June 2018

We investigate the shape transitions of red blood cells flowing in micro-capillaries. A convolutional neural network (CNN) transforms bright-field images of cells into a set of abstract representations. The illustration shows different shape features of the same cell highlighted by the color scheme and dependent on the applied convolution kernel. Our approach allows for a quantitative classification of each recorded cell. According to the prevailing flow conditions, the CNN reveals the formation of two stable shapes, "slippers" and "croissants". Finally, a phase diagram assessed within a range of physiolocial relevant shear rates expresses the shape transition in between these states. Kihm et al.

Image Credit: Stephan Quint

Messages from ISCB

2018 ISCB Innovator Award recognizes M. Madan Babu

Christiana N. Fogg, Diane E. Kovats, Ron Shamir

PLOS Computational Biology: published June 7, 2018 | https://doi.org/10.1371/journal.pcbi.1006164

2018 ISCB Overton Prize awarded to Cole Trapnell

Christiana N. Fogg, Diane E. Kovats, Ron Shamir

PLOS Computational Biology: published June 7, 2018 | https://doi.org/10.1371/journal.pcbi.1006163

Education

Cloud computing applications for biomedical science: A perspective

Vivek Navale, Philip E. Bourne

PLOS Computational Biology: published June 14, 2018 | https://doi.org/10.1371/journal.pcbi.1006144

Research Articles

Computation predicts rapidly adapting mechanotransduction currents cannot account for tactile encoding in Merkel cell-neurite complexes

Gregory J. Gerling, Lingtian Wan, Benjamin U. Hoffman, Yuxiang Wang, Ellen A. Lumpkin

PLOS Computational Biology: published June 29, 2018 | https://doi.org/10.1371/journal.pcbi.1006264

Two critical positions in zinc finger domains are heavily mutated in three human cancer types

Daniel Munro, Dario Ghersi, Mona Singh

PLOS Computational Biology: published June 28, 2018 | https://doi.org/10.1371/journal.pcbi.1006290

Thalamocortical and intracortical laminar connectivity determines sleep spindle properties

Giri P. Krishnan, Burke Q. Rosen, Jen-Yung Chen, Lyle Muller, Terrence J. Sejnowski, Sydney S. Cash, Eric Halgren, Maxim Bazhenov

PLOS Computational Biology: published June 27, 2018 | https://doi.org/10.1371/journal.pcbi.1006171

Age density patterns in patients medical conditions: A clustering approach

Fahad Alhasoun, Faisal Aleissa, May Alhazzani, Luis G. Moyano, Claudio Pinhanez, Marta C. González

PLOS Computational Biology: published June 26, 2018 | https://doi.org/10.1371/journal.pcbi.1006115

Removing contaminants from databases of draft genomes

Jennifer Lu, Steven L. Salzberg

PLOS Computational Biology: published June 25, 2018 | https://doi.org/10.1371/journal.pcbi.1006277

Exploring the single-cell RNA-seq analysis landscape with the scRNA-tools database

Luke Zappia, Belinda Phipson, Alicia Oshlack

PLOS Computational Biology: published June 25, 2018 | https://doi.org/10.1371/journal.pcbi.1006245

The impact of temporal sampling resolution on parameter inference for biological transport models

Jonathan U. Harrison, Ruth E. Baker

PLOS Computational Biology: published June 25, 2018 | https://doi.org/10.1371/journal.pcbi.1006235

Transmission of temporally correlated spike trains through synapses with short-term depression

Alex D. Bird, Magnus J. E. Richardson

PLOS Computational Biology: published June 22, 2018 | https://doi.org/10.1371/journal.pcbi.1006232

Lipidated apolipoprotein E4 structure and its receptor binding mechanism determined by a combined cross-linking coupled to mass spectrometry and molecular dynamics approach

Nicolas Henry, Eva-Maria Krammer, Florian Stengel, Quentin Adams, François Van Liefferinge, Ellen Hubin, Rui Chaves, Rouslan Efremov, Ruedi Aebersold, Guy Vandenbussche, Martine Prévost, Vincent Raussens, Stéphanie Deroo

PLOS Computational Biology: published June 22, 2018 | https://doi.org/10.1371/journal.pcbi.1006165

Control of neurite growth and guidance by an inhibitory cell-body signal

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PLOS Computational Biology: published June 21, 2018 | https://doi.org/10.1371/journal.pcbi.1006218

Community interactions and spatial structure shape selection on antibiotic resistant lineages

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Solving the RNA design problem with reinforcement learning

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PLOS Computational Biology: published June 21, 2018 | https://doi.org/10.1371/journal.pcbi.1006176

Systems modelling of the EGFR-PYK2-c-Met interaction network predicts and prioritizes synergistic drug combinations for triple-negative breast cancer

Sung-Young Shin, Anna-Katharina Müller, Nandini Verma, Sima Lev, Lan K. Nguyen

PLOS Computational Biology: published June 19, 2018 | https://doi.org/10.1371/journal.pcbi.1006192

Reversing allosteric communication: From detecting allosteric sites to inducing and tuning targeted allosteric response

Wei-Ven Tee, Enrico Guarnera, Igor N. Berezovsky

PLOS Computational Biology: published June 18, 2018 | https://doi.org/10.1371/journal.pcbi.1006228

Evolution of chemokine receptors is driven by mutations in the sodium binding site

Bruck Taddese, Madeline Deniaud, Antoine Garnier, Asma Tiss, Hajer Guissouma, Hervé Abdi, Daniel Henrion, Marie Chabbert

PLOS Computational Biology: published June 18, 2018 | https://doi.org/10.1371/journal.pcbi.1006209

Stochastic shielding and edge importance for Markov chains with timescale separation

Deena R. Schmidt, Roberto F. Galán, Peter J. Thomas

PLOS Computational Biology: published June 18, 2018 | https://doi.org/10.1371/journal.pcbi.1006206

Modeling the functions of condensin in chromosome shaping and segregation

Yuji Sakai, Atsushi Mochizuki, Kazuhisa Kinoshita, Tatsuya Hirano, Masashi Tachikawa

PLOS Computational Biology: published June 18, 2018 | https://doi.org/10.1371/journal.pcbi.1006152

Evolutionary dynamics of paroxysmal nocturnal hemoglobinuria

Nathaniel Mon Père, Tom Lenaerts, Jorge M. Pacheco, David Dingli

PLOS Computational Biology: published June 18, 2018 | https://doi.org/10.1371/journal.pcbi.1006133

Classification of red blood cell shapes in flow using outlier tolerant machine learning

Alexander Kihm, Lars Kaestner, Christian Wagner, Stephan Quint

PLOS Computational Biology: published June 15, 2018 | https://doi.org/10.1371/journal.pcbi.1006278

Tellurium notebooks—An environment for reproducible dynamical modeling in systems biology

J. Kyle Medley, Kiri Choi, Matthias König, Lucian Smith, Stanley Gu, Joseph Hellerstein, Stuart C. Sealfon, Herbert M. Sauro

PLOS Computational Biology: published June 15, 2018 | https://doi.org/10.1371/journal.pcbi.1006220

Nonmechanistic forecasts of seasonal influenza with iterative one-week-ahead distributions

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Mechanical evolution of DNA double-strand breaks in the nucleosome

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PLOS Computational Biology: published June 14, 2018 | https://doi.org/10.1371/journal.pcbi.1006224

Hybrid stochastic framework predicts efficacy of prophylaxis against HIV: An example with different dolutegravir prophylaxis schemes

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PLOS Computational Biology: published June 14, 2018 | https://doi.org/10.1371/journal.pcbi.1006155

A biophysical mechanism for preferred direction enhancement in fly motion vision

Alexander Borst

PLOS Computational Biology: published June 13, 2018 | https://doi.org/10.1371/journal.pcbi.1006240

3D morphology-based clustering and simulation of human pyramidal cell dendritic spines

Sergio Luengo-Sanchez, Isabel Fernaud-Espinosa, Concha Bielza, Ruth Benavides-Piccione, Pedro Larrañaga, Javier DeFelipe

PLOS Computational Biology: published June 13, 2018 | https://doi.org/10.1371/journal.pcbi.1006221

Identifying functional groups among the diverse, recombining antigenic var genes of the malaria parasite Plasmodium falciparum from a local community in Ghana

Mary M. Rorick, Edward B. Baskerville, Thomas S. Rask, Karen P. Day, Mercedes Pascual

PLOS Computational Biology: published June 13, 2018 | https://doi.org/10.1371/journal.pcbi.1006174

φ-evo: A program to evolve phenotypic models of biological networks

Adrien Henry, Mathieu Hemery, Paul François

PLOS Computational Biology: published June 11, 2018 | https://doi.org/10.1371/journal.pcbi.1006244

The effect of cell geometry on polarization in budding yeast

Michael Trogdon, Brian Drawert, Carlos Gomez, Samhita P. Banavar, Tau-Mu Yi, Otger Campàs, Linda R. Petzold

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Mechanical positioning of multiple nuclei in muscle cells

Angelika Manhart, Stefanie Windner, Mary Baylies, Alex Mogilner

PLOS Computational Biology: published June 11, 2018 | https://doi.org/10.1371/journal.pcbi.1006208

Changes in parasite traits, rather than intensity, affect the dynamics of infection under external perturbation

Suma Ghosh, Matthew J. Ferrari, Ashutosh K. Pathak, Isabella M. Cattadori

PLOS Computational Biology: published June 11, 2018 | https://doi.org/10.1371/journal.pcbi.1006167

Anticipating epidemic transitions with imperfect data

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Variation of mutational burden in healthy human tissues suggests non-random strand segregation and allows measuring somatic mutation rates

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PLOS Computational Biology: published June 7, 2018 | https://doi.org/10.1371/journal.pcbi.1006233

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Classification of red blood cell shapes in flow using outlier tolerant machine learning

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