Open Access Policy Deposits

Sinha, Rashmi; Zhao, Ni; Goedert, James J; Byrd, Doratha A; Wan, Yunhu; Hua, Xing et al.: Effects of processed meat and drinking water nitrate on oral and fecal microbial populations in a controlled feeding study, 2021

Song, Se Jin; Wang, Jincheng; Martino, Cameron; Jiang, Lingjing; Thompson, Wesley K; Shenhav, Liat et al.: Naturalization of the microbiota developmental trajectory of Cesarean-born neonates after vaginal seeding, 2021

Sun, Zheng; Huang, Shi; Zhang, Meng; Zhu, Qiyun; Haiminen, Niina; Carrieri, Anna Paola et al.: Challenges in benchmarking metagenomic profilers, 2021

Tindle, Courtney; Fuller, MacKenzie; Fonseca, Ayden; Taheri, Sahar; Ibeawuchi, Stella-Rita; Beutler, Nathan et al.: Adult stem cell-derived complete lung organoid models emulate lung disease in COVID-19, 2021

Tripathi, Anupriya; Vázquez-Baeza, Yoshiki; Gauglitz, Julia M; Wang, Mingxun; Dührkop, Kai; Nothias-Esposito, Mélissa et al.: Chemically informed analyses of metabolomics mass spectrometry data with Qemistree, 2021

Tueller, Peter; Maddukuri, Raghav; Paxson, Patrick; Suresh, Vivaswat; Ashok, Arjun; Bland, Madison et al.: FishSense: Underwater RGBD Imaging for Fish Measurement, 2021

Vassena, Marco; Disselkoen, Craig; von Gleissenthall, Klaus; Cauligi, Sunjay; Kıcı, Rami Gökhan; Jhala, Ranjit et al.: Automatically eliminating speculative leaks from cryptographic code with blade, 2021

Vo, Daniella; Singh, Shayal Charisma; Safa, Sara; Sahoo, Debashis: Boolean implication analysis unveils candidate universal relationships in microbiome data, 2021

Wang, Yu-Chen; Wu, Yu-Ting; Li, Tzu-Mao; Chuang, Yung-Yu: Learning to cluster for rendering with many lights, 2021

Wang, Zheng; Usyk, Mykhaylo; Vázquez-Baeza, Yoshiki; Chen, Guo-Chong; Isasi, Carmen R; Williams-Nguyen, Jessica S et al.: Microbial co-occurrence complicates associations of gut microbiome with US immigration, dietary intake and obesity, 2021

Washington, Nicole L; Gangavarapu, Karthik; Zeller, Mark; Bolze, Alexandre; Cirulli, Elizabeth T; Schiabor Barrett, Kelly M et al.: Emergence and rapid transmission of SARS-CoV-2 B.1.1.7 in the United States., 2021

Washington, Nicole L; Gangavarapu, Karthik; Zeller, Mark; Bolze, Alexandre; Cirulli, Elizabeth T; Barrett, Kelly M Schiabor et al.: Genomic epidemiology identifies emergence and rapid transmission of SARS-CoV-2 B.1.1.7 in the United States., 2021

Wu, Zeni; Hullings, Autumn G; Ghanbari, Reza; Etemadi, Arash; Wan, Yunhu; Zhu, Bin et al.: Comparison of fecal and oral collection methods for studies of the human microbiota in two Iranian cohorts, 2021

Xue, Jin; Allaband, Celeste; Zhou, Dan; Poulsen, Orit; Martino, Cameron; Jiang, Lingjing et al.: Influence of Intermittent Hypoxia/Hypercapnia on Atherosclerosis, Gut Microbiome, and Metabolome, 2021

Ying, Wei; Tang, Kechun; Avolio, Ennio; Schilling, Jan M; Pasqua, Teresa; Liu, Matthew A et al.: Immunosuppression of Macrophages Underlies the Cardioprotective Effects of CST (Catestatin), 2021

Zeller, Mark; Gangavarapu, Karthik; Anderson, Catelyn; Smither, Allison R; Vanchiere, John A; Rose, Rebecca et al.: Emergence of an early SARS-CoV-2 epidemic in the United States, 2021

Zeller, Mark; Gangavarapu, Karthik; Anderson, Catelyn; Smither, Allison R; Vanchiere, John A; Rose, Rebecca et al.: Emergence of an early SARS-CoV-2 epidemic in the United States, 2021

Zheng, An; Lamkin, Michael; Zhao, Hanqing; Wu, Cynthia; Su, Hao; Gymrek, Melissa: Deep neural networks identify sequence context features predictive of transcription factor binding, 2021

Zheng, An; Lamkin, Michael; Qiu, Yutong; Ren, Kevin; Goren, Alon; Gymrek, Melissa: A flexible ChIP-sequencing simulation toolkit., 2021

Zhu, Qiyun; Hou, Qiangchuan; Huang, Shi; Ou, Qianying; Huo, Dongxue; Vázquez-Baeza, Yoshiki et al.: Compositional and genetic alterations in Graves’ disease gut microbiome reveal specific diagnostic biomarkers, 2021

Aad, G; Abbott, B; Abbott, DC; Abed Abud, A; Abeling, K; Abhayasinghe, DK et al.: Combination of the W boson polarization measurements in top quark decays using ATLAS and CMS data at s = 8 TeV, 2020

Abbasi, Nazia; Long, Tianyun; Li, Yuxin; Yee, Brian A; Cho, Benjamin S; Hernandez, Juan E et al.: DDX5 promotes oncogene C3 and FABP1 expressions and drives intestinal inflammation and tumorigenesis, 2020

Abdo, Zaid; Blaser, Martin J; Gilbert, Jack A; Knight, Rob; Lozupone, Catherine; Maas, Kendra et al.: Coordinating and Assisting Research at the SARS-CoV-2/Microbiome Nexus, 2020

Alafate, Julaiti; Freund, Yoav; Sandwell, David T; Tozer, Brook: Experimental Design for Bathymetry Editing, 2020

Alweiss, Ryan; Lovett, Shachar; Wu, Kewen; Zhang, Jiapeng: Improved bounds for the sunflower lemma, 2020

Aron, Manju; Park, Sanghui; Lowenthal, Brett M; Gupta, Sounak; Sahoo, Debashis; Cheville, John C et al.: Primary Female Urethral Carcinoma, 2020

Asnicar, Francesco; Thomas, Andrew Maltez; Beghini, Francesco; Mengoni, Claudia; Manara, Serena; Manghi, Paolo et al.: Precise phylogenetic analysis of microbial isolates and genomes from metagenomes using PhyloPhlAn 3.0, 2020

Badal, Varsha D; Vaccariello, Eleonora D; Murray, Emily R; Yu, Kasey E; Knight, Rob; Jeste, Dilip V et al.: The Gut Microbiome, Aging, and Longevity: A Systematic Review, 2020

Bakshi, Ainesh; Diakonikolas, Ilias; Hopkins, Samuel B; Kane, Daniel; Karmalkar, Sushrut; Kothari, Pravesh K: Outlier-Robust Clustering of Gaussians and Other Non-Spherical Mixtures, 2020

Biri, Andreas; Jackson, Neal; Thiele, Lothar; Pannuto, Patrick; Dutta, Prabal: SociTrack: Infrastructure-Free Interaction Tracking through Mobile Sensor Networks, 2020

Bohmann, Kristine; Mirarab, Siavash; Bafna, Vineet; Gilbert, M: Beyond DNA barcoding: The unrealized potential of genome skim data in sample identification., 2020

Bowers, Samuel J; Vargas, Fernando; González, Antonio; He, Shannon; Jiang, Peng; Dorrestein, Pieter C et al.: Repeated sleep disruption in mice leads to persistent shifts in the fecal microbiome and metabolome, 2020

Breuss, Martin W; Antaki, Danny; George, Renee D; Kleiber, Morgan; James, Kiely N; Ball, Laurel L et al.: Autism risk in offspring can be assessed through quantification of male sperm mosaicism, 2020

Burcham, Zachary M; Garneau, Nicole L; Comstock, Sarah S; Tucker, Robin M; Knight, Rob; Metcalf, Jessica L: Patterns of Oral Microbiota Diversity in Adults and Children: A Crowdsourced Population Study, 2020

Bzikadze, Andrey; Pevzner, Pavel: Automated assembly of centromeres from ultra-long error-prone reads., 2020

Callewaert, Chris; Nakatsuji, Teruaki; Knight, Rob; Kosciolek, Tomasz; Vrbanac, Alison; Kotol, Paul et al.: IL-4Rα Blockade by Dupilumab Decreases Staphylococcus aureus Colonization and Increases Microbial Diversity in Atopic Dermatitis., 2020

Canonne, Clément L; Diakonikolas, Ilias; Kane, Daniel M; Stewart, Alistair: Testing Bayesian Networks, 2020

Cauligi, Sunjay; Disselkoen, Craig; Gleissenthall, Klaus V; Tullsen, Dean; Stefan, Deian; Rezk, Tamara et al.: Constant-time foundations for the new spectre era, 2020

Chen, Zhoutao; Pham, Long; Wu, Tsai-Chin; Mo, Guoya; Xia, Yu; Chang, Peter L et al.: Ultralow-input single-tube linked-read library method enables short-read second-generation sequencing systems to routinely generate highly accurate and economical long-range sequencing information, 2020

Dang, Dharanidhar; Taheri, Sahar; Das, Soumita; Ghosh, Pradipta; Prince, Lawrence S; Sahoo, Debashis: Computational Approach to Identifying Universal Macrophage Biomarkers, 2020

Demmer, Ryan T; Ulrich, Angela K; Wiggen, Talia D; Strickland, Ali; Naumchik, Brianna M; Kulasingam, Shalini et al.: SARS-CoV-2 Screening Among Symptom-Free Healthcare Workers, 2020

Dethloff, Frederik; Vargas, Fernando; Elijah, Emmanuel; Quinn, Robert; Park, Dong Ik; Herzog, David P et al.: Paroxetine Administration Affects Microbiota and Bile Acid Levels in Mice, 2020

Diakonikolas, Ilias; Kane, Daniel M; Kontonis, Vasilis; Zarifis, Nikos: Algorithms and SQ Lower Bounds for PAC Learning One-Hidden-Layer ReLU Networks, 2020

Diakonikolas, Ilias; Kane, Daniel M; Manurangsi, Pasin: The Complexity of Adversarially Robust Proper Learning of Halfspaces with Agnostic Noise, 2020

Diakonikolas, Ilias; Kane, Daniel M; Kongsgaard, Daniel: List-Decodable Mean Estimation via Iterative Multi-Filtering, 2020

Diakonikolas, Ilias; Kane, Daniel M; Zarifis, Nikos: Near-Optimal SQ Lower Bounds for Agnostically Learning Halfspaces and ReLUs under Gaussian Marginals, 2020

Diakonikolas, Ilias; Kane, Daniel M; Pensia, Ankit: Outlier Robust Mean Estimation with Subgaussian Rates via Stability, 2020

Diakonikolas, Ilias; Kane, Daniel M: Small Covers for Near-Zero Sets of Polynomials and Learning Latent Variable Models, 2020

Estaki, Mehrbod; Jiang, Lingjing; Bokulich, Nicholas A; McDonald, Daniel; González, Antonio; Kosciolek, Tomasz et al.: QIIME 2 Enables Comprehensive End‐to‐End Analysis of Diverse Microbiome Data and Comparative Studies with Publicly Available Data, 2020

Fedarko, Marcus W; Martino, Cameron; Morton, James T; González, Antonio; Rahman, Gibraan; Marotz, Clarisse A et al.: Visualizing 'omic feature rankings and log-ratios using Qurro., 2020