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location Athens, Greece
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Elected moderator on Unix & Linux. Feel free to @ping me in chat if there's anything I can help you with.

I am a computational biologist with a background in biology, not computers. My PhD work was on gene prediction and comparative genomics but my current research is in systems biology, specifically protein-protein interaction networks.

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1d
comment Why, specifically, does each generation, on average, improve upon the design of the species rather than degrade it?
@augurar ouch, indeed it should. Thanks.
Dec
24
comment Downloading specific yeast genes in an automated manner?
What OS would you do this on? Do you have access to UNIX tools? Also, please show us the rest of the gene names. What identifiers do you have? The answer will depend on what database the identifiers point to.
Dec
22
comment Evolutionary chronology - if any, which species have evolved in the last 100 years
@Chris well, yes and no. I am not suggesting that all resistance to antibiotics happened over the last 100 years, simply that some have which means they can serve as an answer to the OP. There is a huge wealth of evidence that the widespread use of antibiotics has resulted in the development of resistant strains. Of course some such strains already existed but do you deny that others have arisen recently as a direct result of human medical practices?
Dec
3
comment Domains in cell membrane
@WYSIWYG not really. All I know of lipid rafts is what I recall from the relevant classes I took 10 years ago in university. I'm not really competent to elaborate.
Nov
24
comment Do “Giraffe Weevil” males build Nests
Are these photographs of the specimen you found or are they taken from the web? If the latter, the likeliest explanation is that what you found looks very similar but is a different species.
Nov
20
comment Why is the DNA codon table “equal” to the RNA codon table
@Sosi no, the double strands are essential for many things including i) DNA replication ii) error repair (the "right" sequence can be inferred from the opposite strand iii) most importantly, genes can be found on both strands. The sense/antisense is only with respect to a given gene. What is the sense strand for geneX can be the antisense for geneY.
Nov
19
comment Incestual Reproduction in Animals
Since inbreeding can lead to greater chances of genetic abnormalities, it seems reasonable that individuals who avoid it would be selected for in the long run but I don't know of any studies on this.
Nov
17
comment what the best E-value cutoff in the miRNA homology search
Absolutely. Your parameters sound fine. I just wouldn't use an evalue of 10 as a way of determining whether a hit was interesting. I'd leave it at 10 or higher to be sure to get everything and then ignore it and filter on other things as you suggest.
Nov
17
comment Are there any known mutual symbiotic relationships that has more than two agents?
I'm not entirely sure that this constitutes symbiosis. It's a very valid point and +1 but I wonder if someone working in the field would consider it so.
Nov
15
comment what the best E-value cutoff in the miRNA homology search
10? Really? I haven't worked with miRs but 10 seems extremely high. In fact, working on short nucleotide sequences, I wouldn't recommend using the evalue at all. I'd go for plain %id and % coverage instead.
Nov
12
comment Find protein homologs with BLASTp
What species are you comparing? How distant are they? If close enough, "real" homologs should be able to form a single HSP spanning most of the target sequences.
Nov
10
comment Why don't fish groom each other?
@VatsalManot yes, but I think it's applicable to all. In order to be able to eat parasites, you need to be small enough to get at them. Presumably, if you're the same species, you will be too big. Still, as I said, this is pure speculation.
Nov
9
comment How to evolutionary explain menstrural cycles synchronization?
@Chris that's really interesting, I am aware of much anectodal evidence that suggests this is true. The wikipedia link you gave cites PMID:23480070 but I don't have access to it. Do you? Does it indeed confirm that it is a myth (the abstract suggests so but I don't know for sure)?
Nov
4
comment Local BLAST Copy Number per Hit
That depends on how you define a hit. Are we talking about homologous genes from different species? Multiple, slightly different copies of the same gene in a single genome? Multiple, identical copies of a single gene which is repeated in the database?
Nov
4
comment Why are the genomes of some trees so large?
+1. Another interesting point is that there is some evidence that the retrotranspositions of repetitive sequences such as Alu (which represents 10% of the human genome) are activated under conditions of cellular stress and can help shuffle the genome‌​, providing new variety.
Nov
3
comment Do blind people learn Braille equally fast as the sighted?
I'm not sure this is on topic here. It sounds like it might be a better fit for Cognitive Sciences.
Oct
31
comment What is the difference between embryology and developmental biology?
@tel I know, that was just a tongue-in-cheek comment pointing out why not all of developmental biology can be called embryology.
Oct
31
comment What is the difference between embryology and developmental biology?
Do worms have embryos?
Oct
28
comment For how long can a raven stay airborne (a week or more)?
Quite apart from using a mythical story to ask a scientific question, I don't see what makes you think that the raven was flying around all that time. For all you know, and as seems more likely, it drowned. Could you edit your question, remove the biblical references and just ask something specific about an animal's behavior?
Oct
28
comment For how long can a raven stay airborne (a week or more)?
Ah, but is that an African or European pigeon?