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Announcing the Winners of the 2019 PLOS Computational Biology Research Prize

PLOS Computational Biology is pleased to announce the winners of their annual PLOS Computational Biology Research Prize.

In 2017 PLOS Computational Biology launched the “PLOS Computational Biology Research Prize” program with the aim to recognize some of the journal’s most outstanding Research Articles published the previous year in three prize categories: Breakthrough Advance/Innovation, Exemplary Methods/Software, and Public Impact. The 2019 PLOS Computational Biology Research Prize program celebrates Research Articles published in 2018.

Our Editors in Chiefs would like to congratulate the 2019 winners, “These papers represent some of the best research in computational biology, along with many other exceptional papers that were also nominated from among the 500+ research papers published by [PLOS Computational Biology] last year,” says PLOS Computational Biology Editor-in-Chief Jason Papin.

PLOS Computational Biology’s, newly appointed Editor-in-Chief, Feilim Mac Gabhann highlighted how the Research Prize reflects the importance of collaboration in computational biology. If you look at the three awarded papers this year, they have authors from eight different institutions in three different countries.”

Without further ado, PLOS Computational Biology presents the winning papers of the PLOS Computational Biology Research Prize 2019:

Breakthrough Advance/Innovation

A Systematic Atlas of Chaperome Deregulation Topologies Across the Human Cancer Landscape

Ali Hadizadeh Esfahani, Angelina Sverchkova, Julio Saez-Rodriguez, Andreas A. Schuppert, Marc Brehme


Exemplary Methods/Software

Sequence determinants of protein phase behavior from a coarse-grained model

Gregory L. Dignon , Wenwei Zheng , Young C. Kim, Robert B. Best, Jeetain Mittal


Public Impact

PhysiCell: An open source physics-based cell simulator for 3-D multicellular systems.

Ahmadreza Ghaffarizadeh, Randy Heiland, Samuel H. Friedman, Shannon M. Mumenthaler, Paul Macklin


In the first category, Breakthrough Advance/Innovation, we present a study that describes a new meta-PCA based method and associated M-score, including a software tool (Pro2 – Proteostasis Profiler) and its application for the quantification and visualization of systems-level chaperome interactome network deregulation topologies across 22 solid cancers based on TCGA data covering > 10,000 patient biopsies, and selected neurodegenerative diseases based on microarray gene expression data Hadizadeh Esfahani and colleagues explain how the chaperome is a core component of the cellular proteostasis network (PN), which acts to safeguard the native, folded proteome. Global views are obtained on the vast disturbances of this fundamental cellular network of molecular folding machines in the diverse spectrum of human cancers, while differences between functional chaperome families and cancers are revealed. These chaperome alterations lend themselves as candidates towards network-based biomarkers for new approaches to proteostasis adjustment in cancer therapy.

Corresponding author Marc Brehme says, “I am honoured to receive the “PLOS Computational Biology Research Prize 2019 in the category of ‘Breakthrough of Advance’, which recognises the team’s pioneering work in the new area of cancer proteostasis systems biology. The PLOS Computational Biology Research Prize serves as a great incentive to the community to publish in PLOS Computational Biology and provides a fantastic platform to highlight exciting papers published each year”

Taking home the top Exemplary Methods or Software prize is a study that proposed a novel coarse-grained computational framework for studying the liquid-liquid phase separation of intrinsically disordered proteins (IDPs). This model has been applied extensively to make several significant contributions to the field. This model is the first and likely the only available approach which is capable of providing molecular-level details on the sequence-determinants of protein phase separation due to specific disease mutations, the inclusion of a folded domain, and variation of chain length without any experimental input. Using the results from this model, Dignon and colleagues identified a simple relationship between the properties of a single protein chain and the protein phase behaviour (Dignon, Gregory L., et al. “Relation between single-molecule properties and phase behavior of intrinsically disordered proteins.” Proceedings of the National Academy of Sciences115.40 (2018): 9929-9934.), which can be used to make rapid progress in identifying the role of specific amino acids and sequence patterning in the protein phase behavior from simulation and experiment.

Finally, we present the paper taking home the top Public Impact prize. This paper studies how cells interact, communicate, and coordinate to form 3-D multicellular systems.  Ghaffarizadeh and colleagues developed PhysiCell to explore these problems with agent-based models. In PhysiCell, many cell agents move, exchange mechanical forces, grow, divide, communicate, and die. Modelers can attach custom data and functions to each cell to investigate a broad variety of problems. PhysiCell runs efficiently on a desktop, allowing us to run thousands of simulations on supercomputers to explore high-dimensional parameter spaces. The team wanted to reach as many users as possible, so they made sure PhysiCell works on Linux, OSX, Windows and other platforms. In turn, users can convert their PhysiCell models to web-based models (via xml2jupyter) to share their work with the public.

Ghaffarizadeh and colleagues plan to use the funds to support further PhysiCell development, dissemination, and open access publication. Corresponding Author Paul Macklin was  “very honored to receive the PLOS Computational Biology Research Prize in Public Impact. It’s been thrilling to see teams across the US and world use PhysiCell to solve problems we had never considered. We hope to reach more modelers and help them with their multicellular investigations.”

The journal invited the community to nominate their favourite 2018 published Research Articles. From these, nominations the PLOS Computational Biology Research Prize Committee made up of Editorial Board members Nicola Segata, Maricel Kann, Avner Schlessinger, Lilia Iakoucheva, Ilya Ioshikhes, and Shi-Jie Chen, selected the winners. The editorial committee had no conflicts of interest to declare. To help support future work, the corresponding author of each winning paper will receive a $2,000 (USD) prize, with all authors receiving an award certificate.

The three winning studies will join last year’s winners in the online PLOS Computational Biology Research Prize collection.

The team at PLOS Computational Biology would like to thank everyone who nominated and for your support this year. We couldn’t have done it without you.



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