Tortoise Dance Party

About

Um, hi! I'm a microbiologist who uses graph theory and machine learning to study the relationships that bacteria and archaea form with their host organisms. Or, I'm a computer scientist who builds software that uses concepts from evolution to extract knowledge about ecology from large datasets. Or, I'm a data scientist who uses Python to explore biological systems. Or, I'm a physicist that went rouge and defected to the squishy side of science. Take your pick.

This is the six reincarnation of Russell's Blog, and a return to static content for the first time since my ill-fated efforts to build something useful with Apache's XSLT plugin. I mostly use it to talk about science-y things and things that I find vexing or amusing.

I love the natural world. I love the engineered world. I love the people who study both of those worlds. However, there are a lot of things about science and engineering that I don't like. I don't like academic publishers that siphon tens of billions of dollars out of public research and into the hands of their shareholders. I don't like the system of incentives built on top of academic publishing that punishes researchers for fully disclosing their results, methods and thought process. I don't like the way students are treated in the classroom, on campus and by the student loan industry. I don't like the way women are treated in science. I don't like the way people who don't pass as European are treated in science.

Building things and studying the universe is awesome. Everyone should be allowed to play if they want to. I'm here because I think this stuff is fun, but I'm also here because I know it hasn't been fun for a lot of people. I want to help put that right.

Key facts

Talks and stuff

Publications

See also Scholar, ORCID

Refereed Journal Articles

  • 23 Andrew Thaler, S. Kersey Sturdivant, Russell Y. Neches, and J. Jacob Levenson, The OpenCTD: A Low-Cost, Open-Source CTD for Collecting Baseline Oceanographic Data in Coastal Waters, Oceanography, 2024.
  • 22 : Lingjie Meng, Tom O. Delmont, Morgan Gaïa, Eric Pelletier, Antonio Fernàndez-Guerra, Samuel Chaffron, Russell Y. Neches, Junyi Wu, Hiroto Kaneko, Hisashi Endo, and Hiroyuki Ogata. Genomic adaptation of giant viruses in polar oceans, Nature Communications, 2023.
  • 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

Code of Conduct for Vort.org

Vort.org is where I share things that I think are interesting or important. I have comments enabled because I want people to participate. However, I'm not interested in hosting a free-for-all.

  • I am committed to providing a friendly, safe and welcoming environment for all, regardless of level of experience, gender identity and expression, sexual orientation, disability, personal appearance, body size, race, ethnicity, age, religion, nationality, or other similar characteristic.
  • Please avoid using overtly sexual nicknames or other nicknames that might detract from a friendly, safe and welcoming environment for all.
  • Please be kind and courteous. There's no need to be mean or rude.
  • Respect that people have differences of opinion. Every theory starts as an untested hypothesis. Every design or implementation choice carries a trade-off and numerous costs. There may be a right answer, but it isn't enough to be right. It also matters how we get there.
  • Generally speaking, I try my best to document and disclose my methods, data and reasoning and to package them in such a way that you can check them yourself. Critiques that follow suit are more valuable than drive-by complaints.
  • You will be excluded from interaction if you insult, demean or harass anyone. That is not welcome behavior. We interpret the term "harassment" as including the definition in the Citizen Code of Conduct; if you have any lack of clarity about what might be included in that concept, please read their definition. In particular, we don't tolerate behavior that excludes people in socially marginalized groups.
  • Private harassment is also unacceptable. No matter who you are, if you feel you have been or are being harassed or made uncomfortable by a community member, please contact me immediately. Whether you're a regular contributor or a newcomer, I care about making this community a safe place for you.
  • If the problem is my behavior, then my Ph.D. advisor Jonathan Eisen would want to hear about it. He takes these things seriously, and I trust him to hold me accountable.
  • Likewise any spamming, trolling, flaming, baiting or other attention-stealing behavior is not welcome.

This is my personal website, and I am ultimately responsible for enforcing these rules. This leads to one final meta-rule :

  • Don't use the comments to raise issues about how I am enforcing the code of conduct regarding comments. Please direct that feedback to me privately.

(Adapted from the Rust code of conduct.)