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Table of Contents

November 2017

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Predicting HIV-1 neutralization by antibodies using machine learning
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Broadly neutralizing antibodies against HIV-1 are currently investigated in clinical trials as a new treatment option. In order to select an effective antibody therapy, the neutralization sensitivity of the patient's viral strains towards the antibodies must be ensured. Since neutralization assays are too time-consuming and expensive, they are not suitable for routine clinical practice. Applying machine learning on existing neutralization assay data, Hake and Pfeifer developed a model for accurately predicting the neutralization sensitivity of HIV-1 towards antibodies based on the viral envelope sequence. The illustration sketches how the classifier discriminates between susceptible and resistant samples.

Image Credit: Anna Hake

Research Articles

A network diffusion approach to inferring sample-specific function reveals functional changes associated with breast cancer

Sushant Patkar, Assaf Magen, Roded Sharan, Sridhar Hannenhalli

PLOS Computational Biology: published November 30, 2017 | https://doi.org/10.1371/journal.pcbi.1005793

Dynamical compensation and structural identifiability of biological models: Analysis, implications, and reconciliation

Alejandro F. Villaverde, Julio R. Banga

PLOS Computational Biology: published November 29, 2017 | https://doi.org/10.1371/journal.pcbi.1005878

The effect of spatial randomness on the average fixation time of mutants

Suzan Farhang-Sardroodi, Amir H. Darooneh, Moladad Nikbakht, Natalia L. Komarova, Mohammad Kohandel

PLOS Computational Biology: published November 27, 2017 | https://doi.org/10.1371/journal.pcbi.1005864

Strawberry: Fast and accurate genome-guided transcript reconstruction and quantification from RNA-Seq

Ruolin Liu, Julie Dickerson

PLOS Computational Biology: published November 27, 2017 | https://doi.org/10.1371/journal.pcbi.1005851

Initial-state-dependent, robust, transient neural dynamics encode conscious visual perception

Alexis T. Baria, Brian Maniscalco, Biyu J. He

PLOS Computational Biology: published November 27, 2017 | https://doi.org/10.1371/journal.pcbi.1005806

Fragmentation modes and the evolution of life cycles

Yuriy Pichugin, Jorge Peña, Paul B. Rainey, Arne Traulsen

PLOS Computational Biology: published November 22, 2017 | https://doi.org/10.1371/journal.pcbi.1005860

Choose, rate or squeeze: Comparison of economic value functions elicited by different behavioral tasks

Alizée Lopez-Persem, Lionel Rigoux, Sacha Bourgeois-Gironde, Jean Daunizeau, Mathias Pessiglione

PLOS Computational Biology: published November 21, 2017 | https://doi.org/10.1371/journal.pcbi.1005848

Tracking urban human activity from mobile phone calling patterns

Daniel Monsivais, Asim Ghosh, Kunal Bhattacharya, Robin I. M. Dunbar, Kimmo Kaski

PLOS Computational Biology: published November 21, 2017 | https://doi.org/10.1371/journal.pcbi.1005824

Identifying influential neighbors in animal flocking

Li Jiang, Luca Giuggioli, Andrea Perna, Ramón Escobedo, Valentin Lecheval, Clément Sire, Zhangang Han, Guy Theraulaz

PLOS Computational Biology: published November 21, 2017 | https://doi.org/10.1371/journal.pcbi.1005822

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A hierarchical stochastic model for bistable perception

Stefan Albert, Katharina Schmack, Philipp Sterzer, Gaby Schneider

PLOS Computational Biology: published November 20, 2017 | https://doi.org/10.1371/journal.pcbi.1005856

An efficient moments-based inference method for within-host bacterial infection dynamics

David J. Price, Alexandre Breuzé, Richard Dybowski, Piero Mastroeni, Olivier Restif

PLOS Computational Biology: published November 20, 2017 | https://doi.org/10.1371/journal.pcbi.1005841

fluEvidenceSynthesis: An R package for evidence synthesis based analysis of epidemiological outbreaks

Edwin van Leeuwen, Petra Klepac, Dominic Thorrington, Richard Pebody, Marc Baguelin

PLOS Computational Biology: published November 20, 2017 | https://doi.org/10.1371/journal.pcbi.1005838

Optimal synaptic signaling connectome for locomotory behavior in Caenorhabditis elegans: Design minimizing energy cost

Franciszek Rakowski, Jan Karbowski

PLOS Computational Biology: published November 20, 2017 | https://doi.org/10.1371/journal.pcbi.1005834

Multivariate pattern dependence

Stefano Anzellotti, Alfonso Caramazza, Rebecca Saxe

PLOS Computational Biology: published November 20, 2017 | https://doi.org/10.1371/journal.pcbi.1005799

Trade-off and flexibility in the dynamic regulation of the cullin-RING ubiquitin ligase repertoire

Ronny Straube, Meera Shah, Dietrich Flockerzi, Dieter A. Wolf

PLOS Computational Biology: published November 17, 2017 | https://doi.org/10.1371/journal.pcbi.1005869

Cell cycle time series gene expression data encoded as cyclic attractors in Hopfield systems

Anthony Szedlak, Spencer Sims, Nicholas Smith, Giovanni Paternostro, Carlo Piermarocchi

PLOS Computational Biology: published November 17, 2017 | https://doi.org/10.1371/journal.pcbi.1005849

The role of Allee effect in modelling post resection recurrence of glioblastoma

Zoltan Neufeld, William von Witt, Dora Lakatos, Jiaming Wang, Balazs Hegedus, Andras Czirok

PLOS Computational Biology: published November 17, 2017 | https://doi.org/10.1371/journal.pcbi.1005818

The use of ambient humidity conditions to improve influenza forecast

Jeffrey Shaman, Sasikiran Kandula, Wan Yang, Alicia Karspeck

PLOS Computational Biology: published November 16, 2017 | https://doi.org/10.1371/journal.pcbi.1005844

Estimating the probabilities of rare arrhythmic events in multiscale computational models of cardiac cells and tissue

Mark A. Walker, Viatcheslav Gurev, John J. Rice, Joseph L. Greenstein, Raimond L. Winslow

PLOS Computational Biology: published November 16, 2017 | https://doi.org/10.1371/journal.pcbi.1005783

A Bayesian method for detecting pairwise associations in compositional data

Emma Schwager, Himel Mallick, Steffen Ventz, Curtis Huttenhower

PLOS Computational Biology: published November 15, 2017 | https://doi.org/10.1371/journal.pcbi.1005852

A coupled-oscillator model of olfactory bulb gamma oscillations

Guoshi Li, Thomas A. Cleland

PLOS Computational Biology: published November 15, 2017 | https://doi.org/10.1371/journal.pcbi.1005760

A free-boundary model of a motile cell explains turning behavior

Masoud Nickaeen, Igor L. Novak, Stephanie Pulford, Aaron Rumack, Jamie Brandon, Boris M. Slepchenko, Alex Mogilner

PLOS Computational Biology: published November 14, 2017 | https://doi.org/10.1371/journal.pcbi.1005862

A model-based clustering method to detect infectious disease transmission outbreaks from sequence variation

Rosemary M. McCloskey, Art F. Y. Poon

PLOS Computational Biology: published November 13, 2017 | https://doi.org/10.1371/journal.pcbi.1005868

Automated visualization of rule-based models

John Arul Prakash Sekar, Jose-Juan Tapia, James R. Faeder

PLOS Computational Biology: published November 13, 2017 | https://doi.org/10.1371/journal.pcbi.1005857

Predictive model identifies key network regulators of cardiomyocyte mechano-signaling

Philip M. Tan, Kyle S. Buchholz, Jeffrey H. Omens, Andrew D. McCulloch, Jeffrey J. Saucerman

PLOS Computational Biology: published November 13, 2017 | https://doi.org/10.1371/journal.pcbi.1005854

Electrical stimulus artifact cancellation and neural spike detection on large multi-electrode arrays

Gonzalo E. Mena, Lauren E. Grosberg, Sasidhar Madugula, Paweł Hottowy, Alan Litke, John Cunningham, E. J. Chichilnisky, Liam Paninski

PLOS Computational Biology: published November 13, 2017 | https://doi.org/10.1371/journal.pcbi.1005842

Characterizing steady states of genome-scale metabolic networks in continuous cell cultures

Jorge Fernandez-de-Cossio-Diaz, Kalet Leon, Roberto Mulet

PLOS Computational Biology: published November 13, 2017 | https://doi.org/10.1371/journal.pcbi.1005835

Improving virtual screening of G protein-coupled receptors via ligand-directed modeling

Thomas Coudrat, John Simms, Arthur Christopoulos, Denise Wootten, Patrick M. Sexton

PLOS Computational Biology: published November 13, 2017 | https://doi.org/10.1371/journal.pcbi.1005819

Significant associations between driver gene mutations and DNA methylation alterations across many cancer types

Yun-Ching Chen, Valer Gotea, Gennady Margolin, Laura Elnitski

PLOS Computational Biology: published November 10, 2017 | https://doi.org/10.1371/journal.pcbi.1005840

Are there physicochemical differences between allosteric and competitive ligands?

Richard D. Smith, Jing Lu, Heather A. Carlson

PLOS Computational Biology: published November 10, 2017 | https://doi.org/10.1371/journal.pcbi.1005813

A modeling study of budding yeast colony formation and its relationship to budding pattern and aging

Yanli Wang, Wing-Cheong Lo, Ching-Shan Chou

PLOS Computational Biology: published November 9, 2017 | https://doi.org/10.1371/journal.pcbi.1005843

Metabolic dynamics restricted by conserved carriers: Jamming and feedback

Tetsuhiro S. Hatakeyama, Chikara Furusawa

PLOS Computational Biology: published November 7, 2017 | https://doi.org/10.1371/journal.pcbi.1005847

Reading wild minds: A computational assay of Theory of Mind sophistication across seven primate species

Marie Devaine, Aurore San-Galli, Cinzia Trapanese, Giulia Bardino, Christelle Hano, Michel Saint Jalme, Sebastien Bouret, Shelly Masi, Jean Daunizeau

PLOS Computational Biology: published November 7, 2017 | https://doi.org/10.1371/journal.pcbi.1005833

Related Articles

  1. Correction: Reading wild minds: A computational assay of Theory of Mind sophistication across seven primate species

Base pair probability estimates improve the prediction accuracy of RNA non-canonical base pairs

Michael F. Sloma, David H. Mathews

PLOS Computational Biology: published November 6, 2017 | https://doi.org/10.1371/journal.pcbi.1005827

Allosteric modulation of cardiac myosin dynamics by omecamtiv mecarbil

Shaima Hashem, Matteo Tiberti, Arianna Fornili

PLOS Computational Biology: published November 6, 2017 | https://doi.org/10.1371/journal.pcbi.1005826

Insight into glucocorticoid receptor signalling through interactome model analysis

Emyr Bakker, Kun Tian, Luciano Mutti, Constantinos Demonacos, Jean-Marc Schwartz, Marija Krstic-Demonacos

PLOS Computational Biology: published November 6, 2017 | https://doi.org/10.1371/journal.pcbi.1005825

Competitive tuning: Competition's role in setting the frequency-dependence of Ca2+-dependent proteins

Daniel R. Romano, Matthew C. Pharris, Neal M. Patel, Tamara L. Kinzer-Ursem

PLOS Computational Biology: published November 6, 2017 | https://doi.org/10.1371/journal.pcbi.1005820

Individual versus superensemble forecasts of seasonal influenza outbreaks in the United States

Teresa K. Yamana, Sasikiran Kandula, Jeffrey Shaman

PLOS Computational Biology: published November 6, 2017 | https://doi.org/10.1371/journal.pcbi.1005801

mixOmics: An R package for ‘omics feature selection and multiple data integration

Florian Rohart, Benoît Gautier, Amrit Singh, Kim-Anh Lê Cao

PLOS Computational Biology: published November 3, 2017 | https://doi.org/10.1371/journal.pcbi.1005752

A Rescorla-Wagner drift-diffusion model of conditioning and timing

André Luzardo, Eduardo Alonso, Esther Mondragón

PLOS Computational Biology: published November 2, 2017 | https://doi.org/10.1371/journal.pcbi.1005796