Open Access Policy Deposits

McDonald, Daniel; Hyde, Embriette; Debelius, Justine W; Morton, James T; Gonzalez, Antonio; Ackermann, Gail et al.: American Gut: an Open Platform for Citizen Science Microbiome Research, 2018

Michaud, Jennifer M; Thompson, Luke R; Kaul, Drishti; Espinoza, Josh L; Richter, R Alexander; Xu, Zhenjiang Zech et al.: Taxon-specific aerosolization of bacteria and viruses in an experimental ocean-atmosphere mesocosm, 2018

Minich, Jeremiah J; Humphrey, Greg; Benitez, Rodolfo AS; Sanders, Jon; Swafford, Austin; Allen, Eric E et al.: High-Throughput Miniaturized 16S rRNA Amplicon Library Preparation Reduces Costs while Preserving Microbiome Integrity., 2018

Minich, Jeremiah J; Zhu, Qiyun; Janssen, Stefan; Hendrickson, Ryan; Amir, Amnon; Vetter, Russ et al.: KatharoSeq Enables High-Throughput Microbiome Analysis from Low-Biomass Samples, 2018

Minich, Jeremiah J; Zhu, Qiyun; Xu, Zhenjiang Zech; Amir, Amnon; Ngochera, Maxon; Simwaka, Moses et al.: Microbial effects of livestock manure fertilization on freshwater aquaculture ponds rearing tilapia (Oreochromis shiranus) and North African catfish (Clarias gariepinus), 2018

Morton, James T; Toran, Liam; Edlund, Anna; Metcalf, Jessica L; Lauber, Christian; Knight, Rob: Correction for Morton et al., “Uncovering the Horseshoe Effect in Microbial Analyses”, 2018

Naughton, Perry; Roux, Philippe; Schurgers, Curt; Kastner, Ryan; Jaffe, Jules S; Roberts, Paul LD: Self-Localization of a Deforming Swarm of Underwater Vehicles Using Impulsive Sound Sources of Opportunity, 2018

Naughton, Perry; Roux, Philippe; Schurgers, Curt; Kastner, Ryan; Jaffe, Jules S; Roberts, Paul LD: Self-localization of a mobile swarm using noise correlations with local sources of opportunity., 2018

Nguyen, Tanya T; Kosciolek, Tomasz; Eyler, Lisa T; Knight, Rob; Jeste, Dilip V: Overview and systematic review of studies of microbiome in schizophrenia and bipolar disorder, 2018

Nguyen, Nam-phuong D; Deshpande, Viraj; Luebeck, Jens; Mischel, Paul S; Bafna, Vineet: ViFi: accurate detection of viral integration and mRNA fusion reveals indiscriminate and unregulated transcription in proximal genomic regions in cervical cancer, 2018

Pisha, Louis; Hamilton, Sean; Sengupta, Dhiman; Lee, Ching-Hua; Vastare, Krishna; Zubatiy, Tamara et al.: A Wearable Platform for Research in Augmented Hearing., 2018

Quinn, RA; Adem, S; Mills, R; DeRight-Goldasich, L; Humphrey, G; Conrad, DJ et al.: NEUTROPHILIC PROTEOLYSIS IN THE CYSTIC FIBROSIS LUNG FAVORS A PATHOGENIC MICROBIOME, 2018

Quinn, Robert A; Comstock, William; Zhang, Tianyu; Morton, James T; da Silva, Ricardo; Tran, Alda et al.: Niche partitioning of a pathogenic microbiome driven by chemical gradients, 2018

Ramírez, Julian; Rodriquez, Daniel; Qiao, Fang; Warchall, Julian; Rye, Jasmine; Aklile, Eden et al.: Metallic Nanoislands on Graphene for Monitoring Swallowing Activity in Head and Neck Cancer Patients, 2018

Richardson, Joshua B; Dancy, Blair CR; Horton, Cassandra L; Lee, Young S; Madejczyk, Michael S; Xu, Zhenjiang Zech et al.: Exposure to toxic metals triggers unique responses from the rat gut microbiota, 2018

Rozanov, Dmitri V; Rozanov, Nikita D; Chiotti, Kami E; Reddy, Ashok; Wilmarth, Phillip A; David, Larry L et al.: MHC class I loaded ligands from breast cancer cell lines: A potential HLA-I-typed antigen collection, 2018

Rule, Adam; Birmingham, Amanda; Zuniga, Cristal; Altintas, Ilkay; Huang, Shih-Cheng; Knight, Rob et al.: Ten Simple Rules for Reproducible Research in Jupyter Notebooks, 2018

Sahoo, Debashis; Wei, Wei; Auman, Heidi; Hurtado-Coll, Antonio; Carroll, Peter R; Fazli, Ladan et al.: Boolean analysis identifies CD38 as a biomarker of aggressive localized prostate cancer, 2018

Saini, Shubham; Mitra, Ileena; Mousavi, Nima; Fotsing, Stephanie Feupe; Gymrek, Melissa: A reference haplotype panel for genome-wide imputation of short tandem repeats, 2018

Sereti, Konstantina-Ioanna; Nguyen, Ngoc B; Kamran, Paniz; Zhao, Peng; Ranjbarvaziri, Sara; Park, Shuin et al.: Analysis of cardiomyocyte clonal expansion during mouse heart development and injury, 2018

Shalapour, Shabnam; Lin, Xue-Jia; Bastian, Ingmar N; Brain, John; Burt, Alastair D; Aksenov, Alexander A et al.: Author Correction: Inflammation-induced IgA+ cells dismantle anti-liver cancer immunity, 2018

Shen, Lixiang; Mu, Dejun; Cao, Guo; Qin, Maoyuan; Blackstone, Jeremy; Kastner, Ryan: Symbolic execution based test-patterns generation algorithm for hardware Trojan detection, 2018

Shondelmyer, Kaitlyn; Knight, Rob; Sanivarapu, Anusha; Ogino, Shuji; Vanamala, Jairam KP: Ancient <i>Thali</i> Diet: Gut Microbiota, Immunity, and Health., 2018

Sinha, Rashmi; Ahsan, Habibul; Blaser, Martin; Caporaso, J Gregory; Carmical, Joseph Russell; Chan, Andrew T et al.: Next steps in studying the human microbiome and health in prospective studies, Bethesda, MD, May 16–17, 2017, 2018

Smith, Arfon M; Niemeyer, Kyle E; Katz, Daniel S; Barba, Lorena A; Githinji, George; Gymrek, Melissa et al.: Journal of Open Source Software (JOSS): design and first-year review, 2018

Stanislawski, Maggie A; Dabelea, Dana; Wagner, Brandie D; Iszatt, Nina; Dahl, Cecilie; Sontag, Marci K et al.: Gut Microbiota in the First 2 Years of Life and the Association with Body Mass Index at Age 12 in a Norwegian Birth Cohort, 2018

Street, Richard L; Liu, Lin; Farber, Neil J; Chen, Yunan; Calvitti, Alan; Weibel, Nadir et al.: Keystrokes, Mouse Clicks, and Gazing at the Computer: How Physician Interaction with the EHR Affects Patient Participation, 2018

Su, Xiaoquan; Jing, Gongchao; McDonald, Daniel; Wang, Honglei; Wang, Zengbin; Gonzalez, Antonio et al.: Identifying and Predicting Novelty in Microbiome Studies, 2018

Tripathi, Anupriya; Marotz, Clarisse; Gonzalez, Antonio; Vázquez-Baeza, Yoshiki; Song, Jin; Bouslimani, Amina et al.: Are microbiome studies ready for hypothesis-driven research?, 2018

Tripathi, Anupriya; Debelius, Justine; Brenner, David A; Karin, Michael; Loomba, Rohit; Schnabl, Bernd et al.: The gut–liver axis and the intersection with the microbiome, 2018

Tripathi, Anupriya; Melnik, Alexey V; Xue, Jin; Poulsen, Orit; Meehan, Michael J; Humphrey, Gregory et al.: Intermittent Hypoxia and Hypercapnia, a Hallmark of Obstructive Sleep Apnea, Alters the Gut Microbiome and Metabolome, 2018

Tripathi, Anupriya; Debelius, Justine; Brenner, David A; Karin, Michael; Loomba, Rohit; Schnabl, Bernd et al.: Publisher Correction: The gut–liver axis and the intersection with the microbiome, 2018

Vance, ME; Farmer, DK; Novoselac, A; Corsi, R; Ruiz, LH; Abbatt, J et al.: An overview and early results from the HOMEChem indoor air chemistry field campaign, 2018

Vázquez-Baeza, Yoshiki; Gonzalez, Antonio; Xu, Zhenjiang Zech; Washburne, Alex; Herfarth, Hans H; Sartor, R Balfour et al.: Guiding longitudinal sampling in IBD cohorts., 2018

Vrbanac, Alison; Riestra, Angelica M; Coady, Alison; Knight, Rob; Nizet, Victor; Patras, Kathryn A: The murine vaginal microbiota and its perturbation by the human pathogen group B Streptococcus, 2018

Walters, William A; Jin, Zhao; Youngblut, Nicholas; Wallace, Jason G; Sutter, Jessica; Zhang, Wei et al.: Large-scale replicated field study of maize rhizosphere identifies heritable microbes, 2018

Yan, Songbai; Chaudhuri, Kamalika; Javidi, Tara: Active Learning with Logged Data, 2018

Zarrinpar, Amir; Chaix, Amandine; Xu, Zhenjiang Z; Chang, Max W; Marotz, Clarisse A; Saghatelian, Alan et al.: Antibiotic-induced microbiome depletion alters metabolic homeostasis by affecting gut signaling and colonic metabolism, 2018

Zhang, Chicheng; Mukamel, Eran A; Chaudhuri, Kamalika: Spectral Learning of Binomial HMMs for DNA Methylation Data, 2018

Zhou, Yuehai; Song, Aijun; Tong, F; Kastner, Ryan: Distributed compressed sensing based channel estimation for underwater acoustic multiband transmissions., 2018

Zhou, Youlian; Xu, Zhenjiang Zech; He, Yan; Yang, Yunsheng; Liu, Le; Lin, Qianyun et al.: Gut Microbiota Offers Universal Biomarkers across Ethnicity in Inflammatory Bowel Disease Diagnosis and Infliximab Response Prediction, 2018

Amir, Amnon; McDonald, Daniel; Navas-Molina, Jose A; Debelius, Justine; Morton, James T; Hyde, Embriette et al.: Correcting for Microbial Blooms in Fecal Samples during Room-Temperature Shipping, 2017

Amir, Amnon; McDonald, Daniel; Navas-Molina, Jose A; Kopylova, Evguenia; Morton, James T; Xu, Zhenjiang Zech et al.: Deblur Rapidly Resolves Single-Nucleotide Community Sequence Patterns, 2017

Bachan, J; Baden, S; Bonachea, D; Hargrove, P; Hofmeyr, S; Ibrahim, K et al.: UPC++ Programmer’s Guide, v1.0-2017.9, 2017

Bachan, J; Baden, S; Bonachea, D; Hargrove, P; Hofmeyr, S; Ibrahim, K et al.: UPC++ Specification v1.0, Draft 4, 2017

Becker, Andrew; Hu, Wei; Tai, Yu; Brisk, Philip; Kastner, Ryan; Ienne, Paolo: Arbitrary Precision and Complexity Tradeoffs for Gate-Level Information Flow Tracking, 2017

Bonachea, D; Bachan, J; Hargrove, P; Hofmeyr, S; Jacquelin, M; Kamil, A et al.: The UPC++ PGAS library for Exascale Computing: Extended Abstract, 2017

Bowers, Robert M; Kyrpides, Nikos C; Stepanauskas, Ramunas; Harmon-Smith, Miranda; Doud, Devin; Reddy, TBK et al.: Minimum information about a single amplified genome (MISAG) and a metagenome-assembled genome (MIMAG) of bacteria and archaea, 2017

Cai, Shang; Kalisky, Tomer; Sahoo, Debashis; Dalerba, Piero; Feng, Weiguo; Lin, Yuan et al.: A Quiescent Bcl11b High Stem Cell Population Is Required for Maintenance of the Mammary Gland, 2017

Calderon, Joanna; Ayala, Guadalupe X; Elder, John P; Belch, George E; Castro, Iana A; Weibel, Nadir et al.: What Happens When Parents and Children Go Grocery Shopping? An Observational Study of Latino Dyads in Southern California, USA, 2017