Open Access Policy Deposits

Morton, James T; Aksenov, Alexander A; Nothias, Louis Felix; Foulds, James R; Quinn, Robert A; Badri, Michelle H et al.: Learning representations of microbe–metabolite interactions, 2019

Moshiri, Niema; Ragonnet-Cronin, Manon; Wertheim, Joel O; Mirarab, Siavash: FAVITES: simultaneous simulation of transmission networks, phylogenetic trees and sequences, 2019

Moshiri, Niema; Smith, Davey M; Mirarab, Siavash: HIV Care Prioritization using Phylogenetic Branch Length, 2019

Mousavi, Nima; Shleizer-Burko, Sharona; Yanicky, Richard; Gymrek, Melissa: Profiling the genome-wide landscape of tandem repeat expansions., 2019

Mukohyama, Junko; Isobe, Taichi; Hu, Qingjiang; Hayashi, Takanori; Watanabe, Takashi; Maeda, Masao et al.: miR-221 Targets QKI to Enhance the Tumorigenic Capacity of Human Colorectal Cancer Stem Cells, 2019

Musa, Julian; Cidre-Aranaz, Florencia; Aynaud, Marie-Ming; Orth, Martin F; Knott, Maximilian ML; Mirabeau, Olivier et al.: Cooperation of cancer drivers with regulatory germline variants shapes clinical outcomes, 2019

Neekhara, Paarth; Donahue, Chris; Puckette, Miller; Dubnov, Shlomo; McAuley, Julian: Expediting TTS Synthesis with Adversarial Vocoding, 2019

Neekhara, Paarth; Hussain, Shehzeen; Pandey, Prakhar; Dubnov, Shlomo; McAuley, Julian; Koushanfar, Farinaz: Universal Adversarial Perturbations for Speech Recognition Systems, 2019

Nguyen, Tanya T; Kosciolek, Tomasz; Maldonado, Yadira; Daly, Rebecca E; Martin, Averria Sirkin; McDonald, Daniel et al.: Differences in gut microbiome composition between persons with chronic schizophrenia and healthy comparison subjects., 2019

Pandey, Sonalisa; Sahoo, Debashis: Identification of gene expression logical invariants in Arabidopsis, 2019

Pöppl, Alexander; Baden, Scott; Bader, Michael: A UPC++ Actor Library and Its Evaluation On a Shallow Water Proxy Application, 2019

Poudel, Saugat; Tsunemoto, Hannah; Meehan, Michael; Szubin, Richard; Olson, Connor A; Lamsa, Anne et al.: Characterization of CA-MRSA TCH1516 exposed to nafcillin in bacteriological and physiological media., 2019

Prodromou, Andreas; Venkat, Ashish; Tullsen, Dean M: Deciphering Predictive Schedulers for Heterogeneous-ISA Multicore Architectures, 2019

Prodromou, Andreas; Venkat, Ashish; Tullsen, Dean M: Platform-Agnostic Learning-Based Scheduling, 2019

Rajasekaran, Swetha; Selvan, Lakshmi Dhevi Nagarajha; Dotts, Kathleen; Kumar, Ranjith; Rishi, Pukhraj; Khetan, Vikas et al.: Non-coding and Coding Transcriptional Profiles Are Significantly Altered in Pediatric Retinoblastoma Tumors, 2019

Rajkumar, Utkrisht; Turner, Kristen; Luebeck, Jens; Deshpande, Viraj; Chandraker, Manmohan; Mischel, Paul et al.: EcSeg: Semantic Segmentation of Metaphase Images Containing Extrachromosomal DNA, 2019

Rajput, Akanksha; Poudel, Saugat; Tsunemoto, Hannah; Meehan, Michael; Szubin, Richard; Olson, Connor A et al.: Profiling the effect of nafcillin on HA-MRSA D712 using bacteriological and physiological media., 2019

Rubinstein, Mara Roxana; Baik, Jung Eun; Lagana, Stephen M; Han, Richard P; Raab, William J; Sahoo, Debashis et al.: Fusobacterium nucleatum promotes colorectal cancer by inducing Wnt/β‐catenin modulator Annexin A1, 2019

Rule, Adam; Birmingham, Amanda; Zuniga, Cristal; Altintas, Ilkay; Huang, Shih-Cheng; Knight, Rob et al.: Ten simple rules for writing and sharing computational analyses in Jupyter Notebooks., 2019

Sanders, Jon G; Nurk, Sergey; Salido, Rodolfo A; Minich, Jeremiah; Xu, Zhenjiang Z; Zhu, Qiyun et al.: Optimizing sequencing protocols for leaderboard metagenomics by combining long and short reads, 2019

Sarmashghi, Shahab; Bafna, Vineet: Computing the Statistical Significance of Overlap between Genome Annotations with iStat., 2019

Sarmashghi, Shahab; Bohmann, Kristine; P Gilbert, M; Bafna, Vineet; Mirarab, Siavash: Skmer: assembly-free and alignment-free sample identification using genome skims., 2019

Sharon, Gil; Cruz, Nikki Jamie; Kang, Dae-Wook; Gandal, Michael J; Wang, Bo; Kim, Young-Mo et al.: Human Gut Microbiota from Autism Spectrum Disorder Promote Behavioral Symptoms in Mice, 2019

Song, Jin; Woodhams, Douglas C; Martino, Cameron; Allaband, Celeste; Mu, Andre; Javorschi-Miller-Montgomery, Sandrine et al.: Engineering the microbiome for animal health and conservation, 2019

Song, Jin; Sanders, Jon G; Baldassarre, Daniel T; Chaves, Jaime A; Johnson, Nicholas S; Piaggio, Antoinette J et al.: Is there convergence of gut microbes in blood-feeding vertebrates?, 2019

Sprecher, Kate E; Ritchie, Hannah K; Burke, Tina M; Depner, Christopher M; Smits, Alexandra N; Dorrestein, Pieter C et al.: Trait-like vulnerability of higher-order cognition and ability to maintain wakefulness during combined sleep restriction and circadian misalignment, 2019

Strandwitz, Philip; Kim, Ki Hyun; Terekhova, Darya; Liu, Joanne K; Sharma, Anukriti; Levering, Jennifer et al.: GABA-modulating bacteria of the human gut microbiota, 2019

Sun, Zheng; Huang, Shi; Zhu, Pengfei; Yue, Feng; Zhao, Helen; Yang, Ming et al.: A Microbiome-Based Index for Assessing Skin Health and Treatment Effects for Atopic Dermatitis in Children, 2019

Taram, Mohammadkazem; Venkat, Ashish; Tullsen, Dean M: Context-Sensitive Decoding: On-Demand Microcode Customization for Security and Energy Management, 2019

Taram, Mohammadkazem; Venkat, Ashish; Tullsen, Dean M: Context-Sensitive Fencing: Securing Speculative Execution via Microcode Customization., 2019

Taram, Mohammadkazem; Venkat, Ashish; Tullsen, Dean M: Packet Chasing: Spying on Network Packets over a Cache Side-Channel., 2019

Thompson, Luke R; Haroon, Mohamed F; Shibl, Ahmed A; Cahill, Matt J; Ngugi, David K; Williams, Gareth J et al.: Red Sea SAR11 and Prochlorococcus Single-Cell Genomes Reflect Globally Distributed Pangenomes., 2019

Tran, Hao Q; Mills, Robert H; Peters, Nicole V; Holder, Mary K; de Vries, Geert J; Knight, Rob et al.: Associations of the Fecal Microbial Proteome Composition and Proneness to Diet-induced Obesity* [S], 2019

Tripathi, Anupriya; Xu, Zhenjiang Zech; Xue, Jin; Poulsen, Orit; Gonzalez, Antonio; Humphrey, Gregory et al.: Intermittent Hypoxia and Hypercapnia Reproducibly Change the Gut Microbiome and Metabolome across Rodent Model Systems, 2019

Venkat, Ashish; Basavaraj, Harsha; Tullsen, Dean M: Composite-ISA Cores: Enabling Multi-ISA Heterogeneity Using a Single ISA, 2019

Verhaak, Roel; Bafna, Vineet; Mischel, Paul: Extrachromosomal oncogene amplification in tumour pathogenesis and evolution., 2019

Vogtmann, Emily; Chen, Jun; Kibriya, Muhammad G; Amir, Amnon; Shi, Jianxin; Chen, Yu et al.: Comparison of oral collection methods for studies of microbiota, 2019

Weinroth, Margaret D; Britton, Brianna C; McCullough, Kathryn R; Martin, Jennifer N; Geornaras, Ifigenia; Knight, Rob et al.: Ground beef microbiome changes with antimicrobial decontamination interventions and product storage, 2019

White, Ruffin; Caiazza, Gianluca; Cortesi, Agostino; Cho, Young Im; Christensen, Henrik I: Black Block Recorder: Immutable Black Box Logging for Robots via Blockchain, 2019

Wu, Sihan; Turner, Kristen M; Nguyen, Nam; Raviram, Ramya; Erb, Marcella; Santini, Jennifer et al.: Circular ecDNA promotes accessible chromatin and high oncogene expression, 2019

Xu, Zhenjiang Zech; Amir, Amnon; Sanders, Jon; Zhu, Qiyun; Morton, James T; Bletz, Molly C et al.: Calour: an Interactive, Microbe-Centric Analysis Tool, 2019

Yan, Ying; Maurer-Alcalá, Xyrus X; Knight, Rob; Kosakovsky Pond, Sergei L; Katz, Laura A: Single-Cell Transcriptomics Reveal a Correlation between Genome Architecture and Gene Family Evolution in Ciliates., 2019

Zhang, Yanxiao; Li, Ting; Preissl, Sebastian; Amaral, Maria Luisa; Grinstein, Jonathan D; Farah, Elie N et al.: Transcriptionally active HERV-H retrotransposons demarcate topologically associating domains in human pluripotent stem cells, 2019

Zhu, Qiyun; Mai, Uyen; Pfeiffer, Wayne; Janssen, Stefan; Asnicar, Francesco; Sanders, Jon G et al.: Phylogenomics of 10,575 genomes reveals evolutionary proximity between domains Bacteria and Archaea, 2019

Aggarwal, Divesh; Dodis, Yevgeniy; Lovett, Shachar: Non-Malleable Codes from Additive Combinatorics, 2018

Aisenberg, James; Bonet, Maria Luisa; Buss, Sam; Crăciun, Adrian; Istrate, Gabriel: Short proofs of the Kneser–Lovász coloring principle, 2018

Akbari, Ali; Vitti, Joseph J; Iranmehr, Arya; Bakhtiari, Mehrdad; Sabeti, Pardis C; Mirarab, Siavash et al.: Identifying the favored mutation in a positive selective sweep, 2018

Applebaum, Benny; Lovett, Shachar: Algebraic Attacks against Random Local Functions and Their Countermeasures, 2018

Aznar, Nicolas; Ear, Jason; Dunkel, Ying; Sun, Nina; Satterfield, Kendall; He, Fang et al.: Convergence of Wnt, growth factor, and heterotrimeric G protein signals on the guanine nucleotide exchange factor Daple, 2018

Bachan, J; Baden, S; Bonachea, D; Hargrove, P; Hofmeyr, S; Ibrahim, K et al.: UPC++ Programmer’s Guide, v1.0-2018.3.0, 2018