PLoS Computational Biology in 2009
A comprehensive review of the journal's achievements, key research, and impact on computational biology
What does a successful year look like for a scientific journal? Is it the number of groundbreaking papers published, or perhaps a rising impact factor? For PLoS Computational Biology in 2009, it was a year defined by robust growth, a deepening commitment to the scientific community, and the publication of research that would push the boundaries of how we understand life through computation. While the broader scientific world was captivated by the discovery of the human ancestor Ardi and advances in induced pluripotent stem cells, this specialized journal was quietly hitting new strides 7 .
This was a year that saw the journal solidify its role not just as a repository of knowledge, but as a dynamic participant in the evolution of computational biology. It was a year of laying groundwork—for new ways of measuring scientific impact, for more efficient service to authors, and for a deeper understanding of the intricate biological processes that govern life at a cellular level.
The statistics for PLoS Computational Biology in 2009 tell a clear story of expansion and rising influence. The journal recorded a 31% increase in submissions from the previous year, processing a total of 1,204 research articles. Of these, 344 were published, alongside 33 Reviews, Perspectives, and Education articles—a acceptance rate of 29% that reflected the journal's selective standards 1 .
Research Articles Submitted
Research Articles Published
Reviewers
This surge in submissions necessitated a strengthening of the journal's backbone. The Editorial Board welcomed 11 new editors, and the journal was supported by the work of 128 guest editors and a remarkable 1,616 reviewers. This massive community effort ensured that the quality of published work remained high, even as the volume grew 1 . The readership expanded in tandem, with over 14,000 scientists receiving new article alerts, ensuring that the research reached its intended audience quickly and effectively 1 .
Beyond traditional metrics, 2009 was a landmark year for PLoS because of the introduction of article-level metrics. This innovative tool allowed anyone to see, in real time, the impact of a published paper through a variety of lenses—not just citations, but also views, downloads, and media coverage. This provided a more nuanced picture of a paper's influence, revealing, for example, that the popular "Ten Simple Rules" series, while not always highly cited, consistently drew large numbers of readers 1 .
The journal's data also offered a snapshot of the field's hottest areas. Computational neuroscience remained a stronghold, while the modeling of biological systems at various scales emerged as a definite area of growth 1 .
Among the many significant studies published in 2009, one paper exemplifies the power of computational modeling to explain complex biological phenomena: "Computational Model of Membrane Fission Catalyzed by ESCRT-III" by Fabrikant et al. .
Membrane fission—the process where one continuous cellular membrane pinches off to form two separate ones—is fundamental to life. It is crucial for creating transport vesicles inside cells, for the budding of viruses like HIV, and for cell division (cytokinesis). For years, the protein dynamin was the only molecule proven to drive this process. However, a new family of proteins, the ESCRT-III complexes, was found to be essential for fission events that occur in an "inside-out" direction, away from the cell's cytoplasm—a topology that dynamin cannot handle. The mystery was how ESCRT-III proteins achieved this .
The researchers proposed a novel mechanism centered on two mammalian ESCRT-III subunits, CHMP2 and CHMP3. These proteins were known to self-assemble into dome-like structures. The team's computational model proposed the following step-by-step mechanism :
Other ESCRT-III proteins (primarily CHMP4) first deform the membrane to create a bud with an open neck.
CHMP2 and CHMP3 complexes then assemble into a hemispherical dome within the neck of this bud.
The membrane is progressively attached to the outer surface of this protein dome.
As the membrane is pulled taut over the dome, the neck of the bud narrows dramatically into a thin, hourglass-like tube.
This constriction accumulates immense elastic energy in the membrane. The model calculated that the relaxation of this stored energy is sufficient to drive the final fission of the neck.
| Reagent / Tool | Type | Function in the Study |
|---|---|---|
| CHMP2 & CHMP3 Proteins | Protein Complex | The core subjects of the study; self-assemble into the dome-like structures that catalyze fission. |
| CHMP4 Proteins | Protein Complex | Used to generate the initial membrane buds, setting the stage for CHMP2/CHMP3 action. |
| Bending Elastic Model | Computational Model | A mathematical model of lipid bilayers used to calculate the energy dynamics of the membrane. |
| Electron Tomography | Experimental Validation | Provided high-resolution 3D images of the actual CHMP2-CHMP3 dome structures in vitro. |
| Giant Unilamellar Vesicles (GUVs) | Synthetic Membrane | Simplified, model membrane systems used in experiments to observe protein-induced budding and fission. |
Source:
The model was not just theoretical; it was supported by experimental data, including electron tomography images of the dome-like CHMP2-CHMP3 structures. The computations determined the specific amount of energy required from the protein-membrane attachment to drive fission and showed that this energy requirement was biologically feasible .
This work was significant because it provided the first detailed, quantitative mechanism for how ESCRT-III complexes could catalyze the topologically unique "inside-out" membrane fission. It bridged a critical gap in cell biology, showing how a fundamental cellular process is controlled by a precise interplay between protein self-assembly and membrane physics.
| Feature | Dynamin | ESCRT-III (CHMP2/CHMP3) |
|---|---|---|
| Fission Topology | Outward, toward the cytoplasm | Inward, away from the cytoplasm |
| Key Assembly Structure | Helical collar around membrane tubule | Hemispherical dome within membrane neck |
| Membrane Position | Inside the protein scaffold | Outside the protein scaffold |
| Primary Energy Source | GTP hydrolysis | Protein-membrane binding energy |
Source: Adapted from
The broader field of computational biology in 2009 was also being shaped by advances in foundational methods. Comparative genomics was grappling with an "overwhelming list of new genomes," which pushed the development of more powerful computational tools for sequence analysis 2 .
The dominant method for decoding genomes, which involved breaking DNA into random fragments, sequencing them, and then using sophisticated algorithms to reassemble the complete sequence. The Phred-PHRAP-CONSED software pipeline was a standard for this purpose, relying on an "overlap-layout-consensus" algorithm to piece the genomic puzzle back together 2 .
This "fast-growing and current hot topic" allowed scientists to sequence entire communities of unculturable microorganisms directly from environmental samples like soil or water, opening a new window into microbial diversity 2 .
New high-throughput methods like 454 pyrosequencing were coming to the fore, offering massive increases in data output, albeit with the new challenge of assembling much shorter DNA reads 2 .
As 2009 closed, the editors of PLoS Computational Biology looked forward, announcing plans for new article series like "Roots of Bioinformatics" and "Postcards from" conferences to engage younger scientists 1 . They also committed to a crucial, practical goal: reducing the average 45-day time to first decision for authors 1 .
The year was a testament to the power of community. The journal's achievements were "undeniable: we are truly a community journal, the achievements of which result from and depend on the contributions of our authors, readers, editors, and reviewers" 1 . From the macro-level growth in submissions and readership to the micro-level details of a membrane fission mechanism, PLoS Computational Biology in 2009 was a vibrant ecosystem, nurturing the tools, theories, and conversations that would continue to define and expand the field of computational biology for years to come.