The Tattooed Poets Project: Vicki Iorio

We're kicking off this year's Tattooed Poets Project with a tattoo that seems, ahem, apropos-etic:

This poetic foot belongs to Vicki Iorio, a New York poet. She explains the tattoo:

"My group of Long Island poets have the pleasure of reading at the Wyld Chyld Cafe and Tattoo Parlor in Merrick, NY. I watched Tammy Nuzzo-Morgan, the poet laureate of Suffolk County get "poet" tattooed across her shoulder blades. [Tammy will be appearing on the site later this month.] She recited poetry while her back was bleeding, I knew at that moment I would have to get one!

It was a cold January night, Sixx tattooed my right foot with a beautiful scripted "poet." It was a beautiful moment and I love my tat and all it signifies. A slew of woman poets have been tattooed by Sixx. A tattooed sisterhood, indeed."

Here is a poem from Vicki:

Tattoo 56
 
I will get a tattoo next birthday
no one will care
it won't be like birthday 13
when I dyed my hair purple on a shoplift heist
shaved off eyebrows
pierced frozen ears with a needle
hacked off bushy black fur under stockings

I will find an illustrated man
his head bald and shiny
eyes so blue I will see straight through
to his good heart, diamond stud in one ear
massive arms shocking to the touch.

My spider will go willingly to his fly.
I will tell him what I want
where I want it.

After validating plastic worth,
my pirate will lead me to his table
gift me with little hurts
celebrate me electrically
wrap me in gauze
sing the praises of Bacitracin
wish me a happy birthday.

~

Vicki Iorio is a Long Island poet who hangs around tattoo parlors. Her poems have been published in various publications including hell strung and crooked. She is saving up for another tattoo!

Thanks to Vicki for sharing her poetic tattoo and tattoo poem with us here on Tattoosday!

~

This entry is ©2011 Tattoosday.

If you are reading this on another web site other than Tattoosday, without attribution, please note that it has been copied without the author's permission and is in violation of copyright laws. Please feel free to visit http://tattoosday.blogspot.com and read our original content. Please let me know if you saw this elsewhere so I contact the webmaster of the offending site and advise them of this violation in their Terms of Use Agreement.

Tattoos I Know: Beth's Ink Ushers in the New Baseball Season

Well, folks, it's March 31, which means several things, First and foremost, after a long, cold winter, and a rough start to spring, baseball season starts today. And although, the last time I checked, there was a 70% chance of rain for the New York Yankees home opener against the Detroit Tigers today, baseball fans everywhere are just a tad excited that their team's 162 game-long drama is about to begin.

So, it seemed fitting that we share this tattoo, belonging to our cousin Beth:

Photo by Melanie Cohen

Beth is a diehard Yankees fan and she got this inked on September 16, 2005. For the record, the Yankees beat the Toronto Blue Jays north of the border that day 11-10 thanks, in part, to two Robinson Cano home runs and Mariano Rivera's 40th save of the year.

This is one of Beth's three tattoos, a fact not lost on me, as I have been wanting to post her ink on the site ever since we started back in 2007. However, we just never got around to it and this photo was shot last June in New Jersey by my wife, Melanie, at another cousin's baby shower. I thought, at the time, that we would save this picture for the day the Yankees won the World Series, but last year that ambition fell short in the ALCS. So we saved it for Opening Day, instead.

The tattoo was done by Thomi Hawk at K & B Tattooing & Piercing in Hightstown, New Jersey.

I should also add that, back in August 2007, I was sitting in my seat at PNC Bank Arts Center, between sets, when I noticed a very similar tattoo several rows ahead of me. I thought, "Man, that tattoo looks just like Beth's, and in the same spot [on her upper right back] too!" Of course, it was Beth, and we were both unaware that we were attending the show. And to think I spotted her in all that humanity by noticing her tattoo!

I mentioned at the top of the post that it being March 31, meant several things. Aside from Opening Day, it's also opening day for the inkspotting season, as far as I'm concerned. Posts have been few and far between over the past few months and that's about to change. Tomorrow begins National Poetry Month, and we will be embarking on our third annual Tattooed Poets Project: 30 days of tattoos from poets across the country. And, I will assume, that I'll be having regular Tattoosday encounters, which will reappear in May, throughout the month.

Play ball!

Thanks again to Beth for sharing her cool patriotic Yankees tattoo with us here on Tattoosday!

*

This entry is ©2011 Tattoosday.


If you are reading this on another web site other than Tattoosday, without attribution, please note that it has been copied without the author's permission and is in violation of copyright laws. Please feel free to visit http://tattoosday.blogspot.com and read our original content. Please let me know if you saw this elsewhere so I contact the webmaster of the offending site and advise them of this violation in their Terms of Use Agreement.

THROWBACK THURSDAY

PLATINUM SERIES

HANYA MASK

Here is one on a client who came in for his first piece!

Because we ♥ you

Because we ♥ you all so much we currently have a fabulous promotion in all our stores just for you!

One pair of Ali Baba pants for $20 or two for 25!!

Shown here worn in two different ways with our beautiful Om Scarf and Tribal Necklace. xx

ONCE AGAIN ITS ON

Traditional Indian Chai recipe

Why not warm up your morning with a cup of hot Indian Chai tea. Our Merchandise Planner Samara, loves this on a lazy Sunday with a dash of organic honey xx

INGREDIENTS

Spice ingredients for one pot of tea:

1/2 of a star anise star

10-12 whole cloves

6-7 whole allspice

1 heaping teaspoon of cinnamon bark (or 2 short sticks)

6-7 whole white peppercorns

1 cardamon pod opened to the seeds

Other ingredients:

1 cup water

4-6 cups Bonsoy soy milk

2 heaping tablespoons of a high quality full-bodied broad-leaf black tea (Ceylon, or

English Breakfast if a broad-leaf Ceylon is not available) Sugar

METHOD

1 In a 2-qt saucepan, add spices to 1 cup of water. Bring to a boil; remove from heat; let steep for 5-20 minutes, depending on how strong a spice flavor you want.

2 Add 4-6 cups of whole milk to the water and spices. If you don't have Bonsoy soy milk, you can also use non-fat or low-fat milk, just add some cream to it, a few tablespoons. Bring the milk and spice mixture just to a boil and remove from heat.

3 Add the tea to the milk and let steep for 5 to 10 minutes to taste. (Option at this point - reheat to a simmer and remove from heat.) You can add sugar at this point, or serve without sugar and let people put the amount of sugar in they want. Traditionally, sugar is added before serving.

4 Strain into a pot. Serve. Add sugar to taste.

SOUL SUNDAY

FIRST WE PRAY

BiGG Snoop came thru to Represent for Life of the homie Nate DoGG.

You Will Be Remembered!

TRAILER OF THE WEEK

My twitter wrap up of the Joint Genome Institute User Meeting #JGIUM

Off to another meeting so don't have time to write up details of the JGI User Meeting that just ended.  But I am posting my tweets and some related tweets here.  Also, apparently videos of the talks will be available soon. Will try to clean up the style of the posts ASAP but on the road ...





kucsbl CSBL at Korea Univ.
RT @phylogenomics Rob Knight discussing the rationale behind his UNIFRAC metric to comparing communities using phylogeny #JGIUM
5 hours ago Favorite Retweet Reply

CackleofRad CackleofRad
@
@Tideliar @jadebio You know who else I think is awesome? Try @phylogenomics and maybe #JGIUM Not medical per se but cool things in the werks
17 hours ago

phylogenomics Jonathan Eisen

Uy vey: got home from #JGIUM & my kids had chlamydia, anthrax, E. coli, malaria, athletes foot, Helicobacter & giardia yfrog.com/gzk75auj
20 hours ago

phylogenomics Jonathan Eisen
Next up at #JGIUM Dan Distel on Shipworm symbionts - note here is a picture of Dan (foreground) from 1992 cruise http://twitpic.com/4cvb3w
22 hours ago

phylogenomics Jonathan Eisen

Apologies all - have to skip end of #JGIUM - follow this hashtag for other's posts
23 hours ago

phylogenomics Jonathan Eisen
Scholin hacked into unsecured wireless network while on vacation in Death Valley to communicate w/ his sensors in Newport Beach #JGIUM
24 Mar

phylogenomics Jonathan Eisen
Scholin has some of these remote sensors moored off of Newport Beach pier to survey for toxic diatoms #JGIUM
24 Mar

phylogenomics Jonathan Eisen
Holy ecogenomic sensor batman - this remote ESP thing is very cool mbari.org/ESP/esp_2G.htm - can do DNA analysis remotely #JGIUM
24 Mar

phylogenomics Jonathan Eisen
Next up Chris Scholin on remote detection of marine microbes in coastal waters and deep sea #JGIUM
24 Mar

phylogenomics Jonathan Eisen
In the Q and A period for Dan Distel some music has now come on over the speakers #oscars? #exitmusic #JGIUM
24 Mar

phylogenomics Jonathan Eisen
Distel discussing proteomics of shipworm symbionts communities - uses method that focuses on proteins in symbionts not host #JGIUM
24 Mar

phylogenomics Jonathan Eisen
Oh no - Distel mentioned the CaZome when discussing carbohydrate active enzymes in shipworm symbionts #badomicsword #JGIUM
24 Mar

phylogenomics Jonathan Eisen
Distel: the gill symbionts are in addition to symbionts living in the gut that are known to degrade cellulose #JGIUM
24 Mar

phylogenomics Jonathan Eisen
Distel: many (~10) types of closely related bacterial symbionts live inside the cells of shipworm in the gill #JGIUM
24 Mar

phylogenomics Jonathan Eisen
Note - here is a link to my #PLoSONE paper with Distel on the genome of a shipworm symbiont plosone.org/article/info:d… #JGIUM
24 Mar

phylogenomics Jonathan Eisen
Distel: shipworms are very diverse and can live off all sorts of wood & wood like stuff - major wood consuming organisms in ocean #JGIUM
24 Mar

phylogenomics Jonathan Eisen
Dan Distel Works at the Ocean Genome Legacy foundation #JGIUM #coolgroup oglf.org/DistelCV.htm
24 Mar

phylogenomics Jonathan Eisen
Distel: shipworms (which are actually clams) cause billions of dollars of economic damage each year #JGIUM
24 Mar

doe_jgi Joint Genome Inst.
RT @phylogenomics Distel expressing thanks to JGI b/c despite claims by many that sequencing is free, nobody has told his acctg dept #JGIUM
24 Mar

phylogenomics Jonathan Eisen
Distel expressing thanks to JGI b/c despite claims by many that sequencing is free, nobody has told his accounting department #JGIUM
24 Mar

phylogenomics Jonathan Eisen
Next at #JGIUM Dan Distel on shipworm symbionts - note here's a pic of Dan (foreground) from '02 http://www.scancafe.com/p-59386415-38fa9f
24 Mar

sharmanedit Anna Sharman
Wow. MT @phylogenomics [Ed] Buckler: any two corn [maize] plants are as different from each other as humans and chimpanzees #JGIUM
24 Mar

phylogenomics Jonathan Eisen
Next at #JGIUM Mary Ann Moran; Note paper I have w/ her is one Nature fails to make free despite promises nature.com/nature/journal… #opengate
24 Mar

phylogenomics Jonathan Eisen
Buckler described Genotyping by sequencing method from his in press #PLoSOne paper #JGIUM maizegenetics.net/images/stories…
24 Mar

phylogenomics Jonathan Eisen
Buckler suggests the genetic diversity in maize allows it to adapt to local environments better than other species #JGIUM #notbuyingit
24 Mar

phylogenomics Jonathan Eisen
Buckler: genomic domestication analysis w/ Ross-Ibarra lab from #ucdavis: little loss in diversity from landraces -> improved lines #JGIUM
24 Mar

phylogenomics Jonathan Eisen
Buckler: Tripsacum genome has different retrotransposons than maize but otherwise may be useful as source of genetic variants #JGIUM
24 Mar

phylogenomics Jonathan Eisen
Buckler also sequencing Tripsacum - sister genus of maize #JGIUM no chromosomal duplications, very similar gene content to maize
24 Mar

phylogenomics Jonathan Eisen
Buckler: doing maize HAPMAP2 to survey genetic diversity in corn #JGIUM
24 Mar

leonidkruglyak Leonid Kruglyak
So are yeast strains RT @phylogenomics: Buckler: any two corn plants as different as human and chimp #JGIUM #myspeciesisbetterthanyours
24 Mar

phylogenomics Jonathan Eisen
Buckler: any two corn plants are as different from each other as humans and chimpanzees #JGIUM #myspeciesisbetterthanyours
24 Mar

leonidkruglyak Leonid Kruglyak
Ed Buckler RT @phylogenomics: Next up Ed Buckley from Cornell discussing sequencing/using maize genome #JGIUM
24 Mar

phylogenomics Jonathan Eisen
Next up Ed Buckley from Cornell discussing sequencing/using maize genome #JGIUM
24 Mar

sarahcpwilliams sarahcpwilliams
@phylogenomics enjoying yr tweets from #jgium. i'm a big fan of ley and knight. covered their work last year for hhmi: http://bit.ly/g2NEug
24 Mar

phylogenomics Jonathan Eisen
Ley : to study diversity of microbes associated with maize had to get primers that did not amplify chloroplast rDNA #JGIUM
24 Mar

phylogenomics Jonathan Eisen
Ley: doing a QTL experiment on maize/corn treating microbes as their quantitative trait #JGIUM
24 Mar

phylogenomics Jonathan Eisen
Ley now expanding human microbiome GWAS twin study to include surveying microbes all over body #JGIUM
24 Mar

phylogenomics Jonathan Eisen
Ruth Ley: GWAS studies of human twins has IDd many loci that appear to affect microbial diversity - including some immune system loci #JGIUM
24 Mar

phylogenomics Jonathan Eisen
Ruth Ley is now doing GWAS studies w/ human twins where the phenotype they are looking at is microbial diversity #JGIUM #verycool
24 Mar

phylogenomics Jonathan Eisen
Ruth Ley discussing survey of microbes in one child over two years #JGIUM
24 Mar

phylogenomics Jonathan Eisen
Ruth Ley now up at the JGI User Meeting discussing maize, human microbiotas #JGIUM ... Note - I love her work #brilliant
24 Mar

kevinswilson66 Kevin Scott Wilson
@
@phylogenomics : Many thanks for your notes on #JGIUM . I was captivated by them
23 Mar

Symbiologica Juliana Mastronunzio
Thanks for tweets on the JGI meeting #JGIUM from @phylogenomics and @iGenomics.
23 Mar

sdaxen Seth D. Axen
RT @phylogenomics: Schuster: "I would like to finish my talk by discussing sequencing the devil" #JGIUM
23 Mar

Pathh1 Pat Heslop-Harrison
Done that - I found the devil in the detail. RT @phylogenomics: Schuster "like to finish my talk by discussing sequencing the devil" #JGIUM
23 Mar

phylogenomics Jonathan Eisen
Schuster: "I would like to finish my talk by discussing sequencing the devil" #JGIUM
23 Mar

iGenomics Dawei Lin
RT @phylogenomics: Schuster: Stays away from traditional sources of ancient DNA like bone and uses hair #JGIUM
23 Mar

doe_jgi Joint Genome Inst.
RT @phylogenomics Schuster: got .1g of hair from 200 year old mammoth sample from Russia and can get mitochondrial genome #JGIUM #fb
23 Mar

phylogenomics Jonathan Eisen
Schuster: got .1g of hair from 200 year old mammoth sample from Russia and can get mitochondrial genome #JGIUM
23 Mar

phylogenomics Jonathan Eisen
Schuster working on thylacine (tasmanian tiger) mitochondrial genomes #JGIUM thylacine.psu.edu
23 Mar

phylogenomics Jonathan Eisen
For more on mammoth genomics see mammoth.psu.edu #JGIUM
23 Mar

phylogenomics Jonathan Eisen
Schuster: when you sample extinct organisms you have to remember that different samples may come from different times #JGIUM
23 Mar

phylogenomics Jonathan Eisen
Schuster: "You would not believe how much mammoth hair I have washed off myself" #JGIUM
23 Mar

phylogenomics Jonathan Eisen
Schuster: Stays away from traditional sources of ancient DNA like bone and uses hair #JGIUM
23 Mar

phylogenomics Jonathan Eisen
Schuster - redundancy in genome sequencing with ancient genomes helps build quality genome assemblies #JGIUM
23 Mar

phylogenomics Jonathan Eisen
Schuster: one reason to focus on mitochondrial genomes is that there are lots of copies of the genome per cell #JGIUM
23 Mar

phylogenomics Jonathan Eisen
Schuster : "dont forget about mitochondrial genomes" still lots of species that do not have mt genome sequences #JGIUM
23 Mar

phylogenomics Jonathan Eisen
Schuster: discussing mammoths, moas, thylacines, tasmanian devils and polar bears #JGIUM #museomics #conservation #endangered
23 Mar

phylogenomics Jonathan Eisen
For more on Schusters work on extinct species see cidd.psu.edu/people/scs19 #JGIUM
23 Mar

phylogenomics Jonathan Eisen
Next up Stephan Schuster discussing the Genomics of Extinct and Endangered Species #JGIUM #museomics
23 Mar

Energy_Science Energy Science News
@doe_jgi: RT @phylogenomics Why #badomics words can also be very good: a case in study with museomics #JGIUM http://ff.im/-zyA86 #fb
23 Mar

doe_jgi Joint Genome Inst.
RT @phylogenomics Why #badomics words can also be very good: a case in study with museomics #JGIUM http://ff.im/-zyA86 #fb
23 Mar

phylogenomics Jonathan Eisen
Why #badomics words can also be very good: a case in study with museomics #JGIUM http://ff.im/-zyA86
23 Mar

phylogenomics Jonathan Eisen

Eddy Rubin at the #JGIUM is soliciting input from crowd on future needs of the community
23 Mar

Energy_Science Energy Science News
@doe_jgi: #JGIUM bingo anyone? DOE JGI Director Rubin mentions @phylogenomics GEBA project in his talk on future of DOE JGI #fb
23 Mar

phylogenomics Jonathan Eisen

The perils of giving out #badomics word awards - a prior recipient at #JGIUM just told me he's still angry at me phylogenomics.blogspot.com/2009/01/worst-…
23 Mar

doe_jgi Joint Genome Inst.
#JGIUM bingo anyone? DOE JGI Director Rubin mentions @phylogenomics GEBA project in his talk on future of DOE JGI #fb
23 Mar

Energy_Science Energy Science News
@doe_jgi: #JGIUM Rob Knight: "There is one universal tree of life which is why projects such as @phylogenomics GEBA are so critical" #fb
23 Mar

phylogenomics Jonathan Eisen
All I can say is that when I was rejected by HHMI a few yrs ago I felt better when I heard Rob Knight got it b/c, well, he rocks #JGIUM
23 Mar

phylogenomics Jonathan Eisen
Rob Knight - in human microbiome studies you actually need VERY few sequences per sample to get overall trends #JGIUM
23 Mar

phylogenomics Jonathan Eisen
Rob Knight: "There is one universal tree of life" and giving props to my GEBA genomic encyclopedia project #JGIUM
23 Mar

doe_jgi Joint Genome Inst.
#JGIUM Rob Knight: "There is one universal tree of life which is why projects such as @phylogenomics GEBA are so critical" #fb
23 Mar

phylogenomics Jonathan Eisen
Rob Knight discussing the rationale behind his UNIFRAC metric to comparing communities using phylogeny #JGIUM
23 Mar

phylogenomics Jonathan Eisen
Rob Knight discussing how sequencing has gotten so cheap and high throughout that analysis tools are the limiting step in many cases #JGIUM
23 Mar

phylogenomics Jonathan Eisen
Rob Knight now up at #JGIUM - he publishes more cool papers per month than just about anyone in microbial research
23 Mar

phylogenomics Jonathan Eisen
Silver: took sugar secreting cyanobacterium and got macrophage to take them up and they survive a little bit #JGIUM
23 Mar

phylogenomics Jonathan Eisen
Silver: injected sugar secreted cyanobacterium into zebrafish zygotes and get functional fish with cyanos all throughout them #jgium
23 Mar

phylogenomics Jonathan Eisen
Silver: engineered a cyanobacterium secrete sugars so thought maybe they could use this to make photosynthetic animals #JGIUM
23 Mar

phylogenomics Jonathan Eisen
Silver also interested in biohydrogen production #JGIUM but two problems: most hydrogenases are oxygen sensitive and electron competition
23 Mar

phylogenomics Jonathan Eisen
Silver is working on engineering 3hydroxypropionate carbon fixation pathway from Chloroflexus in E. Coli #JGIUM
23 Mar

phylogenomics Jonathan Eisen
Silver claimed that Cyanobacteria are responsible for 50% of photosynthesis on earth but I think that must be too high #JGIUM
23 Mar

phylogenomics Jonathan Eisen
Silver working on redesigning photosynthesis via cyanobacteria #JGIUM - says they need to learn a lot of biology still
23 Mar

phylogenomics Jonathan Eisen
Silver: though she tries to get $$ from basic scion agencies , they never fund her #JGIUM
23 Mar

phylogenomics Jonathan Eisen
Pam Silver: uses "redesign of a system can test our understanding of it's components" to try to get $$ from basic science agencies #JGIUM
23 Mar

phylogenomics Jonathan Eisen
Pam Silver "Biology is the technology of this century" is the message she wants to gt across #JGIUM
23 Mar

phylogenomics Jonathan Eisen
Jerry Tuskan getting some hard but good questions after his talk at #JGIUM - Q and A much more interesting than talks usually
23 Mar

phylogenomics Jonathan Eisen
Next up at #JGIUM Pam Silver - not only brilliant - but also her lab is the source of a good Lady Gaga spoof youtube.com/watch?v=ZilqYp…
23 Mar

phylogenomics Jonathan Eisen

Tuskan using Genome and RNA sequencing and high throughout phenotyping for massive poplar association study #jgium
23 Mar

phylogenomics Jonathan Eisen

At #JGIUM listening to Jerry Tuscan discuss poplar genomics - the place is packed yfrog.com/h82u1nnj
23 Mar

iGenomics Dawei Lin
@
@phylogenomics Terry Hazen talked about it. It can be easily forgot how many people worked behind the scene. #jgium
22 Mar

phylogenomics Jonathan Eisen

Tell me about it: “@iGenomics: It is hard to include all people working on a project into the author list these days. #jgium”
22 Mar

Energy_Science Energy Science News
@doe_jgi: RT @phylogenomics: Personal trivia re: SLAC director Perisis Drell at #JGIUM - previous director Artie Bienenstock was a st...
22 Mar

phylogenomics Jonathan Eisen

Personal trivia re: SLAC director Perisis Drell at #JGIUM - previous director Artie Bienenstock was a student of my grandfather Ben Post
22 Mar

EpiExperts Epigenetics Experts
RT @phylogenomics @doe_jgi: SLAC National Accelerator Lab Director Persis Drell kicks off DOE JGI User Mtg 5pm-use #JGIUM to follow
22 Mar Favorite Retweet Reply

Home is Where the Star Is

Yesterday in Penn Station, I met Jonathan, whose one tattoo caught my eye when I passed him in the Amtrak waiting area.

Except, sometimes, a fragment of a tattoo doesn't necessarily reveal the whole piece. As in Jonathan's case, I saw the back of his arm, and this segment, which resembled (to me, at the time), a crude figure with the beginning of a speech bubble emanating from its mouth:

I felt rather silly, however, when Jonathan agreed to participate and showed me the full tattoo:

The figure I imagined, of course, is really Long Island, and the balloon was the southern tip of the state of New York.

Jonathan explained that he is from Rochester, marked on the tattoo with a star, and that he lived in the same house growing up there for eighteen years. It's a New York state of mind, indeed.

The tattoo was done at Big Joe & Sons Tattooing in White Plains, New York.

Thanks to Jonathan for sharing his stately tattoo with us here on Tattoosday!

This entry is ©2011 Tattoosday.


If you are reading this on another web site other than Tattoosday, without attribution, please note that it has been copied without the author's permission and is in violation of copyright laws. Please feel free to visit http://tattoosday.blogspot.com and read our original content. Please let me know if you saw this elsewhere so I contact the webmaster of the offending site and advise them of this violation in their Terms of Use Agreement.

LET EM KNOW

Drama Beats came thru to get a fresh piece on the inner arm..

Never stop believing

At Tree of Life we never stop believing in ourselves, in others and in the goodness that comes from helping those in need.

THROWBACK THURSDAY

Here is a classic soul record by Weldon Irvine "Morning Sunrise" and a classic track off
Memphis Bleek's album 534 that was sampled from Mr. Irvine's original recording.
Produced by Just Blaze

One Skirt Six Ways

Our beautiful handblock wrap skirts are not only made from 100% cotton and available in a variety of colours and patterns, they can also be worn six different ways - perfect for the girl who can never make her mind up on what to wear!

Why #badomics words can also be very good: a case in study with museomics #JGIUM

Well, my snarky blog style with some of my awards comes with some risks. Today I experienced one of them. Stephan Schuster gave me some serious major grief over a post I wrote a few years ago. In the post I gave him an award for "Worst new omics word" for the word museomics. I gave this award because, well, I don't like the word. I stand by my complaints about the word. But Stephan did highlight ( in his comments to me in the back of the room at the JGI User Meeting) that the word has been remarkably useful at getting money and attention for museum based genomics studies.



So I guess here is the dilemma. I realize new omics words can get attention. Omics is after all very hot still. But I write about #badomics words both because I think it is fun and also because I think people are careless with the language much of the time. Many omics words are really awful with no benefits. But some, fit my criteria as being badomics words, but can have positive benefits. To the public, the word museomics probably conjures up exactly what museum people want - the image of cutting edge science. Though I love museums, to some the conjure up images of dust and cobwebs and crotchety old scientists wandering around the halls in the dark. So the term museomics may indeed turn this on it's head. This term even to me conjures up images of museums doing cool things. So alas, I guess this is a mea culpable of sorts. I still think the word itself is not great. After all, if you think about it, all it really means is doing genomics with museum specimens. But clearly Stephan has a good point ... Getting attention to science is a good thing. So I guess badomics words can be used for good.

I am still going to snark about badomics words. But I will try to make more mention of the potential value they have in spreading science and omics to the masses ....

- Posted using BlogPress from my iPad

The Tattoosday Book Review: Tattooed by the Family Business

I’ll cut right to the chase: if you’re going to buy one tattoo book this spring, make sure it’s Tattooed by The Family Business, a feast for the eyes and a new standard by which all tattoo photography books should be judged.

Simply stated, this book is gorgeous, heavy on high-quality photography, focusing on the wonderful body art created by Mo Coppoletta and his crew of talented tattooists at The Family Business Tattoo Shop, a London-based establishment that has been producing breath-taking work since 2003.

If you're not familiar with Copoletta, or his studio, the book gives readers a peek inside the world of the Family Business. But aside from a one page foreword, and a couple pages of introduction, this lovely book is light on text, and heavy on images from photographers Fredi Marcarini and Chris Terry.

Image copyright: Fredi Marcarini and Chris Terry
Taken from Tattooed by the Family Business (Pavilion)

The two hundred plus pages are filled with lush images of life in the shop and, more importantly, the high quality work created by the artists. Divided up into five sections, titled "The Family," "The Business," "The Art," "The Work," and "The Patrons," this is not just about Coppoletta and his own work. The reader is also introduced to the whole family: Kanae, Mie Satou, Dominique Holmes, Diego Brandini, and Diego Azaldegui.

Some may draw comparisons to the books the American tattoo artist Kat Von D, which I have favorably reviewed in the past on this site. Tattooed by the Family Business is in a different league. It is as you would expect, Von D's books are busy and filled with words and images; whereas Coppoletta's book exudes a classiness to which other artists can only aspire.

In fact, an online review hardly does it justice. Photography dominates and, whereas the tattoo, or the process of tattooing is always at hand, the beauty of the book also lies in its images. Ultimately, I believe, it's what most serious artists want to see in a tattoo book. Although some may criticize that, in some of the photos, the details of the tattoos themselves are lost in the framing of the photograph, I would argue that these images are just as compelling as the close-ups, as one sees the way the tattoos are placed, and how they flow along the lines of the human form.

Image copyright: Fredi Marcarini and Chris Terry
Taken from Tattooed by the Family Business (Pavilion)

Image copyright: Fredi Marcarini and Chris Terry
Taken from Tattooed by the Family Business (Pavilion)

One of the neat features within this volume are several sketches on pages designed to resemble transparencies, where are laid over images of the tattoos themselves. The reader is treated to the full-page two-dimension image from which the artist drew his inspiration, and then can compare it to the end result.

Here on Tattoosday, where most of the tattoos we see are from New York-based artists, I have, in several years, only had the pleasure of encountering Coppoletta's work once, documented here. Therefore, getting to see a more expansive look at his work, as well as that of other artists in The Family Business, is a real pleasure.

Tattooed by the Family Business is a veritable feast. I keep returning to it, marveling at the craftsmanship and beauty of the tattoos. I highly recommend it to artists and aficionados alike. The book is a work of art in and of itself, and the fact that it so beautifully and simply celebrates the art makes it a must-read, a must-relish, and a must-have for every tattoo library.

BROOKLYN

Cappo came through to celebrate the birth of his Baby Girl Brooklyn!

Congrats Homie!

Tepee on the beach

Immerse yourself in beach bleached white wash, wine reds and dramatic blacks to discover your own sea side get-a-way.

PRAY FOR US

SOUL SUNDAY

from: JAMES H.
to: tiangotlost@gmail.com
date: Thu, Mar 10, 2011 at 8:15 AM
subject: Young & Dumb

A friend got me this tattoo years ago and I was told it meant "fear no man". Being young and dumb as most 18 year olds are, I didn't bother to make sure. Now after looking into it a little more, I'm not sure what it is. Please help!!



棺材佬 means "coffin man".

However, the middle character of 木見才 or 木貝才 does not exist in Chinese character list.

Tattoos with exact same error can be seen here & here.

TRAILER OF THE WEEK

The story behind the story of my new #PLoSOne paper on "Stalking the fourth domain of life" #metagenomics #fb

Well, here goes.

This is a post about a paper that has been a long long time coming. Today, a paper of mine is being published in PLoS One. The paper is titled "Stalking the Fourth Domain in Metagenomic Data: Searching for, Discovering, and Interpreting Novel, Deep Branches in Marker Gene Phylogenetic Trees" and is available at http://dx.plos.org/10.1371/journal.pone.0018011. (or if that link does not work you can get a copy here). This paper represents something I started a long time ago and I am going to try to describe the story behind the paper here.

I note - we are not doing a press release for the paper, for a few reasons. But one of them is that, well, I am starting to hate press releases. So I guess this is kind of my press release. But this will be a bit longer than most press releases. I note - my key fear here is that somehow in my communications with the press or in our text in the paper or in this post I will overstate our findings. Here is the punchline - we found some very phylogenetically novel forms of phylogenetic marker genes in metagenomic data. We do not have a conclusive explanation for the origin of these sequences. They may be from novel viruses. The They may be ancient paralogs of the marker genes. Or they may be from a new branch of cellular organisms in the tree of life, distinct from bacteria, archaea or eukaryotes. I think most likely they are from novel viruses. But we just don't know.

UPDATE: Am posting some links here to news stories/blogs about our paper

• Glimpses of the Fourth Domain? by Carl Zimmer at his always stellar "The Loom" 
• Biology's 'dark matter' hints at fourth domain of life by Colin Barras at the New Scientist 
• 21st century science publishing will be multilevel and multimedia by PZ Myers 
• German Radio Story
• Chinese news report
• PLoS One Blog Pick of the Month for March 2011 by Brian Mossop 
• Brazilian news story from @info
• There might be at least one other, previously hidden, domain of life by Francis Martin 
• Pronađen potpuno novi "domen" života
• Craig Venter's study of marine DNA finds new branches on the tree ... Telegraph article #1 
• Scientist finds a whole new 'domain' of life - Telegraph article #2 
• Scientist stumbles on new class of living things - Zee News 
• A new domain of life: Plenty more bugs in the sea from The Economist 
• DNA Analysis Hints At a Fourth Domain of Life - Slashdot
• Check out the video story from Newsy.Com

First - a summary of what we did.

In the paper, we searched through metagenomic data (sequences from environmental samples) for phylogenetically novel sequences for three standard phylogenetic marker genes (ss-rRNA, recA, rpoB). We focused on sequences from the Venter Global Ocean Sampling data set because, well, we started this analysis many years ago when that was the best data set available (more on this below). What we were looking for were evolutionary lineages of these genes that were separate from the branches that corresponded to the three known "Domains" of life (bacteria, archaea and eukaryotes).

To search for such novel lineages in the metagenomic data, we built evolutionary trees using these genes where we included sequences from known organisms (and viruses) as well as sequences from metagenomic data. We then looked through the trees for groups that were both phylogenetically novel and included only environmental data (i.e., they were new compared to known organisms or viruses). This method did not work very well for rRNA sequences (largely because making high quality alignments of short phylogenetically novel rRNA sequences was difficult - more on this below). But with RecA and RpoB homologs we were able to generate what we believe to be robust phylogenetic trees. And in these trees we found evidence for phylogenetically very novel sequences in environmental data.

Figure 1. Phylogenetic tree of the RecA superfamily. 

Figure 3. Phylogenetic tree of the RpoB superfamily

We then propose and discuss four potential mechanisms that could lead to the existence of such evolutionarily novel sequences. The two we consider most likely are the following

1. The sequences could be from novel viruses
2. The sequences could be from a fourth major branch on the tree of life

Unfortunately, we do not actually know what is the source of these sequences. So we cannot determine which of the theories is correct. Obviously if there is a novel lineages of cellular organisms out there, well, that would be cool. But we have no evidence right now if that is what is going on. Personally, I think it is most likely that these novel sequences are from weird viruses. But as far as we can tell, they truly could be from a fourth major branch of cellular organisms and thus even though we did not have the story completely pinned down, we decided to finally write up the paper to get other people to think about this issue.

Below I give all sorts of other details about the project in the following areas

• The history of the project 
• More detail on what is in the paper 
• Follow up analysis and rapid posting with google Know 
• Data deposition in Dryad 
• Who was involved 
• UPDATE: Funding for this work

The history of the project

Well, this is one of those projects for which the history is hard to explain. We started this work in 2004 when I was helping Venter and colleagues analyze the Sargasso Sea metagenome data. I was working at TIGR in 2003, which are the time was a sister institute to some of the institutes affiliated with the J. Craig Venter Institute (JCVI) (it was a complicated time). Craig had led a project to do a massive amount of shotgun sequencing of DNA isolated from the Sargasso Sea, which had been the site of many previous studies of uncultured microbes. And Craig, as well as some of the people working with him including John Heidelberg who was at TIGR, had asked me to help in analysis of the data. So I eventually went to a meeting about the project and got involved. It was quite exciting and I put a lot of effort into helping analyze the data.

As part of my work on the project, I and Martin Wu and Dongying Wu did a variety of phylogenetic studies of genes and gene families. One of these, was a phylogenetic analysis of proteorhodopsin homologs showing massively more diversity in the Sargasso data than in the PCR experiments done by Delong and Beja and others.

Figure 7 from Venter et al. 2004. 

We also did the first "phylotyping" in metagenomic data using genes other than rRNA. We built trees of bacterial ss-rRNAs, RecAs, RpoBs, HSP70s, EF-Tus and EF-Gs and then assigned each sequence to a phylum from the trees. In this analysis we found a variety of interesting things. 

Figure 6 from Venter et al. 2004. 

One thing I did not include in the Sargasso paper was an analysis I did of RecA homologs where I tried to include ALL RecA-like genes from bacteria, archaea, eukaryotes and viruses. The trees I made were a bit unusual but I was not sure that the alignments I had made were robust or that I had found all the RecA-like genes of interest so I did not even show this to Craig et al. at the time.

UPDATE: I note - our work on this project was supported by a grant from the NSF Assembling the Tree of Life program that was awarded to me and Naomi Ward and Karen Nelson. Those funds supported the development of many of the informatics tools we used in this analysis and Martin and Dongying were both working on that project.

After the Sargasso paper was published in 2004 though, I continued to fester about the RecA trees. And I wondered - if instead of trying to classify bacterial sequences into phyla, what if I tried to look for RecAs, rRNAs and other genes that were completely new branches in the tree of life? I got the chance to start to play with this concept again when Venter and crew asked me to help analyze the data coming out of the Global Ocean Sampling project. Again, this project was very exciting and interesting.

As part of the project, I helped Shibu Yooseph and others look into whether the GOS data revealed any completely new types of functionally interesting genes, much like I had shown for proteorhodopsin in the Sargasso data.  

Figure 7 from Yooseph et al. 2007 . Phylogenies Illustrating the Diversity Added by GOS Data to Known Families That We Examined 

And again my mind started wandering towards the question of "OK - so - if there are all these very unusual and novel functionally interesting genes, what about looking for unusual and very novel phylogenetic marker genes"? So finally, I got back to work on the issue.

And so I built a better RecA tree by first pulling out all possible homologs of RecA and RecA like proteins from the GOS data and then building an alignment and a tree. And there they were. Some very f*%&$ novel RecAs - distinct from any previously known RecA like proteins as far as I could tell. And so with help from Dongying and the JCVI crew, we started building a story about novel RecAs. And then we looked at RpoBs. And found novel ones too. And in mid 2006 while Shibu and Doug worked on their papers that were to be submitted to PLoS Biology and I worked on a review paper too, I told Emma Hill (who has since changed her name to Emma Ganley due to some sort of wedding thing) at PLoS Biology about the an analysis that was consistent with the existence of a fourth domain of life. No overstating our findings really - just that we found very novel phylogenetic marker genes. And that I was working on a paper on it. But alas I never got it done, though I was happy to have convinced Venter to send the GOS papers to PLoS Biology and I think the papers that came out were good. Among the papers were my review (Environmental Shotgun Sequencing: Its Potential and Challenges for Studying the Hidden World of Microbes, Doug Rusch's diversity paper The Sorcerer II Global Ocean Sampling Expedition: Northwest Atlantic through Eastern Tropical Pacific and Shibu's protein family paper The Sorcerer II Global Ocean Sampling Expedition: Expanding the Universe of Protein Families as well as many others as part of the Ocean Metagenomics Collection at PLoS.

And in the midst of all of this, we had our first child and we wanted to move back to Northern California to be closer to family (my wife's family is all in the Bay Area and my sister and brother Michael were in N. Cal too). So I applied for jobs and eventually took at job at UC Davis and we moved to Davis. Needless to say, all of that put a bit of a crimp in my work productivity. And once I was up and running at Davis, it just took a long time to get back to the searching for novel deep branches in the tree of life. But finally, we did it (with periodic prodding from Craig Venter). And we put together a paper and got it submitted to PLoS One in October. The reviews were very positive and enormously helpful. And we finally got a revision in January and it was officially accepted in February 2011. Only some seven years after my first work on the project. Whew.

More detail of what is in the paper
Well, I am going to be posting here some additional detail on what is in the paper.

Why we punted on analysis of very novel rRNAs.

The problem with rRNA is that the sequences that come from environmental samples are not complete (i.e. they only correspond to portions of the rRNA genes). Unfortunately, this makes a key step in phylogenetic analysis difficult - the alignment of sequences. We actually found about 200 rRNA sequences that seemed unusual in a phylogenetic sense. However, we were not convinced that the alignments of these fragments to other rRNAs was robust. This is because the alignment of rRNAs is best done making use of the base pairing secondary structure of the molecule and not the base sequence (i.e., primary structure).

With only rRNA fragments, we could not use the secondary structure to do the alignments because you need to whole molecule to determine the best folding. Combined with the fact that we were searching for very distantly related ribosomal RNAs which would be hard to align even if we had the whole molecule, we were stuck for a bit. It seemed impossible to look for really novel organisms.
So that is when we turned to other genes. The key for this is that there are protein coding genes that are universal and that for known organisms show similar patterns to rRNA in trees. In fact, in 1995 I wrote a paper showing that trees of RecA were very similar to trees of rRNA. RpoB is also considered a very robust phylogenetic marker. For organisms that we have in the lab (i.e., cultured) - many people use these other genes for phylogenetic analysis. rRNA has been very important in part because of the ease with which one can PCR amplify it from environmental samples and the fact that it is very hard to PCR amplify protein coding genes from the environment. Metagenomics changes this. With random sequencing, you get data from all genes. This means we can pick and choose genes to analyze for phylogenetic analysis and do not have to rely on rRNA.

So we went after RecA first, because it has been shown to be a good phylogenetic marker for studies of the tree of life. And we found some very novel branches in the RecA tree. And after analyzing these and convincing ourselves that they were indeed phylogenetically very novel we went after RpoB. And also found very novel branches.

So the phylogenetic analysis I think is very robust.

RecA and RpoB as phylogenetic markers

Many genes have been used as alternatives to rRNA genes to build "Trees of Life" including all organisms. Each has their own flavors of advantages and drawbacks. Two commonly used ones are the RecA and RpoB superfamilies.

The many possible explanations for finding novel forms of phylogenetic marker genes

The phylogenetically novel phylogenetic marker genes we found could have many explanations including that they could be ancient paralogs of these genes (but not found in any genomes we have available), they could be from viruses, or they could be from a novel branch on the tree of life. Or our trees could be bad. We think the latter is somewhat unlikely as our analysis has many lines of support. For example our RecA trees are very similar to those from a comprehensive study from M. Nei's lab except they did not include the metagenomic data. But I guess it is still a possibility that our trees are biased in some way (e.g., by long branch attraction or bad alignments)

Follow up analysis and rapid posting via Google Knol

Amazingly and a bit sadly, I think we rushed the paper out. We left out one thing partly by accident - we had done an analysis of the locations from which these novel RecA and RpoB sequences had come. And somehow, in our final push to get the paper out, we left this out. I will be posting this information as soon as possible here and on the PLoS One site.

In addition, after submitting the revision of our paper, we realized that we might be able to do a deeper analysis on one aspect of the work - how RpoB homologs from unusual DNA viruses compared to our novel sequences. We had included some RpoBs from DNA viruses in our analyses but not all that were available. So Dongying Wu did a very rapid additional analysis, adding some additional RpoB homologs to our alignment and making a tree of them. We then wrote a Google Knol about this new tree and submitted the Knol to PLoS Currents "Tree of Life" where it is currently in review. We are publishing the preprint of this Knol to make it available to all even while it is in review.

Figure 2 from Wu and Eisen submitted. 

Data availability

There is a move afoot to make sure all data/tools associated with publications are readily available. We used publicly available sequence data and as much as possible publicly available tools for our work . We are trying to release as much as possible to allow people to re-analyze our work and to do any of the work themselves. We have therefore made use of the Dryad Data deposition service to post some of this material (see http://datadryad.org/handle/10255/dryad.8385).

Who was involved

• Dongying Wu a brilliant "Project Scientist" in my lab led the project (Project Scientist is one of the UC positions that is like what others call "Senior Scientist"). Dongying is simply one of the best bioinformaticians/computational biologists I have ever met. He was first author on many key papers from my lab including the Genomic Encyclopedia paper that came out last year and the glassy winged sharpshooter symbionts paper that came out a few years ago. Dongying worked in my group at TIGR and moved with me to UC Davis and currently splits his time between UC Davis and the DOE Joint Genome Institute. 
• Martin Wu. Martin is an Assistant Professor at the University of Virginia. Prior to that he was a Project Scientist in my lab at Davis and a post-doc in my lab at TIGR. He is also a phenomenal bioinformatician / computational biologist. He developed the AMPHORA software in my lab and also led many genome projects (back when sequencing a genome was hard ...) including that of the first Wolbachia genome and that of a very unusual bug Carboxydothermus hydrogenoformans. Martin helped with some of the genome analyses as part of this work. 
• Aaron Halpern, Doug Rusch and Shibu Yooseph are all bioinformaticians from the J. Craig Venter Institute (Aaron is no longer there). All three helped with different aspects of dealing with and analyzing the GOS data and all three have been remarkably patient as this work dragged on and on. 
• Marv Frazier from the JCVI was helpful in the initial set up and conceptualization of the project. 
• J. Craig Venter is, well, Craig Venter, and he was involved in multiple aspects of the project including thinking about how and where to look for unusual sequences and interpreting some of the results.

UPDATE: Funding for this work

Most of my labs early work on this project was supported by a grant we had from the Assembling the Tree of Life program at the National Science Foundation (grant 0228651 to me and Naomi Ward). In that project we were working on sequencing and analyzing genomes from phyla of bacteria for which genomes were not available at the time. As part of this work we were designing methods to build phylogenetic trees from metagenomic data because we thought that our new genomes would be very useful in helping analyze metagenomic reads and figure out from which phyla they came. Later work on the project was supported by a grant to me, Jessica Green and Katie Pollard from the Gordon and Betty Moore Foundation (grant 1660).

Some questions that might be asked and some answers (based in part on questions I have gotten from reporters). Note if you have other questions please post them here or on the PLOS One site for the paper.

• Why no press release? Well, in part, because I sent information too late (shocking I know) to the Davis Press Office. But also because they have gotten suddenly busy with some Japan earthquake related actions. But also because, well, I really hate a lot of press releases. And finally, my brother had dinner with Carl Zimmer recently and apparently they discussed the possibility of having no press releases associated with papers. So here goes .... 
• Really - what took so long? I would like to say the US Government made us hold back on publishing this until they could look into whether Venter collected ocean data from Roswell, NM or not. But really, the story above is true. We just did not get it done earlier. 
• Why do you not know the source of the DNA (i.e., cells, viruses, etc)? This is why there was a six year wait between discovery and writing this up. We kept thinking we would be able to find the organisms but since I moved from TIGR and started a new job, we just never got around to getting to the source. We therefore decided to open this up to others who will hunt for the source by writing up the paper. 
• Why did you not rename the Unknown 2 group in the RecA tree? We should have renamed our group "Thaumarchaeota" or something like that. When we did the initial analysis our group was novel. And then a few years ago a few groups obtained data from what is thought to be the third major lineage of Archaea - referred to by some as Thaumarchaeota. This is to go with the Euryarchaeota and Crenarchaeota. See http://www.ncbi.nlm.nih.gov/pubmed/20598889 for example. 
• One of the clades in the RecA tree (XRCC2) seems out of place phylogenetically. I can see how that is confusing. The XRCC2 clade is very weird and hard to figure out. It is not the "normal" eukaryotic genes - those are the Rad51/DMC1 genes. One complication with the RecA family is that there have been duplication events to go with the species evolution. And thus eukaryotes have Rad51, DMC1, Rad51B, Rad51C, Rad57, XRCC3 and XRCC2. We tried to figure out where the XRCC2 group should go but it just was hard to place. The statistical support for its position (we used a method called bootstrapping) is low (note the lack of a number on the node where the branch leading to XRCC2 connects to the base of the tree). Most likely that group should be placed with some of the other eukaryotic groups. However, it seems likely that there was a duplication in the lineage leading up to the ancestor of eukaryotes and archaea (some studies have indicated they share a common ancestor to the exclusion of bacteria). Such a duplication would explain why basically all archaea have a RadA and and RadB and all / most eukaryotes have multiple paralogs as well. 
• The Unknown 1 group in the RpoB RecA tree seems to group with phage. What can you say about that? We think unknown 1 is potentially of viral origin but still cannot tell. The fact that is clusters with RecA superfamily members from phage suggests this but it is distant enough from known phage for us to not be confident in any predicted origin. As for derivative forms vs. independent branch - this is one of the big questions about viruses these days. Many viruses encode homologs of "housekeeping" genes found across bacteria, archaea and eukaryotes. And in many cases the viral versions of these genes appear to phylogenetically very novel. This is why the people studying mimivirus (which we refer to) suggest some viruses may in fact represent a fourth branch on the tree of life. It is possible that some viruses are in fact reduced forms of what were once cellular organisms - akin to parasitic intracellular species of bacteria possibly. 
• Why are these phylogenetically novel sequences so low in abundance? This is a key question. I think it would be easy to come up with a theory for these being rare or these being common. They might be rare if their niche is very limited today. Or they might be rare because they could not be very competitive with other organisms. Or they could be rare because they require some unusual interactions with other taxa. In addition, we have only looked carefully at ocean water samples. If these are common somewhere else (e.g., hotsprings, deep subsurface, etc) we would not yet have figured that out. We are looking at additional metagenomic data right now to see fi we can find any locations where relatives of these genes are more common

Some related papers by others worth looking at

• Can identification of a fourth domain of life be made from sequence data alone, and could it be done on Mars?
• Mimivirus: the emerging paradox of quasi-autonomous viruses.
• New evolutionary frontiers from unusual virus genomes
• Phylogenetic and phyletic studies of informational genes in genomes highlight existence of a 4 domain of life including giant viruses.
• Giant viruses, giant chimeras: the multiple evolutionary histories of Mimivirus genes.

Some related papers by me possibly worth looking at

• The Sorcerer II Global Ocean Sampling expedition: northwest Atlantic through eastern tropical Pacific.
• The Sorcerer II Global Ocean Sampling expedition: expanding the universe of protein families.
• Environmental genome shotgun sequencing of the Sargasso Sea. 
• Unsuspected diversity among marine aerobic anoxygenic phototrophs.
• Environmental shotgun sequencing: its potential and challenges for studying the hidden world of microbes.
• A phylogeny-driven genomic encyclopaedia of Bacteria and Archaea.
• A simple, fast, and accurate method of phylogenomic inference. 
• An automated phylogenetic tree-based small subunit rRNA taxonomy and alignment pipeline (STAP).
• PhylOTU: a high-throughput procedure quantifies microbial community diversity and resolves novel taxa from metagenomic data.
• Introducing W.A.T.E.R.S.: a workflow for the alignment, taxonomy, and ecology of ribosomal sequences.

Some related blog posts I have written over the years

• Here's hoping molecular classification/systematics of cultured & uncultured microbes wins #NobelPrize in medicine
• Calling all phylogeneticists - we need your help with metagenomic data
• Scientist Reveals Secret of the Ocean: It's Him

Dongying Wu, Martin Wu, Aaron Halpern, Douglas B. Rusch, Shibu Yooseph, Marvin Frazier,, & J. Craig Venter, Jonathan A. Eisen (2011). Stalking the Fourth Domain in Metagenomic Data: Searching for, Discovering, and Interpreting Novel, Deep Branches in Marker Gene Phylogenetic Trees PLoS One, 6 (3) : 10.1371/journal.pone.0018011