Open Access Policy Deposits

Badal, Varsha Dave; Wright, Dustin; Katsis, Yannis; Kim, Ho-Cheol; Swafford, Austin D; Knight, Rob et al.: Challenges in the construction of knowledge bases for human microbiome-disease associations., 2019

Balaban, Metin; Moshiri, Niema; Mai, Uyen; Jia, Xingfan; Mirarab, Siavash: TreeCluster: Clustering biological sequences using phylogenetic trees, 2019

Balsubramani, Akshay; Dasgupta, Sanjoy; Freund, Yoav; Moran, Shay: An adaptive nearest neighbor rule for classification, 2019

Bansal, Nikhil; Dadush, Daniel; Garg, Shashwat; Lovett, Shachar: The Gram-Schmidt Walk: A Cure for the Banaszczyk Blues, 2019

Bouslimani, Amina; da Silva, Ricardo; Kosciolek, Tomasz; Janssen, Stefan; Callewaert, Chris; Amir, Amnon et al.: The impact of skin care products on skin chemistry and microbiome dynamics, 2019

Byrd, Doratha A; Chen, Jun; Vogtmann, Emily; Hullings, Autumn; Song, Jin; Amir, Amnon et al.: Reproducibility, stability, and accuracy of microbial profiles by fecal sample collection method in three distinct populations, 2019

Cao, Liu; Gurevich, Alexey; Alexander, Kelsey L; Naman, C Benjamin; Leão, Tiago; Glukhov, Evgenia et al.: MetaMiner: A Scalable Peptidogenomics Approach for Discovery of Ribosomal Peptide Natural Products with Blind Modifications from Microbial Communities, 2019

Caussy, Cyrielle; Tripathi, Anupriya; Humphrey, Greg; Bassirian, Shirin; Singh, Seema; Faulkner, Claire et al.: A gut microbiome signature for cirrhosis due to nonalcoholic fatty liver disease, 2019

Chattopadhyay, Eshan; Hatami, Pooya; Hosseini, Kaave; Lovett, Shachar: Pseudorandom Generators from Polarizing Random Walks, 2019

Checinska Sielaff, Aleksandra; Urbaniak, Camilla; Mohan, Ganesh Babu Malli; Stepanov, Victor G; Tran, Quyen; Wood, Jason M et al.: Characterization of the total and viable bacterial and fungal communities associated with the International Space Station surfaces., 2019

Chowdhry, Sudhir; Zanca, Ciro; Rajkumar, Utkrisht; Koga, Tomoyuki; Diao, Yarui; Raviram, Ramya et al.: NAD metabolic dependency in cancer is shaped by gene amplification and enhancer remodelling., 2019

Cristea, Ileana M; Dorrestein, Pieter C; Eisen, Jonathan A; Gilbert, Jack A; Huber, Julie A; Jansson, Janet K et al.: Early-Career Scientists Shaping the World, 2019

Dabydeen, Sarah A; Desai, Arshad; Sahoo, Debashis: Unbiased Boolean analysis of public gene expression data for cell cycle gene identification, 2019

de la Cuesta-Zuluaga, Jacobo; Kelley, Scott T; Chen, Yingfeng; Escobar, Juan S; Mueller, Noel T; Ley, Ruth E et al.: Age- and Sex-Dependent Patterns of Gut Microbial Diversity in Human Adults., 2019

Demmer, RT; Trinh, P; Rosenbaum, M; Li, G; LeDuc, C; Leibel, R et al.: Subgingival Microbiota and Longitudinal Glucose Change: The Oral Infections, Glucose Intolerance and Insulin Resistance Study (ORIGINS), 2019

Diakonikolas, I; Gouleakis, T; Kane, DM; Rao, S: Communication and Memory Efficient Testing of Discrete Distributions, 2019

Diakonikolas, Ilias; Kane, Daniel M: Degree-𝑑 chow parameters robustly determine degree-𝑑 PTFs (and algorithmic applications), 2019

Diakonikolas, Ilias; Kane, Daniel M; Manurangsi, Pasin: Nearly Tight Bounds for Robust Proper Learning of Halfspaces with a Margin, 2019

Diakonikolas, Ilias; Kamath, Gautam; Kane, Daniel; Li, Jerry; Moitra, Ankur; Stewart, Alistair: Robust Estimators in High-Dimensions Without the Computational Intractability, 2019

Diakonikolas, Ilias; Kamath, Gautam; Kane, Daniel M; Li, Jerry; Steinhardt, Jacob; Stewart, Alistair: SEVER: A Robust Meta-Algorithm for Stochastic Optimization, 2019

Dominguez-Bello, Maria Gloria; Godoy-Vitorino, Filipa; Knight, Rob; Blaser, Martin J: Role of the microbiome in human development, 2019

Ezra, Esther; Lovett, Shachar: On the Beck‐Fiala conjecture for random set systems, 2019

Fotsing, Stephanie Feupe; Margoliash, Jonathan; Wang, Catherine; Saini, Shubham; Yanicky, Richard; Shleizer-Burko, Sharona et al.: The impact of short tandem repeat variation on gene expression., 2019

Fragiadakis, Gabriela K; Smits, Samuel A; Sonnenburg, Erica D; Van Treuren, William; Reid, Gregor; Knight, Rob et al.: Links between environment, diet, and the hunter-gatherer microbiome, 2019

Fu, Ting; Coulter, Sally; Yoshihara, Eiji; Oh, Tae Gyu; Fang, Sungsoon; Cayabyab, Fritz et al.: FXR Regulates Intestinal Cancer Stem Cell Proliferation, 2019

Getz, Michael; Swanson, Lee; Sahoo, Debashish; Ghosh, Pradipta; Rangamani, Padmini: A predictive computational model reveals that GIV/girdin serves as a tunable valve for EGFR-stimulated cyclic AMP signals, 2019

Hatami, Hamed; Hatami, Pooya; Lovett, Shachar: Higher-order Fourier Analysis and Applications, 2019

Ho, G; Cidon, A; Gavish, L; Schweighauser, M; Paxson, V; Savage, S et al.: Detecting and characterizing lateral phishing at scale, 2019

Huang, Ming-Xiong; Nichols, Sharon; Robb-Swan, Ashley; Angeles-Quinto, Annemarie; Harrington, Deborah L; Drake, Angela et al.: MEG Working Memory N-Back Task Reveals Functional Deficits in Combat-Related Mild Traumatic Brain Injury, 2019

Iszatt, Nina; Janssen, Stefan; Lenters, Virissa; Dahl, Cecilie; Stigum, Hein; Knight, Rob et al.: Environmental toxicants in breast milk of Norwegian mothers and gut bacteria composition and metabolites in their infants at 1 month, 2019

Jankowska, Marta M; Gaulton, Kyle; Knight, Rob; Patrick, Kevin; Sears, Dorothy D: Neighborhoods to Nucleotides - Advances and gaps for an obesity disparities systems epidemiology model., 2019

Jung, Carrie E; Chopyk, Jessica; Shin, Ji Hyun; Lukacz, Emily S; Brubaker, Linda; Schwanemann, Leila K et al.: Benchmarking urine storage and collection conditions for evaluating the female urinary microbiome., 2019

Kaehler, Benjamin D; Bokulich, Nicholas A; McDonald, Daniel; Knight, Rob; Caporaso, J Gregory; Huttley, Gavin A: Species abundance information improves sequence taxonomy classification accuracy, 2019

Kane, Daniel; Lovett, Shachar; Rao, Sankeerth: The Independence Number of the Birkhoff Polytope Graph, and Applications to Maximally Recoverable Codes, 2019

Kane, Daniel M; Lovett, Shachar; Moran, Shay: Near-optimal Linear Decision Trees for k-SUM and Related Problems, 2019

Kane, Daniel M; Sanna, Carlo; Shallit, Jeffrey: Waring’s Theorem for Binary Powers, 2019

Kaplan, Robert C; Wang, Zheng; Usyk, Mykhaylo; Sotres-Alvarez, Daniela; Daviglus, Martha L; Schneiderman, Neil et al.: Gut microbiome composition in the Hispanic Community Health Study/Study of Latinos is shaped by geographic relocation, environmental factors, and obesity, 2019

Katz Sand, Ilana; Zhu, Yunjiao; Ntranos, Achilles; Clemente, Jose C; Cekanaviciute, Egle; Brandstadter, Rachel et al.: Disease-modifying therapies alter gut microbial composition in MS., 2019

Kirjavainen, Pirkka; Karvonen, Anne; Adams, Rachel; Täubel, Martin; Roponen, Marjut; Tuoresmäki, Pauli et al.: Farm-like indoor microbiota in non-farm homes protects children from asthma development., 2019

Li, Shangzhong; Cha, Seong; Heffner, Kelly; Hizal, Deniz; Bowen, Michael; Chaerkady, Raghothama et al.: Proteogenomic Annotation of Chinese Hamsters Reveals Extensive Novel Translation Events and Endogenous Retroviral Elements., 2019

Lloyd, Colton J; King, Zachary A; Sandberg, Troy E; Hefner, Ying; Olson, Connor A; Phaneuf, Patrick V et al.: The genetic basis for adaptation of model-designed syntrophic co-cultures, 2019

Lloyd-Price, Jason; Arze, Cesar; Ananthakrishnan, Ashwin N; Schirmer, Melanie; Avila-Pacheco, Julian; Poon, Tiffany W et al.: Multi-omics of the gut microbial ecosystem in inflammatory bowel diseases, 2019

Ma, Qianli; Zhuang, Wanqing; Shen, Lifeng; Cottrell, Garrison W: Time series classification with Echo Memory Networks, 2019

Marotz, Clarisse; Sharma, Anukriti; Humphrey, Greg; Gottel, Neil; Daum, Christopher; Gilbert, Jack A et al.: Triplicate PCR reactions for 16S rRNA gene amplicon sequencing are unnecessary, 2019

Martino, Cameron; Morton, James T; Marotz, Clarisse A; Thompson, Luke R; Tripathi, Anupriya; Knight, Rob et al.: A Novel Sparse Compositional Technique Reveals Microbial Perturbations, 2019

McDonald, Daniel; Kaehler, Benjamin; Gonzalez, Antonio; DeReus, Jeff; Ackermann, Gail; Marotz, Clarisse et al.: redbiom: a Rapid Sample Discovery and Feature Characterization System, 2019

Melnik, Alexey V; Vázquez-Baeza, Yoshiki; Aksenov, Alexander A; Hyde, Embriette; McAvoy, Andrew C; Wang, Mingxun et al.: Molecular and Microbial Microenvironments in Chronically Diseased Lungs Associated with Cystic Fibrosis, 2019

Mills, Robert H; Vázquez-Baeza, Yoshiki; Zhu, Qiyun; Jiang, Lingjing; Gaffney, James; Humphrey, Greg et al.: Evaluating Metagenomic Prediction of the Metaproteome in a 4.5-Year Study of a Patient with Crohn's Disease, 2019

Minich, Jeremiah J; Sanders, Jon G; Amir, Amnon; Humphrey, Greg; Gilbert, Jack A; Knight, Rob: Quantifying and Understanding Well-to-Well Contamination in Microbiome Research, 2019

Morton, James T; Marotz, Clarisse; Washburne, Alex; Silverman, Justin; Zaramela, Livia S; Edlund, Anna et al.: Establishing microbial composition measurement standards with reference frames, 2019