Friday, March 23, 2018

Pan-genome of three genera

Here is another example of using Circos diagrams to visualize biological data. This time it is the concept of bacterial pan-genome.

These days sequencing become very cheap and data on bacterial genomes accumulates particularly fast. As of today GeneBank contains information on 131801 bacterial genomes, but thousands more are sequenced every day without being published. Faced with such load of information in their hands researches were able to look deeper in intra-species genome organisation. Having so many genomes allows you to ask questions like, what part of genome common for particular species? What composition of those common features makes a species?

Compared to animals, bacterial genomes are more dynamic as a result of horizontal gene transfer (HGT) between individual cells. Often HGT appears between different strains of same species, but sometimes can go even further, passing genes to other taxonomic groups (families and classes).

 If we take, for example, a genus of bacteria (doesn't matter which) and compare all genomes we have on the global scale there will be three areas. Some areas of genomes are unique, because they usually found only in a few species of the genus. These unique areas often are result of HTG and might find more similarity with species from other genera or even family. Other areas, called variable, are common for almost all species in the genus, but prone to mutation. Finally the third group of regions are specific to particular taxonomic group. These areas called core genome. Both variable and core genome regions make a pan-genome. Pan-genome regions create a signature, typical genome for particular species or genus. Genome that is shared among all members of particular taxon.

In the outer circle green shows core areas in pan-genomes of three genera. Those genes that are shared among more than 90% of all strains used in the analysis.

Second circle is called GC% content. Which basically means what percentage GC bases in particular gene. This matters because genomes that make up a genus usually have similar GC%. In this case for example, Arcobacter usually has 27%, similar to Campylobacter. In the diagram threshold is set to 28% GC and everything over it highlighted red (in light blue area). You can see that Helicobacter has different GC% from other two. It doesn't it somthing wrong, it's just different.

Another important point of GC% graph it allow to see foreign elements. If some genes or genome regions have GC% content significantly different from rest of the genome, it most likely appeared there recently through HGT. If you look at Helicobacter diagram you can easily see that some regions of GC% are not colored red. More interestingly if you look at pan-genome diagram above, you wont find green or grey stripes. These are most likely candidates for Unique regions.

How virulence factors related to pan-genome.

Figure caption: Connection and distribution of virulence factors between pan-genomes of three genera based on all available complete genome sequences. Outer circle 1 showing region similarity ranging 90-100% (indicated in dark green bars) to 80-90% and 70-80% (indicated in light green and gray bars).  Circle 2 shows GC content where upper (indicated in light blue) and lower (light red) boundaries set to 40% and 20%, respectively.  Circle 3 shows histogram of the distribution frequency of variable and core genes where Red bars indicate genes shared by number of strains to each particular cluster, whereas Blue bars represent heterogeneity of number of strains to that cluster. Circle 4 shows virulence, antibiotic resistance and toxin genes identified in pan-genomes of each genus. GenBank identifiers (GIs) from virulence factor database (VFDB) (black), Comprehensive Antibiotic Resistance Database (CARD) (green) and Toxin-antitoxin database (TADB) (blue). IDs shown in Red are connected by lines (in the center) where connecting lines in the center link to the IDs found in pan-genomes of three genera showing homologous virulence factor (blue), antibiotic resistance (green) and toxin (purple) genes.

Tuesday, March 6, 2018

Trascriptome analysis of programmed cell death in Cryphonectria parasitica

This is the first post in series dedicated to my research and project I'm involved in. Also, I'm going to bring here some analysis work I'm doing just to myself. To find out more follow the tags #myresearch and #myanalysis.

This time I'll bring an example of how to use Circos tool to visualize genomic and transcriptomics data. This tool is visually very appealing, but more you put on the graph less useful it becomes.

Before we start I want to introduce one basic concept from mycology, barrage. On figure below barrage shown by arrows and compatible strains' interactions shown by arrowheads.

In a nutshell barrage or incompatibility reaction is a form of innate immune response that causes two genetically distinct fungal strains reject each other. In fungal world most of interactions between strains happen through hyphal fusion or anastomosis. If all immune signals check and no disagreement found two strains fuse and continue to exist as a single individual. But if immune response triggered, two strains form a barrage, a separation wall made out of dead cells. Barrage separates two strains restricting exchange of genetic material. It gives us a glimpse into early evolution of sexual reproduction and immunity. Basically saying if we too different from each other genetically direct exchange of genes may cause more damage than good, so lets have sex instead.

Circular diagram below shows genes differentially expressed in C. parasitica during incompatibility reaction.

This diagram allows to see overall picture of how C. parasitica genes (red dots) behave in relation to genome map. Plus you can compare them to genes of P. anserina (purple) and N. crassa (green) in similar reaction. Not particularly informative, but you certainly can take something out of it.

First of all C. parasitica  has much more upregulated genes (pink area) than other two fungi. Also there are transcriptionally inert areas of genome, showing no gene activation. And finally lack of correlation in expression rate between three species. Basically red dots do not appear together with purple and green, showing different or no expression at all.

Figure caption: Gene differential expression (DE) shown on C. parasitica genome map (11 largest scaffolds).
Diagrams from outside to inside: Black lines show genome map of 11 scaffolds, each tick mark corresponds to 100,000 bp. Inside the outer black lines, blue marks indicate previously annotated genes on JGI C. parasitica genome portal and orange marks indicate novel genes. Novel genes are transcripts which demonstrated detectable level of expression in areas of genome previously not annotated on genome portal. First circle shows expressed genes, and second circle shows DE genes during barrage. Interior to this are C. parasitica gene IDs of DE genes where black IDs indicate genes differentially expressed during barrage only in C. parasitica, green and purple IDs indicate that orthologs of those genes are DE during Heterokaryon Incompatibility (HI) in N. crassa and P. anserina respectively. The inner-most pink, grey and blue bands show plots of individual genes expression. The Y axis indicates genes differential expression in log2 scale. Y axis pink colour indicates upregulated (y> 2), blue – downregulated (y< -2) and grey (2>y>-2) indicate non-DE genes. Red dots indicate C. parasitica genes, green and purple dots indicate DE orthologs during HI in N. crassa and P. anserina respectively.

Monday, September 11, 2017


I always have that uneasy feeling when they try to wash religious orthodoxy's face from all the dirt. It looks clean, but now you can actually see how ugly it is. At some point a horrifying thought visits you, that maybe... maybe!.. it was actually better before. O_o
Because before you could easily argue that this is just a piece of shit, lets get rid of it. But now, it would sound more like a prejudice or personal opinion at best.

They can really argue that hijab and burka protect women from unnecessary attention of horny males. However, completely different story is when they say that nobody forces women to wear hijab or burka. That smells the same as 99.99% of North Koreans support their government (remaining fraction are children who can't speak).

So, I have no stylistic issues with hijab, I'm against fashion policing. But, hijab and burka create nasty dichotomy. If you wear it, you are lawful, good, moral person: here's your husband, here's your allowance. If not, you are disgraceful slut and you deserve whatever bad shit happens to you. No pressure (according to modern islamic apologetic).

They may argue that in western world you have to agree to social norms, so you can get certain benefits of living in society. True.
However, important difference with theocratic societies here is that you free to choose the extent of social norms you accept. Of course you have to acquire basic norms, but nobody forces you to accept whole package. You generally free to make up your own personal set of morals and live perfectly fine.

For women in many islamic states this is not an option. You either accept Islamic Law or you disgraceful slut.

So, don't get too excited when you see picture like one below.

Friday, August 11, 2017

Fight for mental retardation equality

About the recent Google-fired-guy debate over biological differences in males and females when it comes to work in tech or leadership positions.

In short, my opinion is that average person should not care about it at all.

Long: If you a smart girl with IQ over 130 and you decided to hangout only with smart people like you, then prepare to be in predominately male crowd for the rest of your life. Not a big deal. Smart people do not care about penises and vaginas much. If you as IQ130+ person won't be snobbish like that and start to hangout with average people you'll find that all of them, no matter of their sex, are equally stupid. Though sometimes, when you are in a good mood, you can see it as somewhat amusing.

As an average IQ male should I feel pride over the knowledge that there is more males in IQ group over 130?
First, it doesn't change my IQ and second, for a person with IQ 110 there are as much smart men out there as there are smart women. Should a girl with IQ 110 feel bad about the same thing?
For exactly the same reason.

There are biological differences in how brain works between males and females. There is a solid proof of that and it doesn't come from success story magazine. If we look at research on autism there is huge inequality here [1,2]. Ratio of males to females getting autism is like 4.3:1 and this is a general case. Some research shows that for specific cases like Aspergers syndrome it's even worse, like 12:1.

If we start to fight for equality in mental retardation it will be a comedy. We either lower the bar of mental retardation for women (hello XIX century hysteria) or kick out excessive males from care they need. Non of these options are good.

1. Van Wijngaarden-Cremers, P. J. M., et al. (2014). "Gender and Age Differences in the Core Triad of Impairments in Autism Spectrum Disorders: A Systematic Review and Meta-analysis." Journal of Autism and Developmental Disorders 44(3): 627-635.
2. Fombonne, E. (2003). "Epidemiological Surveys of Autism and Other Pervasive Developmental Disorders: An Update." Journal of Autism and Developmental Disorders 33(4): 365-382.

Wednesday, July 19, 2017


Article on opioid epidemics.
While it is really an issue, problem do seems to be a bit overblown.
In these kind of cases I blame how in western countries journalists like first hand experience.
You can never find a report in press generally describing an issue. Informing you on overall matter. It is always have to be accompanied by interviews with real simple folks who got  into it.
Of course it gives the problem a human face, something to relate to. But often it creates biases. As people tend to believe testimonies more than to careful analysis.

Tuesday, May 30, 2017

Gender equality

If at some point government decides to enforce the rule that every workplace has to have exact 50/50 distribution of male and female workers. What you can do to maximise your employment chances?
When they bring you a questionnaire, in line for sex you put none, and declare yourself gender-fluid or gender-neutral. That way your employer can hire you at any quota.

Though for this strategy to work best they have to enforce transgender laws as well. So that at any scrutiny they wouldn't be able to use your birth certificate against you.

Saturday, January 28, 2017


V.V. Shulgin is a person with very interesting history. He was Russian nationalist, monarchist, constitutional monarchy advocate  and one of the members of white movement (called white as opposed to red,old Russia anti-bolshevik movement). Was a member of all sessions of Duma (first Russian parliament). He was among those who accepted abdication of Nicholas II.

So, conservative, nationalist and one who was fighting communists, after all in 1920 wrote this (highlights are mine):

...our ideas jumped over forefront...they (bolsheviks) rebuild Russian army... It might be terrible to acknowledge that, but it's what it is... Bolsheviks raised the Flag of United Russia... Communist International appeared as weapon... to expand Russia's territory...and Moscow power... no one can deny, russian language again rules over 1/6 of the world and all that in the name of Communist International... bolsheviks: 1) rebuilding Russian army; 2) restoring Russian borders... 3) preparing the return of Russia's Tsar.

Valuable lesson here: Some people may appear wise and insightful, by just being narrow minded. It just happens sometimes that time steps on the same tracks with your narrow point of view. Never for long, though.

Monday, January 23, 2017


He said that only 1 out of 3 smokers die from smoking related illnesses. 30% chance. Almost the same as predicted chance of Trump winning the presidency.

I have only one problem with this article. When do this stupid ganre "he said it -- years ago and still didn't correct himself" end?

Saturday, January 14, 2017


Some thoughts about Cambodia.

That was tough experience converting between Riel and USD. And I think they should ban using dollars. It makes everything more expensive. I mean most stuff costs $1, because it's hard to split it further without using local money. Like in Thailand, $1 is about 60 baht. So you can conveniently split dollar at least by 6.


People constantly begging for money almost everywhere. Victims of war, mothers with babies or children with big eyes. Striking thing was not that I never seen it before. I've seen lots of stuff like that back in Russia. It was that I haven't noticed anything like that in Thailand. Still mistery for me.
Sometimes it is interesting what things remind me about my motherland. When I talk with Chinese (esspessially mainland and HK) they remind me Russians by their lifestyle choices and maybe a bit of temperament. And now beggars in Cambodia.

Wednesday, November 30, 2016

Random thoughts

God created everything in 7 days. It's a biblical myth usually called as 6 days creation. But we know that day is one rotation of Earth around the sun. And according to story Earth appears only on "second" day, after the sun (light). So, concidering that it should be called 5ish days creation.

Thursday, November 24, 2016


This is interesting.
So apparently, Exxon accuses Rockefeller to plot a climate change conspiracy against them.
Interesting times indeed.

Sunday, November 6, 2016


Peterson is right that legislature on the subject of pronouns is bad idea. It is rather silly that I can butcher person's name, but must use right pronoun. But he's wrong about being so stubborn on his refusal to call people whatever way they want. At the beginning of term every teacher takes students list in his or her or zie or per class and establishes how students want to be called.

And I have the same issue as Peterson, having a hard time to remember students names. But if there is no law forcing me do so whole pronouns story doesn't make much difference. I can't remember names of 90% of students (well ok, people), but now in addition to that I won't be able to remember their pronouns. In most cases names I remember are students who perform well in class or ask a lot of questions. If student makes those efforts in class, I will make an effort to remember names, nicknames, pronouns etc. I feel it is feir enough. 

Friday, October 21, 2016

Mozart - Requiem

This is one those thing which staed with me since childhood.
An amazing piece of music from first minute till the last.

Sunday, October 9, 2016


Putin threatens to suspended Plutonium treaty. He want US to withdraw forces from Eastern Europe and cancel sanctions against corrupt officials and ones related to annexation of Crimea. 
Considering that US recently cancelled negotiations with him on Syria issues it looks quite interesting. Basically, he's showing that he's wants new negotiations.

Putin clearly demonstrated in recent years that for him process of  negotiations and all this hassle with Americans on the global stage is more important than solving issues on the table. Basically for him longer it lasts the better. Americans realized it long time ago, but only recently started to be practical about it. They started to do the worst! They started to ignore him. And I think it is right thing to do. As one the main rules of internet says: "Don't feed the trolls!".

Biggest problem though, it is absolutely impossible to say what Putin's reaction will be.

Saturday, August 27, 2016

Trump support

Some good thoughts on Trump from Scott Aaronson.

Would Trump moderate his insane “policies” once elected?  I don’t know, but I’d say that electing someone who promises to ignore the rule of law, in the hope that they don’t really mean it, has one of the worst track records of any idea in human history. 

I think people support Trump for the same reason why second-graders support the class clown who calls the teacher a fart-brain to her face.  It’s not that the class literally agrees that the teacher’s cranium is filled with intestinal gases, or considers that an important question to raise.  It’s simply that the clown had the guts to stand up to this scolding authority figure who presumes to tell the class every day what they are and aren’t allowed to think.  (As far as I can tell, this has also been the central operating principle of right-wing shock artists over the decades, from Rush Limbaugh to Ann Coulter to Milo Yiannopoulos.)
The truth is, there’s a movement that’s very effectively wielded social media to remake the public face of progressive activism—to the point where today, progressivism could strike an outside observer as being less about stopping climate change, raising the minimum wage, or investing in public transit than simply about ruining the lives of Brendan Eich and Matt Taylor and Tim Hunt and Erika Christakis and Dongle Guy and Elevator Guy and anyone else who tells the wrong joke, wears the wrong shirt, or sends the wrong email.  It strikes me that this movement never understood the extent to which progressive social values were already winning, with no need for this sort of vindictiveness.  It’s insisted instead on treating its vanquished culture-war enemies as shortsightedly as the Allies treated the Germans at Versailles.
So yes, I do think that the bullying wing of the social-justice left bears at least some minor, indirect responsibility for the rise of Trump.  If you demonstrate enough times that even people who are trying to be decent will still get fired, jeered at, and publicly shamed over the tiniest ideological misstep, then eventually some of those who you’ve frightened might turn toward a demagogue who’s incapable of shame.

Thursday, August 25, 2016

Biologist life

So, I was looking for concise (slim) gene ontology (GO) annotation.
Being concentrated on my writing I opened new browser tab and googled "GO slim".
I feel like that little girl who searched for "wet pussy".

Sunday, July 24, 2016


Let's see if I understand it right.
Pride parade is an event which gather all kinds of people, which support all possible inclusiveness and equality you can only think of.
So blacklivesmatter decided to harass the very crowd they can find the most support from demanding to make Pride parade less inclusive.

Wild thoughts

In a world where mosquitoes sucking fat instead of blood, swamps would be full of rich and glamorous people and Siberia would be a resort.

Saturday, June 11, 2016

Для истории

Следующая война России будет с Казахстаном.