My Ode to Yolo Bypass
Gave my 1st ever talk about Yolo Bypass and my 1st ever talk about Nature Photography. Here it is ...   -------- This is from the" Tree of Life Blog " of Jonathan Eisen, an evolutionary biologist and Open Access advocate at the University of California, Davis. For short updates, follow me on Twitter. -------- (Source: The Tree of Life)
Source: The Tree of Life - January 30, 2024 Category: Microbiology Source Type: blogs

Four years - 1461 straight days - of iNaturalist observations
Well, today is a big day I guess. I just posted an observation to iNaturalist of a hummingbird in my backyard.https://www.inaturalist.org/observations/195397005Not that big a deal unless you are living in some place where it is really cold and you are jealous we have hummingbirds in our yard in Davis, California on December 31.But the context here is important.This entry completes a somewhat crazy run. I have made iNaturalist observations every day for the last four years. That is, every day for the last 1461 days. It all started in January 2020. Before the pandemic reared its ugly head. I decided it mi...
Source: The Tree of Life - December 31, 2023 Category: Microbiology Source Type: blogs

Notes on My Meningioma and Gamma Knife Treatment
So - yesterday I had Gamma Knife treatment at UC Davis for a posterior fossa meningioma that was first found by MRI about 6 years ago. I am going to be collecting my various posts here on the saga. I am also going to post separate posts here about the saga but just wanted to collect some of the other posts for now.Day 1 - September 27, 2023.Posted to many social media channels about my treatment with updates and other details and also got lots and lots and lots of support.Here are some of the posts. LinkedIn Facebook Instagram View this post on InstagramA post shared by Jonathan Eisen (@phylogenomics)View th...
Source: The Tree of Life - September 29, 2023 Category: Microbiology Source Type: blogs

Sanger DNA sequencing services
 Sanger DNA Sequencing ServicesSo I posted a request to multiple social media sites:Question - are there good / cheap services out there to do Sanger sequencing (e.g., for 16S / ITS for taxonomic identification of cultures)? The local Sanger operation we were using shut down.I posted to the following sites:FacebookLinkedIn TwitterBlue SkyMastodonThese are the places that were recommended the mostGENEWIZ from AzentaUC BerkeleyQuintaraEurofinsMcLabThese had single suggestionsMacrogene MR DNA Integrated Genomics Functional Bio U Az. CosmosIDLaragenRetrogenIMRFunctional BiosciencesThese are h...
Source: The Tree of Life - September 21, 2023 Category: Microbiology Source Type: blogs

And today in one of the stranger uses of my work ... " 130 Academic Words Ref from " Jonathan Eisen: Meet your microbes | TED Talk " "
Well, this is certainly a bit wacky.I was, well, Googling myself today and found this.130 Academic Words Ref from " Jonathan Eisen: Meet your microbes | TED Talk " It seems like they took my Ted talkand got key words from it, and then use it to teach about those words in some sort of automated way. And, well, they got a few words wrong but actually the words they chose kind of capture a lot of what my talk was about. So here are a few screenshots of some of these key words -------- This is from the" Tree of Life Blog " of Jonathan Eisen, an evolutionary biologist and Open Access advocate at the University of California,...
Source: The Tree of Life - August 24, 2023 Category: Microbiology Source Type: blogs

Responses to requests for suggestions for quiet air filter for daughter's California dorm room
 So I posted a request for suggestions on various social media sites:" Wanted - recommendations for good / not too expensive / not too loud air filter to get my daughter for her for a small dorm room in California (and thus to filter out pathogens, allergens and smoke ...) "I am going to compile responses here TwitterWanted - recommendations for good / not too expensive / not too loud air filter to get my daughter for her for a small dorm room in California (and thus to filter out pathogens, allergens and smoke ...)— Jonathan Eisen (@phylogenomics)July 23, 2023 Mastodon  Facebook  -------- This is from ...
Source: The Tree of Life - July 23, 2023 Category: Microbiology Source Type: blogs

Summary of responses to request for examples of data sets of microbial genomes with associated phenotypic data
So last week I posted a question to many different places as follows:Wanted - dataset(s) to test bacterial genome analysis / annotation methods. Ideally has many genomes from collection of [interesting] bacteria with associated experimental phenotypes / metadata.On Linked In:Jonathan Jacobs: "All the reference genomes in the ATCC Genome Portal are freely available for non-commercial research purposes. They are also fully authenticated and traceable to physical production lots in our biorepository, and produced under ISO quality management. I ’m biased, but I think we’re producing the quality microbial genomes I’ve ev...
Source: The Tree of Life - June 10, 2023 Category: Microbiology Source Type: blogs

Another day to think, to pause, to ponder.
Panorama of Sycamore Park and the memorial to Karim A bit over 10 years ago I wrote a blog post that I repost all the time. Entitled "A day to think, to pause, to ponder" it was posted on my dad ' s birthday and was about the pain of him dying, by suicide, when I was in college. It was meant as a sad, melancholy post but also one about the importance of compassion and how " we can all do a little bit to improve how we treat other. " When I reposted this one time a few years ago, someone asked me if I had ever met the " Compassion Guy " who frequented downtown Davis and who had a life ' s mission of getting people to t...
Source: The Tree of Life - May 5, 2023 Category: Microbiology Tags: DavisCA UCDavis Karim Majdi Abou Najm David Breaux Kimberlee Guillory compassion Source Type: blogs

Responses to question about functional annotation of metagenomic reads
Posted a question to a few placesHi. We would like to functionally annotate some metagenomic sequencing reads without doing any assembly or binning or read mapping to reference genomes. Just annotate by searching things like nr, PFAM, COGs, etc. Anyone know of tools that do this?— Jonathan Eisen (@phylogenomics)March 29, 2023Humann suggestion  fraggenescan on the raw reads, then use hmmer w/ pfam-A or kegg hmm.EggNog MapperMGRASThttp://mgrast.orgMetawrapYooseph approachhttps://pubmed.ncbi.nlm.nih.gov/27400380/https://pubmed.ncbi.nlm.nih.gov/27585568/mi-faserhttps://bromberglab.org/project/mifaser/ …MGXhttps://micr...
Source: The Tree of Life - April 4, 2023 Category: Microbiology Source Type: blogs

Panoramas from the past ...
In 1997, my then girlfriend (now wife) and I went camping in Death Valley. It was our fourth trip there to camp in grad. school.I brought my Olympus OM1 and did something I thought could be cool with it. I took multiple overlapping pics of landscapes with the idea that I would use Photoshop or some such program to combine them together into large panoramic landscape imagesThe only problem was -- I did not know how to do thatBut when I got home I got the photos developed and scanned them using a scanner I had and merged them with something like Claris Draw. Here is an example - three pics from the Sand Dunes area - and the ...
Source: The Tree of Life - January 20, 2023 Category: Microbiology Source Type: blogs

Well, this is about as scammy / spammy as a journal can get ... putting me on an editorial board I did not agree to be on ...
 So I got an email this AM from "Microorganisms Editorial Office "Dear Prof. Dr. Eisen,We are pleased to inform you that your information has been announced on the webpage of our journal ' s board.Please check that all of your information is correct here:https://www.mdpi.com/journal/microorganismsCool. Cool. Except I never agreed to be on their editorial board. And yet there I am on their web site.https://www.mdpi.com/journal/microorganisms/editors?page_no=3No MDPI Microoorganisms. This is not OK.  -------- This is from the" Tree of Life Blog " of Jonathan Eisen, an evolutionary biologist and Open Access ad...
Source: The Tree of Life - December 19, 2022 Category: Microbiology Source Type: blogs

Lake Arrowhead Microbial Genomics Meeting History
Making a page here with information on the history of the Lake Arrowhead Microbial Genomes meeting.  Please post in comments any additional links to other information.19981998_arrowhead booklet1998_LakeArrowhead notes1998_Arrowhead booklet version 220002000_arrowhead bookletJonathan Eisen talk from 2000  Jonathan Eisen talk on " Phylogenomics of DNA repair " at Lake Arrowhead Small Genomes Meeting 20002002Jonathan Eisen talk from 2002  Jonathan Eisen talk on " Phylogenomics of Microbes " at Lake Arrowhead Small Genomes Meeting 20022004lakearrowhead2004 bookletJonathan Eisen talk from 2004  Jonathan Eisen talk on "...
Source: The Tree of Life - September 11, 2022 Category: Microbiology Source Type: blogs

Wanted - comments on the current @ucdavis COVID plans
 So - I have been publicly and privately critical of some of the recent @ucdavis practices regarding COVID. If you want to know more about my areas of concern see for example this Twitter thread which I posted today: Following up on this I thought I would share the slides I used for my presentation to@Chancellor_May and his leadership group a few weeks ago with my thoughts on the@ucdavis current#COVID response.https://t.co/yKRYU1Gugd1/nhttps://t.co/vD0Cpb795f— Jonathan Eisen (@phylogenomics)August 19, 2022After I posted that, The Chancellor of UC Davis Gary May posted an article with some details of current UC ...
Source: The Tree of Life - August 20, 2022 Category: Microbiology Source Type: blogs

Best pics from Trip to Monterey - Day 1 - May 25, 2022
  Went on a brief trip to Monterey, CA last week. Took lots of pics. Here are some of the better ones. Also seepostings with identifications at iNaturalist.  -------- This is from the" Tree of Life Blog " of Jonathan Eisen, an evolutionary biologist and Open Access advocate at the University of California, Davis. For short updates, follow me on Twitter. -------- (Source: The Tree of Life)
Source: The Tree of Life - June 6, 2022 Category: Microbiology Source Type: blogs

Videos about using the UCSC Genome Browser for analysis of SarsCOV2
 These look pretty useful and thought I would post here. Text is from the UCSC Youtube channelThis 5-part video series is for virologists and public health researchers interested in leveraging the UCSC Genome Browser and web interface to UShER (Ultrafast Sample placement on Existing tRees). These tools are a ' one-stop shop ' to understand SARS-CoV-2 through genome annotations as well as track variants by placing your samples in a phylogenetic tree with millions of other SARS-CoV-2 sequences. Use the SARS-CoV-2 Genome Browser:http://bit.ly/sarscov2browser Visit our SARS-CoV-2 Genome Browser and UShER quick start page ...
Source: The Tree of Life - May 16, 2022 Category: Microbiology Source Type: blogs