Question: What Are The Most Influential Bioinformatics/Computational Biology Papers Of 2011?
18
gravatar for Farhat
6.1 years ago by
Farhat2.8k
Pune, India
Farhat2.8k wrote:

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.

papers • 3.2k views
ADD COMMENTlink modified 6.1 years ago by ALchEmiXt1.9k • written 6.1 years ago by Farhat2.8k
2

A reasonable wiki question, I think.

ADD REPLYlink written 6.1 years ago by David Quigley10k
1

See related question from last year: http://biostar.stackexchange.com/questions/4866/best-papers-on-computational-biology-from-2010

ADD REPLYlink written 6.1 years ago by Casey Bergman17k

I would argue that this is extraordinarily broad.

ADD REPLYlink written 6.1 years ago by Gww2.6k

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.

ADD REPLYlink written 6.1 years ago by Larry_Parnell16k

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

ADD REPLYlink written 6.1 years ago by Farhat2.8k
7
gravatar for Mary
6.1 years ago by
Mary11k
Boston MA area
Mary11k wrote:

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?

ADD COMMENTlink written 6.1 years ago by Mary11k
5
gravatar for Larry_Parnell
6.1 years ago by
Larry_Parnell16k
Boston, MA USA
Larry_Parnell16k wrote:

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.

ADD COMMENTlink modified 6.1 years ago • written 6.1 years ago by Larry_Parnell16k
5
gravatar for ALchEmiXt
6.1 years ago by
ALchEmiXt1.9k
The Netherlands
ALchEmiXt1.9k wrote:

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. :-)

ADD COMMENTlink modified 6.1 years ago • written 6.1 years ago by ALchEmiXt1.9k
4
gravatar for Gjain
6.1 years ago by
Gjain5.1k
Göttingen, Germany
Gjain5.1k wrote:
ADD COMMENTlink modified 6.1 years ago by Michael Schubert6.7k • written 6.1 years ago by Gjain5.1k

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

ADD REPLYlink written 6.1 years ago by Jts1.2k
4
gravatar for Istvan Albert
6.1 years ago by
Istvan Albert ♦♦ 75k
University Park, USA
Istvan Albert ♦♦ 75k wrote:

For me this paper made the most difference:

Reducing the Effects of PCR Amplification and Sequencing Artifacts on 16S rRNA-Based Studies

ADD COMMENTlink written 6.1 years ago by Istvan Albert ♦♦ 75k
1

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

ADD REPLYlink written 6.1 years ago by Larry_Parnell16k

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

ADD REPLYlink written 6.1 years ago by Casey Bergman17k

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

ADD REPLYlink written 6.1 years ago by Istvan Albert ♦♦ 75k
3
gravatar for Jan Kosinski
6.1 years ago by
Jan Kosinski1.6k
Jan Kosinski1.6k wrote:

From protein folding and design:

Computational Design of Proteins Targeting the Conserved Stem Region of Influenza Hemagglutinin

How Fast-Folding Proteins Fold

ADD COMMENTlink written 6.1 years ago by Jan Kosinski1.6k
1
gravatar for David
6.1 years ago by
David70
David70 wrote:

My two cents:

Technical phosphoproteomic and bioinformatic tools useful in cancer research

ADD COMMENTlink written 6.1 years ago by David70
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