Open Access Policy Deposits

Martino, Cameron; McDonald, Daniel; Cantrell, Kalen; Dilmore, Amanda Hazel; Vázquez-Baeza, Yoshiki; Shenhav, Liat et al.: Compositionally Aware Phylogenetic Beta-Diversity Measures Better Resolve Microbiomes Associated with Phenotype, 2022

McGuinness, Rob; Porter, George: Stipulated Smartphones for Students: The Requirements of Modern Technology for Academia, 2022

Mills, Robert H; Dulai, Parambir S; Vázquez-Baeza, Yoshiki; Sauceda, Consuelo; Daniel, Noëmie; Gerner, Romana R et al.: Multi-omics analyses of the ulcerative colitis gut microbiome link Bacteroides vulgatus proteases with disease severity, 2022

Minich, Jeremiah J; Härer, Andreas; Vechinski, Joseph; Frable, Benjamin W; Skelton, Zachary R; Kunselman, Emily et al.: Host biology, ecology and the environment influence microbial biomass and diversity in 101 marine fish species, 2022

Moshiri, Niema: NiemaGraphGen: A memory-efficient global-scale contact network simulation toolkit, 2022

Moshiri, Niema; Fisch, Kathleen M; Birmingham, Amanda; DeHoff, Peter; Yeo, Gene W; Jepsen, Kristen et al.: The ViReflow pipeline enables user friendly large scale viral consensus genome reconstruction, 2022

Narunsky-Haziza, Lian; Sepich-Poore, Gregory D; Livyatan, Ilana; Asraf, Omer; Martino, Cameron; Nejman, Deborah et al.: Pan-cancer analyses reveal cancer-type-specific fungal ecologies and bacteriome interactions, 2022

Needham, Brittany D; Funabashi, Masanori; Adame, Mark D; Wang, Zhuo; Boktor, Joseph C; Haney, Jillian et al.: A gut-derived metabolite alters brain activity and anxiety behaviour in mice, 2022

Park, Jonghun; Bakhtiari, Mehrdad; Popp, Bernt; Wiesener, Michael; Bafna, Vineet: Detecting tandem repeat variants in coding regions using code-adVNTR, 2022

Pekar, Jonathan E; Magee, Andrew; Parker, Edyth; Moshiri, Niema; Izhikevich, Katherine; Havens, Jennifer L et al.: The molecular epidemiology of multiple zoonotic origins of SARS-CoV-2, 2022

Peters, Brandilyn A; Lin, Juan; Qi, Qibin; Usyk, Mykhaylo; Isasi, Carmen R; Mossavar-Rahmani, Yasmin et al.: Menopause Is Associated with an Altered Gut Microbiome and Estrobolome, with Implications for Adverse Cardiometabolic Risk in the Hispanic Community Health Study/Study of Latinos, 2022

Popp, Bernt; Ekici, Arif; Knaup, Karl; Schneider, Karen; Uebe, Steffen; Park, Jonghun et al.: Prevalence of hereditary tubulointerstitial kidney diseases in the German Chronic Kidney Disease study., 2022

Qi, Qibin; Li, Jun; Yu, Bing; Moon, Jee-Young; Chai, Jin C; Merino, Jordi et al.: Host and gut microbial tryptophan metabolism and type 2 diabetes: an integrative analysis of host genetics, diet, gut microbiome and circulating metabolites in cohort studies, 2022

Qin, Youwen; Havulinna, Aki S; Liu, Yang; Jousilahti, Pekka; Ritchie, Scott C; Tokolyi, Alex et al.: Combined effects of host genetics and diet on human gut microbiota and incident disease in a single population cohort, 2022

Ruuskanen, Matti O; Erawijantari, Pande P; Havulinna, Aki S; Liu, Yang; Méric, Guillaume; Tuomilehto, Jaakko et al.: Gut Microbiome Composition Is Predictive of Incident Type 2 Diabetes in a Population Cohort of 5,572 Finnish Adults, 2022

Salo, Virginia C; Pannuto, Pat; Hedgecock, William; Biri, Andreas; Russo, David A; Piersiak, Hannah A et al.: Measuring naturalistic proximity as a window into caregiver–child interaction patterns, 2022

Sauceda, Consuelo; Bayne, Charlie; Sudqi, Khadijeh; Gonzalez, Antonio; Dulai, Parambir S; Knight, Rob et al.: Stool multi-omics for the study of host–microbe interactions in inflammatory bowel disease, 2022

Sepich‐Poore, Gregory D; Guccione, Caitlin; Laplane, Lucie; Pradeu, Thomas; Curtius, Kit; Knight, Rob: Cancer's second genome: Microbial cancer diagnostics and redefining clonal evolution as a multispecies process, 2022

Sfiligoi, Igor; Armstrong, George; Gonzalez, Antonio; McDonald, Daniel; Knight, Rob: Optimizing UniFrac with OpenACC Yields Greater Than One Thousand Times Speed Increase, 2022

Shaffer, Justin P; Carpenter, Carolina S; Martino, Cameron; Salido, Rodolfo A; Minich, Jeremiah J; Bryant, MacKenzie et al.: A comparison of six DNA extraction protocols for 16S, ITS and shotgun metagenomic sequencing of microbial communities, 2022

Shaffer, Justin P; Nothias, Louis-Félix; Thompson, Luke R; Sanders, Jon G; Salido, Rodolfo A; Couvillion, Sneha P et al.: Standardized multi-omics of Earth’s microbiomes reveals microbial and metabolite diversity, 2022

Sholl, Jonathan; Sepich-Poore, Gregory D; Knight, Rob; Pradeu, Thomas: Redrawing therapeutic boundaries: microbiota and cancer, 2022

Sinha, Saptarshi; Castillo, Vanessa; Espinoza, Celia R; Tindle, Courtney; Fonseca, Ayden G; Dan, Jennifer M et al.: COVID-19 lung disease shares driver AT2 cytopathic features with Idiopathic pulmonary fibrosis, 2022

Smart, Mary Anne; Sood, Dhruv; Vaccaro, Kristen: Understanding Risks of Privacy Theater with Differential Privacy, 2022

Subramanian, Rohan; Sahoo, Debashis: Boolean implication analysis of single-cell data predicts retinal cell type markers, 2022

Taram, Mohammadkazem; Venkat, Ashish; Tullsen, Dean M: Mitigating Speculative Execution Attacks via Context-Sensitive Fencing., 2022

Taram, Mohammadkazem; Ren, Xida; Venkat, Ashish; Tullsen, Dean M: SecSMT: Securing SMT Processors against Contention-Based Covert Channels., 2022

Turakhia, Yatish; Thornlow, Bryan; Hinrichs, Angie; McBroome, Jakob; Ayala, Nicolas; Ye, Cheng et al.: Pandemic-scale phylogenomics reveals the SARS-CoV-2 recombination landscape, 2022

Yan, An; McAuley, Julian; Lu, Xing; Du, Jiang; Chang, Eric Y; Gentili, Amilcare et al.: RadBERT: Adapting Transformer-based Language Models to Radiology., 2022

Yatham, Brahmendra; Wang, Shu-Ting; Kim, Dohee; Sarikhani, Parisa; Mahmoudi, Babak; Mahajan, Divya et al.: Yin-Yang: Programming Abstractions for Cross-Domain Multi-Acceleration., 2022

Yen, Alex; Shah, Zeal; Ochoa, Benjamin; Pannuto, Pat; Taneja, Jay: EffiSenseSee, 2022

Young, Colin; Meng, Sarah; Moshiri, Niema: An Evaluation of Phylogenetic Workflows in Viral Molecular Epidemiology, 2022

Zhu, Qiyun; Huang, Shi; Gonzalez, Antonio; McGrath, Imran; McDonald, Daniel; Haiminen, Niina et al.: Phylogeny-Aware Analysis of Metagenome Community Ecology Based on Matched Reference Genomes while Bypassing Taxonomy, 2022

Aksenov, Alexander A; Laponogov, Ivan; Zhang, Zheng; Doran, Sophie LF; Belluomo, Ilaria; Veselkov, Dennis et al.: Auto-deconvolution and molecular networking of gas chromatography-mass spectrometry data., 2021

Alderete, Tanya L; Jones, Roshonda B; Shaffer, Justin P; Holzhausen, Elizabeth A; Patterson, William B; Kazemian, Elham et al.: Early life gut microbiota is associated with rapid infant growth in Hispanics from Southern California, 2021

Allaband, Celeste; Lingaraju, Amulya; Martino, Cameron; Russell, Baylee; Tripathi, Anupriya; Poulsen, Orit et al.: Intermittent Hypoxia and Hypercapnia Alter Diurnal Rhythms of Luminal Gut Microbiome and Metabolome, 2021

Almaraz, Kimberly; Jang, Tyler; Lewis, McKenna; Ngo, Titan; Song, Miranda; Moshiri, Niema: SEPIA: simulation-based evaluation of prioritization algorithms, 2021

Alweiss, Ryan; Lovett, Shachar; Wu, Kewen; Zhang, Jiapeng: Improved bounds for the sunflower lemma, 2021

Ambrosi, Thomas H; Marecic, Owen; McArdle, Adrian; Sinha, Rahul; Gulati, Gunsagar S; Tong, Xinming et al.: Aged skeletal stem cells generate an inflammatory degenerative niche, 2021

Andrade, Gianna; Baca, Rachel E; Liu, Weichen; Schulze, Jurgen; Courtney, Kelly E: Substance Cue Exposure in Virtual Reality: Task Development and Early Results, 2021

Armstrong, George; Cantrell, Kalen; Huang, Shi; McDonald, Daniel; Haiminen, Niina; Carrieri, Anna Paola et al.: Efficient computation of Faith's phylogenetic diversity with applications in characterizing microbiomes, 2021

Armstrong, George; Martino, Cameron; Rahman, Gibraan; Gonzalez, Antonio; Vázquez-Baeza, Yoshiki; Mishne, Gal et al.: Uniform Manifold Approximation and Projection (UMAP) Reveals Composite Patterns and Resolves Visualization Artifacts in Microbiome Data, 2021

Baker, Jonathon L; Morton, James T; Dinis, Márcia; Alvarez, Ruth; Tran, Nini C; Knight, Rob et al.: Deep metagenomics examines the oral microbiome during dental caries, revealing novel taxa and co-occurrences with host molecules, 2021

Bakhtiari, Mehrdad; Park, Jonghun; Ding, Yuan-Chun; Shleizer-Burko, Sharona; Neuhausen, Susan L; Halldórsson, Bjarni V et al.: Variable number tandem repeats mediate the expression of proximal genes, 2021

Bangaru, Sai Praveen; Michel, Jesse; Mu, Kevin; Bernstein, Gilbert; Li, Tzu-Mao; Ragan-Kelley, Jonathan: Systematically differentiating parametric discontinuities, 2021

Behsaz, Bahar; Bode, Edna; Gurevich, Alexey; Shi, Yan-Ni; Grundmann, Florian; Acharya, Deepa et al.: Integrating genomics and metabolomics for scalable non-ribosomal peptide discovery, 2021

Blackstone, Jeremy; Das, Debayan; Althoff, Alric; Sen, Shreyas; Kastner, Ryan: iSTELLAR: intermittent Signature aTtenuation Embedded CRYPTO with Low-Level metAl Routing, 2021

Brogan, Daniel J; Chaverra-Rodriguez, Duverney; Lin, Calvin P; Smidler, Andrea L; Yang, Ting; Alcantara, Lenissa M et al.: Development of a Rapid and Sensitive CasRx-Based Diagnostic Assay for SARS-CoV‑2, 2021

Byrd, Doratha A; Vogtmann, Emily; Wu, Zeni; Han, Yongli; Wan, Yunhu; Clegg‐Lamptey, Joe‐Nat et al.: Associations of fecal microbial profiles with breast cancer and nonmalignant breast disease in the Ghana Breast Health Study, 2021

Cantrell, Kalen; Fedarko, Marcus W; Rahman, Gibraan; McDonald, Daniel; Yang, Yimeng; Zaw, Thant et al.: EMPress Enables Tree-Guided, Interactive, and Exploratory Analyses of Multi-omic Data Sets, 2021