研究テーマ

Theory and numerical methods in phylogenomics, software development and open hardware.

業績

See also Scholar, ORCID

Refereed Journal Articles

• 21 : Antonio Pedro Camargo, Stephen Nayfach, I-Min A. Chen, Krishnaveni Palaniappan, Anna Ratner, Ken Chu, Stephan J. Ritter, T. B. K. Reddy, Supratim Mukherjee, Frederik Schulz, Lee Call, Russell Y. Neches, Tanja Woyke, Natalia N. Ivanova, Emiley A. Eloe-Fadrosh, Nikos C. Kyrpides, and Simon Roux. IMG/VR v4: an expanded database of uncultivated virus genomes within a framework of extensive functional, taxonomic, and ecological metadata. Nucleic Acids Research, 2022
• 20 : David Danko and others including Russell Y. Neches. A global metagenomic map of urban microbiomes and antimicrobial resistance. Cell, May 2021
• 19 : Russell Y Neches, Nikos C Kyrpides, and Christos A Ouzounis. Atypical divergence of SARS-CoV-2 ORF8 from ORF7a within the coronavirus lineage suggests potential stealthy viral strategies in immune evasion. Mbio, 2021
• 18 : Simon Roux, David Páez-Espino, I-Min A Chen, Krishna Palaniappan, Anna Ratner, Ken Chu, T B K Reddy, Stephen Nayfach, Frederik Schulz, Lee Call, Russell Y Neches, Tanja Woyke, Natalia N Ivanova, Emiley A Eloe-Fadrosh, Nikos C Kyrpides. IMG/VR v3: an integrated ecological and evolutionary framework for interrogating genomes of uncultivated viruses. Nucleic Acids Research, 2021
• 17 : Russell Y. Neches, Matthew D. McGee, and Nikos C. Kyrpides. Recombination should not be an afterthought. Nature Reviews Microbiology, 2020
• 16 : David A Coil, Russell Y Neches, Jenna M Lang, Guillaume Jospin, Wendy E Brown, Darlene Cavalier, Jarrad Hampton-Marcell, Jack A Gilbert, and Jonathan A Eisen. Bacterial communities associated with cell phones and shoes. PeerJ, 2020
• 15 : Russell Y Neches and Camille Scott. SuchTree: Fast, thread-safe computations with phylogenetic trees. Journal Open Source Software, 2018
• 14 : Jenna M Lang, David A Coil, Russell Y Neches, Wendy E Brown, Darlene Cavalier, Mark Severance, Jarrad Hampton-Marcell, Jack A Gilbert, and Jonathan A Eisen. A microbial survey of the International Space Station (ISS). PeerJ, 2017
• 13 : Daniel Standage, Ali yari, Lisa J. Cohen, Michael R. Crusoe, Tim Head, Luiz Irber, Shannon EK Joslin, N. B. Kingsley, Kevin D. Murray, Russell Neches, Camille Scott, Ryan Shean, Sascha Steinbiss, Cait Sydney, and C. Titus Brown. khmer release v2.1: software for biological sequence analysis. The Journal of Open Source Software, 2017
• 12 : Russell Y Neches, Kaitlin J Flynn, Luis Zaman, Emily Tung, and Nicholas Pudlo. On the intrinsic sterility of 3D printing. PeerJ, 2016
• 11 : David A Coil, Russell Y Neches, Jenna M Lang, Wendy E Brown, Mark Severance, Darlene Cavalier, and Jonathan A Eisen. Growth of 48 built environment bacterial isolates on board the International Space Station (ISS). PeerJ, 2016
• 10 : Matthew D McGee, Russell Y Neches, and Ole Seehausen. Evaluating genomic divergence and parallelism in replicate ecomorphs from young and old cichlid adaptive radiations. Molecular Ecology, 2016
• 9 : 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, Caroline Chénard, Ian T. Paulsen and Federico M. Lauro. Spatially extensive microbial biogeography of the Indian Ocean provides insights into the unique community structure of a pristine coral atoll. Scientific Reports, 2015
• 8 : Matthew D McGee, Samuel R Borstein, Russell Y Neches, Heinz H Buescher, Ole Seehausen, and Peter C Wainwright. A pharyngeal jaw evolutionary innovation facilitated extinction in Lake Victoria cichlids. Science, 2015
• 7 : Federico M Lauro, Svend Jacob Senstius, Jay Cullen, Russell Y Neches, Rachelle M Jensen, Mark V Brown, Aaron E Darling, Michael Givskov, Diane McDougald, Ron Hoeke, et al. The common oceanographer: crowdsourcing the collection of oceanographic data. PLOS Biology, 2014
• 6 : Elizabeth G Wilbanks, David J Larsen, Russell Y Neches, Andrew I Yao, Chia-Ying Wu, Rachel AS Kjolby, and Marc T Facciotti. A workflow for genome-wide mapping of archaeal transcription factors with ChIP-seq. Nucleic Acids Research, 2012
• 5 : Xingpeng Jiang, Morgan GI Langille, Russell Y Neches, Marie Elliot, Simon A Levin,Jonathan A Eisen, Joshua S Weitz, and Jonathan Dushoff. Functional Biogeography of Ocean Microbes Revealed through Non-Negative Matrix Factorization. PLOS ONE, 2012
• 4 : Russell Y Neches, Steven C Cowley, Pierre-Alexandre Gourdain, and Jean-Noel Leboeuf. The convergence of analytic high-β equilibrium in a finite aspect ratio tokamak. Physics of Plasmas, 2008
• 3 : Pierre-Alexandre Gourdain, Jean-Noel Leboeuf, and Russell Y Neches. Stability of highly shifted equilibria in a large aspect ratio low-field tokamak. Physics of Plasmas, 2007
• 2 : Pierre-Alexandre Gourdain, Jean-Noel Leboeuf, and Russell Y Neches. High-resolution magnetohydrodynamic equilibrium code for unity beta plasmas. Journal of Computational Physics, 2006
• 1 : Pierre-Alexandre Gourdain, Steven C Cowley, Jean-Noel Leboeuf, and Russell Y Neches. Stability of highly shifted equilibria in a large-aspect-ratio tokamak. Physical review letters, 2006

Preprints

• 5 : Andrew Thaler, S Kersey Sturdivant, Russell Neches, and Ian Black. OpenCTD: Construction and operation. MarXiv, 2020
• 4 : David Danko and others including Russell Y Neches. Global genetic cartography of urban metagenomes and antimicrobial resistance. BioRxiv, 2019
• 3 : David A Coil, Russell Y Neches, Jenna M Lang, Guillaume Jospin, Wendy E Brown, Darlene Cavalier, Jarrad Hampton-Marcell, Jack A Gilbert, and Jonathan A Eisen. Bacterial communities associated with cell phones and shoes. PeerJ Preprints, 2019
• 2 : Russell Y Neches, Marc T Facciotti, Phillip M Seitzer, and Elizabeth G Wilbanks. In a fit of pique: Analyzing microbial ChIP-Seq data with Pique. PeerJ Preprints, 2014
• 1 : Russell Y Neches, Kaitlin J Flynn, Luis Zaman, Emily Tung, and Nicholas Pudlo. On the intrinsic sterility of 3D printing. PeerJ Preprints, 2014

 

好きな言葉

Yes, of course duct tape works in a near-vacuum. Duct tape works anywhere. Duct tape is magic and should be worshiped.
Andy Weir – The Martian

The major difference between a thing that might go wrong and a thing that cannot possibly go wrong is that when a thing that cannot possibly go wrong goes wrong it usually turns out to be impossible to get at or repair.
Douglas Adams – Mostly Harmless

This is a planet. Most of it is covered in water but it’s still called Earth.
Terry Pratchett – Wings

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