Search Results - "Neches, Russell Y"

IMG/VR v4: an expanded database of uncultivated virus genomes within a framework of extensive functional, taxonomic, and ecological metadata by Camargo, Antonio Pedro, Nayfach, Stephen, Chen, I-Min A, Palaniappan, Krishnaveni, Ratner, Anna, Chu, Ken, Ritter, Stephan J, Reddy, T B K, Mukherjee, Supratim, Schulz, Frederik, Call, Lee, Neches, Russell Y, Woyke, Tanja, Ivanova, Natalia N, Eloe-Fadrosh, Emiley A, Kyrpides, Nikos C, Roux, Simon

“…Viruses are widely recognized as critical members of all microbiomes. Metagenomics enables large-scale exploration of the global virosphere, progressively…”
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IMG/VR v3: an integrated ecological and evolutionary framework for interrogating genomes of uncultivated viruses by Roux, Simon, Páez-Espino, David, Chen, I-Min A, Palaniappan, Krishna, Ratner, Anna, Chu, Ken, Reddy, T B K, Nayfach, Stephen, Schulz, Frederik, Call, Lee, Neches, Russell Y, Woyke, Tanja, Ivanova, Natalia N, Eloe-Fadrosh, Emiley A, Kyrpides, Nikos C

“…Abstract Viruses are integral components of all ecosystems and microbiomes on Earth. Through pervasive infections of their cellular hosts, viruses can reshape…”
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Atypical Divergence of SARS-CoV-2 Orf8 from Orf7a within the Coronavirus Lineage Suggests Potential Stealthy Viral Strategies in Immune Evasion by Neches, Russell Y, Kyrpides, Nikos C, Ouzounis, Christos A

“…Orf8, one of the most puzzling genes in the SARS lineage of coronaviruses, marks a unique and striking difference in genome organization between SARS-CoV-2 and…”
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Genomic adaptation of giant viruses in polar oceans by Meng, Lingjie, Delmont, Tom O., Gaïa, Morgan, Pelletier, Eric, Fernàndez-Guerra, Antonio, Chaffron, Samuel, Neches, Russell Y., Wu, Junyi, Kaneko, Hiroto, Endo, Hisashi, Ogata, Hiroyuki

“…Despite being perennially frigid, polar oceans form an ecosystem hosting high and unique biodiversity. Various organisms show different adaptive strategies in…”
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On the intrinsic sterility of 3D printing by Neches, Russell Y, Flynn, Kaitlin J, Zaman, Luis, Tung, Emily, Pudlo, Nicholas

“…3D printers that build objects using extruded thermoplastic are quickly becoming commonplace tools in laboratories. We demonstrate that with appropriate…”
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A microbial survey of the International Space Station (ISS) by Lang, Jenna M, Coil, David A, Neches, Russell Y, Brown, Wendy E, Cavalier, Darlene, Severance, Mark, Hampton-Marcell, Jarrad T, Gilbert, Jack A, Eisen, Jonathan A

“…Modern advances in sequencing technology have enabled the census of microbial members of many natural ecosystems. Recently, attention is increasingly being…”
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Functional biogeography of ocean microbes revealed through non-negative matrix factorization by Jiang, Xingpeng, Langille, Morgan G I, Neches, Russell Y, Elliot, Marie, Levin, Simon A, Eisen, Jonathan A, Weitz, Joshua S, Dushoff, Jonathan

“…The direct "metagenomic" sequencing of genomic material from complex assemblages of bacteria, archaea, viruses and microeukaryotes has yielded new insights…”
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Growth of 48 built environment bacterial isolates on board the International Space Station (ISS) by Coil, David A, Neches, Russell Y, Lang, Jenna M, Brown, Wendy E, Severance, Mark, Cavalier, Darlene, Eisen, Jonathan A

“…Background. While significant attention has been paid to the potential risk of pathogenic microbes aboard crewed spacecraft, the non-pathogenic microbes in…”
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Bacterial communities associated with cell phones and shoes by Coil, David A, Neches, Russell Y, Lang, Jenna M, Jospin, Guillaume, Brown, Wendy E, Cavalier, Darlene, Hampton-Marcell, Jarrad, Gilbert, Jack A, Eisen, Jonathan A

“…Every human being carries with them a collection of microbes, a collection that is likely both unique to that person, but also dynamic as a result of…”
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Evaluating genomic divergence and parallelism in replicate ecomorphs from young and old cichlid adaptive radiations by McGee, Matthew D., Neches, Russell Y., Seehausen, Ole

“…Comparative genomic studies of closely related species typically focus on single species pairs at one given stage of divergence. That makes it difficult to…”
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Recombination should not be an afterthought by Neches, Russell Y., McGee, Matthew D., Kyrpides, Nikos C.

“…This month’s Genome Watch highlights how the search for the origins of SARS-CoV-2 emphasizes the need for integrated phylogenetic methods. This month’s Genome…”
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A pharyngeal jaw evolutionary innovation facilitated extinction in Lake Victoria cichlids by McGee, Matthew D., Borstein, Samuel R., Neches, Russell Y., Buescher, Heinz H., Seehausen, Ole, Wainwright, Peter C.

“…Evolutionary innovations, traits that give species access to previously unoccupied niches, may promote speciation and adaptive radiation. Here, we show that…”
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A workflow for genome-wide mapping of archaeal transcription factors with ChIP-seq by Wilbanks, Elizabeth G, Larsen, David J, Neches, Russell Y, Yao, Andrew I, Wu, Chia-Ying, Kjolby, Rachel A S, Facciotti, Marc T

“…Deciphering the structure of gene regulatory networks across the tree of life remains one of the major challenges in postgenomic biology. We present a novel…”
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Spatially extensive microbial biogeography of the Indian Ocean provides insights into the unique community structure of a pristine coral atoll by Jeffries, Thomas C., Ostrowski, Martin, Williams, Rohan B., Xie, Chao, Jensen, Rachelle M., Grzymski, Joseph J., Senstius, Svend Jacob, Givskov, Michael, Hoeke, Ron, Philip, Gayle K., Neches, Russell Y., Drautz-Moses, Daniela I., Chénard, Caroline, Paulsen, Ian T., Lauro, Federico M.

“…Microorganisms act both as drivers and indicators of perturbations in the marine environment. In an effort to establish baselines to predict the response of…”
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Correction: A microbial survey of the International Space Station (ISS) by Lang, Jenna M, Coil, David A, Neches, Russell Y, Brown, Wendy E, Cavalier, Darlene, Severance, Mark, Hampton-Marcell, Jarrad T, Gilbert, Jack A, Eisen, Jonathan A

“…[This corrects the article DOI: 10.7717/peerj.4029.]…”
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Cartography of opportunistic pathogens and antibiotic resistance genes in a tertiary hospital environment by Chng, Kern Rei, Li, Chenhao, Bertrand, Denis, Ng, Amanda Hui Qi, Kwah, Junmei Samantha, Low, Hwee Meng, Tong, Chengxuan, Natrajan, Maanasa, Zhang, Michael Hongjie, Xu, Licheng, Ko, Karrie Kwan Ki, Ho, Eliza Xin Pei, Av-Shalom, Tamar V., Teo, Jeanette Woon Pei, Khor, Chiea Chuen, Chen, Swaine L., Mason, Christopher E., Ng, Oon Tek, Marimuthu, Kalisvar, Ang, Brenda, Nagarajan, Niranjan

“…Although disinfection is key to infection control, the colonization patterns and resistomes of hospital-environment microbes remain underexplored. We report…”
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THE OpenCTD: A LOW-COST, OPEN-SOURCE CTD FOR COLLECTING BASELINE OCEANOGRAPHIC DATA IN COASTAL WATERS by Thaler, Andrew, Sturdivant, S. Kersey, Neches, Russell Y., Levenson, J. Jacob

“…CTDs, devices that measure salinity (via conductivity), temperature, and depth in the ocean, are essential for almost all marine scientific research, whether…”
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SuchTree: Fast, thread-safe computations with phylogenetic trees by Y. Neches, Russell, Scott, Camille

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Prediction of Ecological Function in the Microbiome Using Machine Learning on the Graph Spectra of Coevolving Subnetworks by Neches, Russell Y

“…Chapter 1. We propose a method for predicting the ecological function of host-associated microbes using neural networks trained on a feature space of labeled…”
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