Forum:What Are The Most Influential Bioinformatics/Computational Biology Papers Of 2011?
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10.0 years ago
Farhat ★ 2.9k

Since the year is coming to an end, this may be a good time to check out the best of 2011. I would prefer to not include reviews and the like in this.

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A reasonable wiki question, I think.

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I would argue that this is extraordinarily broad.

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I can agree with GWW. Take out "best" and add "influential." I think it is more important to see which papers are influencing how research will be planned and undertaken.

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changed to influential, which is what I was aiming at.

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Mary 11k

I think one of the ones that caused the most buzz in my sphere was the Ion Torrent one. Everyone was waiting for that....

Paper itself: An integrated semiconductor device enabling non-optical genome sequencing

Dan MacArthur's take on it: How accurate is the new Ion Torrent genome, really?

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One paper that will influence my work is Stochastic state transitions give rise to phenotypic equilibrium in populations of cancer cells by Gupta et al. Importantly, the authors show that subpopulations of cells purified for a given phenotypic state return towards equilibrium proportions over time, explaining this with Markov models. I would like to examine their conclusions in terms of metabolic diseases, eg type 2 diabetes and dyslipidemia.

I also think that a key event of 2011 is the growing realization that the genome is the basic unit of interrogation. It is increasingly easier to begin to address a biological question by looking genome-wide, then drawing focus on the biological implications of a few select genes.

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10.0 years ago
ALchEmiXt ★ 1.9k

This paper of Salzberg et al in Genome Research "GAGE: A critical evaluation of genome assemblies and assembly algorithms" (quite recent) is very actual for our research; "Which de novo assembler to choose in short read assembly...and more importantly how to assess which is the best for YOUR situation (e.g. the E-size as alternative/addition for/to N50."

This paper provides some ways to look at it which may be applicable to making a well-understood choice. Not just the choice of the assembler available at the server or because a collegue is using it fine. :-)

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You have an extra hypen at the end of the first link

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Thanks you! Quite relevant to upcoming work in which I will be involved.

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Agreed, hadn't seen this and already forwarded to colleagues!

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the field is very exciting and I hope to be working in it - yet as it turns out (and my early experiences substantiate this) separating the wheat from the chaff is unexpectedly challenging

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