Open Access Policy Deposits

Bachan, J; Baden, S; Bonachea, Dan; Hargrove, P; Hofmeyr, S; Jacquelin, M et al.: UPC++ Programmer’s Guide, v1.0-2018.9.0, 2018

Bachan, J; Baden, S; Bonachea, D; Hargrove, P; Hofmeyr, S; Ibrahim, K et al.: UPC++ Specification v1.0, Draft 6, 2018

Bachan, John; Baden, Scott; Bonachea, Dan; Hargrove, Paul; Hofmeyr, Steven; Jacquelin, Mathias et al.: UPC++ Specification v1.0, Draft 8, 2018

Bakhtiari, Mehrdad; Shleizer-Burko, Sharona; Gymrek, Melissa; Bansal, Vikas; Bafna, Vineet: Targeted genotyping of variable number tandem repeats with adVNTR, 2018

Beame, P; Fleming, N; Impagliazzo, R; Kolokolova, A; Pankratov, D; Pitassi, T et al.: Stabbing planes, 2018

Belk, Aeriel; Xu, Zhenjiang Zech; Carter, David O; Lynne, Aaron; Bucheli, Sibyl; Knight, Rob et al.: Microbiome Data Accurately Predicts the Postmortem Interval Using Random Forest Regression Models., 2018

Beyter, Doruk; Lin, Miin; Yu, Yanbao; Pieper, Rembert; Bafna, Vineet: ProteoStorm: An Ultrafast Metaproteomics Database Search Framework., 2018

Boast, Alexander P; Weyrich, Laura S; Wood, Jamie R; Metcalf, Jessica L; Knight, Rob; Cooper, Alan: Coprolites reveal ecological interactions lost with the extinction of New Zealand birds, 2018

Bokulich, Nicholas A; Kaehler, Benjamin D; Rideout, Jai Ram; Dillon, Matthew; Bolyen, Evan; Knight, Rob et al.: Optimizing taxonomic classification of marker-gene amplicon sequences with QIIME 2’s q2-feature-classifier plugin, 2018

Bowers, Robert M; Kyrpides, Nikos C; Stepanauskas, Ramunas; Harmon-Smith, Miranda; Doud, Devin; Reddy, TBK et al.: Correction: Corrigendum: Minimum information about a single amplified genome (MISAG) and a metagenome-assembled genome (MIMAG) of bacteria and archaea, 2018

Canonne, Clément L; Diakonikolas, Ilias; Kane, Daniel M; Stewart, Alistair: Testing conditional independence of discrete distributions, 2018

Carmosino, Marco L; Impagliazzo, Russell; Lovett, Shachar; Mihajlin, Ivan: Hardness Amplification for Non-Commutative Arithmetic Circuits, 2018

Cekanaviciute, Egle; Pröbstel, Anne-Katrin; Thomann, Anna; Runia, Tessel F; Casaccia, Patrizia; Katz Sand, Ilana et al.: Multiple Sclerosis-Associated Changes in the Composition and Immune Functions of Spore-Forming Bacteria., 2018

Cheng, Yu; Diakonikolas, Ilias; Kane, Daniel M; Stewart, Alistair: Robust Learning of Fixed-Structure Bayesian Networks, 2018

Costea, Paul I; Hildebrand, Falk; Arumugam, Manimozhiyan; Bäckhed, Fredrik; Blaser, Martin J; Bushman, Frederic D et al.: Enterotypes in the landscape of gut microbial community composition., 2018

DeFrancesco, Laura: Erratum: California voters and CIRM—will lightning strike twice?, 2018

DeFrancesco, Laura: Erratum: California voters and CIRM-will lightning strike twice?, 2018

Diakonikolas, Ilias; Kane, Daniel M; Stewart, Alistair: Learning geometric concepts with nasty noise, 2018

Diakonikolas, Ilias; Kane, Daniel M; Stewart, Alistair: List-decodable robust mean estimation and learning mixtures of spherical gaussians, 2018

Diakonikolas, Ilias; Kane, Daniel M; Stewart, Alistair: Sharp Bounds for Generalized Uniformity Testing, 2018

Donaldson, GP; Ladinsky, MS; Yu, KB; Sanders, JG; Yoo, BB; Chou, W-C et al.: Gut microbiota utilize immunoglobulin A for mucosal colonization., 2018

Fang, Xin; Monk, Jonathan M; Nurk, Sergey; Akseshina, Margarita; Zhu, Qiyun; Gemmell, Christopher et al.: Metagenomics-Based, Strain-Level Analysis of <i>Escherichia coli</i> From a Time-Series of Microbiome Samples From a Crohn's Disease Patient., 2018

Franzosa, Eric A; McIver, Lauren J; Rahnavard, Gholamali; Thompson, Luke R; Schirmer, Melanie; Weingart, George et al.: Species-level functional profiling of metagenomes and metatranscriptomes, 2018

Fulbright, Scott P; Robbins-Pianka, Adam; Berg-Lyons, Donna; Knight, Rob; Reardon, Kenneth F; Chisholm, Stephen T: Bacterial community changes in an industrial algae production system., 2018

Gilbert, Jack A; Blaser, Martin J; Caporaso, J Gregory; Jansson, Janet K; Lynch, Susan V; Knight, Rob: Current understanding of the human microbiome., 2018

Gilbert, Jack A; Jansson, Janet K; Knight, Rob: Earth Microbiome Project and Global Systems Biology., 2018

Gonzalez, Antonio; Navas-Molina, Jose A; Kosciolek, Tomasz; McDonald, Daniel; Vázquez-Baeza, Yoshiki; Ackermann, Gail et al.: Qiita: rapid, web-enabled microbiome meta-analysis, 2018

Gopalan, Parikshit; Kane, Daniel M; Meka, Raghu: Pseudorandomness via the Discrete Fourier Transform, 2018

Hatami, Hamed; Hosseini, Kaave; Lovett, Shachar: Structure of Protocols for XOR Functions, 2018

Hillmann, Benjamin; Al-Ghalith, Gabriel A; Shields-Cutler, Robin R; Zhu, Qiyun; Gohl, Daryl M; Beckman, Kenneth B et al.: Evaluating the Information Content of Shallow Shotgun Metagenomics, 2018

Hua, Zheng-Shuang; Qu, Yan-Ni; Zhu, Qiyun; Zhou, En-Min; Qi, Yan-Ling; Yin, Yi-Rui et al.: Genomic inference of the metabolism and evolution of the archaeal phylum Aigarchaeota, 2018

Janssen, Stefan; McDonald, Daniel; Gonzalez, Antonio; Navas-Molina, Jose A; Jiang, Lingjing; Xu, Zhenjiang Zech et al.: Phylogenetic Placement of Exact Amplicon Sequences Improves Associations with Clinical Information, 2018

Jiang, Weihua; Zheng, Siyuan; Zhou, Yuehai; Tong, F; Kastner, Ryan: Exploiting time varying sparsity for underwater acoustic communication via dynamic compressed sensing., 2018

Kahn, Suzana A; Wang, Xin; Nitta, Ryan T; Gholamin, Sharareh; Theruvath, Johanna; Hutter, Gregor et al.: Publisher Correction: Notch1 regulates the initiation of metastasis and self-renewal of Group 3 medulloblastoma, 2018

Kane, Daniel M; Palmer, Joseph; Pelayo, Alvaro: Classifying Toric and Semitoric Fans by Lifting Equations from SL₂(Z), 2018

Kane, DM; Lovett, S; Moran, S: Generalized comparison trees for point-location problems, 2018

Kane, DM; Palmer, J; Pelayo, Á: Minimal models of compact symplectic semitoric manifolds, 2018

Kane, Daniel M; Lovett, Shachar; Moran, Shay: Near-optimal linear decision trees for k-SUM and related problems, 2018

Kaplanis, Joanna; Gordon, Assaf; Shor, Tal; Weissbrod, Omer; Geiger, Dan; Wahl, Mary et al.: Quantitative analysis of population-scale family trees with millions of relatives, 2018

Kapono, Clifford A; Morton, James T; Bouslimani, Amina; Melnik, Alexey V; Orlinsky, Kayla; Knaan, Tal Luzzatto et al.: Creating a 3D microbial and chemical snapshot of a human habitat, 2018

Lapek, John D; Mills, Robert H; Wozniak, Jacob M; Campeau, Anaamika; Fang, Ronnie H; Wei, Xiaoli et al.: Defining Host Responses during Systemic Bacterial Infection through Construction of a Murine Organ Proteome Atlas, 2018

Lavrinienko, Anton; Mappes, Tapio; Tukalenko, Eugene; Mousseau, Timothy A; Møller, Anders P; Knight, Rob et al.: Environmental radiation alters the gut microbiome of the bank vole Myodes glareolus, 2018

Lee, Dajung; Mehta, Nirja; Shearer, Alexandria; Kastner, Ryan: A hardware accelerated system for high throughput cellular image analysis, 2018

Lovett, Shachar; Regev, Oded: A counterexample to a strong variant of the Polynomial Freiman-Ruzsa conjecture in Euclidean space, 2018

Mao, Baolei; Hu, Wei; Althoff, Alric; Matai, Janarbek; Tai, Yu; Mu, Dejun et al.: Quantitative Analysis of Timing Channel Security in Cryptographic Hardware Design, 2018

Maricic, Igor; Marrero, Idania; Eguchi, Akiko; Nakamura, Ryota; Johnson, Casey D; Dasgupta, Suryasarathi et al.: Differential Activation of Hepatic Invariant NKT Cell Subsets Plays a Key Role in Progression of Nonalcoholic Steatohepatitis., 2018

Marotz, Clarisse A; Sanders, Jon G; Zuniga, Cristal; Zaramela, Livia S; Knight, Rob; Zengler, Karsten: Improving saliva shotgun metagenomics by chemical host DNA depletion, 2018

Maurer-Alcalá, Xyrus X; Knight, Rob; Katz, Laura A; Orias, Eduardo; Cavalcanti, Andre; Frapporti, Andrea et al.: Exploration of the Germline Genome of the Ciliate Chilodonella uncinata through Single-Cell Omics (Transcriptomics and Genomics), 2018

Maurer-Alcalá, Xyrus X; Yan, Ying; Pilling, Olivia; Knight, Rob; Katz, Laura A: “Twisted Tales: Insights into Genome Diversity of Ciliates Using Single-Cell ‘omics”, 2018

McCall, Laura-Isobel; Tripathi, Anupriya; Vargas, Fernando; Knight, Rob; Dorrestein, Pieter C; Siqueira-Neto, Jair L: Experimental Chagas disease-induced perturbations of the fecal microbiome and metabolome, 2018