maximizes genotyping density and reveals structural impacts on fungal resistance in melon},
  author={Vaughn, Justin N and Branham, Sandra E and Abernathy, Brian and Hulse-Kemp, Amanda M and Rivers, Adam R and Levi, Amnon and Wechter, William P},
  journal={Nature Communications},
  volume={13},
  number={1},
  pages={7897},
  year={2022},
  publisher={Nature Publishing Group UK London}
}

@article{valles2023rna,
  title={{RNA} virus discoveries in the electric ant, \emph{Wasmannia auropunctata}},
  author={Valles, Steven M and Zhao, Chaoyang and Rivers, Adam R and Iwata, Ryo L and Oi, David H and Cha, Dong H and Collignon, R Max and Cox, Nastassja A and Morton, Gary J and Calcaterra, Luis A},
  journal={Virus Genes},
  pages={1--14},
  year={2023},
  publisher={Springer US New York}
}

@article{poudel2022guidemaker,
  title={GuideMaker: Software to design CRISPR-Cas guide {RNA} pools in non-model genomes},
  author={Poudel, Ravin and Rodriguez, Lidimarie Trujillo and Reisch, Christopher R and Rivers, Adam R},
  journal={GigaScience},
  volume={11},
  year={2022},
  publisher={Oxford Academic}
}

@article{guard2021homopolymer,
  title={AT Homopolymer Strings in \emph{Salmonella enterica} Subspecies I Contribute to Speciation and Serovar Diversity},
  author={Guard, Jean and Rivers, Adam R and Vaughn, Justin N and Rothrock, Michael J and Oladeinde, Adelumola H and Shah, Devendra H},
  journal={Microorganisms},
  volume={9},
  number={10},
  pages={2075},
  year={2021},
  publisher={Multidisciplinary Digital Publishing Institute}
}

@article{foxx2021advancing,
  title={Advancing equity and inclusion in microbiome research and training},
  author={Foxx, Alicia J and Franco Mel{\'e}ndez, Karla P and Hariharan, Janani and Kozik, Ariangela J and Wattenburger, Cassandra J and Godoy-Vitorino, Filipa and Rivers, Adam R},
  journal={Msystems},
  volume={6},
  number={5},
  pages={e01151--21},
  year={2021},
  publisher={American Society for Microbiology 1752 N St., NW, Washington, DC}
}

@article{rivers2022gross,
  title={Gross Morphology of Diseased Tissues in \emph{Nezara viridula} (Hemiptera: Pentatomidae) and Molecular Characterization of an Associated {Microsporidian}},
  author={Rivers, Adam R and Grodowitz, Michael J and Miles, Godfrey P and Allen, Margaret L and Elliott, Brad and Weaver, Mark and Bon, Marie-Claude and Rojas, M Guadalupe and Morales-Ramos, Juan},
  journal={Journal of Insect Science},
  volume={22},
  number={2},
  pages={4},
  year={2022},
  publisher={Oxford University Press US}
}
@article{Poudel2021,
abstract = {Background CRISPR-Cas systems have expanded the possibilities for gene editing in bacteria and eukaryotes. There are many excellent tools for designing the CRISPR-Cas guide RNAs for model organisms with standard Cas enzymes. GuideMaker is intended as a fast and easy-to-use design tool for atypical projects with 1) non-standard Cas enzymes, 2) non-model organisms, or 3) projects that need to design a panel of guide RNAs (gRNA) for genome-wide screens.
Findings GuideMaker can rapidly design gRNAs for gene targets across the genome from a degenerate protospacer adjacent motif (PAM) and a GenBank file. The tool applies Hierarchical Navigable Small World (HNSW) graphs to speed up the comparison of guide RNAs. This allows the user to design gRNAs targeting all genes in a typical bacterial genome in about 1-2 minutes.
Conclusions Guidemaker enables the rapid design of genome-wide gRNA for any CRISPR-Cas enzyme in non-model organisms. While GuideMaker is designed with prokaryotic genomes in mind, it can efficiently process smaller eukaryotic genomes as well. GuideMaker is available as command-line software, a stand-alone web application, and a tool in the CyCverse Discovery Environment. All versions are available under a Creative Commons CC0 1.0 Universal Public Domain Dedication.},
author = {Poudel, Ravin and Rodriguez, Lidimarie Trujillo and Reisch, Christopher R. and Rivers, Adam R.},
doi = {10.1101/2021.06.28.450164},
file = {:Users/rivers/Library/Application Support/Mendeley Desktop/Downloaded/Poudel et al. - 2021 - GuideMaker Software to design CRISPR-Cas guide RNA pools in non-model genomes.pdf:pdf},
journal = {bioRxiv},
month = {jun},
pages = {2021.06.28.450164},
publisher = {Cold Spring Harbor Laboratory},
title = {{GuideMaker: Software to design CRISPR-Cas guide RNA pools in non-model genomes}},
url = {https://www.biorxiv.org/content/10.1101/2021.06.28.450164v1 https://www.biorxiv.org/content/10.1101/2021.06.28.450164v1.abstract},
year = {2021}
}
@article{Guard2021,
abstract = {Adenine and thymine homopolymer strings of at least 8 nucleotides (AT 8+mers) were characterized in \emph{Salmonella enterica} subspecies I and other Eubacteria. Incidence of the motif differed between Eubacteria but not between Salmonella enterica serotypes. Of 481 AT 8+mers loci in serovars Typhimurium, Enteritidis, and Gallinarum, 35 (12.3\%) had mutations. We propose that the AT 8+mer motif identifies genomes with optimal gene content and provides self-recognition that facilitates efficient genome repair. A theory that genome regeneration accounts for both serovar diversity and persistence of predominant Salmonella serovars associated provides a new framework for investigating root causes of foodborne illness.},
author = {Guard, Jean and Rivers, Adam R and Vaughn, Justin N and {Michael J Rothrock}, Jr and Oladeinde, Adelumola and Shah, Devendra H},
doi = {10.20944/PREPRINTS202106.0384.V1},
file = {:Users/rivers/Library/Application Support/Mendeley Desktop/Downloaded/Guard et al. - 2021 - AT Homopolymer Strings as a Motif for Self-Recognition and Repair of Genomes in Salmonella enterica Subspecies I.pdf:pdf},
keywords = {Salmonella enterica,food safety,genome,recombination,serotype,single nucleotide polymorphisms,theory},
journal = {Preprints},
month = {jun},
publisher = {Preprints},
title = {{AT Homopolymer Strings as a Motif for Self-Recognition and Repair of Genomes in \emph{Salmonella enterica} Subspecies I}},
url = {https://www.preprints.org/manuscript/202106.0384/v1},
year = {2021}
}

@article{Fernandezbaca2021a,
	title        = {{Rice plant-soil microbiome interactions driven by root and shoot biomass}},
	author       = {Fernandez-baca, Cristina P. and Rivers, Adam R. and Maul, Jude E. and Kim, Woojae and Poudel, Ravin and McClung, Anna M. and Roberts, Daniel P. and Reddy, Vangimalla R. and Barnaby, Jinyoung Y.},
	year         = 2021,
	month        = mar,
	journal      = {Diversity},
	publisher    = {MDPI AG},
	volume       = 13,
	number       = 3,
	pages        = 125,
	doi          = {10.3390/d13030125},
	issn         = 14242818,
	url          = {https://doi.org/10.3390/d13030125},
	abstract     = {Plant?soil microbe interactions are complex and affected by many factors including soil type, edaphic conditions, plant genotype and phenotype, and developmental stage. The rice rhizo-sphere microbial community composition of nine recombinant inbred lines (RILs) and their parents, Francis and Rondo, segregating for root and shoot biomass, was determined using metagenomic sequencing as a means to examine how biomass phenotype influences the rhizosphere community. Two plant developmental stages were studied, heading and physiological maturity, based on root and shoot biomass growth patterns across the selected genotypes. We used partial least squares (PLS) regression analysis to examine plant trait?driven microbial populations and identify microbial species, functions, and genes corresponding to root and shoot biomass as well as developmental stage patterns. Species identified correlated with increases in either root or shoot biomass were widely present in soil and included species involved in nitrogen cycling (Anaeromyxobacter spp.) and methane production (Methanocella avoryzae), as well as known endophytes (Bradyrhizobium spp.). Additionally, PLS analysis allowed us to explore the relationship of developmental stage with species, microbial functions, and genes. Many of the community functions and genes observed during the heading stage were representative of cell growth (e.g., carbohydrate and nitrogen metabo-lism), while functions correlated with physiological maturity were indicative of cell decay. These results are consistent with the hypothesis that microbial communities exist whose metabolic and gene functions correspond to plant biomass traits.},
	keywords     = {Heading and physiological maturity stage,Partial Least Squares (PLS) regression analysis,Recombinant inbred lines,Rhizosphere microbiome,Rice,Root and shoot biomass,Shotgun metagenomic sequencing}
}
@article{Fernandezbaca2021b,
	title        = {{Changes in rhizosphere soil microbial communities across plant developmental stages of high and low methane emitting rice genotypes}},
	author       = {Fernandez-Baca, Cristina P. and Rivers, Adam R. and Kim, Woojae and Iwata, Ryo and McClung, Anna M. and Roberts, Daniel P. and Reddy, Vangimalla R. and Barnaby, Jinyoung Y.},
	year         = 2021,
	month        = may,
	journal      = {Soil Biology and Biochemistry},
	publisher    = {Elsevier Ltd},
	volume       = 156,
	pages        = 108233,
	doi          = {10.1016/j.soilbio.2021.108233},
	issn         = {00380717},
	abstract     = {Rice production is an important source of methane accounting for 11\% of global anthropogenic emissions. Methane emissions can be effectively reduced by management practices and cultivar selection. However, whether cultivars lower methane emissions primarily through mediating whole microbial community shifts or through more targeted interactions with methane-cycling microbes is not understood. Here, we sequenced the soil metagenomes associated with two rice recombinant inbred lines (RILs) along with their parents, Francis and Rondo, displaying a range of low to high methane emitting phenotypes. Methane emissions and rhizosphere soil microbial communities were sampled at booting, heading, grain fill, and maturity growth stages to evaluate how plant development impacted rhizosphere communities. Methane emissions were low at booting and increased during heading and grain fill stages where peak methane emissions were observed and returned to basal levels at maturity. In response to genotype and plant developmental stage, we observed changes in rhizosphere microbial community structure in several methanogenic archaea as well as bacterial methane oxidizers and sulfur cyclers. Rice genotype played a larger role in influencing the soil microbial community structure during the reproductive phases of booting and heading as compared to the ripening phases (grain fill and maturity). Francis showed lower methane emissions and relative abundance of methanogen populations during the heading stage where methane emissions were highest for the other genotypes. This indicated that the reduced methane emissions trait was associated with small changes in the composition of methanogens rather than wholesale community shifts. This finding suggests future breeding efforts can focus on reducing methane emissions during high methane emitting phases (i.e., reproductive phases) by selecting genotypes that have lower methanogen populations and higher methanotroph populations during these developmental stages.},
	keywords     = {Methane,Methanogens,Methanotrophs,Rhizosphere,Rice}
}
@article{Smith2019,
	title        = {{Genomic signatures for sedimentary microbial utilization of phytoplankton detritus in a fast-flowing estuary}},
	author       = {Smith, Maria W. and Herfort, Lydie and Rivers, Adam R. and Simon, Holly M.},
	year         = 2019,
	journal      = {Frontiers in Microbiology},
	volume       = 10,
	pages        = 2475,
	doi          = {10.3389/fmicb.2019.02475}
}
@article{Paez-Espino2017,
	title        = {{IMG/VR: A database of cultured and uncultured DNA viruses and retroviruses}},
	author       = {Paez-Espino, David and Chen, I. Min A. and Palaniappan, Krishna and Ratner, Anna and Chu, Ken and Szeto, Ernest and Pillay, Manoj and Huang, Jinghua and Markowitz, Victor M. and Nielsen, Torben and Huntemann, Marcel and Reddy, T. B.K. and Pavlopoulos, Georgios A. and Sullivan, Matthew B. and Campbell, Barbara J. and Chen, Feng and McMahon, Katherine and Hallam, Steve J. and Denef, Vincent and Cavicchioli, Ricardo and Caffrey, Sean M. and Streit, Wolfgang R. and Webster, John and Handley, Kim M. and Salekdeh, Ghasem H. and Tsesmetzis, Nicolas and Setubal, Joao C. and Pope, Phillip B. and Liu, Wen Tso and Rivers, Adam R. and Ivanova, Natalia N. and Kyrpides, Nikos C.},
	year         = 2017,
	month        = jan,
	journal      = {Nucleic Acids Research},
	publisher    = {Oxford University Press},
	volume       = 45,
	number       = {D1},
	pages        = {D457--D465},
	doi          = {10.1093/nar/gkw1030},
	issn         = 13624962,
	abstract     = {Viruses represent the most abundant life forms on the planet. Recent experimental and computational improvements have led to a dramatic increase in the number of viral genome sequences identified primarily from metagenomic samples. As a result of the expanding catalog of metagenomic viral sequences, there exists a need for a comprehensive computational platform integrating all these sequences with associated metadata and analytical tools. Here we present IMG/VR (https://img.jgi.doe.gov/vr/), the largest publicly available database of 3908 isolate reference DNA viruses with 264 413 computationally identified viral contigs from {\textgreater}6000 ecologically diverse metagenomic samples. Approximately half of the viral contigs are grouped into genetically distinct quasi-species clusters. Microbial hosts are predicted for 20 000 viral sequences, revealing nine microbial phyla previously unreported to be infected by viruses. Viral sequences can be queried using a variety of associated metadata, including habitat type and geographic location of the samples, or taxonomic classification according to hallmark viral genes. IMG/VR has a user-friendly interface that allows users to interrogate all integrated data and interact by comparingwith external sequences, thus serving as an essential resource in the viral genomics community.},
	file         = {:Users/rivers/Library/Application Support/Mendeley Desktop/Downloaded/Paez-Espino et al. - 2017 - IMGVR A database of cultured and uncultured DNA viruses and retroviruses(2).pdf:pdf}
}
@article{Lamit2017,
	title        = {{Patterns and drivers of fungal community depth stratification in Sphagnum peat}},
	author       = {Lamit, Louis J. and Romanowicz, Karl J. and Potvin, Lynette R. and Rivers, Adam R. and Singh, Kanwar and Lennon, Jay T. and Tringe, Susannah G. and Kane, Evan S. and Lilleskov, Erik A.},
	year         = 2017,
	month        = jul,
	journal      = {FEMS microbiology ecology},
	volume       = 93,
	number       = 7,
	doi          = {10.1093/femsec/fix082},
	issn         = 15746941,
	abstract     = {Peatlands store an immense pool of soil carbon vulnerable to microbial oxidation due to drought and intentional draining. We used amplicon sequencing and quantitative PCR to (i) examine how fungi are influenced by depth in the peat profile, water table and plant functional group at the onset of a multiyear mesocosm experiment, and (ii) test if fungi are correlated with abiotic variables of peat and pore water. We hypothesized that each factor influenced fungi, but that depth would have the strongest effect early in the experiment. We found that (i) communities were strongly depth stratified; fungi were four times more abundant in the upper (10-20 cm) than the lower (30-40 cm) depth, and dominance shifted from ericoid mycorrhizal fungi to saprotrophs and endophytes with increasing depth; (ii) the influence of plant functional group was depth dependent, with Ericaceae structuring the community in the upper peat only; (iii) water table had minor influences; and (iv) communities strongly covaried with abiotic variables, including indices of peat and pore water carbon quality. Our results highlight the importance of vertical stratification to peatland fungi, and the depth dependency of plant functional group effects, which must be considered when elucidating the role of fungi in peatland carbon dynamics.},
	file         = {:Users/rivers/Library/Application Support/Mendeley Desktop/Downloaded/Lamit et al. - 2017 - Patterns and drivers of fungal community depth stratification in Sphagnum peat(3).pdf:pdf},
	keywords     = {Ericaceae,ericoid mycorrhiza,peat,sedge,soil depth,water table}
}
@article{Bolyen2019,
	title        = {{Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2}},
	author       = {Bolyen, Evan and Rideout, Jai Ram and Dillon, Matthew R. and Bokulich, Nicholas A. and Abnet, Christian C. and Al-Ghalith, Gabriel A. and Alexander, Harriet and Alm, Eric J. and Arumugam, Manimozhiyan and Asnicar, Francesco and Bai, Yang and Bisanz, Jordan E. and Bittinger, Kyle and Brejnrod, Asker and Brislawn, Colin J. and Brown, C. Titus and Callahan, Benjamin J. and Caraballo-Rodr{\'{i}}guez, Andr{\'{e}}s Mauricio and Chase, John and Cope, Emily K. and {Da Silva}, Ricardo and Diener, Christian and Dorrestein, Pieter C. and Douglas, Gavin M. and Durall, Daniel M. and Duvallet, Claire and Edwardson, Christian F. and Ernst, Madeleine and Estaki, Mehrbod and Fouquier, Jennifer and Gauglitz, Julia M. and Gibbons, Sean M. and Gibson, Deanna L. and Gonzalez, Antonio and Gorlick, Kestrel and Guo, Jiarong and Hillmann, Benjamin and Holmes, Susan and Holste, Hannes and Huttenhower, Curtis and Huttley, Gavin A. and Janssen, Stefan and Jarmusch, Alan K. and Jiang, Lingjing and Kaehler, Benjamin D. and Kang, Kyo Bin and Keefe, Christopher R. and Keim, Paul and Kelley, Scott T. and Knights, Dan and Koester, Irina and Kosciolek, Tomasz and Kreps, Jorden and Langille, Morgan G. I. and Lee, Joslynn and Ley, Ruth and Liu, Yong-Xin and Loftfield, Erikka and Lozupone, Catherine and Maher, Massoud and Marotz, Clarisse and Martin, Bryan D. and McDonald, Daniel and McIver, Lauren J. and Melnik, Alexey V. and Metcalf, Jessica L. and Morgan, Sydney C. and Morton, Jamie T. and Naimey, Ahmad Turan and Navas-Molina, Jose A. and Nothias, Louis Felix and Orchanian, Stephanie B. and Pearson, Talima and Peoples, Samuel L. and Petras, Daniel and Preuss, Mary Lai and Pruesse, Elmar and Rasmussen, Lasse Buur and Rivers, Adam and Robeson, Michael S. and Rosenthal, Patrick and Segata, Nicola and Shaffer, Michael and Shiffer, Arron and Sinha, Rashmi and Song, Se Jin and Spear, John R. and Swafford, Austin D. and Thompson, Luke R. and Torres, Pedro J. and Trinh, Pauline and Tripathi, Anupriya and Turnbaugh, Peter J. and Ul-Hasan, Sabah and van der Hooft, Justin J. J. and Vargas, Fernando and V{\'{a}}zquez-Baeza, Yoshiki and Vogtmann, Emily and von Hippel, Max and Walters, William and Wan, Yunhu and Wang, Mingxun and Warren, Jonathan and Weber, Kyle C. and Williamson, Charles H. D. and Willis, Amy D. and Xu, Zhenjiang Zech and Zaneveld, Jesse R. and Zhang, Yilong and Zhu, Qiyun and Knight, Rob and Caporaso, J. Gregory},
	year         = 2019,
	month        = aug,
	journal      = {Nature Biotechnology},
	publisher    = {Nature Publishing Group},
	volume       = 37,
	number       = 8,
	pages        = {852--857},
	doi          = {10.1038/s41587-019-0209-9},
	issn         = {1087-0156},
	url          = {http://www.nature.com/articles/s41587-019-0209-9},
	file         = {:Users/rivers/Library/Application Support/Mendeley Desktop/Downloaded/Bolyen et al. - 2019 - Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2.pdf:pdf},
	keywords     = {Microbiome,Software}
}
@article{Valles2019,
	title        = {{Nine new RNA viruses associated with the fire ant Solenopsis invicta from its native range}},
	author       = {Valles, Steven M. and Rivers, Adam R.},
	year         = 2019,
	month        = jun,
	journal      = {Virus Genes},
	publisher    = {Springer US},
	volume       = 55,
	number       = 3,
	pages        = {368--380},
	doi          = {10.1007/s11262-019-01652-4},
	issn         = {0920-8569},
	url          = {http://link.springer.com/10.1007/s11262-019-01652-4},
	file         = {:Users/rivers/Library/Application Support/Mendeley Desktop/Downloaded/Valles, Rivers - 2019 - Nine new RNA viruses associated with the fire ant Solenopsis invicta from its native range.pdf:pdf}
}
@article{Bowers2017,
	title        = {{Minimum information about a single amplified genome (MISAG) and a metagenome-assembled genome (MIMAG) of bacteria and archaea}},
	author       = {Bowers, Robert M and Kyrpides, Nikos C. and Stepanauskas, Ramunas and Harmon-Smith, Miranda and Doud, Devin and Reddy, T B K and Schulz, Frederik and Jarett, Jessica and Rivers, Adam R and Eloe-Fadrosh, Emiley A. and Tringe, Susannah G and Ivanova, Natalia N and Copeland, Alex and Clum, Alicia and Becraft, Eric D and Malmstrom, Rex R and Birren, Bruce and Podar, Mircea and Bork, Peer and Weinstock, George M and Garrity, George M and Dodsworth, Jeremy a and Yooseph, Shibu and Sutton, Granger and Gl{\"{o}}ckner, Frank O and Gilbert, Jack A. and Nelson, William C and Hallam, Steven J. and Jungbluth, Sean P and Ettema, Thijs J. G. and Tighe, Scott and Konstantinidis, Konstantinos T. and Liu, Wen-Tso and Baker, Brett J and Rattei, Thomas and Eisen, Jonathan A. and Hedlund, Brian P and McMahon, Katherine D and Fierer, Noah and Knight, Rob and Finn, Robert D. and Cochrane, Guy and Karsch-Mizrachi, Ilene and Tyson, Gene W. and Rinke, Christian and Kyrpides, Nikos C. and Schriml, Lynn and Garrity, George M and Hugenholtz, Philip and Sutton, Granger and Yilmaz, Pelin and Meyer, Folker and Gl{\"{o}}ckner, Frank O and Gilbert, Jack A. and Knight, Rob and Finn, Robert D. and Cochrane, Guy and Karsch-Mizrachi, Ilene and Lapidus, Alla and Meyer, Folker and Yilmaz, Pelin and Parks, Donovan H. and Eren, AM M and Schriml, Lynn and Banfield, Jillian F. and Hugenholtz, Philip and Woyke, Tanja and Doud, Devin and Reddy, T B K and Jarett, Jessica and Rivers, Adam R and Eloe-Fadrosh, Emiley A. and Tringe, Susannah G and Ivanova, Natalia N and Copeland, Alex and Clum, Alicia and Becraft, Eric D and Malmstrom, Rex R and Birren, Bruce and Schriml, Lynn and Podar, Mircea and Bork, Peer and Weinstock, George M and Banfield, Jillian F. and Garrity, George M and Hugenholtz, Philip and Parks, Donovan H. and Tyson, Gene W. and Rinke, Christian and Dodsworth, Jeremy a and Yooseph, Shibu and Sutton, Granger and Yilmaz, Pelin and Glockner, Franz Oliver and Meyer, Folker and Gilbert, Jack A. and Nelson, William C and Hallam, Steven J. and Jungbluth, Sean P and Ettema, Thijs J. G. and Tighe, Scott and Konstantinidis, Konstantinos T. and Liu, Wen-Tso and Baker, Brett J and Rattei, Thomas and Eisen, Jonathan A. and Hedlund, Brian P and McMahon, Katherine D and Fierer, Noah and Knight, Rob and Finn, Robert D. and Karsch-Mizrachi, Ilene and Eren, AM M and Woyke, Tanja},
	year         = 2017,
	month        = aug,
	journal      = {Nature Biotechnology},
	publisher    = {Nature Research},
	volume       = {in press},
	number       = 8,
	pages        = {725--731},
	doi          = {10.1038/nbt.3893},
	issn         = {1087-0156},
	url          = {http://www.nature.com/doifinder/10.1038/nbt.3893},
	file         = {:Users/rivers/Documents/Paperwork/manuscripts/nbt.3893.pdf:pdf}
}
@article{McIntyre2005,
	title        = {{Individual- and Assemblage-Level Effects of Anthropogenic Sedimentation on Snails in Lake Tanganyika}},
	author       = {Mcintyre, Peter B. and Michel, Ellinor and France, Kristin and Rivers, Adam and Hakizimana, Paul and Cohen, Andrew S},
	year         = 2005,
	journal      = {Conservation Biology},
	volume       = 19,
	number       = 1,
	pages        = 171,
	doi          = {10.1111/j.1523-1739.2005.00456.x},
	isbn         = {0888-8892},
	issn         = {08888892},
	url          = {http://dx.doi.org/10.1111/j.1523-1739.2005.00456.x},
	abstract     = {Human impacts on aquatic biodiversity are often measured at the assemblage or community level, although it has been suggested that individual-level measures are more sensitive. We evaluated the effects of anthropogenic sedimentation on endemics snails in Lake Tanganyika, East Africa, by comparing assemblage-level (i.e., species richness, evennes, and abundance) and individual-level (i.e., frequencies of predation and parasitism, fecal organic content, life history) data between sediment-disturbed and reference sites. Previous studies have indicated that sedimentation kills snails and reduce mollusc diversity in this system, but we found little evidence of changes in species richness, evenness, or snail abundance at the levels of sedimentation recorded. In contrast, individual-level data revealed a variety of differences associated with sedimentation. Frequencies of shell scarring by predatory crabs and castration by parasitic trematodes were significantly lower at disturbed sites, indicating shifts in interspecific interactions. Snails ingested large amounts of inorganic sediments at disturbed sites, suggesting a reduction in food quality. In addition, sedimentation was associated with a large downward shift in size distribution within some species and reproduction at smaller size. These strong patterns in individual-level data contrast with the lack of effects at the assemblage level. We argue that incorporating individual-level measures will often enhance the sensitivity of impact surveys and may reveal effects of disturbance on important interspecific interactions.},
	file         = {:Users/rivers/Library/Application Support/Mendeley Desktop/Downloaded/McIntyre et al. - 2005 - Individual- and Assemblage-Level Effects of Anthropogenic Sedimentation on Snails in Lake Tanganyika.pdf:pdf},
	keywords     = {Lavigeria,Mcintyre2005,crab,life history,parasitism,predation,trematode},
	mendeley-tags = {Mcintyre2005}
}
@article{Teske2009,
	title        = {{A molecular and physiological survey of a diverse collection of hydrothermal vent Thermococcus and Pyrococcus isolates.}},
	author       = {Teske, Andreas and Edgcomb, Virginia and Rivers, Adam R and Thompson, Janelle R and de Alvin, Vera Gomez and Molyneaux, Stephen J and Wirsen, Carl O and {de Vera Gomez}, Alvin and Molyneaux, Stephen J and Wirsen, Carl O},
	year         = 2009,
	month        = nov,
	journal      = {Extremophiles : life under extreme conditions},
	publisher    = {Springer Japan},
	volume       = 13,
	number       = 6,
	pages        = {905--15},
	doi          = {10.1007/s00792-009-0278-7},
	isbn         = {1431-0651},
	issn         = {1433-4909},
	url          = {http://www.ncbi.nlm.nih.gov/pubmed/19763742 http://dx.doi.org/10.1007/s00792-009-0278-7},
	abstract     = {Strains of hyperthermophilic anaerobic hydrothermal vent archaea maintained in the culture collection assembled by Holger Jannasch at the Woods Hole Oceanographic Institution between 1984 and 1998 were identified and partially characterized by Denaturing Gradient Gel Electrophoresis, 16S rRNA gene sequencing, and by growth tests at different temperatures and on different organic carbon and nitrogen sources. All strains were members of the genera Thermococcus and Pyrococcus. The greatest phylogenetic diversity was found in strains from a single Guaymas Basin core isolated by serial dilution from four different depth horizons of heated sediment incubated at the corresponding in situ temperatures. In contrast, geographically distinct vent locations and sample materials yielded a lower diversity of isolates when enriched under uniform temperature regimes and without prior dilution of the source material.},
	file         = {:Users/rivers/Library/Application Support/Mendeley Desktop/Downloaded/Teske et al. - 2009 - A molecular and physiological survey of a diverse collection of hydrothermal vent Thermococcus and Pyrococcus isol.pdf:pdf},
	keywords     = {16S,16S: genetics,Bacterial,Bacterial: genetics,Bacteriological Techniques,Biomedical and Life Sciences,Culture Media,DNA,Geologic Sediments,Geologic Sediments: microbiology,Hot Springs,Hot Springs: microbiology,Marine Biology,Mexico,Molecular Sequence Data,Phylogeny,Pyrococcus,Pyrococcus: classification,Pyrococcus: genetics,Pyrococcus: growth {\&} development,Pyrococcus: isolation {\&} purification,Pyrococcus: metabolism,RNA,Ribosomal,Ribotyping,Species Specificity,Temperature,Teske2009,Thermococcus,Thermococcus: classification,Thermococcus: genetics,Thermococcus: growth {\&} development,Thermococcus: isolation {\&} purification,Thermococcus: metabolism},
	mendeley-tags = {Teske2009},
	pmid         = 19763742
}
@article{Rivers2009,
	title        = {{Iron stress genes in marine Synechococcus and the development of a flow cytometric iron stress assay}},
	author       = {Rivers, Adam R and Jakuba, Rachel Wisniewski and Webb, Eric A},
	year         = 2009,
	journal      = {Environmental Microbiology},
	volume       = 11,
	number       = 2,
	pages        = {382--396},
	doi          = {10.1111/j.1462-2920.2008.01778.x},
	isbn         = {1462-2920},
	url          = {http://dx.doi.org/10.1111/j.1462-2920.2008.01778.x},
	abstract     = {Marine Synechococcus are frequently found in environments where iron (Fe) is a limiting nutrient. To understand their capacity to respond to Fe stress, we screened picoplankton genomes and the Global Ocean Survey metagenome for known Fe stress genes. Many open ocean strains of Synechococcus lack most known genes for Fe stress, while coastal and upwelling strains contain many, suggesting that maintaining multiple Fe limitation compensation strategies is not a selective advantage in the open ocean. All genomes contained iron deficiency-induced protein A (IdiA) and its complementary Fe3+ transport proteins. The ubiquity of IdiA was exploited to develop an in situ Fe stress bioassay based on immunolabelling and flow cytometry. As a test of field applicability, we used the assay on natural Synechococcus populations from one station in the Costa Rica Upwelling Dome where total Fe ranged from {\textless}0.08 to 0.14†nM in the upper water column. The bioassay found Fe stress in 5201354{\%} of the population. Based on our findings, we believe that when reactive strains are present this assay can reveal environmental and clade-specific differences in the response of Synechococcus to Fe stress.},
	file         = {:Users/rivers/Library/Application Support/Mendeley Desktop/Downloaded/Rivers, Jakuba, Webb - 2009 - Iron stress genes in marine Synechococcus and the development of a flow cytometric iron stress assay.pdf:pdf},
	keywords     = {Rivers2009},
	mendeley-tags = {Rivers2009}
}
@article{Rivers2018,
	title        = {{ITSxpress: Software to rapidly trim internally transcribed spacer sequences with quality scores for marker gene analysis}},
	author       = {Rivers, Adam R. and Weber, Kyle C. and Gardner, Terrence G. and Liu, Shuang and Armstrong, Shalamar D.},
	year         = 2018,
	month        = sep,
	journal      = {F1000Research},
	volume       = 7,
	pages        = 1418,
	doi          = {10.12688/f1000research.15704.1},
	issn         = {2046-1402},
	url          = {https://f1000research.com/articles/7-1418/v1},
	abstract     = {{\textless}p{\textgreater}The internally transcribed spacer (ITS) region between the small subunit ribosomal RNA gene and large subunit ribosomal RNA gene is a widely used phylogenetic marker for fungi and other taxa. The eukaryotic ITS contains the conserved 5.8S rRNA and is divided into the ITS1 and ITS2 hypervariable regions. These regions are variable in length and are amplified using primers complementary to the conserved regions of their flanking genes. Previous work has shown that removing the conserved regions results in more accurate taxonomic classification. An existing software program, ITSx, is capable of trimming FASTA sequences by matching hidden Markov model profiles to the ends of the conserved genes using the software suite HMMER. ITSxpress was developed to extend this technique from marker gene studies using Operational Taxonomic Units (OTU's) to studies using exact sequence variants; a method used by the software packages Dada2, Deblur, QIIME 2, and Unoise. The sequence variant approach uses the quality scores of each read to identify sequences that are statistically likely to represent real sequences. ITSxpress enables this by processing FASTQ rather than FASTA files. The software also speeds up the trimming of reads by a factor of 14-23 times on a 4-core computer by temporarily clustering highly similar sequences that are common in amplicon data and utilizing optimized parameters for Hmmsearch. ITSxpress is available as a QIIME 2 plugin and a stand-alone application installable from the Python package index, Bioconda, and Github.{\textless}/p{\textgreater}},
	file         = {:Users/rivers/Library/Application Support/Mendeley Desktop/Downloaded/Rivers et al. - 2018 - ITSxpress Software to rapidly trim internally transcribed spacer sequences with quality scores for marker gene an.pdf:pdf},
	keywords     = {Amplicon sequencing,ITS,QIIME,internally transcribed spacer,marker gene sequencing,trimming}
}
@article{Rivers2013,
	title        = {{An online calculator for marine phytoplankton iron culturing experiments}},
	author       = {Rivers, Adam R. and Rose, Andrew L. and Webb, Eric A.},
	year         = 2013,
	month        = aug,
	journal      = {Journal of Phycology},
	volume       = 49,
	number       = 5,
	pages        = {1017--1021},
	doi          = {10.1111/jpy.12107},
	issn         = {00223646},
	url          = {http://doi.wiley.com/10.1111/jpy.12107},
	editor       = {Raven, J.},
	file         = {:Users/rivers/Library/Application Support/Mendeley Desktop/Downloaded/Rivers, Rose, Webb - 2013 - An online calculator for marine phytoplankton iron culturing experiments.pdf:pdf}
}
@article{Moran2013,
	title        = {{Sizing up metatranscriptomics.}},
	shorttitle   = {ISME J},
	author       = {Moran, Mary Ann and Satinsky, Brandon and Gifford, Scott M and Luo, Haiwei and Rivers, Adam and Chan, Leong-Keat and Meng, Jun and Durham, Bryndan P and Shen, Chen and Varaljay, Vanessa A and Smith, Christa B and Yager, Patricia L and Hopkinson, Brian M},
	year         = 2013,
	month        = feb,
	journal      = {The ISME journal},
	publisher    = {International Society for Microbial Ecology},
	volume       = 7,
	number       = 2,
	pages        = {237--43},
	doi          = {10.1038/ismej.2012.94},
	issn         = {1751-7370},
	url          = {http://dx.doi.org/10.1038/ismej.2012.94},
	abstract     = {A typical marine bacterial cell in coastal seawater contains only ∼200 molecules of mRNA, each of which lasts only a few minutes before being degraded. Such a surprisingly small and dynamic cellular mRNA reservoir has important implications for understanding the bacterium's responses to environmental signals, as well as for our ability to measure those responses. In this perspective, we review the available data on transcript dynamics in environmental bacteria, and then consider the consequences of a small and transient mRNA inventory for functional metagenomic studies of microbial communities.},
	file         = {:Users/rivers/Library/Application Support/Mendeley Desktop/Downloaded/Moran et al. - 2013 - Sizing up metatranscriptomics.pdf:pdf},
	keywords     = {Bacteria,Bacteria: genetics,Bacterial Proteins,Bacterial Proteins: analysis,Bacterial Proteins: genetics,Half-Life,Metagenomics,RNA, Bacterial,RNA, Bacterial: analysis,RNA, Bacterial: genetics,RNA, Messenger,RNA, Messenger: analysis,RNA, Messenger: genetics,Seawater,Seawater: microbiology,Transcriptome,Water Microbiology},
	pmid         = 22931831
}
@article{Beier2015,
	title        = {{The transcriptional response of prokaryotes to phytoplankton-derived dissolved organic matter in seawater}},
	author       = {Beier, Sara and Rivers, Adam R. and Moran, Mary Ann and Obernosterer, Ingrid},
	year         = 2015,
	month        = oct,
	journal      = {Environmental Microbiology},
	volume       = 17,
	number       = 10,
	pages        = {3466--3480},
	doi          = {10.1111/1462-2920.12434},
	issn         = 14622912,
	url          = {http://doi.wiley.com/10.1111/1462-2920.12434 http://www.ncbi.nlm.nih.gov/pubmed/24612402},
	abstract     = {To better understand the functional responses in prokaryotes to dissolved organic matter (DOM), we compared the transcriptional pattern of natural prokaryotic communities grown in continuous cultures on seawater amended with phytoplankton-derived DOM. Metatranscriptomic reads were classified taxonomically (by genomic binning) and functionally (using Kyoto Encyclopedia of Genes and Genomes), and the relative gene expression of individual taxa (genome bins) was compared with the total community response. In the first experiment comparing seawater and seawater amended with diatom-derived DOM, metatranscriptomes revealed pronounced differences in pathways involved in carbohydrate and lipid metabolism. In the second experiment comparing seawater amended with cyanobacteria- and diatom-derived DOM, metatranscriptomes had similar functional profiles, likely reflecting more similar DOM regimes in this experimental setup. Among the five most abundant taxa investigated in more detail, two featured pronounced differences in transcript abundance between treatments suggesting that they were specialized in the use of only one of the two DOM regimes. However, these two taxa were less involved in carbohydrate metabolism than others and had few genes that were significantly regulated in response to the DOM source. Our results indicate that both substrate composition and the competitive interplay of community members were decisive for the functional response of a microbial system.},
	file         = {:Users/rivers/Library/Application Support/Mendeley Desktop/Downloaded/Beier et al. - 2015 - The transcriptional response of prokaryotes to phytoplankton-derived dissolved organic matter in seawater.pdf:pdf},
	pmid         = 24612402
}
@article{Rivers2016,
	title        = {{Experimental Identification of Small Non-Coding RNAs in the Model Marine Bacterium Ruegeria pomeroyi DSS-3}},
	author       = {Rivers, Adam R. and Burns, Andrew S. and Chan, Leong-Keat and Moran, Mary Ann},
	year         = 2016,
	month        = mar,
	journal      = {Frontiers in Microbiology},
	publisher    = {Frontiers},
	volume       = 7,
	doi          = {10.3389/fmicb.2016.00380},
	issn         = {1664-302X},
	url          = {http://journal.frontiersin.org/article/10.3389/fmicb.2016.00380/abstract},
	abstract     = {In oligotrophic ocean waters where bacteria are often subjected to chronic nutrient limitation, community transcriptome sequencing has pointed to the presence of highly abundant small RNAs (sRNAs). The role of sRNAs in regulating response to nutrient stress was investigated in a model heterotrophic marine bacterium Ruegeria pomeroyi grown in continuous culture under carbon (C) and nitrogen (N) limitation. RNAseq analysis identified 99 putative sRNAs. Sixty-nine were cis-encoded and located antisense to a presumed target gene. Thirty were trans-encoded and initial target prediction was performed computationally. The most prevalent functional roles of genes anti-sense to the cis-sRNAs were transport, cell-cell interactions, signal transduction, and transcriptional regulation. Most sRNAs were transcribed equally under both C and N limitation, and may be involved in a general stress response. However, 14 were regulated differentially between the C and N treatments and may respond to specific nutrient limitations. A network analysis of the predicted target genes of the R. pomeroyi cis-sRNAs indicated that they average fewer connections than typical protein-encoding genes, and appear to be more important in peripheral or niche-defining functions encoded in the pan genome.},
	file         = {:Users/rivers/Library/Application Support/Mendeley Desktop/Downloaded/Rivers et al. - 2016 - Experimental Identification of Small Non-Coding RNAs in the Model Marine Bacterium Ruegeria pomeroyi DSS-3.pdf:pdf},
	keywords     = {Roseobacter,Ruegeria pomeroyi DSS-3,SRNAs,ncRNAs,small RNAs},
	language     = {English}
}
@article{Rivers2014,
	title        = {{An Updated genome annotation for the model marine bacterium Ruegeria pomeroyi DSS-3.}},
	author       = {Rivers, Adam R and Smith, Christa B and Moran, Mary Ann},
	year         = 2014,
	month        = jan,
	journal      = {Standards in genomic sciences},
	publisher    = {BioMed Central},
	volume       = 9,
	number       = 1,
	pages        = 11,
	doi          = {10.1186/1944-3277-9-11},
	issn         = {1944-3277},
	url          = {http://standardsingenomics.biomedcentral.com/articles/10.1186/1944-3277-9-11},
	abstract     = {When the genome of Ruegeria pomeroyi DSS-3 was published in 2004, it represented the first sequence from a heterotrophic marine bacterium. Over the last ten years, the strain has become a valuable model for understanding the cycling of sulfur and carbon in the ocean. To ensure that this genome remains useful, we have updated 69 genes to incorporate functional annotations based on new experimental data, and improved the identification of 120 protein-coding regions based on proteomic and transcriptomic data. We review the progress made in understanding the biology of R. pomeroyi DSS-3 and list the changes made to the genome.},
	file         = {:Users/rivers/Library/Application Support/Mendeley Desktop/Downloaded/Rivers, Smith, Moran - 2014 - An Updated genome annotation for the model marine bacterium Ruegeria pomeroyi DSS-3.pdf:pdf},
	keywords     = {Animal Genetics and Genomics,Microbial Genetics and Genomics,Plant Genetics {\&} Genomics},
	language     = {En},
	pmid         = 25780504
}
@article{Kemp2015,
	title        = {{Spatial Homogeneity of Bacterial Communities Associated with the Surface Mucus Layer of the Reef-Building Coral Acropora palmata.}},
	author       = {Kemp, Dustin W and Rivers, Adam R and Kemp, Keri M and Lipp, Erin K and Porter, James W and Wares, John P},
	year         = 2015,
	month        = jan,
	journal      = {PloS one},
	publisher    = {Public Library of Science},
	volume       = 10,
	number       = 12,
	pages        = {e0143790},
	doi          = {10.1371/journal.pone.0143790},
	issn         = {1932-6203},
	url          = {http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0143790},
	abstract     = {Coral surface mucus layer (SML) microbiota are critical components of the coral holobiont and play important roles in nutrient cycling and defense against pathogens. We sequenced 16S rRNA amplicons to examine the structure of the SML microbiome within and between colonies of the threatened Caribbean reef-building coral Acropora palmata in the Florida Keys. Samples were taken from three spatially distinct colony regions-uppermost (high irradiance), underside (low irradiance), and the colony base-representing microhabitats that vary in irradiance and water flow. Phylogenetic diversity (PD) values of coral SML bacteria communities were greater than surrounding seawater and lower than adjacent sediment. Bacterial diversity and community composition was consistent among the three microhabitats. Cyanobacteria, Bacteroidetes, Alphaproteobacteria, and Proteobacteria, respectively were the most abundant phyla represented in the samples. This is the first time spatial variability of the surface mucus layer of A. palmata has been studied. Homogeneity in the microbiome of A. palmata contrasts with SML heterogeneity found in other Caribbean corals. These findings suggest that, during non-stressful conditions, host regulation of SML microbiota may override diverse physiochemical influences induced by the topographical complexity of A. palmata. Documenting the spatial distribution of SML microbes is essential to understanding the functional roles these microorganisms play in coral health and adaptability to environmental perturbations.},
	file         = {:Users/rivers/Library/Application Support/Mendeley Desktop/Downloaded/Kemp et al. - 2015 - Spatial Homogeneity of Bacterial Communities Associated with the Surface Mucus Layer of the Reef-Building Coral Acr.pdf:pdf},
	pmid         = 26659364
}
@article{Beier2015a,
	title        = {{Phenotypic plasticity in heterotrophic marine microbial communities in continuous cultures.}},
	shorttitle   = {ISME J},
	author       = {Beier, Sara and Rivers, Adam R and Moran, Mary Ann and Obernosterer, Ingrid},
	year         = 2015,
	month        = may,
	journal      = {The ISME journal},
	publisher    = {International Society for Microbial Ecology},
	volume       = 9,
	number       = 5,
	pages        = {1141--51},
	doi          = {10.1038/ismej.2014.206},
	issn         = {1751-7370},
	url          = {http://dx.doi.org/10.1038/ismej.2014.206},
	abstract     = {Phenotypic plasticity (PP) is the development of alternate phenotypes of a given taxon as an adaptation to environmental conditions. Methodological limitations have restricted the quantification of PP to the measurement of a few traits in single organisms. We used metatranscriptomic libraries to overcome these challenges and estimate PP using the expressed genes of multiple heterotrophic organisms as a proxy for traits in a microbial community. The metatranscriptomes captured the expression response of natural marine bacterial communities grown on differing carbon resource regimes in continuous cultures. We found that taxa with different magnitudes of PP coexisted in the same cultures, and that members of the order Rhodobacterales had the highest levels of PP. In agreement with previous studies, our results suggest that continuous culturing may have specifically selected for taxa featuring a rather high range of PP. On average, PP and abundance changes within a taxon contributed equally to the organism's change in functional gene abundance, implying that both PP and abundance mediated observed differences in community function. However, not all functional changes due to PP were directly reflected in the bulk community functional response: gene expression changes in individual taxa due to PP were partly masked by counterbalanced expression of the same gene in other taxa. This observation demonstrates that PP had a stabilizing effect on a community's functional response to environmental change.},
	file         = {:Users/rivers/Library/Application Support/Mendeley Desktop/Downloaded/Beier et al. - 2015 - Phenotypic plasticity in heterotrophic marine microbial communities in continuous cultures.pdf:pdf},
	keywords     = {Alphaproteobacteria,Alphaproteobacteria: physiology,Bacterial,Computational Biology,Cyanobacteria,Cyanobacteria: physiology,Diatoms,Ecosystem,Gene Expression Profiling,Gene Expression Regulation,Heterotrophic Processes,Phenotype,Phylogeny,Seawater,Seawater: microbiology,Transcriptome,Water Microbiology},
	pmid         = 25397947
}
@article{Bolyen2018,
	title        = {{QIIME 2: Reproducible, interactive, scalable, and extensible microbiome data science}},
	author       = {Bolyen, Evan and Rideout, Jai Ram and Dillon, Matthew R and Bokulich, Nicholas A and Abnet, Christian and Al-Ghalith, Gabriel A and Alexander, Harriet and Alm, Eric J and Arumugam, Manimozhiyan and Asnicar, Francesco and Bai, Yang and Bisanz, Jordan E and Bittinger, Kyle and Brejnrod, Asker and Brislawn, Colin J and Brown, C Titus and Callahan, Benjamin J and Caraballo-Rodr{\'{i}}guez, Andr{\'{e}}s Mauricio and Chase, John and Cope, Emily and Silva, Ricardo Da and Dorrestein, Pieter C and Douglas, Gavin M and Durall, Daniel M and Duvallet, Claire and Edwardson, Christian F and Ernst, Madeleine and Estaki, Mehrbod and Fouquier, Jennifer and Gauglitz, Julia M and Gibson, Deanna L and Gonzalez, Antonio and Gorlick, Kestrel and Guo, Jiarong and Hillmann, Benjamin and Holmes, Susan and Holste, Hannes and Huttenhower, Curtis and Huttley, Gavin and Janssen, Stefan and Jarmusch, Alan K and Jiang, Lingjing and Kaehler, Benjamin and Kang, Kyo Bin and Keefe, Christopher R and Keim, Paul and Kelley, Scott T and Knights, Dan and Koester, Irina and Kosciolek, Tomasz and Kreps, Jorden and Langille, Morgan GI and Lee, Joslynn and Ley, Ruth and Liu, Yong-Xin and Loftfield, Erikka and Lozupone, Catherine and Maher, Massoud and Marotz, Clarisse and Martin, Bryan D and McDonald, Daniel and McIver, Lauren J and Melnik, Alexey V and Metcalf, Jessica L and Morgan, Sydney C and Morton, Jamie and Naimey, Ahmad Turan and Navas-Molina, Jose A and Nothias, Louis Felix and Orchanian, Stephanie B and Pearson, Talima and Peoples, Samuel L and Petras, Daniel and Preuss, Mary Lai and Pruesse, Elmar and Rasmussen, Lasse Buur and Rivers, Adam and {Michael S Robeson}, II and Rosenthal, Patrick and Segata, Nicola and Shaffer, Michael and Shiffer, Arron and Sinha, Rashmi and Song, Se Jin and Spear, John R and Swafford, Austin D and Thompson, Luke R and Torres, Pedro J and Trinh, Pauline and Tripathi, Anupriya and Turnbaugh, Peter J and Ul-Hasan, Sabah and van der Hooft, Justin JJ and Vargas, Fernando and V{\'{a}}zquez-Baeza, Yoshiki and Vogtmann, Emily and von Hippel, Max and Walters, William and Wan, Yunhu and Wang, Mingxun and Warren, Jonathan and Weber, Kyle C and Williamson, Chase HD and Willis, Amy D and Xu, Zhenjiang Zech and Zaneveld, Jesse R and Zhang, Yilong and Zhu, Qiyun and Knight, Rob and Caporaso, J Gregory},
	year         = 2018,
	month        = dec,
	journal      = {PeerJ Preprints},
	publisher    = {PeerJ Inc.},
	number       = {e27295v1},
	doi          = {10.7287/peerj.preprints.27295v2},
	issn         = {2167-9843},
	file         = {:Users/rivers/Library/Application Support/Mendeley Desktop/Downloaded/Bolyen et al. - 2018 - QIIME 2 Reproducible, interactive, scalable, and extensible microbiome data science(3).pdf:pdf},
	keywords     = {bioinformatics,data science,microbial ecology,microbiome,reproducibility,software}
}
@article{Rivers2013a,
	title        = {{Transcriptional response of bathypelagic marine bacterioplankton to the Deepwater Horizon oil spill.}},
	author       = {Rivers, Adam R and Sharma, Shalabh and Tringe, Susannah G and Martin, Jeffrey and Joye, Samantha B and Moran, Mary Ann},
	year         = 2013,
	month        = aug,
	journal      = {The ISME journal},
	publisher    = {Nature Publishing Group},
	volume       = 19,
	number       = 1,
	pages        = {1--15},
	doi          = {10.1038/ismej.2013.129},
	issn         = {1751-7370},
	url          = {http://www.ncbi.nlm.nih.gov/pubmed/23902988},
	abstract     = {The Deepwater Horizon blowout released a massive amount of oil and gas into the deep ocean between April and July 2010, stimulating microbial blooms of petroleum-degrading bacteria. To understand the metabolic response of marine microorganisms, we sequenced ∼66 million community transcripts that revealed the identity of metabolically active microbes and their roles in petroleum consumption. Reads were assigned to reference genes from ∼2700 bacterial and archaeal taxa, but most assignments (39{\%}) were to just six genomes representing predominantly methane- and petroleum-degrading Gammaproteobacteria. Specific pathways for the degradation of alkanes, aromatic compounds and methane emerged from the metatranscriptomes, with some transcripts assigned to methane monooxygenases representing highly divergent homologs that may degrade either methane or short alkanes. The microbial community in the plume was less taxonomically and functionally diverse than the unexposed community below the plume; this was due primarily to decreased species evenness resulting from Gammaproteobacteria blooms. Surprisingly, a number of taxa (related to SAR11, Nitrosopumilus and Bacteroides, among others) contributed equal numbers of transcripts per liter in both the unexposed and plume samples, suggesting that some groups were unaffected by the petroleum inputs and blooms of degrader taxa, and may be important for re-establishing the pre-spill microbial community structure.The ISME Journal advance online publication, 1 August 2013; doi:10.1038/ismej.2013.129.},
	file         = {:Users/rivers/Library/Application Support/Mendeley Desktop/Downloaded/Rivers et al. - 2013 - Transcriptional response of bathypelagic marine bacterioplankton to the Deepwater Horizon oil spill.pdf:pdf},
	keywords     = {deepwater horizon,methane oxidation,oil degradation,transcriptomics},
	pmid         = 23902988
}
@article{Boyles2020,
	title        = {{Under-the-Radar Dengue Virus Infections in Natural Populations of Aedes aegypti Mosquitoes}},
	author       = {Boyles, Sean M. and Mavian, Carla N. and Finol, Esteban and Ukhanova, Maria and Stephenson, Caroline J. and Hamerlinck, Gabriela and Kang, Seokyoung and Baumgartner, Caleb and Geesey, Mary and Stinton, Israel and Williams, Katie and Mathias, Derrick K. and Prosperi, Mattia and Mai, Volker and Salemi, Marco and Buckner, Eva A. and Lednicky, John A. and Rivers, Adam R. and Dinglasan, Rhoel R.},
	year         = 2020,
	month        = apr,
	journal      = {mSphere},
	publisher    = {American Society for Microbiology Journals},
	volume       = 5,
	number       = 2,
	doi          = {10.1128/mSphere.00316-20},
	issn         = {2379-5042},
	url          = {http://msphere.asm.org/lookup/doi/10.1128/mSphere.00316-20},
	abstract     = {The incidence of locally acquired dengue infections increased during the last decade in the United States, compelling a sustained research effort concerning the dengue mosquito vector, Aedes aegypti , and its microbiome, which has been shown to influence virus transmission success. We examined the ?metavirome? of four populations of Aedes aegypti mosquitoes collected in 2016 to 2017 in Manatee County, FL. Unexpectedly, we discovered that dengue virus serotype 4 (DENV4) was circulating in these mosquito populations, representing the first documented case of such a phenomenon in the absence of a local DENV4 human case in this county over a 2-year period. We confirmed that all of the mosquito populations carried the same DENV4 strain, assembled its full genome, validated infection orthogonally by reverse transcriptase PCR, traced the virus origin, estimated the time period of its introduction to the Caribbean region, and explored the viral genetic signatures and mosquito-specific virome associations that potentially mediated DENV4 persistence in mosquitoes. We discuss the significance of prolonged maintenance of the DENV4 infections in A. aegypti that occurred in the absence of a DENV4 human index case in Manatee County with respect to the inability of current surveillance paradigms to detect mosquito vector infections prior to a potential local outbreak.},
	editor       = {Pipas, James M.},
	file         = {:Users/rivers/Desktop/mSphere-2020-Boyles-e00316-20.full.pdf:pdf}
}
@article{Peters2020,
	title        = {{Harnessing AI to Transform Agriculture and Inform Agricultural Research}},
	author       = {Peters, Debra P. C. and Rivers, Adam and Hatfield, Jerry L. and Lemay, Danielle G. and Liu, Simon and Basso, Bruno},
	year         = 2020,
	month        = may,
	journal      = {IT Professional},
	volume       = 22,
	number       = 3,
	pages        = {16--21},
	doi          = {10.1109/MITP.2020.2986124},
	issn         = {1520-9202},
	url          = {https://ieeexplore.ieee.org/document/9098014/},
	file         = {:Users/rivers/Library/Application Support/Mendeley Desktop/Downloaded/Peters et al. - 2020 - Harnessing AI to Transform Agriculture and Inform Agricultural Research.pdf:pdf}
}
@article{Sudduth2020,
	title        = {{AI Down on the Farm}},
	author       = {Sudduth, Kenneth A. and Woodward-Greene, M. Jennifer and Penning, Bryan W. and Locke, Martin A. and Rivers, Adam R. and Veum, Kristen S.},
	year         = 2020,
	month        = may,
	journal      = {IT Professional},
	volume       = 22,
	number       = 3,
	pages        = {22--26},
	doi          = {10.1109/MITP.2020.2986104},
	issn         = {1520-9202},
	url          = {https://ieeexplore.ieee.org/document/9098007/},
	file         = {:Users/rivers/Library/Application Support/Mendeley Desktop/Downloaded/Sudduth et al. - 2020 - AI Down on the Farm.pdf:pdf}
}

license: MIT

repository: arivers/cv

license_type: permissive

repo_name: arivers/cv

branch_name: refs/heads/master

extension: bib


text:
@InProceedings{hennig14,
  supplementary = {Supplementary:henning14-supp.zip},
  title = {{Probabilistic Solutions to Differential Equations and their Application to Riemannian Statistics}},
  author = {Hennig, Philipp and Hauberg, Søren},
  pages = {347-355},
  abstract = {We study a probabilistic numerical method for the solution of both boundary and initial value problems that returns a joint Gaussian process posterior over the solution. Such methods have concrete value in the statistics on Riemannian manifolds, where non-analytic ordinary differential equations are involved in virtually all computations. The probabilistic formulation permits marginalising the uncertainty of the numerical solution such that statistics are less sensitive to inaccuracies. This leads to new Riemannian algorithms for mean value computations and principal geodesic analysis. Marginalisation also means results can be less precise than point estimates, enabling a noticeable speed-up over the state of the art. Our approach is an argument for a wider point that uncertainty caused by numerical calculations should be tracked throughout the pipeline of machine learning algorithms.},
}

repository: mreid/papersite

repo_name: mreid/papersite

gha_license_id: MIT

gha_language: TeX