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Recombination should not be an afterthought

Russell Y Neches, Matthew D McGee, Nikos C Kyrpides
2020 Nature Reviews Microbiology  
As recombination behaviour is a major risk factor for developing vaccines and treatments for SARS-CoV-2, why were early efforts to Recombination should not be an afterthought Russell Y.  ...  Neches, Matthew D. McGee and Nikos C. Kyrpides  ... 
doi:10.1038/s41579-020-00451-1 pmid:32958891 pmcid:PMC7503439 fatcat:jv3njof5jvd5lafgbedydpoqzm

On the intrinsic sterility of 3D printing

Russell Y. Neches, Kaitlin J. Flynn, Luis Zaman, Emily Tung, Nicholas Pudlo
2016 PeerJ  
Funding Russell Neches was supported by an Alfred P. Sloan Foundation grant to Jonathan Eisen.  ...  2014a; Neches, 2014d; Neches, 2014e; Neches, 2014b; Neches, 2014c) .  ...  Author Contributions • Russell Y. Neches, Kaitlin J.  ... 
doi:10.7717/peerj.2661 pmid:27920950 pmcid:PMC5136128 fatcat:o6jyadcbm5fgtkqkublgymweim

SuchTree: Fast, thread-safe computations with phylogenetic trees

Russell Y. Neches, Camille Scott
2018 Journal of Open Source Software  
Neches et al., (2018) . SuchTree: Fast, thread-safe computations with phylogenetic trees. Journal of Open Source Software, 3(26), 678.  ... 
doi:10.21105/joss.00678 fatcat:tdoy5pnn2vdpnmw26wpkavhsbm

Untapped viral diversity in global soil metagenomes [article]

Emily B. Graham, David Paez-Espino, Colin Brislawn, Russell Y. Neches, Kirsten S. Hofmockel, Ruonan Wu, Nikos C. Kyrpides, Janet K. Jansson, Jason E. McDermott
2019 bioRxiv   pre-print
L 8 _ P S E D 2 /8 2 -2 5 6 30 |G a0 12 63 80 _1 00 00 12 53 1_ 1/ 1 14|G a008 1455 _100 0068 750; 1/2 G 9M X Y 4_ H Y PV G /7 1-23 0 F9F55 4_FU SOF/8 1-253 0 7 |G a0 0 6 8  ...  CT T/ 27 3-46 3 2 5 |G a0 1 2 63 7 7_ 1 0 00 0 08 2 42 ;2 /2 C 7 Y S F 2 _ N E C H 7/ 8 0 -2 5 6 B 2J 61 7 _ N O S P 7/ 1 0 0-2 8 4 S8 B8 I7_ PE NO 1/7 8-2 38 K 9 G G Y 7  ... 
doi:10.1101/583997 fatcat:jbp5264ttvbj5koeoz3l5wrmmy

Bacterial communities associated with cell phones and shoes

David A. Coil, Russell Y. Neches, Jenna M. Lang, Guillaume Jospin, Wendy E. Brown, Darlene Cavalier, Jarrad Hampton-Marcell, Jack A. Gilbert, Jonathan A. Eisen
2020 PeerJ  
Neches (2020, February 13). ryneches/shoephone: Community analysis of cell phones and shoes : Project MERCCURI (Version 1.1).  ...  Availability The following information was supplied regarding data availability: All data analysis, metadata, supporting files and intermediate analysis files are available at Zenodo: Guillaume Jospin, & Russell  ...  Coil and Russell Y.  ... 
doi:10.7717/peerj.9235 pmid:32551196 pmcid:PMC7292020 fatcat:a57hgwkpprez3ac7ojgrhhcndy

Functional Biogeography of Ocean Microbes Revealed through Non-Negative Matrix Factorization

Xingpeng Jiang, Morgan G. I. Langille, Russell Y. Neches, Marie Elliot, Simon A. Levin, Jonathan A. Eisen, Joshua S. Weitz, Jonathan Dushoff, Matthias Horn
2012 PLoS ONE  
The direct "metagenomic" sequencing of genomic material from complex assemblages of bacteria, archaea, viruses and microeukaryotes has yielded new insights into the structure of microbial communities. For example, analysis of metagenomic data has revealed the existence of previously unknown microbial taxa whose spatial distributions are limited by environmental conditions, ecological competition, and dispersal mechanisms. However, differences in genotypes that might lead biologists to designate
more » ... two microbes as taxonomically distinct need not necessarily imply differences in ecological function. Hence, there is a growing need for large-scale analysis of the distribution of microbial function across habitats. Here, we present a framework for investigating the biogeography of microbial function by analyzing the distribution of protein families inferred from environmental sequence data across a global collection of sites. We map over 6,000,000 protein sequences from unassembled reads from the Global Ocean Survey dataset to 8214 protein families, generating a protein family relative abundance matrix that describes the distribution of each protein family across sites. We then use non-negative matrix factorization (NMF) to approximate these protein family profiles as linear combinations of a small number of ecological components. Each component has a characteristic functional profile and site profile. Our approach identifies common functional signatures within several of the components. We use our method as a filter to estimate functional distance between sites, and find that an NMF-filtered measure of functional distance is more strongly correlated with environmental distance than a comparable PCA-filtered measure. We also find that functional distance is more strongly correlated with environmental distance than with geographic distance, in agreement with prior studies. We identify similar protein functions in several components and suggest that functional co-occurrence across metagenomic samples could lead to future methods for de-novo functional prediction. We conclude by discussing how NMF, and other dimension reduction methods, can help enable a macroscopic functional description of marine ecosystems.
doi:10.1371/journal.pone.0043866 pmid:23049741 pmcid:PMC3445553 fatcat:6wvh64nyz5fl7dpym76mnqvsoy

A microbial survey of the International Space Station (ISS)

Jenna M. Lang, David A. Coil, Russell Y. Neches, Wendy E. Brown, Darlene Cavalier, Mark Severance, Jarrad T. Hampton-Marcell, Jack A. Gilbert, Jonathan A. Eisen
2017 PeerJ  
Coil, Russell Y. Neches and Wendy E. Brown conceived and designed the experiments, reviewed drafts of the paper. • Darlene Cavalier, Mark Severance and Jonathan A.  ... 
doi:10.7717/peerj.4029 pmid:29492330 pmcid:PMC5827671 fatcat:w6gpihxlcndp7p4oedng5q3bmu

Growth of 48 built environment bacterial isolates on board the International Space Station (ISS)

David A. Coil, Russell Y. Neches, Jenna M. Lang, Wendy E. Brown, Mark Severance, Darlene Cavalier, Jonathan A. Eisen
2016 PeerJ  
. • Russell Y. Neches conceived and designed the experiments, performed the experiments, analyzed the data, prepared figures and/or tables, reviewed drafts of the paper. • Jenna M.  ... 
doi:10.7717/peerj.1842 pmid:27019789 pmcid:PMC4806633 fatcat:6g5hkjf3yrac7aqza736lidnxq

Atypical Divergence of SARS-CoV-2 Orf8 from Orf7a within the Coronavirus Lineage Suggests Potential Stealthy Viral Strategies in Immune Evasion

Russell Y. Neches, Nikos C. Kyrpides, Christos A. Ouzounis, Diane E. Griffin
2021 mBio  
[I,L,V][K,R][I,V,Y]}.  ...  Neches et al. ® January/February 2021 Volume 12 Issue 1 e03014-20 4 Neches et al.  ... 
doi:10.1128/mbio.03014-20 pmid:33468697 fatcat:o3sqaue5yzh2hfsuck6tr5baem

A workflow for genome-wide mapping of archaeal transcription factors with ChIP-seq

Elizabeth G. Wilbanks, David J. Larsen, Russell Y. Neches, Andrew I. Yao, Chia-Ying Wu, Rachel A. S. Kjolby, Marc T. Facciotti
2012 Nucleic Acids Research  
protein-DNA binding events were detected using Pique, a novel microbially focused and freely available peak calling application (available at https://, version tag: halo_egw) (Neches  ...  identify binding sites using our open source software package Pique, which reports the candidate binding site's enrichment as the ratio of sequence coverage in the IP data relative to a background control (Neches  ... 
doi:10.1093/nar/gks063 pmid:22323522 pmcid:PMC3378898 fatcat:pny3swh7lrf4hhvf5rwn2f2noe

Spatially extensive microbial biogeography of the Indian Ocean provides insights into the unique community structure of a pristine coral atoll

Thomas C. Jeffries, Martin Ostrowski, Rohan B. Williams, Chao Xie, Rachelle M. Jensen, Joseph J. Grzymski, Svend Jacob Senstius, Michael Givskov, Ron Hoeke, Gayle K. Philip, Russell Y. Neches, Daniela I. Drautz-Moses (+3 others)
2015 Scientific Reports  
We gratefully acknowledge the many volunteers and scientists who sailed S/Y Indigo V during the Indian Ocean passage from Cape Town to Singapore:  ... 
doi:10.1038/srep15383 pmid:26481089 pmcid:PMC4611231 fatcat:qpiusvgdefgxvckgpw3txx5ijy

Global Genetic Cartography of Urban Metagenomes and Anti-Microbial Resistance [article]

David C Danko, Daniela Bezdan, Ebrahim Afshinnekoo, Sofia Ahsanuddin, Josue Alicea, Chandrima Bhattacharya, Malay Bhattacharyya, Ran Blekhman, Daniel J Butler, Eduardo Castro-Nallar, Ana M Canas, Aspassia D Chatziefthimiou (+65 others)
2019 bioRxiv   pre-print
Although studies have shown that urban environments and mass-transit systems have geospatially distinct metagenomes, no study has ever systematically studied these dense, human/microbial ecosystems around the world. To address this gap in knowledge, we created a global metagenomic and antimicrobial resistance (AMR) atlas of urban mass transit systems from 58 cities, spanning 3,741 samples and 4,424 taxonomically-defined microorganisms collected for three years. The map provides annotated,
more » ... tial data about microbial strains, functional genetics, antimicrobial resistance, and novel genetic elements, including 10,928 novel predicted viral species. Urban microbiomes often resemble human commensal microbiomes from the skin and airways but contain a consistent "core" of 61 species which are predominantly not human commensal species. These data also show that AMR density across cities varies by several orders of magnitude with many AMRs present on plasmids with cosmopolitan distributions. Conversely, samples may be accurately (91.4%) classified to their city-of-origin using a linear support vector machine over taxa. Together, these results constitute a high-resolution global metagenomic atlas, which enables the discovery of new genetic components of the built human environment, forensic application, and an essential first draft of the global AMR burden of the world's cities
doi:10.1101/724526 fatcat:c653fsd4czhepptt7nhkkg6d64

Page 251 of CORROSION Vol. 5, Issue 7 [page]

J JACKSON, Hedley V., Jefferson Chemical Co., Port Neches, Tex. JACKSON, Russell, Rust-Proofing, Inc., 1220 East Henshaw Rd., Phoenix, Ariz. JELINEK, F.  ...  JOHNSON, Russell K., Darling Valve & Manu- facturing Co., Williamsport, Pa. For mail: 70 Pine St., New York, N. Y. JOHNSON, William W., The Texas Co., Box 712, Port Arthur, Tex.  ... 

Page 394 of Current Geographical Publications Vol. 9, Issue 10 [page]

1946 Current Geographical Publications  
- 394 «- Russell, Je Co, 113 Russell Cortez, Fernando, 176 Russia, Academy of sciences, 174 Russia.  ...  Y.-Vt., “198 Salerno, Ase, 111, 251 Sales, Apolonio, 67 Salinas quad., Puerto Rico, "66 Salis, Re.  ... 

Page 533 of Teachers College Record Vol. 26, Issue 6 [page]

1925 Teachers College Record  
Russell, Olivia—Teacher of Spanish and history, High School, Lakewood, | aes Russo, Salvatore V. H.—Instructor in fine arts, University of Oklahoma, Norman, Okla.  ...  Schwieger, Dorothy—Religious educa- tion and membership secretary, Y. W. C. A., St. Paul, Minn.  ... 
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